[Debian-med-packaging] Bug#1049735: bolt-lmm: Fails to build binary packages again after successful build

[Lucas Nussbaum]

Source: bolt-lmm
Version: 2.4.1+dfsg-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 bolt-lmm
> dpkg-buildpackage: info: source version 2.4.1+dfsg-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
>  debian/rules clean
> dh clean --sourcedirectory=src
>    dh_auto_clean -O--sourcedirectory=src
> 	cd src && make -j8 clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
> rm -f *.o
> rm -f bolt
> make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
>    dh_autoreconf_clean -O--sourcedirectory=src
>    dh_clean -O--sourcedirectory=src
>  debian/rules binary
> dh binary --sourcedirectory=src
>    dh_update_autotools_config -O--sourcedirectory=src
>    dh_autoreconf -O--sourcedirectory=src
>    dh_auto_configure -O--sourcedirectory=src
>    debian/rules override_dh_auto_build-indep
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> cd /<<PKGBUILDDIR>>/example/ && \
> 	tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner
> EUR_subset.bed
> EUR_subset.bim
> EUR_subset.dosage.chr17first100
> EUR_subset.dosage.chr22last100.gz
> EUR_subset.dosage.indivs
> EUR_subset.dosage2.chr17first100.gz
> EUR_subset.dosage2.chr17first100.map
> EUR_subset.dosage2.chr17second100
> EUR_subset.dosage2.chr17second100.map
> EUR_subset.dosage2.chr22last100.gz
> EUR_subset.dosage2.chr22last100.map
> EUR_subset.dosage2FileList.txt
> EUR_subset.exclude
> EUR_subset.exclude2
> EUR_subset.fam
> EUR_subset.impute2.chr17first100.gz
> EUR_subset.impute2.chr17second100
> EUR_subset.impute2.chr22last100.gz
> EUR_subset.impute2.indivs
> EUR_subset.impute2FileList.txt
> EUR_subset.modelSnps
> EUR_subset.modelSnps2
> EUR_subset.pheno.covars
> EUR_subset.pheno2.covars
> EUR_subset.remove
> example.dosage2Snps.stats
> example.dosageSnps.stats
> example.impute2Snps.stats
> example.log
> example.stats
> example_reml2.log
> examples.tar.xz
> tar: examples.tar.xz: file changed as we read it
> run_example.sh
> run_example_reml2.sh
> make[1]: *** [debian/rules:13: override_dh_auto_build-indep] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:10: 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/bolt-lmm_2.4.1+dfsg-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.