[Debian-med-packaging] Bug#1048006: python-pybedtools: Fails to build source after successful build

[Lucas Nussbaum]

Source: python-pybedtools
Version: 0.9.0-4
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 python-pybedtools
> dpkg-buildpackage: info: source version 0.9.0-4
> 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,sphinxdoc --buildsystem=pybuild
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> /bin/rm -rf fakehome .eggs .pybuild
> /bin/rm -rf debian/python3-pybedtools debian/files
> /bin/rm -rf pybedtools.egg-info
> /bin/rm -rf pybedtools/scripts/__pycache__/
> /bin/rm -rf pybedtools/contrib/__pycache__/
> /bin/rm -rf pybedtools/__pycache__/
> find pybedtools -name "*.so" -o -name "*.o" | xargs -r rm
> rm -rf build
> /bin/rm -rf pybedtools/cbedtools.cpp pybedtools/featurefuncs.cpp
> find docs/source/autodocs/ -name "*.rst" | xargs -r /bin/rm
> # dh_auto_clean
> 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 python-pybedtools using existing ./python-pybedtools_0.9.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file docs/source/autodocs/pybedtools.contrib.plotting.Track.rst, use --include-removal to override
> dpkg-source: warning: file python-pybedtools-0.9.0/pybedtools/version.py has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.add_color.rst
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.extend_fields.rst
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.five_prime.rst
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.greater_than.rst
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.less_than.rst
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst
>  python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.three_prime.rst
>  python-pybedtools-0.9.0/pybedtools/version.py
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/python-pybedtools_0.9.0-4.diff.axznIW
> 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/python-pybedtools_0.9.0-4_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.