[Debian-med-packaging] Bug#1045634: rna-star: Fails to build source after successful build

[Lucas Nussbaum]

Source: rna-star
Version: 2.7.10b+dfsg-2
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 rna-star
> dpkg-buildpackage: info: source version 2.7.10b+dfsg-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --sourcedirectory=source
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> cd source && /usr/bin/make clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/source'
> 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/source'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--sourcedirectory=source
>    dh_clean -O--sourcedirectory=source
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building rna-star using existing ./rna-star_2.7.10b+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to source/STAR-avx: binary file contents changed
> dpkg-source: error: add source/STAR-avx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STAR-avx' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STAR-avx2: binary file contents changed
> dpkg-source: error: add source/STAR-avx2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STAR-avx2' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STAR-plain: binary file contents changed
> dpkg-source: error: add source/STAR-plain in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STAR-plain' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STAR-sse3: binary file contents changed
> dpkg-source: error: add source/STAR-sse3 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STAR-sse3' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STAR-sse4.1: binary file contents changed
> dpkg-source: error: add source/STAR-sse4.1 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STAR-sse4.1' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STAR-ssse3: binary file contents changed
> dpkg-source: error: add source/STAR-ssse3 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STAR-ssse3' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STARlong-avx: binary file contents changed
> dpkg-source: error: add source/STARlong-avx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STARlong-avx' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STARlong-avx2: binary file contents changed
> dpkg-source: error: add source/STARlong-avx2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STARlong-avx2' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STARlong-plain: binary file contents changed
> dpkg-source: error: add source/STARlong-plain in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STARlong-plain' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STARlong-sse3: binary file contents changed
> dpkg-source: error: add source/STARlong-sse3 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STARlong-sse3' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STARlong-sse4.1: binary file contents changed
> dpkg-source: error: add source/STARlong-sse4.1 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STARlong-sse4.1' will not be represented in diff
> dpkg-source: error: cannot represent change to source/STARlong-ssse3: binary file contents changed
> dpkg-source: error: add source/STARlong-ssse3 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'source/STARlong-ssse3' 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/rna-star_2.7.10b+dfsg-2_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.