[Debian-med-packaging] Bug#1043663: clonalorigin: Fails to build source after successful build

[Lucas Nussbaum]

Source: clonalorigin
Version: 1.0-6
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 clonalorigin
> dpkg-buildpackage: info: source version 1.0-6
> 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 --sourcedirectory=warg
>    dh_auto_clean -O--sourcedirectory=warg
> 	cd warg && make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>/warg'
> Making distclean in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/src'
> test -z "warg" || rm -f warg
> rm -f *.o
> test -z "profilerun.sh.log" || rm -f profilerun.sh.log
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f config.h stamp-h1
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test -z "profilerun.sh.trs" || rm -f profilerun.sh.trs
> test . = "." || test -z "" || rm -f 
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f ./.deps/warg-data.Po
> rm -f ./.deps/warg-metropolis.Po
> rm -f ./.deps/warg-move.Po
> rm -f ./.deps/warg-moveaddedge.Po
> rm -f ./.deps/warg-moveageclonal.Po
> rm -f ./.deps/warg-movedelta.Po
> rm -f ./.deps/warg-moveedgechange.Po
> rm -f ./.deps/warg-movegreedytree.Po
> rm -f ./.deps/warg-moveregraftclonal.Po
> rm -f ./.deps/warg-moveremedge.Po
> rm -f ./.deps/warg-moverho.Po
> rm -f ./.deps/warg-movescaletree.Po
> rm -f ./.deps/warg-movesitechange.Po
> rm -f ./.deps/warg-movetheta.Po
> rm -f ./.deps/warg-movetimechange.Po
> rm -f ./.deps/warg-mpiutils.Po
> rm -f ./.deps/warg-node.Po
> rm -f ./.deps/warg-param.Po
> rm -f ./.deps/warg-recedge.Po
> rm -f ./.deps/warg-rectree.Po
> rm -f ./.deps/warg-rng.Po
> rm -f ./.deps/warg-tree.Po
> rm -f ./.deps/warg-wargxml.Po
> rm -f ./.deps/warg-weakarg.Po
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
> Making distclean in scripts
> make[2]: Entering directory '/<<PKGBUILDDIR>>/warg/scripts'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/scripts'
> make[2]: Entering directory '/<<PKGBUILDDIR>>/warg'
> test -z "src/*.gcda src/*.gcno" || rm -f src/*.gcda src/*.gcno
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
>    dh_autoreconf_clean -O--sourcedirectory=warg
>    dh_clean -O--sourcedirectory=warg
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building clonalorigin using existing ./clonalorigin_1.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: info: local changes detected, the modified files are:
>  clonalorigin-1.0/warg/src/simulatedData.xmfa
>  clonalorigin-1.0/warg/src/testout
>  clonalorigin-1.0/warg/src/truth.xml
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/clonalorigin_1.0-6.diff.IHIr_Y
> 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/clonalorigin_1.0-6_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.