From 526fdca703ac676cef9ba53be8803a4e60d27021 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Feb 2025 00:48:44 -0500 Subject: [PATCH] Update rdeval to 0.0.5 (#53619) * Update rdeval to 0.0.5 * edit patches --------- Co-authored-by: mencian --- recipes/rdeval/0001-Makefile.patch | 34 ++++++ ...file.patch => 0002-gfalibs-Makefile.patch} | 0 recipes/rdeval/Makefile.patch | 26 ----- recipes/rdeval/build_failure.linux-64.yaml | 104 ------------------ .../rdeval/build_failure.linux-aarch64.yaml | 104 ------------------ recipes/rdeval/build_failure.osx-64.yaml | 104 ------------------ recipes/rdeval/build_failure.osx-arm64.yaml | 104 ------------------ recipes/rdeval/foo.patch | 38 ------- recipes/rdeval/meta.yaml | 14 +-- 9 files changed, 41 insertions(+), 487 deletions(-) create mode 100644 recipes/rdeval/0001-Makefile.patch rename recipes/rdeval/{gfalibs-Makefile.patch => 0002-gfalibs-Makefile.patch} (100%) delete mode 100644 recipes/rdeval/Makefile.patch delete mode 100644 recipes/rdeval/build_failure.linux-64.yaml delete mode 100644 recipes/rdeval/build_failure.linux-aarch64.yaml delete mode 100644 recipes/rdeval/build_failure.osx-64.yaml delete mode 100644 recipes/rdeval/build_failure.osx-arm64.yaml delete mode 100644 recipes/rdeval/foo.patch diff --git a/recipes/rdeval/0001-Makefile.patch b/recipes/rdeval/0001-Makefile.patch new file mode 100644 index 0000000000000..558fe0ab16311 --- /dev/null +++ b/recipes/rdeval/0001-Makefile.patch @@ -0,0 +1,34 @@ +diff --git a/Makefile b/Makefile +index 1682ec3..d9991ae 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,5 +1,5 @@ +-CXX ?= g++ +-INCLUDE_DIR += -I./include -I./gfalibs/include ++CXX ?= $(CXX) ++INCLUDE_DIR += -I./include -I./gfalibs/include -I$(PREFIX)/include + WARNINGS = -Wall -Wextra + + CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) $(CFLAGS) +@@ -12,7 +12,11 @@ SOURCE = src + INCLUDE = include + BINDIR := $(BUILD)/.o + +-LDFLAGS += -pthread ++ifeq ($(origin LDFLAGS), undefined) ++ LDFLAGS := -pthread ++else ++ LDFLAGS := $(LDFLAGS) -pthread ++endif + LIBS = -lz -lcrypto -lhts + + OBJS := main input reads +@@ -30,7 +34,7 @@ head: $(BINS) gfalibs | $(BUILD) + all: head validate regenerate + + $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) +- $(CXX) $(CXXFLAGS) $(EVP) -c $(SOURCE)/$(notdir $@).cpp -o $@ ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(EVP) -c $(SOURCE)/$(notdir $@).cpp -o $@ + + .PHONY: gfalibs + gfalibs: diff --git a/recipes/rdeval/gfalibs-Makefile.patch b/recipes/rdeval/0002-gfalibs-Makefile.patch similarity index 100% rename from recipes/rdeval/gfalibs-Makefile.patch rename to recipes/rdeval/0002-gfalibs-Makefile.patch diff --git a/recipes/rdeval/Makefile.patch b/recipes/rdeval/Makefile.patch deleted file mode 100644 index fd23495377e3d..0000000000000 --- a/recipes/rdeval/Makefile.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/Makefile b/Makefile -index 7ec8f12..d81d842 100644 ---- a/Makefile -+++ b/Makefile -@@ -12,7 +12,11 @@ SOURCE = src - INCLUDE = include - BINDIR := $(BUILD)/.o - --LDFLAGS += -pthread -+ifeq ($(origin LDFLAGS), undefined) -+ LDFLAGS := -pthread -+else -+ LDFLAGS := $(LDFLAGS) -pthread -+endif - LIBS = -lz -lcrypto -lhts - - OBJS := main input reads -@@ -27,7 +31,7 @@ head: $(BINS) gfalibs | $(BUILD) - all: head validate regenerate - - $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) -- $(CXX) $(CXXFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ -+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ - - .PHONY: gfalibs - gfalibs: diff --git a/recipes/rdeval/build_failure.linux-64.yaml b/recipes/rdeval/build_failure.linux-64.yaml deleted file mode 100644 index 6d8aeff9481d0..0000000000000 --- a/recipes/rdeval/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - 2024-12-11T16:57:32 noarch Writing patched repodata - 2024-12-11T16:57:32 noarch Building current_repodata subset - 2024-12-11T16:57:32 noarch Writing current_repodata subset - 2024-12-11T16:57:32 noarch Writing index HTML - /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). - It should be a path to a folder. - Forcing conda-build to use the