[Debian-med-packaging] Bug#1044536: fasta3: Fails to build source after successful build

[Lucas Nussbaum]

Source: fasta3
Version: 36.3.8i.14-Nov-2020-1
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 fasta3
> dpkg-buildpackage: info: source version 36.3.8i.14-Nov-2020-1
> 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 --sourcedirectory src
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> if [ -d src ]; then cd src && /usr/bin/make -f "../make/Makefile.linux64" clean-up; fi
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> rm -f *.o  fasta36 ssearch36 lalign36 fasts36 fastx36 tfastx36 fasty36 tfasty36 tfasts36 fastm36 tfastm36 fastf36 tfastf36 glsearch36 ggsearch36 map_db; 	rm -rf ../bin/*
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--sourcedirectory=src
>    dh_clean -O--sourcedirectory=src
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building fasta3 using existing ./fasta3_36.3.8i.14-Nov-2020.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file bin/README, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_m1.rfx
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_m1.rss
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_mc.lal
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_mc.lal_bl62
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_mc.lal_z3
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_mw.lal
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_mw.lal_bl62
>  fasta3-36.3.8i.14-Nov-2020/test/results/test2G_mw.lal_z3
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_m1.rfx
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_m1.rss
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_mc.lal
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_mc.lal_bl62
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_mc.lal_z3
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_mw.lal
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_mw.lal_bl62
>  fasta3-36.3.8i.14-Nov-2020/test/results/test_mw.lal_z3
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/fasta3_36.3.8i.14-Nov-2020-1.diff.hR_Wgd
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> 
> 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/fasta3_36.3.8i.14-Nov-2020-1_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.