[Debian-med-packaging] Bug#1048510: python-skbio: Fails to build source after successful build

[Lucas Nussbaum]

Source: python-skbio
Version: 0.5.8-4
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-skbio
> dpkg-buildpackage: info: source version 0.5.8-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe 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>>'
> if [ "`find . -name "*.pyo"`" = "" ] ; then echo no need to clean up ; else dh_auto_clean; fi
> no need to clean up
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> find ./skbio -name '*.so' -delete
> find ./skbio -name '*.o' -delete
> rm -rf doc/build build doc/source/generated
> find doc -name *.doctree -delete
> rm -rf .pybuild
> rm -f scikit_bio.egg-info/PKG-INFO scikit_bio.egg-info/SOURCES.txt scikit_bio.egg-info/dependency_links.txt scikit_bio.egg-info/requires.txt scikit_bio.egg-info/top_level.txt
> rm -f skbio/alignment/_ssw_wrapper.c skbio/diversity/_phylogenetic.c skbio/stats/__subsample.c skbio/metadata/_intersection.c
> mv simde-sse2.h.orig simde-sse2.h || true
> mv: cannot stat 'simde-sse2.h.orig': No such file or directory
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building python-skbio using existing ./python-skbio_0.5.8.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file simde-sse2.h, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file skbio/metadata/_intersection.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file skbio/alignment/_ssw_wrapper.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file skbio/stats/__subsample.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file skbio/diversity/_phylogenetic.c, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  python-skbio-0.5.8/skbio/stats/distance/_cutils.c
>  python-skbio-0.5.8/skbio/stats/ordination/_cutils.c
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/python-skbio_0.5.8-4.diff.QvA4ng
> 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-skbio_0.5.8-4_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.