recipe file. - warnings.warn( - WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 - Adding in variants from internal_defaults - Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml - Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml - Attempting to finalize metadata for rdeval - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Getting pinned dependencies: ...working... done - BUILD START: ['rdeval-0.0.2-h077b44d_2.tar.bz2'] - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Solving environment (_h_env): ...working... done - - ## Package Plan ## - - environment location: /opt/conda/conda-bld/rdeval_1733936252875/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - - - The following NEW packages will be INSTALLED: - - _libgcc_mutex: 0.1-conda_forge conda-forge - _openmp_mutex: 4.5-2_gnu conda-forge - libgcc: 14.2.0-h77fa898_1 conda-forge - libgomp: 14.2.0-h77fa898_1 conda-forge - libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge - libzlib: 1.3.1-hb9d3cd8_2 conda-forge - zlib: 1.3.1-hb9d3cd8_2 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Solving environment (_build_env): ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Solving environment (_test_env): ...working... done - - ## Package Plan ## - - environment location: /opt/conda/conda-bld/rdeval_1733936252875/_build_env - - - The following NEW packages will be INSTALLED: - - _libgcc_mutex: 0.1-conda_forge conda-forge - _openmp_mutex: 4.5-2_gnu conda-forge - binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge - binutils_linux-64: 2.43-h4852527_2 conda-forge - gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge - gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge - gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge - gxx_linux-64: 13.3.0-h6834431_7 conda-forge - kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge - ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge - libgcc: 14.2.0-h77fa898_1 conda-forge - libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge - libgomp: 14.2.0-h77fa898_1 conda-forge - libsanitizer: 13.3.0-heb74ff8_1 conda-forge - libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge - libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge - make: 4.4.1-hb9d3cd8_2 conda-forge - sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge - tzdata: 2024b-hc8b5060_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip - Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip - Success - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build - try_download(m, no_download_source=False, raise_error=True) - File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download - source.provide(metadata) - File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide - unpack( - File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack - src_path, unhashed_fn = download_to_cache( - File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache - raise RuntimeError( - RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' -# Last 100 lines of the build log. diff --git a/recipes/rdeval/build_failure.linux-aarch64.yaml b/recipes/rdeval/build_failure.linux-aarch64.yaml deleted file mode 100644 index 7043d8a29e1cb..0000000000000 --- a/recipes/rdeval/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - 2024-12-10T17:23:35 linux-64 Writing current_repodata subset - 2024-12-10T17:23:35 linux-64 Writing index HTML - 2024-12-10T17:23:35 noarch Writing current_repodata subset - 2024-12-10T17:23:35 noarch Writing index HTML - 2024-12-10T17:23:35 linux-aarch64 Writing current_repodata subset - 2024-12-10T17:23:35 linux-aarch64 Writing index HTML - /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). - It should be a path to a folder. - Forcing conda-build to use the recipe file. - warnings.warn( - WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 - Adding in variants from internal_defaults - Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml - Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml - Attempting to finalize metadata for rdeval - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Getting pinned