Source: clustalo Version: 1.2.4-7 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 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 > <[email protected]> > 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.
