[Debian-med-packaging] Bug#1043996: biosquid: Fails to build source after successful build

Lucas Nussbaum lucas at debian.org
Sun Aug 13 14:17:55 BST 2023 

Source: biosquid
Version: 1.9g+cvs20050121-12
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 biosquid
> dpkg-buildpackage: info: source version 1.9g+cvs20050121-12
> 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
> 	rm -f debian/biosquid.debhelper.log debian/libsquid-dev.debhelper.log debian/libsquid1.debhelper.log
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 	make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "libsquid.la" || rm -f libsquid.la
> rm -rf .libs _libs
>  rm -f afetch alistat compalign compstruct revcomp seqsplit seqstat sfetch shuffle sindex sreformat translate weight
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> rm -f ./so_locations
> test -z "Testsuite/Makefile squid.h libsquid.pc" || rm -f Testsuite/Makefile squid.h libsquid.pc
> rm -f squidconf.h stamp-h1
> test . = "." || test -z "" || rm -f 
> rm -f libtool config.lt
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f ./.deps/afetch_main.Po
> rm -f ./.deps/aligneval.Po
> rm -f ./.deps/alistat_main.Po
> rm -f ./.deps/cluster.Po
> rm -f ./.deps/compalign_main.Po
> rm -f ./.deps/compstruct_main.Po
> rm -f ./.deps/eps.Po
> rm -f ./.deps/iupac.Po
> rm -f ./.deps/libsquid_la-a2m.Plo
> rm -f ./.deps/libsquid_la-aligneval.Plo
> rm -f ./.deps/libsquid_la-alignio.Plo
> rm -f ./.deps/libsquid_la-clustal.Plo
> rm -f ./.deps/libsquid_la-cluster.Plo
> rm -f ./.deps/libsquid_la-dayhoff.Plo
> rm -f ./.deps/libsquid_la-dirichlet.Plo
> rm -f ./.deps/libsquid_la-eps.Plo
> rm -f ./.deps/libsquid_la-file.Plo
> rm -f ./.deps/libsquid_la-getopt.Plo
> rm -f ./.deps/libsquid_la-gki.Plo
> rm -f ./.deps/libsquid_la-hsregex.Plo
> rm -f ./.deps/libsquid_la-iupac.Plo
> rm -f ./.deps/libsquid_la-msa.Plo
> rm -f ./.deps/libsquid_la-msf.Plo
> rm -f ./.deps/libsquid_la-phylip.Plo
> rm -f ./.deps/libsquid_la-revcomp.Plo
> rm -f ./.deps/libsquid_la-rk.Plo
> rm -f ./.deps/libsquid_la-selex.Plo
> rm -f ./.deps/libsquid_la-seqencode.Plo
> rm -f ./.deps/libsquid_la-shuffle.Plo
> rm -f ./.deps/libsquid_la-sqerror.Plo
> rm -f ./.deps/libsquid_la-sqio.Plo
> rm -f ./.deps/libsquid_la-squidcore.Plo
> rm -f ./.deps/libsquid_la-sre_ctype.Plo
> rm -f ./.deps/libsquid_la-sre_math.Plo
> rm -f ./.deps/libsquid_la-sre_random.Plo
> rm -f ./.deps/libsquid_la-sre_stack.Plo
> rm -f ./.deps/libsquid_la-sre_string.Plo
> rm -f ./.deps/libsquid_la-ssi.Plo
> rm -f ./.deps/libsquid_la-stockholm.Plo
> rm -f ./.deps/libsquid_la-stopwatch.Plo
> rm -f ./.deps/libsquid_la-translate.Plo
> rm -f ./.deps/libsquid_la-types.Plo
> rm -f ./.deps/libsquid_la-vectorops.Plo
> rm -f ./.deps/libsquid_la-weight.Plo
> rm -f ./.deps/libsquid_la-wuss.Plo
> rm -f ./.deps/revcomp.Po
> rm -f ./.deps/revcomp_main.Po
> rm -f ./.deps/seqsplit_main.Po
> rm -f ./.deps/seqstat_main.Po
> rm -f ./.deps/sfetch_main.Po
> rm -f ./.deps/shuffle.Po
> rm -f ./.deps/shuffle_main.Po
> rm -f ./.deps/sindex_main.Po
> rm -f ./.deps/sre_math.Po
> rm -f ./.deps/sre_stack.Po
> rm -f ./.deps/sreformat_main.Po
> rm -f ./.deps/translate.Po
> rm -f ./.deps/translate_main.Po
> rm -f ./.deps/weight.Po
> rm -f ./.deps/weight_main.Po
> rm -f ./.deps/wuss.Po
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f configure
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
> 	rm -f -- ./install-sh ./squidconf.h.in\~ ./aclocal.m4 ./config.guess ./autom4te.cache/requests ./autom4te.cache/traces.2 ./autom4te.cache/output.2 ./autom4te.cache/output.1 ./autom4te.cache/traces.1 ./autom4te.cache/output.0 ./autom4te.cache/traces.0 ./Makefile.in ./compile ./ltmain.sh ./configure ./depcomp ./squidconf.h.in ./missing
> 	rm -f debian/autoreconf.before debian/autoreconf.after
>    dh_clean
> 	rm -f debian/debhelper-build-stamp
> 	cp -an --reflink=auto debian/.debhelper/bucket/files/6256efe9320ee8690c8be56bb851415d90efe4d27a67fe374efd28a6c6733153 debian/.debhelper/bucket/files/6256efe9320ee8690c8be56bb851415d90efe4d27a67fe374efd28a6c6733153.tmp
> 	mv debian/.debhelper/bucket/files/6256efe9320ee8690c8be56bb851415d90efe4d27a67fe374efd28a6c6733153.tmp config.sub
> 	rm -f debian/.debhelper/bucket/index
> 	rm -rf debian/.debhelper/
> 	rm -f -- debian/biosquid.substvars debian/libsquid1.substvars debian/libsquid-dev.substvars debian/files
> 	rm -fr -- debian/biosquid/ debian/tmp/ debian/libsquid1/ debian/libsquid-dev/
> 	find .  \( \( \
> 		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
> 	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
> 		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
> 		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
> 		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
> 		\) -exec rm -f {} + \) -o \
> 		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building biosquid using existing ./biosquid_1.9g+cvs20050121.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to libsquid.a:
> dpkg-source: error:   new version is symlink to .libs/libsquid.a
> 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 Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file squidconf.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/biosquid_1.9g+cvs20050121-12_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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