[Debian-med-packaging] Bug#1048635: unicycler: Fails to build source after successful build

[Lucas Nussbaum]

Source: unicycler
Version: 0.5.0+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 unicycler
> dpkg-buildpackage: info: source version 0.5.0+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 --with python3 --buildsystem=pybuild
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> find . -name __pycache__ -type d | xargs rm -rf
> make distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Platform: Linux
> Compiler: g++ 13.2.0
> rm -f unicycler/src/scoredalignment.o unicycler/src/minimap_align.o unicycler/src/ref_seqs.o unicycler/src/random_alignments.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/hit.o unicycler/src/consensus_align.o unicycler/src/global_align.o unicycler/src/semi_global_align.o unicycler/src/string_functions.o unicycler/src/miniasm_assembly.o unicycler/src/start_end_align.o unicycler/src/path_align.o unicycler/src/minimap/misc.o unicycler/src/minimap/map.o unicycler/src/minimap/sdust.o unicycler/src/minimap/bseq.o unicycler/src/minimap/sketch.o unicycler/src/minimap/kthread.o unicycler/src/minimap/index.o unicycler/src/semi_global_align_exhaustive.o 
> unicycler/src/overlap_align.o unicycler/src/kmers.o
> rm -f unicycler/cpp_functions.so
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building unicycler using existing ./unicycler_0.5.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: newly created empty file '.pybuild/cpython3_3.11_unicycler/build/unicycler/__init__.py' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_unicycler/build/unicycler/cpp_functions.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_unicycler/build/unicycler/cpp_functions.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_unicycler/build/unicycler/cpp_functions.so' will not be represented in diff
> dpkg-source: warning: file unicycler-0.5.0+dfsg/unicycler.egg-info/SOURCES.txt has no final newline (either original or modified version)
> 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/unicycler_0.5.0+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.