[Debian-med-packaging] Bug#1049745: beast2-mcmc: Fails to build binary packages again after successful build

[Lucas Nussbaum]

Source: beast2-mcmc
Version: 2.7.5+dfsg-1
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).

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/DoubleBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> ----------------------------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package beast2-mcmc
> dpkg-buildpackage: info: source version 2.7.5+dfsg-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
>  debian/rules clean
> dh clean --with javahelper
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # skip as it needs patches applied, only remove our files generated manually
> # with antlr4.
> if [ -e debian/treeparser ]; then \
>     rm src/beast/base/evolution/tree/treeparser/*.java; \
>     mv debian/treeparser/*.java src/beast/base/evolution/tree/treeparser; \
> fi
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    jh_clean
>    dh_clean
>  debian/rules binary
> dh binary --with javahelper
>    dh_update_autotools_config
>    dh_autoreconf
>    debian/rules execute_before_dh_auto_configure
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # Replacing upstream .java files generated by a recent antlr4 with ones
> # generated on-the-fly with Debian-packaged antlr4.
> mkdir debian/treeparser
> mkdir: cannot create directory ‘debian/treeparser’: File exists
> make[1]: *** [debian/rules:44: execute_before_dh_auto_configure] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:24: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.


The full build log is available from:
http://qa-logs.debian.net/2023/08/16/beast2-mcmc_2.7.5+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.