[Debian-med-packaging] Bug#1045461: reapr: Fails to build source after successful build

[Lucas Nussbaum]

Source: reapr
Version: 1.0.18+dfsg-5
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 reapr
> dpkg-buildpackage: info: source version 1.0.18+dfsg-5
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Michael R. Crusoe <michael.crusoe at gmail.com>
>  dpkg-source --before-build .
>  fakeroot debian/rules clean
> dh clean
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf /<<PKGBUILDDIR>>/debian/man_src/*.html /<<PKGBUILDDIR>>/debian/man_src/*.?
> rm -rf /<<PKGBUILDDIR>>/debian/man
> rm -rf /<<PKGBUILDDIR>>/debian/test
> dh_auto_clean --
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building reapr using existing ./reapr_1.0.18+dfsg.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to src/bam2fcdEstimate: binary file contents changed
> dpkg-source: error: add src/bam2fcdEstimate 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/bam2fcdEstimate' will not be represented in diff
> dpkg-source: error: cannot represent change to src/bam2fcdEstimate.o: binary file contents changed
> dpkg-source: error: add src/bam2fcdEstimate.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/bam2fragCov: binary file contents changed
> dpkg-source: error: add src/bam2fragCov 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/bam2fragCov' will not be represented in diff
> dpkg-source: error: cannot represent change to src/bam2fragCov.o: binary file contents changed
> dpkg-source: error: add src/bam2fragCov.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/bam2insert: binary file contents changed
> dpkg-source: error: add src/bam2insert 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/bam2insert' will not be represented in diff
> dpkg-source: error: cannot represent change to src/bam2insert.o: binary file contents changed
> dpkg-source: error: add src/bam2insert.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/bam2perfect: binary file contents changed
> dpkg-source: error: add src/bam2perfect 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/bam2perfect' will not be represented in diff
> dpkg-source: error: cannot represent change to src/bam2perfect.o: binary file contents changed
> dpkg-source: error: add src/bam2perfect.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/coveragePlot.o: binary file contents changed
> dpkg-source: error: add src/coveragePlot.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/errorWindow.o: binary file contents changed
> dpkg-source: error: add src/errorWindow.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/fa2gaps: binary file contents changed
> dpkg-source: error: add src/fa2gaps 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/fa2gaps' will not be represented in diff
> dpkg-source: error: cannot represent change to src/fa2gaps.o: binary file contents changed
> dpkg-source: error: add src/fa2gaps.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/fa2gc: binary file contents changed
> dpkg-source: error: add src/fa2gc 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/fa2gc' will not be represented in diff
> dpkg-source: error: cannot represent change to src/fa2gc.o: binary file contents changed
> dpkg-source: error: add src/fa2gc.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/fasta.o: binary file contents changed
> dpkg-source: error: add src/fasta.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/histogram.o: binary file contents changed
> dpkg-source: error: add src/histogram.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/make_plots: binary file contents changed
> dpkg-source: error: add src/make_plots 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/make_plots' will not be represented in diff
> dpkg-source: error: cannot represent change to src/make_plots.o: binary file contents changed
> dpkg-source: error: add src/make_plots.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/n50: binary file contents changed
> dpkg-source: error: add src/n50 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/n50' will not be represented in diff
> dpkg-source: error: cannot represent change to src/n50.o: binary file contents changed
> dpkg-source: error: add src/n50.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/scaff2contig: binary file contents changed
> dpkg-source: error: add src/scaff2contig 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/scaff2contig' will not be represented in diff
> dpkg-source: error: cannot represent change to src/scaff2contig.o: binary file contents changed
> dpkg-source: error: add src/scaff2contig.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/task_break: binary file contents changed
> dpkg-source: error: add src/task_break 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/task_break' will not be represented in diff
> dpkg-source: error: cannot represent change to src/task_break.o: binary file contents changed
> dpkg-source: error: add src/task_break.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/task_fcdrate: binary file contents changed
> dpkg-source: error: add src/task_fcdrate 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/task_fcdrate' will not be represented in diff
> dpkg-source: error: cannot represent change to src/task_fcdrate.o: binary file contents changed
> dpkg-source: error: add src/task_fcdrate.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/task_gapresize: binary file contents changed
> dpkg-source: error: add src/task_gapresize 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/task_gapresize' will not be represented in diff
> dpkg-source: error: cannot represent change to src/task_gapresize.o: binary file contents changed
> dpkg-source: error: add src/task_gapresize.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/task_score: binary file contents changed
> dpkg-source: error: add src/task_score 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/task_score' will not be represented in diff
> dpkg-source: error: cannot represent change to src/task_score.o: binary file contents changed
> dpkg-source: error: add src/task_score.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/task_stats: binary file contents changed
> dpkg-source: error: add src/task_stats 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/task_stats' will not be represented in diff
> dpkg-source: error: cannot represent change to src/task_stats.o: binary file contents changed
> dpkg-source: error: add src/task_stats.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/trianglePlot.o: binary file contents changed
> dpkg-source: error: add src/trianglePlot.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/utils.o: binary file contents changed
> dpkg-source: error: add src/utils.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 29
> 
> 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/reapr_1.0.18+dfsg-5_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.