Source: bio-tradis Version: 1.4.5+dfsg2-1 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-sab-20230813 ftbfs-source-after-build User: [email protected] 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 bio-tradis > dpkg-buildpackage: info: source version 1.4.5+dfsg2-1 > dpkg-buildpackage: info: source distribution unstable > dpkg-buildpackage: info: source changed by Michael R. Crusoe > <[email protected]> > dpkg-source --before-build . > fakeroot debian/rules clean > dh clean > dh_auto_clean > make -j8 distclean > make[1]: Entering directory '/<<PKGBUILDDIR>>' > rm -f \ > blib/script/add_tradis_tags blib/script/bacteria_tradis \ > blib/script/check_tradis_tags blib/script/combine_tradis_plots \ > blib/script/filter_tradis_tags blib/script/remove_tradis_tags \ > blib/script/tradis_comparison.R blib/script/tradis_essentiality.R \ > blib/script/tradis_gene_insert_sites blib/script/tradis_merge_plots \ > blib/script/tradis_plot > "/usr/bin/perl" "-MExtUtils::Manifest=fullcheck" -e fullcheck > rm -f \ > Tradis.bso Tradis.def \ > Tradis.exp Tradis.x \ > blib/arch/auto/Bio/Tradis/extralibs.all \ > blib/arch/auto/Bio/Tradis/extralibs.ld Makefile.aperl \ > *.a *.o \ > *perl.core MYMETA.json \ > MYMETA.yml blibdirs.ts \ > core core.*perl.*.? \ > core.[0-9] core.[0-9][0-9] \ > core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \ > core.[0-9][0-9][0-9][0-9][0-9] libTradis.def \ > mon.out perl \ > perl perl.exe \ > perlmain.c pm_to_blib \ > pm_to_blib.ts so_locations \ > tmon.out > rm -rf \ > blib > mv Makefile Makefile.old > /dev/null 2>&1 > rm -f \ > Makefile Makefile.old > rm -rf \ > Bio-Tradis-1.4.5 > No such file: BioTraDISTutorial.pdf > No such file: t/data/FilterTags/expected.caa.fastq > No such file: t/data/FilterTags/expected.tna.fastq > No such file: t/data/RemoveTags/expected.rm.caa.fastq > No such file: t/data/RemoveTags/expected.rm.tna.fastq > Not in MANIFEST: .pc/.quilt_patches > Not in MANIFEST: .pc/.quilt_series > Not in MANIFEST: .pc/.version > Not in MANIFEST: .pc/applied-patches > Not in MANIFEST: .pc/samtools1.10/lib/Bio/Tradis/Samtools.pm > Not in MANIFEST: > debian/.debhelper/generated/bio-tradis/dh_installchangelogs.dch.trimmed > Not in MANIFEST: > debian/.debhelper/generated/bio-tradis/installed-by-dh_install > Not in MANIFEST: > debian/.debhelper/generated/bio-tradis/installed-by-dh_installdocs > Not in MANIFEST: > debian/.debhelper/generated/bio-tradis/installed-by-dh_installman > Not in MANIFEST: debian/bio-tradis.debhelper.log > Not in MANIFEST: debian/bio-tradis.substvars > Not in MANIFEST: debian/bio-tradis/DEBIAN/control > Not in MANIFEST: debian/bio-tradis/DEBIAN/md5sums > Not in MANIFEST: debian/bio-tradis/usr/bin/add_tradis_tags > Not in MANIFEST: debian/bio-tradis/usr/bin/bacteria_tradis > Not in MANIFEST: debian/bio-tradis/usr/bin/check_tradis_tags > Not in MANIFEST: debian/bio-tradis/usr/bin/combine_tradis_plots > Not in MANIFEST: debian/bio-tradis/usr/bin/filter_tradis_tags > Not in MANIFEST: debian/bio-tradis/usr/bin/remove_tradis_tags > Not in MANIFEST: debian/bio-tradis/usr/bin/tradis_comparison > Not in MANIFEST: debian/bio-tradis/usr/bin/tradis_essentiality > Not in MANIFEST: debian/bio-tradis/usr/bin/tradis_gene_insert_sites > Not in MANIFEST: debian/bio-tradis/usr/bin/tradis_merge_plots > Not in MANIFEST: debian/bio-tradis/usr/bin/tradis_plot > Not in MANIFEST: > debian/bio-tradis/usr/share/doc/bio-tradis/changelog.Debian.gz > Not in MANIFEST: debian/bio-tradis/usr/share/doc/bio-tradis/changelog.gz > Not in MANIFEST: debian/bio-tradis/usr/share/doc/bio-tradis/copyright > Not in MANIFEST: debian/bio-tradis/usr/share/doc/bio-tradis/NEWS.Debian.gz > Not in MANIFEST: debian/bio-tradis/usr/share/doc/bio-tradis/README.Debian > Not in MANIFEST: debian/bio-tradis/usr/share/doc/bio-tradis/README.md.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/add_tradis_tags.1p.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/bacteria_tradis.1p.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/check_tradis_tags.1p.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man1/combine_tradis_plots.1p.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/filter_tradis_tags.1p.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/remove_tradis_tags.1p.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/tradis_comparison.1.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/tradis_essentiality.1.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man1/tradis_gene_insert_sites.1p.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man1/tradis_plot.1p.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man3/Bio::Tradis.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::AddTagsToSeq.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::Exceptions.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::InsertSite.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CombinePlots.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::AddTags.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::CheckTags.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::FilterFastqTags.