[Debian-med-packaging] Bug#1042657: khmer: FTBFS with Sphinx 7.1, docutils 0.20: error: invalid command 'build_sphinx'
Lucas Nussbaum
lucas at debian.org
Sun Jul 30 19:23:34 BST 2023
Source: khmer
Version: 3.0.0~a3+dfsg-4
Severity: important
Tags: ftbfs
User: python-modules-team at lists.alioth.debian.org
Usertags: sphinx7.1
Hi,
khmer fails to build with Sphinx 7.1 and docutils 0.20, both of which
are currently available in experimental.
Relevant part (hopefully):
> x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -fopenmp
> copying build/lib.linux-x86_64-cpython-311/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -> khmer
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli
> Creating /<<PKGBUILDDIR>>/fakehome/.local/lib/python3.11/site-packages/khmer.egg-link (link to .)
> Adding khmer 3.0.0a3 to easy-install.pth file
> Installing interleave-reads.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing trim-low-abund.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing normalize-by-median.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing abundance-dist.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing extract-long-sequences.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing annotate-partitions.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing split-paired-reads.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing abundance-dist-single.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing sample-reads-randomly.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing find-knots.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing merge-partitions.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing count-median.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing load-graph.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing filter-abund-single.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing partition-graph.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing extract-paired-reads.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing filter-stoptags.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing unique-kmers.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing do-partition.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing fastq-to-fasta.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing readstats.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing make-initial-stoptags.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing extract-partitions.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing load-into-counting.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
> Installing filter-abund.py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
>
> Installed /<<PKGBUILDDIR>>
> Processing dependencies for khmer==3.0.0a3
> Searching for screed==1.1.2
> Best match: screed 1.1.2
> Adding screed 1.1.2 to easy-install.pth file
> Installing screed script to /<<PKGBUILDDIR>>/fakehome/.local/bin
>
> Using /usr/lib/python3/dist-packages
> Finished processing dependencies for khmer==3.0.0a3
> *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation.
> /usr/lib/python3/dist-packages/setuptools/dist.py:745: SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
>
> ********************************************************************************
> Usage of dash-separated 'include-dirs' will not be supported in future
> versions. Please use the underscore name 'include_dirs' instead.
>
> By 2023-Sep-26, you need to update your project and remove deprecated calls
> or your builds will no longer be supported.
>
> See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
> ********************************************************************************
>
> !!
> opt = self.warn_dash_deprecation(opt, section)
> /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
> !!
>
> ********************************************************************************
> Requirements should be satisfied by a PEP 517 installer.
> If you are using pip, you can try `pip install --use-pep517`.
> ********************************************************************************
>
> !!
> dist.fetch_build_eggs(dist.setup_requires)
> WARNING: The wheel package is not available.
> /usr/lib/python3/dist-packages/setuptools/dist.py:745: SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
>
> ********************************************************************************
> Usage of dash-separated 'include-dirs' will not be supported in future
> versions. Please use the underscore name 'include_dirs' instead.
>
> By 2023-Sep-26, you need to update your project and remove deprecated calls
> or your builds will no longer be supported.
>
> See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
> ********************************************************************************
>
> !!
> opt = self.warn_dash_deprecation(opt, section)
> usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
> or: setup.py --help [cmd1 cmd2 ...]
> or: setup.py --help-commands
> or: setup.py cmd --help
>
> error: invalid command 'build_sphinx'
> make[1]: *** [debian/rules:20: override_dh_auto_build] Error 1
The full build log is available from:
http://qa-logs.debian.net/2023/07/30/exp/khmer_3.0.0~a3+dfsg-4_unstable_sphinx-exp.log
Please see [1] for Sphinx changelog and [2] for Docutils changelog.
Also see [3] for the list of deprecated/removed APIs in Sphinx and possible
alternatives to them.
Some notable changes in Sphinx 6 and Sphinx 7:
- Sphinx no longer includes jquery.js and underscore.js by default.
Please use python3-sphinxcontrib.jquery package if you are using a custom
template and it still needs jquery.
- The setup.py build_sphinx command was removed. Please instead call
sphinx-build or "python3 -m sphinx" directly.
- For packages using the extlinks extension, the caption should contain
exactly one "%s" placeholder (if caption is not None).
In case you have questions, please Cc sphinx at packages.debian.org on reply.
[1]: https://www.sphinx-doc.org/en/master/changes.html
[2]: https://repo.or.cz/docutils.git/blob/refs/tags/docutils-0.20.1:/RELEASE-NOTES.txt
[3]: https://www.sphinx-doc.org/en/master/extdev/deprecated.html#dev-deprecated-apis
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=sphinx7.1;users=python-modules-team@lists.alioth.debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=sphinx7.1&fusertaguser=python-modules-team@lists.alioth.debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
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