Your message dated Sat, 21 Feb 2026 09:04:46 +0000
with message-id <[email protected]>
and subject line Bug#1044465: fixed in gubbins 3.4.3-3
has caused the Debian Bug report #1044465,
regarding gubbins: Fails to build source after successful build
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1044465: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1044465
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: gubbins
Version: 3.3.0-2
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 gubbins
> dpkg-buildpackage: info: source version 3.3.0-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <[email protected]>
> 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.
--- End Message ---
--- Begin Message ---
Source: gubbins
Source-Version: 3.4.3-3
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
gubbins, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated gubbins package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 21 Feb 2026 09:30:44 +0100
Source: gubbins
Architecture: source
Version: 3.4.3-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1044465 1128512
Changes:
gubbins (3.4.3-3) unstable; urgency=medium
.
* remove-numba-temporarily.patch: update.
Cleanup occurrences of numba in python/setup.py.
Thanks to Adrian Bunk (Closes: #1128512)
* d/clean: also cleanup leftover csv files. (Closes: #1044465)
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Files:
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