Skip to content

Commit

Permalink
build failures with log
Browse files Browse the repository at this point in the history
  • Loading branch information
@aliciaaevans
aliciaaevans committed Dec 15, 2023
1 parent 5a91151 commit fee0e3f
Show file tree
Hide file tree
Showing 4 changed files with 193 additions and 0 deletions.
95 changes: 95 additions & 0 deletions recipes/bioconductor-musicatk/build_failure.linux-64.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,98 @@ reason: |-
ERRO Task processing failed: API error (500): {"message":"write /usr/local/lib/libgoogle_cloud_cpp_dialogflow_cx.so.2.12.0: no space left on device"}
category: |-
compiler error
log: |-
.07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] SERR [Dec 15 07:05:52] ERRO Task processing failed: API error (500): {"message":"write /usr/local/lib/libgoogle_cloud_cpp_dialogflow_cx.so.2.12.0: no space left on device"}
07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] SERR
07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] ERRO Task processing failed: Unexpected exit code [1] of container [c84c2e941721 step-698cd8abd9], container preserved
.07:06:42 BIOCONDA INFO (OUT) ........
07:06:42 BIOCONDA INFO (ERR) Traceback (most recent call last):
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/mulled-build", line 10, in <module>
07:06:42 BIOCONDA INFO (ERR) sys.exit(main())
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 414, in main
07:06:42 BIOCONDA INFO (ERR) sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 243, in mull_targets
07:06:42 BIOCONDA INFO (ERR) ret = involucro_context.exec_command(involucro_args)
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 287, in exec_command
07:06:42 BIOCONDA INFO (ERR) shutil.rmtree('./build')
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 718, in rmtree
07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(fd, path, onerror)
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd
07:06:42 BIOCONDA INFO (ERR) onerror(os.unlink, fullname, sys.exc_info())
07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd
07:06:42 BIOCONDA INFO (ERR) os.unlink(entry.name, dir_fd=topfd)
07:06:42 BIOCONDA INFO (ERR) PermissionError: [Errno 13] Permission denied: 'pcre2_set_callout.3'
07:06:42 BIOCONDA ERROR COMMAND FAILED (exited with 1): mulled-build build-and-test bioconductor-musicatk=1.12.0--r43hdfd78af_0 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && Rscript -e "library('"'"'musicatk'"'"')"' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/involucro
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package
p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/utils.py", line 697, in run
raise sp.CalledProcessError(returncode, masked_cmds, output=output)
subprocess.CalledProcessError: Command '['mulled-build', 'build-and-test', 'bioconductor-musicatk=1.12.0--r43hdfd78af_0', '-n', 'biocontainers', '--test', 'bash -c \'/usr/local/env-execute true && . /usr/local/env-activate.sh && Rscript -e "library(\'"\'"\'musicatk\'"\'"\')"\'', '--channels', 'conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults', '--involucro-path', '/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/involucro']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd
os.unlink(entry.name, dir_fd=topfd)
PermissionError: [Errno 13] Permission denied: 'pcre2_set_callout.3'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/bin/bioconda-utils", line 8, in <module>
sys.exit(main())
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 1114, in main
argh.dispatch_commands([
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 328, in dispatch_commands
dispatch(parser, *args, **kwargs)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 260, in _call
result = function(*positional, **keywords)
File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 137, in wrapper
func(*args, **kwargs)
File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 66, in wrapper
func(*args, **kwargs)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 492, in build
success = build_recipes(recipe_folder, config, recipes,
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/build.py", line 421, in build_recipes
res = build(recipe=recipe,
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/build.py", line 185, in build
pkg_test.test_package(pkg_path, base_image=base_image,
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package
p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 827, in __exit__
self.cleanup()
File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 831, in cleanup
self._rmtree(self.name)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 813, in _rmtree
_shutil.rmtree(name, onerror=onerror)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 718, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
[Previous line repeated 1 more time]
File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 798, in onerror
resetperms(_os.path.dirname(path))
File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 794, in resetperms
_os.chmod(path, 0o700)
PermissionError: [Errno 1] Operation not permitted: '/tmp/tmpeaviicao/build/dist/man/man3'
Error: Process completed with exit code 1.
55 changes: 55 additions & 0 deletions recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,58 @@ reason: |-
package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed
category: |-
dependency issue
log: |-
02:31:45 BIOCONDA INFO (OUT) RuntimeError: Solver could not find solution.Mamba failed to solve:
02:31:45 BIOCONDA INFO (OUT) - r-base 4.3.*
02:31:45 BIOCONDA INFO (OUT) - r-httr
02:31:45 BIOCONDA INFO (OUT) - nodejs 14.*
02:31:45 BIOCONDA INFO (OUT) - r-git2r
02:31:45 BIOCONDA INFO (OUT) - bioconductor-s4vectors >=0.40.0,<0.41.0
02:31:45 BIOCONDA INFO (OUT) - r-rappdirs
02:31:45 BIOCONDA INFO (OUT) - bioconductor-rcwl >=1.18.0,<1.19.0
