[Debian-med-packaging] Bug#1043697: bowtie: Fails to build source after successful build

[Lucas Nussbaum]

Source: bowtie
Version: 1.3.1-1
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 bowtie
> dpkg-buildpackage: info: source version 1.3.1-1
> 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
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f .bowtie*
> dh_auto_clean
> 	make -j8 clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-build-s-debug bowtie-build-l-debug bowtie-align-s-debug bowtie-align-l-debug bowtie-inspect-s-debug bowtie-inspect-l-debug \
> bowtie_prof \
> bowtie-build-s.exe bowtie-build-l.exe bowtie-align-s.exe bowtie-align-l.exe bowtie-inspect-s.exe bowtie-inspect-l.exe bowtie-build-s-debug.exe bowtie-build-l-debug.exe bowtie-align-s-debug.exe bowtie-align-l-debug.exe bowtie-inspect-s-debug.exe bowtie-inspect-l-debug.exe bowtie_prof.exe \
> bowtie-src.zip bowtie-bin.zip
> rm -f *.core
> rm -f bowtie-align-s-master* bowtie-align-s-no-io*
> rm -rf .lib .include
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building bowtie using existing ./bowtie_1.3.1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: newly created empty file '.simple_tests.2.fq' will not be represented in diff
> dpkg-source: warning: file bowtie-1.3.1/.simple_tests.fq has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to .simple_tests.tmp.1.ebwt: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.1.ebwt in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.1.ebwtl: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.1.ebwtl in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.2.ebwt: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.2.ebwt in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.2.ebwtl: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.2.ebwtl in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.3.ebwt: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.3.ebwt in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.3.ebwtl: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.3.ebwtl in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file bowtie-1.3.1/.simple_tests.tmp.4.ebwt has no final newline (either original or modified version)
> dpkg-source: warning: file bowtie-1.3.1/.simple_tests.tmp.4.ebwtl has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to .simple_tests.tmp.rev.1.ebwt: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.rev.1.ebwt in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.rev.1.ebwtl: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.rev.1.ebwtl in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.rev.2.ebwt: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.rev.2.ebwt in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .simple_tests.tmp.rev.2.ebwtl: binary file contents changed
> dpkg-source: error: add .simple_tests.tmp.rev.2.ebwtl in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to __pycache__/bowtie-buildcpython-311.pyc: binary file contents changed
> dpkg-source: error: add __pycache__/bowtie-buildcpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> 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/bowtie_1.3.1-1_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.