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotCombine.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotTradis.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RemoveFastqTags.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RunMapping.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisAnalysis.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisBam.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::DetectTags.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Exception.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::FilterTags.3pm.gz > Not in MANIFEST: debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Map.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Bam.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Cigar.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Fastq.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RemoveTags.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RunTradis.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Samtools.3pm.gz > Not in MANIFEST: > debian/bio-tradis/usr/share/man/man3/Bio::Tradis::TradisPlot.3pm.gz > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/AddTagsToSeq.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/Exceptions.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/InsertSite.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/CombinePlots.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/AddTags.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/CheckTags.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/FilterFastqTags.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotCombine.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotTradis.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RemoveFastqTags.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RunMapping.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisAnalysis.pm > Not in MANIFEST: > debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisBam.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/DetectTags.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/Exception.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/FilterTags.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/Map.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Bam.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Cigar.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Fastq.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/RemoveTags.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/RunTradis.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/Samtools.pm > Not in MANIFEST: debian/bio-tradis/usr/share/perl5/Bio/Tradis/TradisPlot.pm > Not in MANIFEST: debian/changelog > Not in MANIFEST: debian/control > Not in MANIFEST: debian/copyright > Not in MANIFEST: debian/createmanpages > Not in MANIFEST: debian/debhelper-build-stamp > Not in MANIFEST: debian/docs > Not in MANIFEST: debian/files > Not in MANIFEST: debian/install > Not in MANIFEST: debian/manpages > Not in MANIFEST: debian/mans/tradis_comparison.1 > Not in MANIFEST: debian/mans/tradis_essentiality.1 > Not in MANIFEST: debian/mans/tradis_merge_plots.1 > Not in MANIFEST: debian/NEWS > Not in MANIFEST: debian/patches/samtools1.10 > Not in MANIFEST: debian/patches/series > Not in MANIFEST: debian/README.Debian > Not in MANIFEST: debian/rules > Not in MANIFEST: debian/source/format > Not in MANIFEST: debian/tests/pkg-perl/smoke-skip > Not in MANIFEST: debian/upstream/metadata > Not in MANIFEST: debian/watch > Not in MANIFEST: expected.bwa.nohead.mapped > Not in MANIFEST: expected.smalt.nohead.mapped > Not in MANIFEST: mapped.nohead.out > Not in MANIFEST: output.fastq > Not in MANIFEST: test.plot.unzipped > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > dh_clean > dpkg-source -b . > dpkg-source: info: using source format '3.0 (quilt)' > dpkg-source: info: building bio-tradis using existing > ./bio-tradis_1.4.5+dfsg2.orig.tar.xz > dpkg-source: info: using patch list from debian/patches/series > dpkg-source: warning: ignoring deletion of file > t/data/FilterTags/expected.caa.fastq, use --include-removal to override > dpkg-source: warning: ignoring deletion of file > t/data/FilterTags/expected.tna.fastq, use --include-removal to override > dpkg-source: warning: ignoring deletion of file > t/data/RemoveTags/expected.rm.tna.fastq, use --include-removal to override > dpkg-source: warning: ignoring deletion of file > t/data/RemoveTags/expected.rm.caa.fastq, use --include-removal to override > dpkg-source: info: local changes detected, the modified files are: > bio-tradis-1.4.5+dfsg2/expected.bwa.nohead.mapped > bio-tradis-1.4.5+dfsg2/expected.smalt.nohead.mapped > bio-tradis-1.4.5+dfsg2/mapped.nohead.out > bio-tradis-1.4.5+dfsg2/output.fastq > bio-tradis-1.4.5+dfsg2/test.plot.unzipped > dpkg-source: error: aborting due to unexpected upstream changes, see > /tmp/bio-tradis_1.4.5+dfsg2-1.diff.7LfaJF > 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/bio-tradis_1.4.5+dfsg2-1_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.
