Source: ghmm Version: 0.9~rc3-4 Severity: minor Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-sab-20230813 ftbfs-source-after-build User: debian...@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 ghmm > dpkg-buildpackage: info: source version 0.9~rc3-4 > dpkg-buildpackage: info: source distribution unstable > dpkg-buildpackage: info: source changed by Andreas Tille <ti...@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 clean; fi > make[2]: Entering directory '/<<PKGBUILDDIR>>' > Making clean in ghmm > make[3]: Entering directory '/<<PKGBUILDDIR>>/ghmm' > Making clean in . > make[4]: Entering directory '/<<PKGBUILDDIR>>/ghmm' > test -z "libghmm.la" || rm -f libghmm.la > rm -f ./so_locations > rm -rf .libs _libs > rm -f *.o > rm -f *.lo > make[4]: Leaving directory '/<<PKGBUILDDIR>>/ghmm' > make[3]: Leaving directory '/<<PKGBUILDDIR>>/ghmm' > Making clean in tools > make[3]: Entering directory '/<<PKGBUILDDIR>>/tools' > Making clean in . > make[4]: Entering directory '/<<PKGBUILDDIR>>/tools' > rm -f probdist cluster scluster smix_hmm > rm -rf .libs _libs > rm -f *.o > rm -f *.lo > make[4]: Leaving directory '/<<PKGBUILDDIR>>/tools' > make[3]: Leaving directory '/<<PKGBUILDDIR>>/tools' > Making clean in tests > make[3]: Entering directory '/<<PKGBUILDDIR>>/tests' > Making clean in data > make[4]: Entering directory '/<<PKGBUILDDIR>>/tests/data' > Making clean in . > make[5]: Entering directory '/<<PKGBUILDDIR>>/tests/data' > rm -rf .libs _libs > rm -f *.lo > make[5]: Leaving directory '/<<PKGBUILDDIR>>/tests/data' > make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests/data' > make[4]: Entering directory '/<<PKGBUILDDIR>>/tests' > test -z "ghmm.log ghmm.sum site.exp site.bak" || rm -f ghmm.log ghmm.sum > site.exp site.bak > rm -rf .libs _libs > rm -f randvar_test root_finder_test coin_toss_test two_states_three_symbols > libxml-test chmm chmm_test shmm_viterbi_test test_gsl_ran_gaussian_tail > sequences_test sequences_old_format label_higher_order_test read_fa mcmc > rm -f *.o > test -z "root_finder_test.log coin_toss_test.log two_states_three_symbols.log > libxml-test.log chmm.log chmm_test.log shmm_viterbi_test.log > test_gsl_ran_gaussian_tail.log sequences_test.log sequences_old_format.log > label_higher_order_test.log read_fa.log mcmc.log" || rm -f > root_finder_test.log coin_toss_test.log two_states_three_symbols.log > libxml-test.log chmm.log chmm_test.log shmm_viterbi_test.log > test_gsl_ran_gaussian_tail.log sequences_test.log sequences_old_format.log > label_higher_order_test.log read_fa.log mcmc.log > test -z "root_finder_test.trs coin_toss_test.trs two_states_three_symbols.trs > libxml-test.trs chmm.trs chmm_test.trs shmm_viterbi_test.trs > test_gsl_ran_gaussian_tail.trs sequences_test.trs sequences_old_format.trs > label_higher_order_test.trs read_fa.trs mcmc.trs" || rm -f > root_finder_test.trs coin_toss_test.trs two_states_three_symbols.trs > libxml-test.trs chmm.trs chmm_test.trs shmm_viterbi_test.trs > test_gsl_ran_gaussian_tail.trs sequences_test.trs sequences_old_format.trs > label_higher_order_test.trs read_fa.trs mcmc.trs > test -z "test-suite.log" || rm -f test-suite.log > rm -f *.lo > make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests' > make[3]: Leaving directory '/<<PKGBUILDDIR>>/tests' > Making clean in ghmmwrapper > make[3]: Entering directory '/<<PKGBUILDDIR>>/ghmmwrapper' > /usr/bin/python3 setup.py clean > /<<PKGBUILDDIR>>/ghmmwrapper/setup.py:38: DeprecationWarning: The distutils > package is deprecated and slated for removal in Python 3.12. Use setuptools > or check PEP 632 for potential alternatives > from distutils.core import setup,Extension > running clean > removing 'build/temp.linux-x86_64-3.11' (and everything under it) > rm -f message.txt > make[3]: Leaving directory '/<<PKGBUILDDIR>>/ghmmwrapper' > Making clean in HMMEd > make[3]: Entering directory '/<<PKGBUILDDIR>>/HMMEd' > /usr/bin/python3 setup.py clean > /<<PKGBUILDDIR>>/HMMEd/setup.py:38: DeprecationWarning: The distutils package > is deprecated and slated for removal in Python 3.12. Use setuptools or check > PEP 632 for potential alternatives > from distutils.core import setup,Extension > running clean > make[3]: Leaving directory '/<<PKGBUILDDIR>>/HMMEd' > make[3]: Entering directory '/<<PKGBUILDDIR>>' > rm -rf .libs _libs > rm -f *.lo > make[3]: Leaving directory '/<<PKGBUILDDIR>>' > make[2]: Leaving directory '/<<PKGBUILDDIR>>' > find . -name Makefile -delete > find . \( -name "*.o" -o -name "*.lo" \) -delete > rm -f ghmmwrapper/ghmmwrapper.py ghmmwrapper/ghmmwrapper_wrap.c > rm -rf HMMEd/build/ ghmmwrapper/build/ > rm -f config.h config.log config.status > rm -f libtool stamp-h1 tests/chmm_test.2JNcXz > rm -f tools/ghmm-config > rm -rf ghmm/.deps/ tests/.deps/ tools/.deps/ > 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 ghmm using existing ./ghmm_0.9~rc3.orig.tar.gz > dpkg-source: info: using patch list from debian/patches/series > 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 config.h.in, 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 tests/Makefile.in, use > --include-removal to override > dpkg-source: warning: ignoring deletion of file tests/data/Makefile.in, use > --include-removal to override > dpkg-source: warning: ignoring deletion of file ghmmwrapper/Makefile.in, use > --include-removal to override > dpkg-source: warning: ignoring deletion of file HMMEd/Makefile.in, use > --include-removal to override > dpkg-source: warning: ignoring deletion of file tools/Makefile.in, use > --include-removal to override > dpkg-source: warning: ignoring deletion of file ghmm/Makefile.in, use > --include-removal to override > dpkg-source: info: local changes detected, the modified files are: > ghmm-0.9~rc3/ghmm/ghmmconfig.h > dpkg-source: error: aborting due to unexpected upstream changes, see > /tmp/ghmm_0.9~rc3-4.diff.iMqRFW > 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/ghmm_0.9~rc3-4_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.
