[Debian-med-packaging] Bug#1043849: clustalo: Fails to build source after successful build
Lucas Nussbaum
lucas at debian.org
Sun Aug 13 14:17:57 BST 2023
Source: clustalo
Version: 1.2.4-7
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 clustalo
> dpkg-buildpackage: info: source version 1.2.4-7
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe at debian.org>
> dpkg-source --before-build .
> debian/rules clean
> dh clean
> dh_auto_clean
> make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> Making distclean in hhalign
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/hhalign'
> rm -rf .libs _libs
> test -z "libhhalign.la" || rm -f libhhalign.la
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> rm -f ./so_locations
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f ./.deps/hhalign.Plo
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
> Making distclean in squid
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
> rm -rf .libs _libs
> test -z "libsquid.la" || rm -f libsquid.la
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f ./so_locations
> test . = "." || test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f ./.deps/a2m.Plo
> rm -f ./.deps/aligneval.Plo
> rm -f ./.deps/alignio.Plo
> rm -f ./.deps/clustal.Plo
> rm -f ./.deps/cluster.Plo
> rm -f ./.deps/dayhoff.Plo
> rm -f ./.deps/eps.Plo
> rm -f ./.deps/file.Plo
> rm -f ./.deps/getopt.Plo
> rm -f ./.deps/gki.Plo
> rm -f ./.deps/gsi.Plo
> rm -f ./.deps/gsi64.Plo
> rm -f ./.deps/hsregex.Plo
> rm -f ./.deps/iupac.Plo
> rm -f ./.deps/msa.Plo
> rm -f ./.deps/msf.Plo
> rm -f ./.deps/phylip.Plo
> rm -f ./.deps/revcomp.Plo
> rm -f ./.deps/rk.Plo
> rm -f ./.deps/selex.Plo
> rm -f ./.deps/seqencode.Plo
> rm -f ./.deps/shuffle.Plo
> rm -f ./.deps/sqerror.Plo
> rm -f ./.deps/sqio.Plo
> rm -f ./.deps/squidcore.Plo
> rm -f ./.deps/sre_ctype.Plo
> rm -f ./.deps/sre_math.Plo
> rm -f ./.deps/sre_random.Plo
> rm -f ./.deps/sre_string.Plo
> rm -f ./.deps/ssi.Plo
> rm -f ./.deps/stack.Plo
> rm -f ./.deps/stockholm.Plo
> rm -f ./.deps/stopwatch.Plo
> rm -f ./.deps/translate.Plo
> rm -f ./.deps/types.Plo
> rm -f ./.deps/vectorops.Plo
> rm -f ./.deps/weight.Plo
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/squid'
> Making distclean in kmpp
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/kmpp'
> rm -rf .libs _libs
> test -z "libkmpp.la" || rm -f libkmpp.la
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f ./so_locations
> test . = "." || test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f ./.deps/KMeans.Plo
> rm -f ./.deps/KmTree.Plo
> rm -f ./.deps/KmUtils.Plo
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/kmpp'
> Making distclean in clustal
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/clustal'
> rm -rf .libs _libs
> test -z "libclustal.la" || rm -f libclustal.la
> rm -f *.o
> rm -f *.lo
> rm -f ./so_locations
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/hhalign_wrapper.Plo
> rm -f ./.deps/ktuple_pair.Plo
> rm -f ./.deps/list.Plo
> rm -f ./.deps/log.Plo
> rm -f ./.deps/mbed.Plo
> rm -f ./.deps/muscle_tree.Plo
> rm -f ./.deps/muscle_upgma.Plo
> rm -f ./.deps/pair_dist.Plo
> rm -f ./.deps/progress.Plo
> rm -f ./.deps/seq.Plo
> rm -f ./.deps/symmatrix.Plo
> rm -f ./.deps/tree.Plo
> rm -f ./.deps/util.Plo
> rm -f ./.deps/weights.Plo
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/clustal'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "libclustalo.la" || rm -f libclustalo.la
> rm -f clustalo
> rm -rf .libs _libs
> rm -f *.o
> rm -f ./so_locations
> rm -f *.lo
> rm -f *.tab.c
> 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>>/src'
> rm -f ./.deps/clustal-omega.Plo
> rm -f ./.deps/main.Po
> rm -f ./.deps/mymain.Po
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "clustalo.pc Doxyfile" || rm -f clustalo.pc Doxyfile
> rm -f libtool config.lt
> test . = "." || test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean
> debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> rm -f _configs.sed
> rm -rf doc
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building clustalo using existing ./clustalo_1.2.4.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file Doxyfile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file install-sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file aclocal.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file INSTALL, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file ltmain.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 depcomp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file missing, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltsugar.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/lt~obsolete.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltversion.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/libtool.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltoptions.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/config.h.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/hhalign/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/clustal/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/kmpp/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/squid/Makefile.in, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
> clustalo-1.2.4/src/clustal-omega-config.h
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/clustalo_1.2.4-7.diff.tSz35L
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
>
> 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/clustalo_1.2.4-7_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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