Your message dated Tue, 17 Dec 2024 18:19:13 +0000
with message-id <[email protected]>
and subject line Bug#1045517: fixed in infernal 1.1.5-3
has caused the Debian Bug report #1045517,
regarding infernal: Fails to build source after successful build
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1045517: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1045517
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: infernal
Version: 1.1.4-1
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: [email protected]
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 <[email protected]>
> 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.
--- End Message ---
--- Begin Message ---
Source: infernal
Source-Version: 1.1.5-3
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
infernal, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated infernal package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 17 Dec 2024 18:38:04 +0100
Source: infernal
Architecture: source
Version: 1.1.5-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1045517
Changes:
infernal (1.1.5-3) unstable; urgency=medium
.
* Fix clean target
Closes: #1045517
* Standards-Version: 4.7.0 (routine-update)
* Drop ${shlibs:Depends} from doc package
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Files:
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