[Debian-med-packaging] Bug#1048122: ska: Fails to build source after successful build

[Lucas Nussbaum]

Source: ska
Version: 1.0+dfsg-2.1
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 ska
> dpkg-buildpackage: info: source version 1.0+dfsg-2.1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Bastian Germann <bage at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f  build/DNA.o  build/general.o  build/kmers.o  build/sk_align.o  build/sk_alleles.o  build/sk_compare.o  build/sk_distance.o  build/sk_fasta.o  build/sk_fastq.o  build/sk_find.o  build/sk_humanise.o  build/sk_info.o  build/sk_merge.o  build/sk_refalign.o  build/sk_summary.o  build/sk_type.o  build/sk_unique.o  build/sk_weed.o  build/ska.o
> rm -f bin/ska
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building ska using existing ./ska_1.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to tests/DNA.o: binary file contents changed
> dpkg-source: error: add tests/DNA.o 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/DNA_unittest: binary file contents changed
> dpkg-source: error: add tests/DNA_unittest in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/DNA_unittest' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/general.o: binary file contents changed
> dpkg-source: error: add tests/general.o 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/general_unittest: binary file contents changed
> dpkg-source: error: add tests/general_unittest in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/general_unittest' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/gtest-all.o: binary file contents changed
> dpkg-source: error: add tests/gtest-all.o 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/gtest_main.a: binary file contents changed
> dpkg-source: error: add tests/gtest_main.a 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/gtest_main.o: binary file contents changed
> dpkg-source: error: add tests/gtest_main.o 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/kmers.o: binary file contents changed
> dpkg-source: error: add tests/kmers.o 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/kmers_unittest: binary file contents changed
> dpkg-source: error: add tests/kmers_unittest in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/kmers_unittest' will not be represented in diff
> 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/ska_1.0+dfsg-2.1_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.