[Debian-med-packaging] Bug#1045517: infernal: Fails to build source after successful build
Lucas Nussbaum
lucas at debian.org
Sun Aug 13 20:20:48 BST 2023
Source: infernal
Version: 1.1.4-1
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 infernal
> dpkg-buildpackage: info: source version 1.1.4-1
> 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
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> if [ -r Makefile ]; then /usr/bin/make distclean; fi
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> SUBDIR src
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> SUBDIR impl_sse
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/impl_sse'
> rm -f libinfernal-impl.stamp
> rm -f *.o *~ Makefile.bak core sse_cmsearch TAGS gmon.out cscope.out
> rm -f *.gcno
> for prog in sse_cmsearch; do \
> if test -d $prog.dSYM; then rm -rf $prog.dSYM; fi ;\
> done
> CLEAN impl_sse
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/impl_sse'
> rm -f *.o *~ Makefile.bak core cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmscan cmsearch cmstat trcyk bandcyk-montecarlo-test bandcyk-truncation-test cp9-test sub_cm-test truncyk_check cm_tophits_benchmark cm_tophits_utest itest_brute TAGS gmon.out
> rm -f libinfernal.a libinfernal-src.stamp
> rm -f *.gcno
> rm -f cscope.out
> for prog in cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmscan cmsearch cmstat trcyk bandcyk-montecarlo-test bandcyk-truncation-test cp9-test sub_cm-test truncyk_check cm_tophits_benchmark cm_tophits_utest itest_brute; do \
> if test -d $prog.dSYM; then rm -rf $prog.dSYM; fi ;\
> done
> CLEAN src
> SUBDIR impl_sse
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/impl_sse'
> rm -f libinfernal-impl.stamp
> rm -f *.o *~ Makefile.bak core sse_cmsearch TAGS gmon.out cscope.out
> rm -f *.gcno
> for prog in sse_cmsearch; do \
> if test -d $prog.dSYM; then rm -rf $prog.dSYM; fi ;\
> done
> CLEAN impl_sse
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/impl_sse'
> rm -f Makefile config.h
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> SUBDIR rmark
> make[3]: Entering directory '/<<PKGBUILDDIR>>/rmark'
> rm -f *.o *~ rmark-create rmark-rocplot TAGS
> rm -f *.gcno
> for prog in rmark-create rmark-rocplot; do \
> if test -d $prog.dSYM; then rm -rf $prog.dSYM; fi ;\
> done
> CLEAN rmark
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/rmark'
> SUBDIR testsuite
> make[3]: Entering directory '/<<PKGBUILDDIR>>/testsuite'
> rm -f *.gcno *.gcda *.gcov
> rm -f *.o *~
> CLEAN testsuite
> rm -f Makefile
> rm -f esltmp[a-z][a-z][0-9][0-9]*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/testsuite'
> SUBDIR documentation
> make[3]: Entering directory '/<<PKGBUILDDIR>>/documentation'
> SUBDIR userguide
> make[4]: Entering directory '/<<PKGBUILDDIR>>/documentation/userguide'
> rm -f latex.log
> rm -f main.aux main.bbl main.blg main.log main.toc x.log *~
> CLEAN userguide
> if test "x." != "x."; then \
> for texfile in cmbuild.tex copyright.tex filter.tex format_prior.tex formats.tex install.tex intro.tex macros.tex main.tex scores.tex titlepage.tex tutorial.tex diffoptions.tex; do \
> rm -f $texfile ;\
> done ;\
> fi
> rm -f symlinks.stamp
> rm -f titlepage.tex copyright.tex manpages.tex
> rm -f Userguide.pdf
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/documentation/userguide'
> SUBDIR man
> make[4]: Entering directory '/<<PKGBUILDDIR>>/documentation/man'
> rm -f *~
> rm -f *.man
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/documentation/man'
> rm -f *~
> rm -f Makefile
> CLEAN documentation
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/documentation'
> SUBDIR hmmer
> make[3]: Entering directory '/<<PKGBUILDDIR>>/hmmer'
> SUBDIR src
> make[4]: Entering directory '/<<PKGBUILDDIR>>/hmmer/src'
> SUBDIR impl_sse
> make[5]: Entering directory '/<<PKGBUILDDIR>>/hmmer/src/impl_sse'
> CLEAN impl_sse
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/src/impl_sse'
> CLEAN src
> SUBDIR impl_sse
> make[5]: Entering directory '/<<PKGBUILDDIR>>/hmmer/src/impl_sse'
> CLEAN impl_sse
