[Debian-med-packaging] Bug#1049476: hmmer2: Fails to build binary packages again 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-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).

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/DoubleBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> ------------------------------------------------------------------------------------------------------------------------
> 
> 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 .
> dpkg-buildpackage: info: host architecture amd64
>  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>>'
>  debian/rules binary
> dh binary
>    dh_prep
>    debian/rules override_dh_auto_install
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_install -- prefix=/<<PKGBUILDDIR>>/debian/tmp
> # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1:
> rename 's/^hmm/hmm2/;' /<<PKGBUILDDIR>>/debian/tmp/bin/*
> cd /<<PKGBUILDDIR>>/debian/tmp/bin; rename 's/^hmm/hmm2/;' *
> /bin/sh: 1: cd: can't cd to /<<PKGBUILDDIR>>/debian/tmp/bin
> cd /<<PKGBUILDDIR>>/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' *
> /bin/sh: 1: cd: can't cd to /<<PKGBUILDDIR>>/debian/tmp/share/man/man1
> mv /<<PKGBUILDDIR>>/debian/tmp/share/man/man1/hmm2er.1 /<<PKGBUILDDIR>>/debian/tmp/share/man/man1/hmmer2.1
> mv: cannot stat '/<<PKGBUILDDIR>>/debian/tmp/share/man/man1/hmm2er.1': No such file or directory
> make[1]: *** [debian/rules:50: override_dh_auto_install] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:15: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.


The full build log is available from:
http://qa-logs.debian.net/2023/08/16/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.