[Debian-med-packaging] Bug#1046065: hmmer2: Fails to build source after successful build

[Lucas Nussbaum]

Source: hmmer2
Version: 2.3.2+dfsg-8
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 hmmer2
> dpkg-buildpackage: info: source version 2.3.2+dfsg-8
> 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
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf binaries
> rm config.log config.status
> rm -rf autom4te.cache
> rm -f *.o *~ Makefile.bak core TAGS gmon.out
> rm Makefile
> (cd src;       make distclean)
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> rm -f *.o *~ Makefile.bak core hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch  TAGS gmon.out libhmmer.a
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> rm -f Makefile 
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> (cd testsuite; make distclean)
> make[2]: Entering directory '/<<PKGBUILDDIR>>/testsuite'
> make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/testsuite'
> rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/testsuite'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/testsuite'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> if [ -e configure_not_used ] ; then mv configure_not_used configure; fi
> rm -f configure.ac
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2pfam
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2fetch
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2align
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2emit
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2calibrate
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2index
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2build
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2convert
> dpkg-source: error: unwanted binary file: debian/tmp/bin/hmm2search
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2-doc/changelog.Debian.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2-doc/NOTES.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2-doc/changelog.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2/tutorial/pkinase.sto.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2/tutorial/rrm.sto.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2/tutorial/globins630.fa.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2/tutorial/globins50.msf.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2/tutorial/rrm.hmm.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2-doc/usr/share/doc/hmmer2/tutorial/fn3.sto.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/lib/hmmer2/hmmindex
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/lib/hmmer2/hmmpfam
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2pfam
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2fetch
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2align
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2emit
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2calibrate
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2index
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2build
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2convert
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/bin/hmm2search
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2pfam.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2convert.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2build.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmmer2.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2fetch.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2search.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2emit.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2index.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2calibrate.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/man/man1/hmm2align.1.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/doc/hmmer2/NEWS.Debian.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/doc/hmmer2/changelog.Debian.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/doc/hmmer2/NOTES.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/doc/hmmer2/changelog.gz
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/doc/hmmer2/examples/fn3-bin
> dpkg-source: error: unwanted binary file: debian/hmmer2/usr/share/doc/hmmer2/examples/fn3-bin-swap
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/19/cb4d842246146a9d9d8235d1237cf398c5d97f.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/6f/c1c7db7515d2ed5d6d4e6f0c09daeafee545eb.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/e5/5ecaf607616cbef097daf7db8eb05f9009e894.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/bd/88f0a149e2c0f7b5b852a7a5abd3acae05b134.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/70/2512f571c568ae3d30ef75a2681be1ba5a1554.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/92/743d2ef7095c1407e7a11cd6bad8a4f9d9250d.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/46/8eef128f0799b6ed1f1bb57b44ff6c6fdfaeb4.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/6e/f48b6504f37c7f8e5edbff21f02df413ee2537.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.build-id/dc/6b7ce0469d359b7b72e1636f5dc5bae1fdfe2d.debug
> dpkg-source: error: unwanted binary file: debian/.debhelper/hmmer2/dbgsym-root/usr/lib/debug/.dwz/x86_64-linux-gnu/hmmer2.debug
> dpkg-source: error: unwanted binary file: debian/libhmmer2-dev/usr/share/doc/libhmmer2-dev/changelog.Debian.gz
> dpkg-source: error: unwanted binary file: debian/libhmmer2-dev/usr/share/doc/libhmmer2-dev/NOTES.gz
> dpkg-source: error: unwanted binary file: debian/libhmmer2-dev/usr/share/doc/libhmmer2-dev/changelog.gz
> dpkg-source: error: detected 58 unwanted binary files (add them in debian/source/include-binaries to allow their inclusion).
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 255
> 
> 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/hmmer2_2.3.2+dfsg-8_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.