Source: snakemake Version: 5.10.0-2 Severity: important Tags: ftbfs User: python-modules-t...@lists.alioth.debian.org Usertags: sphinx2.4
Hi, snakemake fails to build with Sphinx 2.4, currently available in experimental. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > dh_auto_build > I: pybuild base:217: /usr/bin/python3 setup.py build > running build > running build_py > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/rules.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/executors.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/dag.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/persistence.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/checkpoints.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/parser.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/__main__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/decorators.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/benchmark.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/scheduler.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/logging.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/notebook.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/wrapper.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/workflow.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/script.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/jobs.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/_version.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/io.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/shell.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/gui.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/cwl.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/stats.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/exceptions.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/common.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/output_index.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/resources.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/utils.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/XRootD.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/dropbox.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/GS.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/NCBI.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/S3Mocked.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/webdav.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/SFTP.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/gridftp.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/gfal.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/AzureStorage.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/S3.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/EGA.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/FTP.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/iRODS.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > copying snakemake/remote/HTTP.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/remote > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/report > copying snakemake/report/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/report > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/caching > copying snakemake/caching/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/caching > copying snakemake/caching/hash.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/caching > copying snakemake/caching/local.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/caching > copying snakemake/caching/remote.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/caching > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/deployment > copying snakemake/deployment/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/deployment > copying snakemake/deployment/conda.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/deployment > copying snakemake/deployment/singularity.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/deployment > copying snakemake/deployment/env_modules.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/deployment > copying snakemake/report.css -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/jobscript.sh -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/gui.html -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake > copying snakemake/report/table.html -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/report > copying snakemake/report/report.html -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/report > UPDATING > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/_version.py > set > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/snakemake/_version.py > to '5.10.0' > PATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/bin:/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/bin:/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games > \ > PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_snakemake/build \ > python3 setup.py build_sphinx > running build_sphinx > Running Sphinx v2.4.3 > making output directory... done > building [mo]: targets for 0 po files that are out of date > building [html]: targets for 33 source files that are out of date > updating environment: [new config] 33 added, 0 changed, 0 removed > reading sources... [ 3%] api_reference/internal/modules > reading sources... [ 6%] api_reference/internal/snakemake > /usr/lib/python3/dist-packages/sphinx/util/compat.py:30: > RemovedInSphinx30Warning: The config variable "source_parsers" is deprecated. > Please update your extension for the parser and remove the setting. > warnings.warn('The config variable "source_parsers" is deprecated. ' > /usr/lib/python3/dist-packages/sphinx/util/compat.py:36: > RemovedInSphinx30Warning: app.add_source_parser() does not support suffix > argument. Use app.add_source_suffix() instead. > app.add_source_parser(suffix, parser) > > Exception occurred: > File "/usr/lib/python3/dist-packages/sphinx/util/docstrings.py", line 24, > in prepare_docstring > lines = s.expandtabs(tabsize).splitlines() > AttributeError: 'member_descriptor' object has no attribute 'expandtabs' > The full traceback has been saved in /tmp/sphinx-err-wxiq7_57.log, if you > want to report the issue to the developers. > Please also report this if it was a user error, so that a better error > message can be provided next time. > A bug report can be filed in the tracker at > <https://github.com/sphinx-doc/sphinx/issues>. Thanks! > make[1]: *** [debian/rules:35: override_dh_auto_build] Error 1 The full build log is available from: http://qa-logs.debian.net/2020/03/26/snakemake_5.10.0-2_unstable_sphinx243.log Please see [1] for Sphinx changelog, which may give a hint of what changes in Sphinx caused this error. Also see [2] for the list of deprecated/removed APIs and possible alternatives to them. Sphinx 2.4 is going to be uploaded to unstable in a couple of weeks. When that happens, the severity of this bug will be bumped to serious. In case you have questions, please Cc sph...@packages.debian.org on reply. [1]: https://www.sphinx-doc.org/en/2.0/changes.html [2]: https://www.sphinx-doc.org/en/2.0/extdev/deprecated.html#dev-deprecated-apis A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.