[Debichem-devel] Bug#1045215: mdanalysis: Fails to build source after successful build

[Lucas Nussbaum]

Source: mdanalysis
Version: 2.5.0+dfsg1-2
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 mdanalysis
> dpkg-buildpackage: info: source version 2.5.0+dfsg1-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Drew Parsons <dparsons at debian.org>
>  dpkg-source --before-build .
> dpkg-source: info: using options from mdanalysis-2.5.0+dfsg1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
>  fakeroot debian/rules clean
> dh clean --with python3,sphinxdoc --buildsystem=pybuild
>    dh_auto_clean -O--buildsystem=pybuild
>    debian/rules execute_after_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f .duecredit.p
> rm -f package/MDAnalysis/authors.py
> rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \
>   package/MDAnalysis/analysis/encore/cutils.c \
>   package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \
>   package/MDAnalysis/lib/_augment.cpp \
>   package/MDAnalysis/lib/_cutil.cpp \
>   package/MDAnalysis/lib/c_distances.c \
>   package/MDAnalysis/lib/c_distances_openmp.c \
>   package/MDAnalysis/lib/formats/cython_util.c \
>   package/MDAnalysis/lib/formats/libdcd.c \
>   package/MDAnalysis/lib/formats/libmdaxdr.c \
>   package/MDAnalysis/lib/nsgrid.cpp \
>   package/MDAnalysis/lib/qcprot.c
> rm -rf package/MDAnalysis.egg-info
> rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz  testsuite/MDAnalysisTests/data/*/.*_offsets.npz
> rm -rf testsuite/.pytest_cache
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
>  dpkg-source -b .
> dpkg-source: info: using options from mdanalysis-2.5.0+dfsg1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building mdanalysis using existing ./mdanalysis_2.5.0+dfsg1.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/.adk_oplsaa.trr_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/.adk_oplsaa.xtc_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/.cobrotoxin.trr_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/.cobrotoxin.xtc_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/.surface.trr_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/.xtc_test_only_10_frame_10_atoms.xtc_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/.xyz_random_walk.xtc_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/analysis/.YiiP_lipids.xtc_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/coordinates/.test.trr_offsets.lock' will not be represented in diff
> dpkg-source: warning: newly created empty file 'testsuite/MDAnalysisTests/data/coordinates/.test.xtc_offsets.lock' will not be represented in diff
> dpkg-source: info: local changes detected, the modified files are:
>  mdanalysis-2.5.0+dfsg1/package/MDAnalysis/coordinates/timestep.cpp
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/mdanalysis_2.5.0+dfsg1-2.diff.QZjbD4
> 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/mdanalysis_2.5.0+dfsg1-2_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.