[Debian-med-packaging] Bug#1044467: genometools: Fails to build source after successful build
Lucas Nussbaum
lucas at debian.org
Sun Aug 13 17:56:56 BST 2023
Source: genometools
Version: 1.6.2+ds-3
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild
Hi,
This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).
This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.
More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> --------------------------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package genometools
> dpkg-buildpackage: info: source version 1.6.2+ds-3
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
> dpkg-source --before-build .
> debian/rules clean
> dh clean --with python3
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> mkdir -p obj
> /usr/bin/make cleanup
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf lib
> find obj -name '*.o' -delete
> rm -f obj/amalgamation.c
> rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests
> /usr/bin/make -s -C ./doc/devguide clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/devguide'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/devguide'
> /usr/bin/make -s -C ./doc/manuals clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manuals'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manuals'
> rm -f doc/manuals/api_reference.tex \
> doc/manuals/gtscript_reference.tex
> find doc . -name "*.toc" -delete
> rm -f www/genometools.org/htdocs/images/callbacks.png \
> www/genometools.org/htdocs/images/parsed.png \
> www/genometools.org/htdocs/images/constructed.png \
> doc/manuals/annotationsketch.pdf
> rm -f www/genometools.org/htdocs/examples.html
> rm -rf doc/manpages
> find testdata \( -name '*.esq' -o -name '*.sds' -o -name '*.ssp' \
> -o -name '*.ois' -o -name '*.al1' \) \
> -a ! \( -name 'foo.[36][24].*' \) -delete
> find obj -name '*.splint' -delete
> find obj -name '*.check' -delete
> find obj -name '*.sb' -delete
> rm -rf bin obj
> rm -rf gtpython/build
> /usr/bin/make -s -C ./doc/manuals cleanup
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manuals'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manuals'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> cd doc/manuals; /usr/bin/make cleanup
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc/manuals'
> rm -f *.aux *.log *.bbl *.blg *.dvi *.mer *.mct *.mbd comment.cut
> rm -f *.out *.toc
> rm -f U89959.fna read[12].fna
> rm -f reads.al1 reads.esq reads.lcp reads.llv reads.prj reads.suf
> rm -f tallymer-tmp.tex
> rm -f tagerator-tmp.tex Q1.gz pck-human.*
> rm -f readjoiner.pdf hop.pdf ltrharvest.pdf ltrdigest.pdf uniquesub.pdf matstat.pdf mgth.pdf packedindex.pdf repfind.pdf tallymer.pdf tagerator.pdf genomediff.pdf
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc/manuals'
> # should be deleted inside doc/manuals/Makefile
> rm -f doc/manuals/annotationsketch.out \
> doc/manuals/api_reference.tex \
> doc/manuals/gtscript_reference.tex
> find doc . -name "*.toc" -delete
> find testdata \( -name '*.ois' -or -name '*.sds' -or -name '*.esq' -or \
> -name '*.ssp' -or -name '*.des' -or -name "*.md5" \) -and \( -not \
> -name '*foo.32.*' -not -name '*foo.64.*' \) -delete
> rm -f www/genometools.org/htdocs/images/callbacks.png \
> www/genometools.org/htdocs/images/parsed.png \
> www/genometools.org/htdocs/images/constructed.png \
> doc/manuals/annotationsketch.pdf
> rm -f www/genometools.org/htdocs/examples.html \
> www/genometools.org/htdocs/libgenometools.html
> rm -rf gtpython/build
> rm -rf obj
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_clean
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building genometools using existing ./genometools_1.6.2+ds.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file www/genometools.org/htdocs/libgenometools.html, use --include-removal to override
> dpkg-source: warning: file genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/__init__.py has no final newline (either original or modified version)
> dpkg-source: warning: file genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/version.py has no final newline (either original or modified version)
> dpkg-source: warning: file genometools-1.6.2+ds/gtpython/GenomeTools.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/.pydistutils.cfg
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/__init__.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/__init__.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/block.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/canvas.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/color.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/custom_track.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/custom_track_example.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/diagram.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/feature_index.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/feature_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/graphics.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/image_info.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/layout.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/rec_map.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/annotationsketch/style.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/__init__.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/alphabet.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/array.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/encseq.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/error.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/gtrange.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/gtstr.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/readmode.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/str_array.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/core/warning.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/dlload.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/__init__.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/add_introns_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/anno_db.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/comment_node.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/custom_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/custom_stream_example.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/custom_visitor.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/custom_visitor_example.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/dup_feature_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/eof_node.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/feature_index.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/feature_node.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/feature_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/genome_node.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/genome_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/gff3_in_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/gff3_out_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/gff3_visitor.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/inter_feature_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/merge_feature_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/meta_node.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/node_visitor.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/rdb.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/region_node.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/sequence_node.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/sort_stream.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/extended/strand.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/props.py
> genometools-1.6.2+ds/.pybuild/cpython3_3.11/build/gt/version.py
> genometools-1.6.2+ds/gtpython/GenomeTools.egg-info/PKG-INFO
> genometools-1.6.2+ds/gtpython/GenomeTools.egg-info/SOURCES.txt
> genometools-1.6.2+ds/gtpython/GenomeTools.egg-info/dependency_links.txt
> genometools-1.6.2+ds/gtpython/GenomeTools.egg-info/top_level.txt
> genometools-1.6.2+ds/www/genometools.org/htdocs/docs.html
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/genometools_1.6.2+ds-3.diff.B1ntAY
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/13/genometools_1.6.2+ds-3_unstable.log
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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