[Debian-med-packaging] Bug#1043774: bio-tradis: Fails to build source after successful build

[Lucas Nussbaum]

Source: bio-tradis
Version: 1.4.5+dfsg2-1
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 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 <michael.crusoe at gmail.com>
>  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.