[Debian-med-packaging] Bug#1043915: augustus: Fails to build source after successful build

[Lucas Nussbaum]

Source: augustus
Version: 3.5.0+dfsg-3
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 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 <satta at debian.org>
>  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.