Source: primer3 Version: 2.6.1-4 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 primer3 > dpkg-buildpackage: info: source version 2.6.1-4 > dpkg-buildpackage: info: source distribution unstable > dpkg-buildpackage: info: source changed by Ãtienne Mollier > <[email protected]> > dpkg-source --before-build . > debian/rules clean > dh clean --sourcedirectory=src > dh_auto_clean -O--sourcedirectory=src > cd src && make -j8 clean > make[1]: Entering directory '/<<PKGBUILDDIR>>/src' > no windows > rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test > primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a > libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 > libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 > liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int > core ../*~ > cd ../test/; make clean > make[2]: Entering directory '/<<PKGBUILDDIR>>/test' > make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make > rule. > echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; > > > CLEAN UP TEST DIRECTORIES > > > rm -rf primer_list_tmp/* > rm -rf primer1_list_tmp/* > rm -rf primer1_th_list_tmp/* > rm -rf th-w-other-tasks_list_tmp/* > rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak > rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher* > rm -f *.tmp *.bak *.tmp.err *~ > rm -f hyb_probe_only.for hyb_probe_only.int > rm -f right_only.for right_only.rev left_only.for > rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for > rm -f pcr_primers.rev pcr_primers.for > rm -f pick_primer_list_and_file_flag_th_[1-4].for > pick_primer_list_and_file_flag_th_[1-4].rev > rm -f pick_primer_list_and_file_flag_th_[1-4].int > rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev > rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind > rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind > rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind > rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind > rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind > rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind > rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind > rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind > rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind > rm -f *.vg.core.* # core files from crashed valgrind test > rm -f ./core # in case we crashed and left a core file > make[2]: Leaving directory '/<<PKGBUILDDIR>>/test' > make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' > dh_autoreconf_clean -O--sourcedirectory=src > dh_clean -O--sourcedirectory=src > dpkg-source -b . > dpkg-source: info: using source format '3.0 (quilt)' > dpkg-source: info: building primer3 using existing ./primer3_2.6.1.orig.tar.gz > dpkg-source: info: using patch list from debian/patches/series > dpkg-source: error: cannot represent change to > src/debian/primer3/usr/bin/amplicon3_core: binary file contents changed > dpkg-source: error: add src/debian/primer3/usr/bin/amplicon3_core in > debian/source/include-binaries if you want to store the modified binary in > the debian tarball > dpkg-source: warning: executable mode 0755 of > 'src/debian/primer3/usr/bin/amplicon3_core' will not be represented in diff > dpkg-source: error: cannot represent change to > src/debian/primer3/usr/bin/long_seq_tm_test: binary file contents changed > dpkg-source: error: add src/debian/primer3/usr/bin/long_seq_tm_test in > debian/source/include-binaries if you want to store the modified binary in > the debian tarball > dpkg-source: warning: executable mode 0755 of > 'src/debian/primer3/usr/bin/long_seq_tm_test' will not be represented in diff > dpkg-source: error: cannot represent change to > src/debian/primer3/usr/bin/ntdpal: binary file contents changed > dpkg-source: error: add src/debian/primer3/usr/bin/ntdpal in > debian/source/include-binaries if you want to store the modified binary in > the debian tarball > dpkg-source: warning: executable mode 0755 of > 'src/debian/primer3/usr/bin/ntdpal' will not be represented in diff > dpkg-source: error: cannot represent change to > src/debian/primer3/usr/bin/ntthal: binary file contents changed > dpkg-source: error: add src/debian/primer3/usr/bin/ntthal in > debian/source/include-binaries if you want to store the modified binary in > the debian tarball > dpkg-source: warning: executable mode 0755 of > 'src/debian/primer3/usr/bin/ntthal' will not be represented in diff > dpkg-source: error: cannot represent change to > src/debian/primer3/usr/bin/oligotm: binary file contents changed > dpkg-source: error: add src/debian/primer3/usr/bin/oligotm in > debian/source/include-binaries if you want to store the modified binary in > the debian tarball > dpkg-source: warning: executable mode 0755 of > 'src/debian/primer3/usr/bin/oligotm' will not be represented in diff > dpkg-source: error: cannot represent change to > src/debian/primer3/usr/bin/primer3_core: binary file contents changed > dpkg-source: error: add src/debian/primer3/usr/bin/primer3_core in > debian/source/include-binaries if you want to store the modified binary in > the debian tarball > dpkg-source: warning: executable mode 0755 of > 'src/debian/primer3/usr/bin/primer3_core' will not be represented in diff > dpkg-source: error: cannot represent change to > src/debian/primer3/usr/bin/primer3_masker: binary file contents changed > dpkg-source: error: add src/debian/primer3/usr/bin/primer3_masker in > debian/source/include-binaries if you want to store the modified binary in > the debian tarball > dpkg-source: warning: executable mode 0755 of > 'src/debian/primer3/usr/bin/primer3_masker' will not be represented in diff > dpkg-source: error: unrepresentable changes to source > dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1 > > 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/primer3_2.6.1-4_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.
