[Debian-med-packaging] Bug#1047333: ivar: Fails to build source after successful build

[Lucas Nussbaum]

Source: ivar
Version: 1.4.2+dfsg-2
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 ivar
> dpkg-buildpackage: info: source version 1.4.2+dfsg-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building ivar using existing ./ivar_1.4.2+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file config.h.in, use --include-removal to override
> dpkg-source: warning: executable mode 0755 of 'config.status' will not be represented in diff
> dpkg-source: error: cannot represent change to data/trim_isize.bam: binary file contents changed
> dpkg-source: error: add data/trim_isize.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 'src/.dirstamp' will not be represented in diff
> dpkg-source: error: cannot represent change to src/alignment.o: binary file contents changed
> dpkg-source: error: add src/alignment.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/allele_functions.o: binary file contents changed
> dpkg-source: error: add src/allele_functions.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/call_consensus_pileup.o: binary file contents changed
> dpkg-source: error: add src/call_consensus_pileup.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/call_variants.o: binary file contents changed
> dpkg-source: error: add src/call_variants.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/get_common_variants.o: binary file contents changed
> dpkg-source: error: add src/get_common_variants.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/get_masked_amplicons.o: binary file contents changed
> dpkg-source: error: add src/get_masked_amplicons.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/interval_tree.o: binary file contents changed
> dpkg-source: error: add src/interval_tree.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/ivar: binary file contents changed
> dpkg-source: error: add src/ivar 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/ivar' will not be represented in diff
> dpkg-source: error: cannot represent change to src/ivar.o: binary file contents changed
> dpkg-source: error: add src/ivar.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/parse_gff.o: binary file contents changed
> dpkg-source: error: add src/parse_gff.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/primer_bed.o: binary file contents changed
> dpkg-source: error: add src/primer_bed.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/ref_seq.o: binary file contents changed
> dpkg-source: error: add src/ref_seq.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/remove_reads_from_amplicon.o: binary file contents changed
> dpkg-source: error: add src/remove_reads_from_amplicon.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/suffix_tree.o: binary file contents changed
> dpkg-source: error: add src/suffix_tree.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/trim_primer_quality.o: binary file contents changed
> dpkg-source: error: add src/trim_primer_quality.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 tests/check_allele_depth: binary file contents changed
> dpkg-source: error: add tests/check_allele_depth in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_allele_depth' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_amplicon_search: binary file contents changed
> dpkg-source: error: add tests/check_amplicon_search in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_amplicon_search' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_common_variants: binary file contents changed
> dpkg-source: error: add tests/check_common_variants in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_common_variants' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_consensus: binary file contents changed
> dpkg-source: error: add tests/check_consensus in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_consensus' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_consensus_min_depth: binary file contents changed
> dpkg-source: error: add tests/check_consensus_min_depth in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_consensus_min_depth' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_consensus_min_insert_threshold: binary file contents changed
> dpkg-source: error: add tests/check_consensus_min_insert_threshold in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_consensus_min_insert_threshold' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_consensus_seq_id: binary file contents changed
> dpkg-source: error: add tests/check_consensus_seq_id in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_consensus_seq_id' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_consensus_threshold: binary file contents changed
> dpkg-source: error: add tests/check_consensus_threshold in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_consensus_threshold' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_getmasked: binary file contents changed
> dpkg-source: error: add tests/check_getmasked in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_getmasked' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_interval_tree: binary file contents changed
> dpkg-source: error: add tests/check_interval_tree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_interval_tree' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_isize_trim: binary file contents changed
> dpkg-source: error: add tests/check_isize_trim in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_isize_trim' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_primer_bed: binary file contents changed
> dpkg-source: error: add tests/check_primer_bed in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_primer_bed' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_primer_trim: binary file contents changed
> dpkg-source: error: add tests/check_primer_trim in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_primer_trim' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_primer_trim_edge_cases: binary file contents changed
> dpkg-source: error: add tests/check_primer_trim_edge_cases in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_primer_trim_edge_cases' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_quality_trim: binary file contents changed
> dpkg-source: error: add tests/check_quality_trim in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_quality_trim' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_quality_trim.o: binary file contents changed
> dpkg-source: error: add tests/check_quality_trim.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 tests/check_removereads: binary file contents changed
> dpkg-source: error: add tests/check_removereads in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_removereads' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_trim: binary file contents changed
> dpkg-source: error: add tests/check_trim in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_trim' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_unpaired_trim: binary file contents changed
> dpkg-source: error: add tests/check_unpaired_trim in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_unpaired_trim' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/check_variants: binary file contents changed
> dpkg-source: error: add tests/check_variants in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'tests/check_variants' will not be represented in diff
> dpkg-source: error: cannot represent change to tests/test_allele_depth.o: binary file contents changed
> dpkg-source: error: add tests/test_allele_depth.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 tests/test_amplicon_search.o: binary file contents changed
> dpkg-source: error: add tests/test_amplicon_search.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 tests/test_call_consensus_from_plup.o: binary file contents changed
> dpkg-source: error: add tests/test_call_consensus_from_plup.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 tests/test_common_variants.o: binary file contents changed
> dpkg-source: error: add tests/test_common_variants.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 tests/test_consensus_min_depth.o: binary file contents changed
> dpkg-source: error: add tests/test_consensus_min_depth.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 tests/test_consensus_min_insert_threshold.o: binary file contents changed
> dpkg-source: error: add tests/test_consensus_min_insert_threshold.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 tests/test_consensus_seq_id.o: binary file contents changed
> dpkg-source: error: add tests/test_consensus_seq_id.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 tests/test_consensus_threshold.o: binary file contents changed
> dpkg-source: error: add tests/test_consensus_threshold.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 tests/test_getmasked.o: binary file contents changed
> dpkg-source: error: add tests/test_getmasked.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 tests/test_interval_tree.o: binary file contents changed
> dpkg-source: error: add tests/test_interval_tree.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 tests/test_isize_trim.o: binary file contents changed
> dpkg-source: error: add tests/test_isize_trim.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 tests/test_primer_bed.o: binary file contents changed
> dpkg-source: error: add tests/test_primer_bed.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 tests/test_primer_trim.o: binary file contents changed
> dpkg-source: error: add tests/test_primer_trim.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 tests/test_primer_trim_edge_cases.o: binary file contents changed
> dpkg-source: error: add tests/test_primer_trim_edge_cases.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 tests/test_removereads.o: binary file contents changed
> dpkg-source: error: add tests/test_removereads.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 tests/test_trim.o: binary file contents changed
> dpkg-source: error: add tests/test_trim.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 tests/test_unpaired_trim.o: binary file contents changed
> dpkg-source: error: add tests/test_unpaired_trim.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 tests/test_variants.o: binary file contents changed
> dpkg-source: error: add tests/test_variants.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/ivar_1.4.2+dfsg-2_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.