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/src/impl_sse'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/src'
> SUBDIR profmark
> make[4]: Entering directory '/<<PKGBUILDDIR>>/hmmer/profmark'
> CLEAN profmark
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/profmark'
> SUBDIR testsuite
> make[4]: Entering directory '/<<PKGBUILDDIR>>/hmmer/testsuite'
> CLEAN testsuite
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/testsuite'
> SUBDIR documentation
> make[4]: Entering directory '/<<PKGBUILDDIR>>/hmmer/documentation'
> SUBDIR userguide
> make[5]: Entering directory '/<<PKGBUILDDIR>>/hmmer/documentation/userguide'
> SUBDIR inclusions
> make[6]: Entering directory '/<<PKGBUILDDIR>>/hmmer/documentation/userguide/inclusions'
> CLEAN inclusions
> make[6]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/documentation/userguide/inclusions'
> CLEAN userguide
> SUBDIR inclusions
> make[6]: Entering directory '/<<PKGBUILDDIR>>/hmmer/documentation/userguide/inclusions'
> CLEAN inclusions
> make[6]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/documentation/userguide/inclusions'
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/documentation/userguide'
> SUBDIR man
> make[5]: Entering directory '/<<PKGBUILDDIR>>/hmmer/documentation/man'
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/documentation/man'
> CLEAN documentation
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/documentation'
> SUBDIR ../easel
> make[4]: Entering directory '/<<PKGBUILDDIR>>/easel'
> SUBDIR documentation
> make[5]: Entering directory '/<<PKGBUILDDIR>>/easel/documentation'
> CLEAN documentation
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/easel/documentation'
> SUBDIR testsuite
> make[5]: Entering directory '/<<PKGBUILDDIR>>/easel/testsuite'
> CLEAN testsuite
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/easel/testsuite'
> SUBDIR miniapps
> make[5]: Entering directory '/<<PKGBUILDDIR>>/easel/miniapps'
> CLEAN miniapps
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/easel/miniapps'
> CLEAN easel
> SUBDIR documentation
> make[5]: Entering directory '/<<PKGBUILDDIR>>/easel/documentation'
> CLEAN documentation
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/easel/documentation'
> SUBDIR testsuite
> make[5]: Entering directory '/<<PKGBUILDDIR>>/easel/testsuite'
> CLEAN testsuite
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/easel/testsuite'
> SUBDIR miniapps
> make[5]: Entering directory '/<<PKGBUILDDIR>>/easel/miniapps'
> CLEAN miniapps
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/easel/miniapps'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/easel'
> SUBDIR libdivsufsort
> make[4]: Entering directory '/<<PKGBUILDDIR>>/hmmer/libdivsufsort'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/hmmer/libdivsufsort'
> rm: cannot remove 'config.log': No such file or directory
> rm: cannot remove 'config.status': No such file or directory
> make[3]: [Makefile:175: distclean] Error 1 (ignored)
> CLEAN hmmer
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/hmmer'
> CLEAN infernal
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> cd documentation/userguide && if [ -r Makefile ]; then make distclean; fi
> cd easel/documentation && if [ -r Makefile ]; then make distclean; fi
> dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1
> rm -f testsuite/i49.tbl
> 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 infernal using existing ./infernal_1.1.4.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to easel/easel:
> dpkg-source: error: new version is symlink to ../easel
> dpkg-source: error: old version is nonexistent
> dpkg-source: warning: ignoring deletion of file install-sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file configure, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file easel/decoy_config.h.in, use --include-removal to override
> dpkg-source: error: unrepresentable changes to source
> 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/infernal_1.1.4-1_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.
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