[Debian-med-packaging] Bug#1046620: htseq: Fails to build source after successful build

[Lucas Nussbaum]

Source: htseq
Version: 1.99.2-1
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 htseq
> dpkg-buildpackage: info: source version 1.99.2-1
> 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 --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 
> /bin/sh: 1: git: not found
> /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
> !!
> 
>         ********************************************************************************
>         Requirements should be satisfied by a PEP 517 installer.
>         If you are using pip, you can try `pip install --use-pep517`.
>         ********************************************************************************
> 
> !!
>   dist.fetch_build_eggs(dist.setup_requires)
> WARNING: The wheel package is not available.
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_htseq/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
> # setup.py creates some symlinks in clean target
> # remove these links to keep source tree clean
> for link in 'src' 'HTSeq' 'doc' 'scripts' 'test' ; do \
>   if [ -L ${link} ] ; then rm ${link} ; fi \
> done
> 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 htseq using existing ./htseq_1.99.2.orig.tar.gz
> dpkg-source: warning: ignoring deletion of file src/StepVector.py, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  htseq-1.99.2/HTSeq.egg-info/PKG-INFO
>  htseq-1.99.2/HTSeq.egg-info/SOURCES.txt
>  htseq-1.99.2/HTSeq.egg-info/requires.txt
>  htseq-1.99.2/HTSeq/StepVector.py
>  htseq-1.99.2/src/StepVector_wrap.cxx
>  htseq-1.99.2/src/_HTSeq.c
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/htseq_1.99.2-1.diff.h3ecYO
> 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/htseq_1.99.2-1_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.