Your message dated Mon, 02 Mar 2026 18:21:27 +0000
with message-id <[email protected]>
and subject line Bug#1047333: fixed in ivar 1.4.4+dfsg-2
has caused the Debian Bug report #1047333,
regarding ivar: 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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--
1047333: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1047333
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ivar
Version: 1.4.2+dfsg-2
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 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 <[email protected]>
> 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.
--- End Message ---
--- Begin Message ---
Source: ivar
Source-Version: 1.4.4+dfsg-2
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ivar, 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.
Santiago Vila <[email protected]> (supplier of updated ivar 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: Mon, 02 Mar 2026 18:55:00 +0100
Source: ivar
Architecture: source
Version: 1.4.4+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1047333
Changes:
ivar (1.4.4+dfsg-2) unstable; urgency=medium
.
* Team upload.
* Fix clean target. Closes: #1047333.
* Drop "Rules-Requires-Root: no" (default).
* Drop "Priority: optional" (default).
* Update standards-version.
* Simplify salsa-ci.yml.
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