[Debian-med-packaging] Bug#1046514: proteinortho: Fails to build source after successful build

[Lucas Nussbaum]

Source: proteinortho
Version: 6.2.3+dfsg-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 proteinortho
> dpkg-buildpackage: info: source version 6.2.3+dfsg-1
> 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
>    dh_auto_clean
> 	make -j8 clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.*
> rm -rf src/lapack-3.8.0/
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building proteinortho using existing ./proteinortho_6.2.3+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: newly created empty file 'remove.graph.done' will not be represented in diff
> dpkg-source: warning: file proteinortho-6.2.3+dfsg/test_diamond.proteinortho.html has no final newline (either original or modified version)
> dpkg-source: warning: file proteinortho-6.2.3+dfsg/test_singles_diamond.proteinortho.html has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
>  proteinortho-6.2.3+dfsg/test/C_clean.faa
>  proteinortho-6.2.3+dfsg/test_diamond.blast-graph
>  proteinortho-6.2.3+dfsg/test_diamond.info
>  proteinortho-6.2.3+dfsg/test_diamond.proteinortho-graph
>  proteinortho-6.2.3+dfsg/test_diamond.proteinortho-graph.summary
>  proteinortho-6.2.3+dfsg/test_diamond.proteinortho.html
>  proteinortho-6.2.3+dfsg/test_diamond.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_lapack.err
>  proteinortho-6.2.3+dfsg/test_lapack.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_lapack_K5.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_lapack_P3_K5.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_lapack_P4.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_lapack_ring4_K5.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_power.err
>  proteinortho-6.2.3+dfsg/test_power.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_power_ring4_K5.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_singles_diamond.blast-graph
>  proteinortho-6.2.3+dfsg/test_singles_diamond.info
>  proteinortho-6.2.3+dfsg/test_singles_diamond.proteinortho-graph
>  proteinortho-6.2.3+dfsg/test_singles_diamond.proteinortho-graph.summary
>  proteinortho-6.2.3+dfsg/test_singles_diamond.proteinortho.html
>  proteinortho-6.2.3+dfsg/test_singles_diamond.proteinortho.tsv
>  proteinortho-6.2.3+dfsg/test_singles_diamond.test
>  proteinortho-6.2.3+dfsg/test_singles_diamond.true
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/proteinortho_6.2.3+dfsg-1.diff.1ngYFC
> 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/proteinortho_6.2.3+dfsg-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.