[Debian-med-packaging] Bug#1043871: biomaj3-cli: Fails to build source after successful build

[Lucas Nussbaum]

Source: biomaj3-cli
Version: 3.1.11-4
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 biomaj3-cli
> dpkg-buildpackage: info: source version 3.1.11-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --with python3 --buildsystem=pybuild
>    dh_auto_clean -O--buildsystem=pybuild
> I: pybuild base:275: python3.11 setup.py clean 
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_biomaj-cli/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
>    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 biomaj3-cli using existing ./biomaj3-cli_3.1.11.orig.tar.xz
> dpkg-source: warning: file biomaj3-cli-3.1.11/biomaj_cli.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
>  biomaj3-cli-3.1.11/biomaj_cli.egg-info/PKG-INFO
>  biomaj3-cli-3.1.11/biomaj_cli.egg-info/SOURCES.txt
>  biomaj3-cli-3.1.11/biomaj_cli.egg-info/dependency_links.txt
>  biomaj3-cli-3.1.11/biomaj_cli.egg-info/requires.txt
>  biomaj3-cli-3.1.11/biomaj_cli.egg-info/top_level.txt
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/biomaj3-cli_3.1.11-4.diff.nv9OoN
> 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/biomaj3-cli_3.1.11-4_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.