[Debian-med-packaging] Bug#1048393: pirs: Fails to build source after successful build

[Lucas Nussbaum]

Source: pirs
Version: 2.0.2+dfsg-11
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 pirs
> dpkg-buildpackage: info: source version 2.0.2+dfsg-11
> 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=src
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 	cd src && make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> Making distclean in pirs
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/pirs'
> test -z "pirs" || rm -f pirs
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f ./.deps/BaseCallingProfile.Po
> rm -f ./.deps/GCBiasProfile.Po
> rm -f ./.deps/IndelProfile.Po
> rm -f ./.deps/InputStream.Po
> rm -f ./.deps/MaskQvalsByEamss.Po
> rm -f ./.deps/OutputStream.Po
> rm -f ./.deps/Profile.Po
> rm -f ./.deps/SFMT.Po
> rm -f ./.deps/main.Po
> rm -f ./.deps/mt19937-64.Po
> rm -f ./.deps/pirs_diploid.Po
> rm -f ./.deps/pirs_simulate.Po
> rm -f ./.deps/util.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/pirs'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f config.h stamp-h1
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> cd src && ./srclean.sh >/dev/null 2>/dev/null || true
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--sourcedirectory=src
>    dh_clean -O--sourcedirectory=src
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building pirs using existing ./pirs_2.0.2+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to src/stator/gcContCvgBias/gc_coverage_bias: binary file contents changed
> dpkg-source: error: add src/stator/gcContCvgBias/gc_coverage_bias in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'src/stator/gcContCvgBias/gc_coverage_bias' will not be represented in diff
> dpkg-source: error: cannot represent change to src/stator/gcContCvgBias/main.o: binary file contents changed
> dpkg-source: error: add src/stator/gcContCvgBias/main.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/stator/gcContCvgBias/self_util.h.gch: binary file contents changed
> dpkg-source: error: add src/stator/gcContCvgBias/self_util.h.gch in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/stator/gcContCvgBias/self_util.o: binary file contents changed
> dpkg-source: error: add src/stator/gcContCvgBias/self_util.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/stator/gcContCvgBias/stat_soap_coverage.h.gch: binary file contents changed
> dpkg-source: error: add src/stator/gcContCvgBias/stat_soap_coverage.h.gch in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/stator/gcContCvgBias/stat_soap_coverage.o: binary file contents changed
> dpkg-source: error: add src/stator/gcContCvgBias/stat_soap_coverage.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> 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/pirs_2.0.2+dfsg-11_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.