[Debian-med-packaging] Bug#1045400: mrbayes: Fails to build source after successful build

[Lucas Nussbaum]

Source: mrbayes
Version: 3.2.7a-6
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 mrbayes
> dpkg-buildpackage: info: source version 3.2.7a-6
> 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
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "mb" || rm -f mb
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f config.h stamp-h1
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/mb-bayes.Po
> rm -f ./.deps/mb-best.Po
> rm -f ./.deps/mb-command.Po
> rm -f ./.deps/mb-likelihood.Po
> rm -f ./.deps/mb-mbbeagle.Po
> rm -f ./.deps/mb-mcmc.Po
> rm -f ./.deps/mb-model.Po
> rm -f ./.deps/mb-proposal.Po
> rm -f ./.deps/mb-sumpt.Po
> rm -f ./.deps/mb-utils.Po
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making distclean in doc
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> Making distclean in manual
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
> test -z "Manual_MrBayes_v3.2.aux Manual_MrBayes_v3.2.bbl Manual_MrBayes_v3.2.blg Manual_MrBayes_v3.2.log Manual_MrBayes_v3.2.toc" || rm -f Manual_MrBayes_v3.2.aux Manual_MrBayes_v3.2.bbl Manual_MrBayes_v3.2.blg Manual_MrBayes_v3.2.log Manual_MrBayes_v3.2.toc
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> test -z "Manual_MrBayes_v3.2.pdf" || rm -f Manual_MrBayes_v3.2.pdf
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
> Making distclean in tutorial
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
> test -z "MBDating.aux MBDating.bbl MBDating.blg MBDating.log MBDating.out" || rm -f MBDating.aux MBDating.bbl MBDating.blg MBDating.log MBDating.out
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> test -z "MBDating.pdf" || rm -f MBDating.pdf
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> Making distclean in examples
> make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building mrbayes using existing ./mrbayes_3.2.7a.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file aclocal.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file configure, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file am-aux/install-sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file am-aux/compile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file am-aux/depcomp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file am-aux/missing, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file examples/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/config.h.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file doc/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file doc/tutorial/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file doc/tutorial/MBDating.pdf, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file doc/manual/Manual_MrBayes_v3.2.pdf, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file doc/manual/Makefile.in, use --include-removal to override
> dpkg-source: error: cannot represent change to mb: binary file contents changed
> dpkg-source: error: add mb in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'mb' will not be represented in diff
> dpkg-source: error: cannot represent change to mb-mpi: binary file contents changed
> dpkg-source: error: add mb-mpi in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'mb-mpi' 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/mrbayes_3.2.7a-6_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.