[Debian-med-packaging] Bug#1044832: fastml: Fails to build source after successful build

[Lucas Nussbaum]

Source: fastml
Version: 3.11-3
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 fastml
> dpkg-buildpackage: info: source version 3.11-3
> 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>>'
> dh_auto_clean
> 	make -j8 clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> cd libs;make clean
> cd programs;make clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/libs'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/programs'
> cd fastml && make clean
> cd phylogeny && make clean
> cd gainLoss && make clean
> cd indelCoder && make clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
> rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml  fastml.debug fastml.doubleRep *.o
> make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
> rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss  gainLoss.debug gainLoss.doubleRep *.o
> make[4]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
> rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a   *.o
> make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/indelCoder'
> rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder  indelCoder.debug indelCoder.doubleRep *.o
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/indelCoder'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/gainLoss'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/libs/phylogeny'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f libs/phylogeny/make.dep \
>       programs/fastml/make.dep \
>       programs/gainLoss/make.dep \
>       programs/indelCoder/make.dep
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building fastml using existing ./fastml_3.11.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file programs/gainLoss/make.dep, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file programs/indelCoder/make.dep, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file programs/fastml/make.dep, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file libs/phylogeny/#Makefile#, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file libs/phylogeny/make.dep, use --include-removal to override
> dpkg-source: error: cannot represent change to bin/fastml: binary file contents changed
> dpkg-source: error: add bin/fastml in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'bin/fastml' will not be represented in diff
> dpkg-source: error: cannot represent change to bin/gainLoss: binary file contents changed
> dpkg-source: error: add bin/gainLoss in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'bin/gainLoss' will not be represented in diff
> dpkg-source: error: cannot represent change to bin/indelCoder: binary file contents changed
> dpkg-source: error: add bin/indelCoder in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'bin/indelCoder' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/checkTreeLikelihoodGivenBranches: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/checkTreeLikelihoodGivenBranches in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/checkTreeLikelihoodGivenBranches' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/doubleRep: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/doubleRep in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/doubleRep' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/given2seqEstimateTheDistBetweenThem: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/given2seqEstimateTheDistBetweenThem in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/given2seqEstimateTheDistBetweenThem' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/given2seqEstimateTheDistBetweenThemGamma: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/given2seqEstimateTheDistBetweenThemGamma in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/given2seqEstimateTheDistBetweenThemGamma' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/given2seqEstimateTheDistanceK2P: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/given2seqEstimateTheDistanceK2P in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/given2seqEstimateTheDistanceK2P' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/given2seqTheDistBetweenThem-3: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/given2seqTheDistBetweenThem-3 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/given2seqTheDistBetweenThem-3' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/readTreeWithComments: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/readTreeWithComments in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/readTreeWithComments' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/splitMap_test: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/splitMap_test in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/splitMap_test' will not be represented in diff
> dpkg-source: error: cannot represent change to libs/phylogeny/tests/split_test: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/split_test in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'libs/phylogeny/tests/split_test' 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/fastml_3.11-3_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.