Source: genomethreader Version: 1.7.3+dfsg-7 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build User: [email protected] 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 <[email protected]> > 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.
