[Debian-med-packaging] Bug#1047512: tnseq-transit: Fails to build source after successful build

[Lucas Nussbaum]

Source: tnseq-transit
Version: 3.2.7-1
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 tnseq-transit
> dpkg-buildpackage: info: source version 3.2.7-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Étienne Mollier <emollier at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --with python3 --buildsystem=pybuild
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> I: pybuild base:275: python3.11 setup.py clean 
> /usr/lib/python3/dist-packages/setuptools/dist.py:745: SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
> 
>         ********************************************************************************
>         Usage of dash-separated 'description-file' will not be supported in future
>         versions. Please use the underscore name 'description_file' instead.
> 
>         By 2023-Sep-26, you need to update your project and remove deprecated calls
>         or your builds will no longer be supported.
> 
>         See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
>         ********************************************************************************
> 
> !!
>   opt = self.warn_dash_deprecation(opt, section)
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build' (and everything under it)
> 'build/bdist.linux-x86_64' does not exist -- can't clean it
> 'build/scripts-3.11' does not exist -- can't clean it
> rm -rf tests_invalid_data
> rm -rf tnseq_transit.egg-info
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building tnseq-transit using existing ./tnseq-transit_3.2.7.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of symlink tests/H37Rv.fna
> dpkg-source: error: cannot represent change to tests/data/test-multicontig.fna.bwt: binary file contents changed
> dpkg-source: error: add tests/data/test-multicontig.fna.bwt 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/data/test-multicontig.fna.pac: binary file contents changed
> dpkg-source: error: add tests/data/test-multicontig.fna.pac 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/data/test-multicontig.fna.sa: binary file contents changed
> dpkg-source: error: add tests/data/test-multicontig.fna.sa 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/tnseq-transit_3.2.7-1_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.