Your message dated Sat, 18 Nov 2023 08:24:17 +0000
with message-id <[email protected]>
and subject line Bug#1043915: fixed in augustus 3.5.0+dfsg-4
has caused the Debian Bug report #1043915,
regarding augustus: 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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--
1043915: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1043915
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: augustus
Version: 3.5.0+dfsg-3
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 augustus
> dpkg-buildpackage: info: source version 3.5.0+dfsg-3
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Sascha Steinbiss <[email protected]>
> dpkg-source --before-build .
> debian/rules clean
> dh clean
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> /usr/bin/make -C auxprogs/bam2hints clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
> rm -f bam2hints.o bam2hints ../../bin/bam2hints
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/bam2hints'
> /usr/bin/make -C auxprogs/homGeneMapping clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
> cd src; make clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
> rm -f homGeneMapping gene.o genome.o sqliteDB.o
> rm -f ../../../bin/homGeneMapping
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
> if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py
> --clean homGeneMapping ; fi
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping'
> /usr/bin/make -C auxprogs/joingenes clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/joingenes'
> rm -f *.o joingenes ../../bin/joingenes
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/joingenes'
> /usr/bin/make -C auxprogs/aln2wig clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
> rm -f aln2wig aln2wig.o ../../bin/aln2wig
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/aln2wig'
> /usr/bin/make -C auxprogs/bam2wig clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
> rm -f bam2wig.o bam2wig
> rm -f ../../bin/bam2wig
> if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py
> --clean bam2wig ; fi
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
> /usr/bin/make -C auxprogs/compileSpliceCands clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
> rm -f compileSpliceCands *.o ../../bin/compileSpliceCands
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
> /usr/bin/make -C auxprogs/filterBam clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
> (cd src; make clean;)
> make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
> rm -f *~ filterBam.o initOptions.o printElapsedTime.o MatePairs.o
> PairednessCoverage.o BamToolsAccess.o
> rm -f filterBam
> rm -f ../../../bin/filterBam
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
> rm -rf bin
> rm -f debian/*substvars
> rm -f debian/mansrc/*.1
> find . -name "__pycache__" | xargs -r rm -r
> find src -name "*.o" | xargs -r rm
> find auxprogs -name "*.o" | xargs -r rm
> rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining
> src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore
> src/prepareAlign
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_clean
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building augustus using existing
> ./augustus_3.5.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to auxprogs/utrrnaseq/utrrnaseq:
> binary file contents changed
> dpkg-source: error: add auxprogs/utrrnaseq/utrrnaseq in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of 'auxprogs/utrrnaseq/utrrnaseq'
> will not be represented in diff
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/bam2hints/tmp/test.s.sorted.bam: binary file contents
> changed
> dpkg-source: error: add tests/short/auxprogs/bam2hints/tmp/test.s.sorted.bam
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_paired.paired.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_paired.paired.sam.bam in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_paired.paired_maxIntronLen100.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_paired.paired_maxIntronLen100.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_paired.paired_pairwiseAlignments.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_paired.paired_pairwiseAlignments.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise.paired_pairwiseAlignments.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise.paired_pairwiseAlignments.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.best.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.best.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.no_options.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.no_options.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.paired_pairwiseAlignments.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.paired_pairwiseAlignments.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.uniq.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd.uniq.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.best.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.best.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.no_options.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.no_options.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.paired_pairwiseAlignments.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.paired_pairwiseAlignments.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.uniq.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_pairwise_calmd_seq_with_equalsigns.uniq.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.best.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.best.sam.bam in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.minCover99.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.minCover99.sam.bam
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.noIntrons.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.noIntrons.sam.bam
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.noIntrons_insertLimit15.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.noIntrons_insertLimit15.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.no_minCover.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.no_minCover.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.no_minId.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.no_minId.sam.bam
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.no_minId_no_minCover.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.no_minId_no_minCover.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.no_options.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.no_options.sam.bam
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.not_paired.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.not_paired.sam.bam
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.uniq.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.uniq.sam.bam in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> tests/short/auxprogs/filterbam/result_files/example_single.uniqThresh1_1.sam.bam:
> binary file contents changed
> dpkg-source: error: add
> tests/short/auxprogs/filterbam/result_files/example_single.uniqThresh1_1.sam.bam
> in debian/source/include-binaries if you want to store the modified binary
> in the debian tarball
> dpkg-source: warning: newly created empty file
> 'tests/short/examples/results/test_format_and_error_out/augustus.err' 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/augustus_3.5.0+dfsg-3_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: augustus
Source-Version: 3.5.0+dfsg-4
Done: Sascha Steinbiss <[email protected]>
We believe that the bug you reported is fixed in the latest version of
augustus, 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.
Sascha Steinbiss <[email protected]> (supplier of updated augustus 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: SHA256
Format: 1.8
Date: Sat, 18 Nov 2023 08:21:25 +0100
Source: augustus
Architecture: source
Version: 3.5.0+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Sascha Steinbiss <[email protected]>
Closes: 1043915
Changes:
augustus (3.5.0+dfsg-4) unstable; urgency=medium
.
* Ensure multiple builds can be done in same directory.
Done by ensuring the directory is cleaned correctly.
Closes: #1043915
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