[Debian-med-packaging] Bug#1049212: vcfanno: Fails to build source after successful build

[Lucas Nussbaum]

Source: vcfanno
Version: 0.3.5+ds-1
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 vcfanno
> dpkg-buildpackage: info: source version 0.3.5+ds-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --buildsystem=golang --with=golang
>    dh_auto_clean -O--buildsystem=golang
>    dh_autoreconf_clean -O--buildsystem=golang
>    dh_clean -O--buildsystem=golang
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building vcfanno using existing ./vcfanno_0.3.5+ds.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file tests/notbgz/notbgz.vcf.gz, use --include-removal to override
> dpkg-source: error: cannot represent change to docs/examples/gff_sv/genes.gff3.gz.tbi: binary file contents changed
> dpkg-source: error: add docs/examples/gff_sv/genes.gff3.gz.tbi in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to example/ex.bam: binary file contents changed
> dpkg-source: error: add example/ex.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 example/ex.bam.bai: binary file contents changed
> dpkg-source: error: add example/ex.bam.bai in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to example/exac.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add example/exac.vcf.gz.tbi in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to example/fitcons.bed.gz.tbi: binary file contents changed
> dpkg-source: error: add example/fitcons.bed.gz.tbi 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/astar/astar.anno.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/astar/astar.anno.vcf.gz.tbi 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/by_alt_float/annotation.tsv.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/by_alt_float/annotation.tsv.gz.tbi 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/citest/at/testexon.bed.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/citest/at/testexon.bed.gz.tbi 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/citest/dummyexons.bed.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/citest/dummyexons.bed.gz.tbi 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/data/multiple-alts.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/data/multiple-alts.vcf.gz.tbi 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/data/number.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/data/number.vcf.gz.tbi 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/dbnsfp/dbNSFP_ex.txt.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/dbnsfp/dbNSFP_ex.txt.gz.tbi 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/dbnsfp/dbNSFP_example.txt.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/dbnsfp/dbNSFP_example.txt.gz.tbi 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/id-test/cosmic.small.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/id-test/cosmic.small.vcf.gz.tbi 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/id-test/dbsnp.small.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/id-test/dbsnp.small.vcf.gz.tbi 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/id-test/small.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/id-test/small.vcf.gz.tbi 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/multiple-alts/ma-db.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/multiple-alts/ma-db.vcf.gz.tbi 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/notbgz/gno.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/notbgz/gno.vcf.gz.tbi 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/overwrite-multiple-alts/a/whole.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/overwrite-multiple-alts/a/whole.vcf.gz.tbi 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/overwrite-multiple-alts/b/cadd_indels.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/overwrite-multiple-alts/b/cadd_indels.vcf.gz.tbi 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/overwrite-multiple-alts/b/whole_genome_snv_slice.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/overwrite-multiple-alts/b/whole_genome_snv_slice.vcf.gz.tbi 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/ref-alt-test/tmp_annotation.txt.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/ref-alt-test/tmp_annotation.txt.gz.tbi 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/ref-alt-test/tmp_calls.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/ref-alt-test/tmp_calls.vcf.gz.tbi 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/testVA/test-gnomad.vcf.gz.tbi: binary file contents changed
> dpkg-source: error: add tests/testVA/test-gnomad.vcf.gz.tbi 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 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/vcfanno_0.3.5+ds-1_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.