[Debian-med-packaging] Bug#1047681: smalt: Fails to build source after successful build

[Lucas Nussbaum]

Source: smalt
Version: 0.7.6-12
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 smalt
> dpkg-buildpackage: info: source version 0.7.6-12
> 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
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 	make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in misc
> make[3]: Entering directory '/<<PKGBUILDDIR>>/misc'
> test -z "simread fetchseq splitreads mixreads splitmates readstats trunkreads basqcol simqual" || rm -f simread fetchseq splitreads mixreads splitmates readstats trunkreads basqcol simqual
> 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 -rf ./.deps
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/misc'
> Making distclean in test
> make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
> Making distclean in data
> make[4]: Entering directory '/<<PKGBUILDDIR>>/test/data'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/test/data'
> Making distclean in .
> make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
> test -z "sequenceReverseComplement_test smalt_Xali_test    " || rm -f sequenceReverseComplement_test smalt_Xali_test    
> 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
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
> rm -rf ./.deps
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
> Making distclean in src
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "smalt" || rm -f smalt
> test -z "libseq.a libsgm.a" || rm -f libseq.a libsgm.a
> 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 -rf ./.deps
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making distclean in .
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f config.h stamp-h1
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -rf test/*.pyc misc/*.pyc test/tmp
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building smalt using existing ./smalt_0.7.6.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to misc/__pycache__/SAM.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add misc/__pycache__/SAM.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/__pycache__/formats.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add test/__pycache__/formats.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/__pycache__/testdata.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add test/__pycache__/testdata.cpython-311.pyc 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/smalt_0.7.6-12_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.