[Debian-med-packaging] Bug#1044465: gubbins: Fails to build source after successful build

[Lucas Nussbaum]

Source: gubbins
Version: 3.3.0-2
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 gubbins
> dpkg-buildpackage: info: source version 3.3.0-2
> 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
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "libgubbins.la" || rm -f libgubbins.la
> rm -rf .libs _libs
> rm -f *.o
> test -z "run_all_tests.log" || rm -f run_all_tests.log
>  rm -f run_all_tests
>  rm -f gubbins
> rm -f *.lo
> rm -f ../tests/*.o
> rm -f *.tab.c
> test -z "run_all_tests.trs" || rm -f run_all_tests.trs
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f ../tests/.deps/.dirstamp
> rm -f ./so_locations
> rm -f ../tests/.dirstamp
> rm -f ../tests/.deps/run_all_tests-check_branch_sequences.Po
> rm -f ../tests/.deps/run_all_tests-check_gubbins.Po
> rm -f ../tests/.deps/run_all_tests-check_parse_phylip.Po
> rm -f ../tests/.deps/run_all_tests-check_snp_searching.Po
> rm -f ../tests/.deps/run_all_tests-check_snp_sites.Po
> rm -f ../tests/.deps/run_all_tests-check_vcf_parsing.Po
> rm -f ../tests/.deps/run_all_tests-helper_methods.Po
> rm -f ../tests/.deps/run_all_tests-run_all_tests.Po
> rm -f ./.deps/Newickform.Plo
> rm -f ./.deps/alignment_file.Plo
> rm -f ./.deps/block_tab_file.Plo
> rm -f ./.deps/branch_sequences.Plo
> rm -f ./.deps/csv_of_snp_sites.Plo
> rm -f ./.deps/fasta_of_snp_sites.Plo
> rm -f ./.deps/gff_file.Plo
> rm -f ./.deps/gubbins.Plo
> rm -f ./.deps/main.Po
> rm -f ./.deps/parse_phylip.Plo
> rm -f ./.deps/parse_vcf.Plo
> rm -f ./.deps/phylip_of_snp_sites.Plo
> rm -f ./.deps/seqUtil.Plo
> rm -f ./.deps/snp_searching.Plo
> rm -f ./.deps/snp_sites.Plo
> rm -f ./.deps/string_cat.Plo
> rm -f ./.deps/tree_scaling.Plo
> rm -f ./.deps/tree_statistics.Plo
> rm -f ./.deps/vcf.Plo
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making distclean in release
> make[2]: Entering directory '/<<PKGBUILDDIR>>/release'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/release'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f 
> rm -f config.h stamp-h1
> rm -f libtool config.lt
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> rm -rf python/*.egg-info python/build  python/Makefile
> find . -name "*.pyc" -delete
> rm -rf python/output_alignment python/tmp*
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building gubbins using existing ./gubbins_3.3.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file tests/data/multiple_recombinations.tre, use --include-removal to override
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_branch_sequences.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_branch_sequences.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_branch_sequences.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_branch_sequences.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_gubbins.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_gubbins.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_gubbins.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_gubbins.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_parse_phylip.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_parse_phylip.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_parse_phylip.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_parse_phylip.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_snp_searching.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_snp_searching.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_snp_searching.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_snp_searching.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_snp_sites.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_snp_sites.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_snp_sites.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_snp_sites.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_vcf_parsing.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_vcf_parsing.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-check_vcf_parsing.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-check_vcf_parsing.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-helper_methods.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-helper_methods.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-helper_methods.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-helper_methods.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-run_all_tests.gcda: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-run_all_tests.gcda in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/run_all_tests-run_all_tests.gcno: binary file contents changed
> dpkg-source: error: add tests/run_all_tests-run_all_tests.gcno in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> 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/gubbins_3.3.0-2_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.