02:31:45 BIOCONDA INFO (OUT) - bioconductor-biocfilecache >=2.10.0,<2.11.0
02:31:45 BIOCONDA INFO (OUT)
02:31:45 BIOCONDA INFO (OUT) with channels:
02:31:45 BIOCONDA INFO (OUT) - file:///opt/host-conda-bld
02:31:45 BIOCONDA INFO (OUT) - conda-forge
02:31:45 BIOCONDA INFO (OUT) - bioconda
02:31:45 BIOCONDA INFO (OUT) - defaults
02:31:45 BIOCONDA INFO (OUT)
02:31:45 BIOCONDA INFO (OUT) The reported errors are:
02:31:45 BIOCONDA INFO (OUT) - Encountered problems while solving:
02:31:45 BIOCONDA INFO (OUT) - - package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed
02:31:45 BIOCONDA INFO (OUT) -
02:31:45 BIOCONDA INFO (OUT)
02:31:45 BIOCONDA INFO (OUT) During handling of the above exception, another exception occurred:
02:31:45 BIOCONDA INFO (OUT)
02:31:45 BIOCONDA INFO (OUT) Traceback (most recent call last):
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in <module>
02:31:45 BIOCONDA INFO (OUT) sys.exit(main())
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
02:31:45 BIOCONDA INFO (OUT) call_conda_build(action, config)
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
02:31:45 BIOCONDA INFO (OUT) result = api.build(
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
02:31:45 BIOCONDA INFO (OUT) return build_tree(
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
02:31:45 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats,
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build
02:31:45 BIOCONDA INFO (OUT) output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)])
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs
02:31:45 BIOCONDA INFO (OUT) for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False):
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set
02:31:45 BIOCONDA INFO (OUT) conda_packages = finalize_outputs_pass(
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass
02:31:45 BIOCONDA INFO (OUT) fm = finalize_metadata(
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata
02:31:45 BIOCONDA INFO (OUT) build_unsat, host_unsat = add_upstream_pins(m,
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins
02:31:45 BIOCONDA INFO (OUT) host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host',
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files
02:31:45 BIOCONDA INFO (OUT) deps, actions, unsat = get_env_dependencies(m, env, m.config.variant,
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies
02:31:45 BIOCONDA INFO (OUT) actions = environ.get_install_actions(tmpdir, tuple(dependencies), env,
02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions
02:31:45 BIOCONDA INFO (OUT) raise err
02:31:45 BIOCONDA INFO (OUT) conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base==4.3.0=h0fc540b_0"), MatchSpec("icu[version='>=72.1,<73.0a0']")}
37 changes: 37 additions & 0 deletions recipes/bioconductor-rjmcmcnucleosomes/build_failure.osx-64.yaml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
recipe_sha: 57c464f557d893513c8a51289794676d266d43f1471676f3bcf810b5a60c4160 # The commit 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.
reason: |-
./Nucleosome.h:13:10: fatal error: 'gsl/gsl_randist.h' file not found
category: |-
compiler error
log: |-
3:29:52 BIOCONDA INFO (OUT) x86_64-apple-darwin13.4.0-clang++ -I"$PREFIX/lib/R/include" -DNDEBUG `gsl-config --cflags` -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c NucleoDirichlet.cpp -o NucleoDirichlet.o
29:52 BIOCONDA INFO (ERR) /bin/sh: gsl-config: command not found
29:58 BIOCONDA INFO (ERR) In file included from NucleoDirichlet.cpp:7:
29:58 BIOCONDA INFO (ERR) In file included from ./NucleoDirichlet.h:12:
29:58 BIOCONDA INFO (ERR) ./Nucleosome.h:13:10: fatal error: 'gsl/gsl_randist.h' file not found
29:58 BIOCONDA INFO (ERR) #include <gsl/gsl_randist.h>
29:58 BIOCONDA INFO (ERR) ^~~~~~~~~~~~~~~~~~~
29:58 BIOCONDA INFO (ERR) 1 error generated.
29:58 BIOCONDA INFO (ERR) make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rjmcmcnucleosomes_1702610665714/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/etc/Makeconf:200: NucleoDirichlet.o] Error 1
29:58 BIOCONDA INFO (ERR) ERROR: compilation failed for package ‘RJMCMCNucleosomes’
29:58 BIOCONDA INFO (ERR) * removing ‘/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rjmcmcnucleosomes_1702610665714/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/RJMCMCNucleosomes’
29:58 BIOCONDA INFO (ERR) Traceback (most recent call last):
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
29:58 BIOCONDA INFO (ERR) sys.exit(main())
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
29:58 BIOCONDA INFO (ERR) call_conda_build(action, config)
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
29:58 BIOCONDA INFO (ERR) result = api.build(
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
29:58 BIOCONDA INFO (ERR) return build_tree(
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
29:58 BIOCONDA INFO (ERR) packages_from_this = build(metadata, stats,
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build
29:58 BIOCONDA INFO (ERR) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env
29:58 BIOCONDA INFO (ERR) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
29:58 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ
29:58 BIOCONDA INFO (ERR) raise subprocess.CalledProcessError(proc.returncode, _args)
29:58 BIOCONDA INFO (ERR) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rjmcmcnucleosomes_1702610665714/work/conda_build.sh']' returned non-zero exit status 1.
6 changes: 6 additions & 0 deletions recipes/bioconductor-sccomp/build_failure.osx-64.yaml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
recipe_sha: c6c86a551617ab192acea3543c4da0aa9ddee063ff6e7204b82211c508530538 # The commit 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.
reason: |-
nothing provides requested r-rstan >=2.26.0
category: |-
dependency issue

0 comments on commit fee0e3f

Please sign in to comment.