Your message dated Sun, 01 Dec 2024 12:21:35 +0000
with message-id <[email protected]>
and subject line Bug#1045454: fixed in primer3 2.6.1-5
has caused the Debian Bug report #1045454,
regarding primer3: 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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--
1045454: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1045454
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: primer3
Source-Version: 2.6.1-5
Done: Ananthu C V <[email protected]>
We believe that the bug you reported is fixed in the latest version of
primer3, 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.
Ananthu C V <[email protected]> (supplier of updated primer3 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: SHA512
Format: 1.8
Date: Sun, 01 Dec 2024 17:24:55 +0530
Source: primer3
Architecture: source
Version: 2.6.1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Ananthu C V <[email protected]>
Closes: 1045454
Changes:
primer3 (2.6.1-5) unstable; urgency=medium
.
* Team upload.
* Clean up source directory properly (Closes: #1045454)
* Use execute_after hook over overrides in d/rules
* Bump standards version to 4.7.0 (no changes needed)
* Correct patch header metadata
* Drop deprecated an-trap macro from manpage
Checksums-Sha1:
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28b7395b0de7f04628fb08c962c4d0cedb8c949e 6540 primer3_2.6.1-5_amd64.buildinfo
Checksums-Sha256:
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Files:
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28b989a292909a073f143fabc5d430ee 13976 science optional
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