Your message dated Wed, 07 Feb 2024 14:40:02 +0000
with message-id <[email protected]>
and subject line Bug#1044649: fixed in ghmm 0.9~rc3-5
has caused the Debian Bug report #1044649,
regarding ghmm: Fails to build source after successful build
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1044649: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1044649
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ghmm
Version: 0.9~rc3-4
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 ghmm
> dpkg-buildpackage: info: source version 0.9~rc3-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <[email protected]>
> 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.
--- End Message ---
--- Begin Message ---
Source: ghmm
Source-Version: 0.9~rc3-5
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ghmm, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated ghmm package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 07 Feb 2024 15:25:59 +0100
Source: ghmm
Architecture: source
Version: 0.9~rc3-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1044649 1056673
Changes:
ghmm (0.9~rc3-5) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* Standards-Version: 4.6.2 (routine-update)
* Avoid explicitly specifying -Wl,--as-needed linker flag.
* Fix: SyntaxWarning: "is" with a literal. Did you mean "=="?
* Fix clean target
Closes: #1044649
* Install additional header files needed for autopkgtest
* Explain in README.Debian that Python3 interface is broken
.
[ Komolehin Israel Timilehin ]
* Add autopkgtest
.
[ Sébastien Villemot ]
* Remove build-dependency on libatlas-base-dev
Closes: #1056673
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--- End Message ---