dependencies: ...working... done - BUILD START: ['rdeval-0.0.2-h1e84f2d_2.tar.bz2'] - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Solving environment (_h_env): ...working... done - - ## Package Plan ## - - environment location: /opt/conda/conda-bld/rdeval_1733851416889/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - - - The following NEW packages will be INSTALLED: - - _openmp_mutex: 4.5-2_gnu conda-forge - libgcc: 14.2.0-he277a41_1 conda-forge - libgomp: 14.2.0-he277a41_1 conda-forge - libstdcxx: 14.2.0-h3f4de04_1 conda-forge - libzlib: 1.3.1-h86ecc28_2 conda-forge - zlib: 1.3.1-h86ecc28_2 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Solving environment (_build_env): ...working... done - Reloading output folder (file:///opt/host-conda-bld): ...working... done - Solving environment (_test_env): ...working... done - - ## Package Plan ## - - environment location: /opt/conda/conda-bld/rdeval_1733851416889/_build_env - - - The following NEW packages will be INSTALLED: - - _openmp_mutex: 4.5-2_gnu conda-forge - binutils_impl_linux-aarch64: 2.43-h4c662bb_2 conda-forge - binutils_linux-aarch64: 2.43-hf1166c9_2 conda-forge - gcc_impl_linux-aarch64: 13.3.0-hcdea9b6_1 conda-forge - gcc_linux-aarch64: 13.3.0-h1cd514b_7 conda-forge - gxx_impl_linux-aarch64: 13.3.0-h1211b58_1 conda-forge - gxx_linux-aarch64: 13.3.0-h2864abd_7 conda-forge - kernel-headers_linux-aarch64: 4.18.0-h05a177a_18 conda-forge - ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge - libgcc: 14.2.0-he277a41_1 conda-forge - libgcc-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge - libgomp: 14.2.0-he277a41_1 conda-forge - libsanitizer: 13.3.0-ha58e236_1 conda-forge - libstdcxx: 14.2.0-h3f4de04_1 conda-forge - libstdcxx-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge - make: 4.4.1-h2a6d0cb_2 conda-forge - sysroot_linux-aarch64: 2.17-h5b4a56d_18 conda-forge - tzdata: 2024b-hc8b5060_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip - Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip - Success - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build - try_download(m, no_download_source=False, raise_error=True) - File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download - source.provide(metadata) - File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide - unpack( - File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack - src_path, unhashed_fn = download_to_cache( - File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache - raise RuntimeError( - RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' -# Last 100 lines of the build log. diff --git a/recipes/rdeval/build_failure.osx-64.yaml b/recipes/rdeval/build_failure.osx-64.yaml deleted file mode 100644 index c72468886192c..0000000000000 --- a/recipes/rdeval/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - It should be a path to a folder. - Forcing conda-build to use the recipe file. - warnings.warn( - WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 - Adding in variants from internal_defaults - Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml - Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml - Attempting to finalize metadata for rdeval - Reloading output folder (local): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (local): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (local): ...working... done - Getting pinned dependencies: ...working... done - BUILD START: ['rdeval-0.0.2-h2ec61ea_2.tar.bz2'] - Reloading output folder (local): ...working... done - Solving environment (_h_env): ...working... done - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733868175370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - - - The following NEW packages will be INSTALLED: - - libcxx: 19.1.5-hf95d169_0 conda-forge - libzlib: 1.3.1-hd23fc13_2 conda-forge - zlib: 1.3.1-hd23fc13_2 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder (local): ...working... done - Solving environment (_build_env): ...working... done - Reloading output folder (local): ...working... done - Solving environment (_test_env): ...working... done - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733868175370/_build_env - - - The following NEW packages will be INSTALLED: - - ca-certificates: 2024.8.30-h8857fd0_0 conda-forge - cctools_osx-64: 1010.6-h00edd4c_2 conda-forge - clang: 18.1.8-default_h179603d_5 conda-forge - clang-18: 18.1.8-default_h0c94c6a_5 conda-forge - clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge - clang_osx-64: 18.1.8-h7e5c614_23 conda-forge - clangxx: 18.1.8-default_h179603d_5 conda-forge - clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge - clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge - compiler-rt: 18.1.8-h1020d70_1 conda-forge - compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge - ld64_osx-64: 951.9-hc8d1a19_2 conda-forge - libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge - libcxx: 19.1.5-hf95d169_0 conda-forge - libcxx-devel: 18.1.8-h7c275be_7 conda-forge - libiconv: 1.17-hd75f5a5_2 conda-forge - libllvm18: 18.1.8-h9ce406d_2 conda-forge - liblzma: 5.6.3-hd471939_1 conda-forge - libxml2: 2.13.5-he8ee3e7_1 conda-forge - libzlib: 1.3.1-hd23fc13_2 conda-forge - llvm-tools: 18.1.8-h9ce406d_2 conda-forge - llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge - make: 4.4.1-h00291cd_2 conda-forge - ncurses: 6.5-hf036a51_1 conda-forge - openssl: 3.4.0-hd471939_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1300.6.5-h390ca13_0 conda-forge - zstd: 1.5.6-h915ae27_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip - Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip - Success - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build - try_download(m, no_download_source=False, raise_error=True) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download - source.provide(metadata) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide - unpack( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack - src_path, unhashed_fn = download_to_cache( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache - raise RuntimeError( - RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' -# Last 100 lines of the build log. diff --git a/recipes/rdeval/build_failure.osx-arm64.yaml b/recipes/rdeval/build_failure.osx-arm64.yaml deleted file mode 100644 index 92d31a1bd4cfb..0000000000000 --- a/recipes/rdeval/build_failure.osx-arm64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Forcing conda-build to use the recipe file. - warnings.warn( - WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 - Adding in variants from internal_defaults - Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml - Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml - Attempting to finalize metadata for rdeval - Reloading output folder (local): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (local): ...working... done - Getting pinned dependencies: ...working... done - Reloading output folder (local): ...working... done - Getting pinned dependencies: ...working... done - BUILD START: ['rdeval-0.0.2-hda5e58c_2.tar.bz2'] - Reloading output folder (local): ...working... done - Solving environment (_h_env): ...working... done - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733970186660/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - - - The following NEW packages will be INSTALLED: - - libcxx: 19.1.5-ha82da77_0 conda-forge - libzlib: 1.3.1-h8359307_2 conda-forge - zlib: 1.3.1-h8359307_2 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder (local): ...working... done - Solving environment (_build_env): ...working... done - Reloading output folder (local): ...working... done - Solving environment (_test_env): ...working... done - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733970186660/_build_env - - - The following NEW packages will be INSTALLED: - - ca-certificates: 2024.8.30-hf0a4a13_0 conda-forge - cctools_osx-arm64: 1010.6-h908b477_2 conda-forge - clang: 18.1.8-default_h675cc0c_5 conda-forge - clang-18: 18.1.8-default_h5c12605_5 conda-forge - clang_impl_osx-arm64: 18.1.8-h2ae9ea5_23 conda-forge - clang_osx-arm64: 18.1.8-h07b0088_23 conda-forge - clangxx: 18.1.8-default_h675cc0c_5 conda-forge - clangxx_impl_osx-arm64: 18.1.8-h555f467_23 