[Debian-med-packaging] Bug#1049588: nim-hts: Fails to build binary packages again after successful build

[Lucas Nussbaum]

Source: nim-hts
Version: 0.3.19+ds-1
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).

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/DoubleBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> -------------------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package nim-hts
> dpkg-buildpackage: info: source version 0.3.19+ds-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh at debian.org>
>  dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
>  debian/rules clean
> dh clean
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> # remnants from testing
> rm -f ____t.vcf t.gz ti.txt.gz ti.txt.gz.csi
> rm -f tests/run tests/HG02002.bam.csi tests/auxtest tests/newsample.vcf tests/outmissing.vcf tests/outv.vcf tests/outz.vcf tests/sample.fa.fai tests/all tests/htstest tests/bgzftest tests/bamtest
> rm -rf tests/nimcache
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
> 	rm -f debian/debhelper-build-stamp
> 	rm -rf debian/.debhelper/
> 	rm -f -- debian/nim-hts-dev.substvars debian/nim-hts-examples.substvars debian/files
> 	rm -fr -- debian/nim-hts-dev/ debian/tmp/ debian/nim-hts-examples/
> 	find .  \( \( \
> 		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
> 	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
> 		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
> 		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
> 		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
> 		\) -exec rm -f {} + \) -o \
> 		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
>  debian/rules binary
> dh binary
>    dh_update_autotools_config
>    dh_autoreconf
>    debian/rules override_dh_auto_build
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_build
> # Regenerate repacked files
> cat tests/sa.sam | samtools view -Sb - > tests/sa.bam
> samtools index tests/sa.bam tests/sa.bam.bai
> cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam
> samtools index tests/HG02002.bam tests/HG02002.bam.bai
> tabix tests/test.vcf.gz
> [tabix] the index file exists. Please use '-f' to overwrite.
> make[1]: *** [debian/rules:15: override_dh_auto_build] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:6: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.


The full build log is available from:
http://qa-logs.debian.net/2023/08/16/nim-hts_0.3.19+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.