[Debian-med-packaging] Bug#1047821: libseqlib: Fails to build source after successful build

[Lucas Nussbaum]

Source: libseqlib
Version: 1.2.0+dfsg-10
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 libseqlib
> dpkg-buildpackage: info: source version 1.2.0+dfsg-10
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Étienne Mollier <emollier at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --with pkgkde_symbolshelper
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "libseqlib.la" || rm -f libseqlib.la
> rm -rf .libs _libs
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> rm -f ./so_locations
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f ./.deps/libseqlib_la-BFC.Plo
> rm -f ./.deps/libseqlib_la-BWAWrapper.Plo
> rm -f ./.deps/libseqlib_la-BamHeader.Plo
> rm -f ./.deps/libseqlib_la-BamReader.Plo
> rm -f ./.deps/libseqlib_la-BamRecord.Plo
> rm -f ./.deps/libseqlib_la-BamWriter.Plo
> rm -f ./.deps/libseqlib_la-FastqReader.Plo
> rm -f ./.deps/libseqlib_la-FermiAssembler.Plo
> rm -f ./.deps/libseqlib_la-GenomicRegion.Plo
> rm -f ./.deps/libseqlib_la-ReadFilter.Plo
> rm -f ./.deps/libseqlib_la-RefGenome.Plo
> rm -f ./.deps/libseqlib_la-SeqPlot.Plo
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "libseqlib.pc" || rm -f libseqlib.pc
> rm -f config.h stamp-h1
> rm -f libtool config.lt
> 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>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building libseqlib using existing ./libseqlib_1.2.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file src/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/seqtools/Makefile.in, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  libseqlib-1.2.0+dfsg/src/seqtools/Makefile
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/libseqlib_1.2.0+dfsg-10.diff.SH0LYd
> 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/libseqlib_1.2.0+dfsg-10_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.