[Debian-med-packaging] Bug#1045454: primer3: Fails to build source after successful build

Sun Aug 13 20:21:07 BST 2023

Source: primer3
Version: 2.6.1-4
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 primer3
> dpkg-buildpackage: info: source version 2.6.1-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Ã‰tienne Mollier <emollier at debian.org>
>  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.