[Debian-med-packaging] Bug#1046060: minimap2: Fails to build source after successful build

[Lucas Nussbaum]

Source: minimap2
Version: 2.24+dfsg-3
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 minimap2
> dpkg-buildpackage: info: source version 2.24+dfsg-3
> 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 --with python3
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 	make -j8 clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -fr gmon.out *.o a.out minimap2 sdust minimap2-lite *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> cd tex && make clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/tex'
> rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/tex'
> rm -f MT-human.mmi
> rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf
> rm -f libminimap2.a
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building minimap2 using existing ./minimap2_2.24+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11/build/mappy.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11/build/mappy.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11/build/mappy.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> 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/minimap2_2.24+dfsg-3_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.