conda-forge - clangxx_osx-arm64: 18.1.8-h07b0088_23 conda-forge - compiler-rt: 18.1.8-h856b3c1_1 conda-forge - compiler-rt_osx-arm64: 18.1.8-h832e737_1 conda-forge - icu: 75.1-hfee45f7_0 conda-forge - ld64_osx-arm64: 951.9-hfc0fa09_2 conda-forge - libclang-cpp18.1: 18.1.8-default_h5c12605_5 conda-forge - libcxx: 19.1.5-ha82da77_0 conda-forge - libcxx-devel: 18.1.8-h6dc3340_7 conda-forge - libiconv: 1.17-h0d3ecfb_2 conda-forge - libllvm18: 18.1.8-h5090b49_2 conda-forge - liblzma: 5.6.3-h39f12f2_1 conda-forge - libxml2: 2.13.5-h178c5d8_1 conda-forge - libzlib: 1.3.1-h8359307_2 conda-forge - llvm-tools: 18.1.8-h5090b49_2 conda-forge - llvm-tools-18: 18.1.8-h5090b49_2 conda-forge - make: 4.4.1-hc9fafa5_2 conda-forge - ncurses: 6.5-h7bae524_1 conda-forge - openssl: 3.4.0-h39f12f2_0 conda-forge - sigtool: 0.1.3-h44b9a77_0 conda-forge - tapi: 1300.6.5-h03f4b80_0 conda-forge - zstd: 1.5.6-hb46c0d2_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip - Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip - Success - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build - try_download(m, no_download_source=False, raise_error=True) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download - source.provide(metadata) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide - unpack( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack - src_path, unhashed_fn = download_to_cache( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache - raise RuntimeError( - RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' -# Last 100 lines of the build log. diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch deleted file mode 100644 index 417701560725a..0000000000000 --- a/recipes/rdeval/foo.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/Makefile b/Makefile -index 5823f28..6f4a60f 100644 ---- a/Makefile -+++ b/Makefile -@@ -1,5 +1,5 @@ --CXX ?= g++ --INCLUDE_DIR = -I./include -I./gfalibs/include -+CXX ?= ${CXX} -+INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include - WARNINGS = -Wall -Wextra - - CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) -@@ -12,8 +12,8 @@ SOURCE = src - INCLUDE = include - BINDIR := $(BUILD)/.o - --LDFLAGS := -pthread --LIBS = -lz -+LDFLAGS := -pthread -L${PREFIX}/lib -+LIBS := -lz -lpthread - - OBJS := main input reads - BINS := $(addprefix $(BINDIR)/, $(OBJS)) -@@ -22,12 +22,12 @@ BINS := $(addprefix $(BINDIR)/, $(OBJS)) - GFALIBS_DIR := $(CURDIR)/gfalibs - - head: $(BINS) gfalibs | $(BUILD) -- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS) -+ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS) - - all: head validate regenerate - - $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) -- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ -+ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) - - .PHONY: gfalibs - gfalibs: diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index af1f86091f035..ae6ae078df86e 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -1,5 +1,5 @@ {% set name = "rdeval" %} -{% set version = "0.0.4" %} +{% set version = "0.0.5" %} package: name: {{ name|lower }} @@ -7,15 +7,15 @@ package: source: url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip - sha256: 905a5bece7551de25896dcd6b48d1921f1df63635a80b0bc5605a8c57c37d5eb + sha256: c7e0466eabff90d39742a7df749018c81c7e425027667fa4a880897dbdccd70a patches: - - Makefile.patch - - gfalibs-Makefile.patch + - 0001-Makefile.patch + - 0002-gfalibs-Makefile.patch build: number: 0 run_exports: - - {{ pin_subpackage(name|lower, max_pin="x.x") }} + - {{ pin_subpackage(name|lower, max_pin="x.x.x") }} requirements: build: @@ -35,12 +35,12 @@ test: about: home: https://github.com/vgl-hub/{{ name }} - summary: A general purpose, multithreaded read analysis and manipulation tool. + summary: "A general purpose, multithreaded read analysis and manipulation tool." license: MIT license_family: MIT license_file: LICENSE dev_url: https://github.com/vgl-hub/{{ name }} - doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md + doc_url: "https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md" extra: additional-platforms: