[Debian-med-packaging] Bug#1044649: ghmm: Fails to build source after successful build

Sun Aug 13 17:56:56 BST 2023

Source: ghmm
Version: 0.9~rc3-4
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 ghmm
> dpkg-buildpackage: info: source version 0.9~rc3-4
> 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
>    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.