[R-pkg-team] Bug#1047493: r-bioc-rhtslib: Fails to build source after successful build

[Lucas Nussbaum]

Source: r-bioc-rhtslib
Version: 2.2.0+dfsg-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 r-bioc-rhtslib
> dpkg-buildpackage: info: source version 2.2.0+dfsg-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 --buildsystem R
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> find src -name "*.o" -delete
> find src -name "*.pico" -delete
> rm -f src/*/libhts.a src/*/libhts.so*
> rm -f src/*/version.h
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=R
>    dh_clean -O--buildsystem=R
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building r-bioc-rhtslib using existing ./r-bioc-rhtslib_2.2.0+dfsg.orig.tar.xz
> dpkg-source: info: local changes detected, the modified files are:
>  r-bioc-rhtslib-2.2.0+dfsg/src/htslib-1.15.1/config_vars.h
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/r-bioc-rhtslib_2.2.0+dfsg-1.diff.BWtbVg
> 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/r-bioc-rhtslib_2.2.0+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.