[Debian-med-packaging] Bug#1049675: genomethreader: Fails to build binary packages again after successful build
Lucas Nussbaum
lucas at debian.org
Wed Aug 16 08:42:49 BST 2023
Source: genomethreader
Version: 1.7.3+dfsg-7
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild
Hi,
This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).
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/DoubleBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> ----------------------------------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package genomethreader
> dpkg-buildpackage: info: source version 1.7.3+dfsg-7
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Sascha Steinbiss <satta at debian.org>
> dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
> debian/rules clean
> dh clean
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata
> rm -rf /<<PKGBUILDDIR>>/debian/man
> rm -f debian/*substvars
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_clean
> debian/rules binary
> dh binary
> dh_update_autotools_config
> dh_autoreconf
> dh_auto_configure
> debian/rules override_dh_auto_build
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> make licensemanager=no opt=yes 64bit=yes
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> make[2]: Nothing to be done for 'all'.
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make licensemanager=no opt=yes 64bit=yes train
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> make[2]: Nothing to be done for 'train'.
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> debian/rules override_dh_auto_test
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> make licensemanager=no 64bit=yes test
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
> BSSMDIR=/<<PKGBUILDDIR>>/bin/bssm GTHDATADIR=/<<PKGBUILDDIR>>/gthdata/gth \
> CCACHE_DISABLE=yes HOME=/home/user42 GTHTESTDATADIR= \
> ruby -I. testsuite.rb \
> -testdata /<<PKGBUILDDIR>>/testdata -bin /<<PKGBUILDDIR>>/bin -cur /<<PKGBUILDDIR>> \
> -gtruby /<<PKGBUILDDIR>>/gtruby
> 1: gth : ok
> 2: gth -help : ok
> 3: gth -help+ : ok
> 4: gth -version : ok
> 5: gth regression test (assertion in gthsafilter) : ok
> 6: gth regression test (-gff3out -intermediate) : ok
> 7: gth regression test (-gff3out -intermediate -fastdp) : ok
> 8: gth regression test (-gff3out -skipalignmentout) : ok
> 9: gth regression test (-gff3out -skipalignmentout -fastdp) : ok
> 10: gth regression test (-gff3out -intermediate -o) : ok
> 11: gth regression test (-gff3out -skipalignmentout -o) : ok
> 12: gthconsensus regression test (-gff3out -intermediate) : ok
> 13: gthconsensus regression test (-gff3out -skipalignmentout) : ok
> 14: gthconsensus regression test (-gff3out -intermediate -o) : ok
> 15: gthconsensus regression test (-gff3out -skipalignmentout -o): ok
> 16: gth regression test (-exondistri) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test16 ]
> 17: gth regression test (-introndistri) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test17 ]
> 18: gth regression test (-refseqcovdistri) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test18 ]
> 19: gth regression test (all distributions) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test19 ]
> 20: gth regression test (-skipindexcheck) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test20 ]
> 21: gth regression test (index reconstruction) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test21 ]
> 22: gth regression test (-createindicesonly & -noautoindex) : ok
> 23: gth regression test (coverage assertion) : ok
> 24: gth -gff3out -intermediate (long intron files) : ok
> 25: gth -gff3out -skipalignmentout (long intron files) : ok
> 26: gth -gff3out -frompos (correct positions in sequence region): ok
> 27: gth -gff3out -intermediate (correct reverse positions) : ok
> 28: gth arabidopsis : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test28 ]
> 29: gth illegal character in protein file : ok
> 30: align_dna : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test30 ]
> 31: gth -gff3descranges (single exon) : ok
> 32: gthconsensus -help : ok
> 33: gthconsensus -help+ : ok
> 34: gthconsensus empty_file : ok
> 35: gthconsensus empty_file.gz : ok
> 36: gthconsensus empty_file.bz2 : ok
> 37: gthbssmfileinfo (arabidopsis) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test37 ]
> 38: gthbssmfileinfo (human) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test38 ]
> 39: gthbssmprint (arabidopsis) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test39 ]
> 40: gthbssmprint (human) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test40 ]
> 41: gthbssmrmsd (arabidopsis) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test41 ]
> 42: gthbssmtrain (examples from manual) : ok
> 43: gthbssmtrain (file, no introns) : ok
> 44: gthbssmtrain (file, introns) : ok
> 45: gthbssmtrain (stdin, no introns) : ok
> 46: gthbssmtrain (stdin, introns) : ok
> 47: gthbssmtrain (short intron) : ok
> 48: gthunit : ok
> 49: fastdp 01 : ok
> 50: fastdp (U89959) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test50 ]
> 51: fastdp (U89959, introncutout) : failed
> [ problem: unexpected return code: 1 != 0
> in: /<<PKGBUILDDIR>>/testsuite/stest_testsuite/test51 ]
> make[2]: *** [Makefile:475: test] Error 1
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: *** [debian/rules:45: override_dh_auto_test] Error 2
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:26: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/16/genomethreader_1.7.3+dfsg-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.
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