Your message dated Thu, 09 Apr 2020 09:34:37 +0000
with message-id <[email protected]>
and subject line Bug#955056: fixed in snakemake 5.10.0-3
has caused the Debian Bug report #955056,
regarding snakemake: FTBFS with Sphinx 2.4: AttributeError: 'member_descriptor'
object has no attribute 'expandtabs'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
955056: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955056
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: snakemake
Version: 5.10.0-2
Severity: important
Tags: ftbfs
User: [email protected]
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 [email protected] 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.
--- End Message ---
--- Begin Message ---
Source: snakemake
Source-Version: 5.10.0-3
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
snakemake, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated snakemake package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 09 Apr 2020 11:09:24 +0200
Source: snakemake
Architecture: source
Version: 5.10.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 955056
Changes:
snakemake (5.10.0-3) unstable; urgency=medium
.
* Team upload.
.
[ Rebecca N. Palmer ]
* Exclude lazy_property to make Sphinx succeed.
Closes: #955056
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--- End Message ---
