Source: khmer Version: 3.0.0~a3+dfsg-4 Severity: important Tags: ftbfs User: python-modules-t...@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 sph...@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-t...@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-t...@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