[Debian-med-packaging] Bug#1043640: beast-mcmc: Fails to build source after successful build

[Lucas Nussbaum]

Source: beast-mcmc
Version: 1.10.4+dfsg-5
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 beast-mcmc
> dpkg-buildpackage: info: source version 1.10.4+dfsg-5
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andrius Merkys <merkys at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --with javahelper
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f native/*\.o native/*\.so native/*\.so\.*
> ant clean
> Buildfile: /<<PKGBUILDDIR>>/build.xml
> 
> clean:
>    [delete] Deleting directory /<<PKGBUILDDIR>>/build
> 
> BUILD SUCCESSFUL
> Total time: 0 seconds
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    jh_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building beast-mcmc using existing ./beast-mcmc_1.10.4+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/VERSION HISTORY.txt has no final newline (either original or modified version)
> dpkg-source: warning: executable mode 0755 of 'release/Linux/BEASTv1.10.4/bin/beast' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'release/Linux/BEASTv1.10.4/bin/beauti' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'release/Linux/BEASTv1.10.4/bin/loganalyser' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'release/Linux/BEASTv1.10.4/bin/logcombiner' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'release/Linux/BEASTv1.10.4/bin/treeannotator' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'release/Linux/BEASTv1.10.4/bin/treestat' will not be represented in diff
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/ContinuousTraits/DarwinsFinches.nex has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/Data/Primates_starting_tree.nex has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/DiscreteTraits/H5N1_HA.nex has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/DiscreteTraits/phylogeneticGLM/batRABV.fas has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/DiscreteTraits/phylogeneticGLM/hostDistances.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/ecmdata/freqs_k_unrest.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/ecmdata/freqs_zs.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/ecmdata/inirates.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/ecmdata/norates.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/ecmdata/rates_k_unrest.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/ecmdata/rates_zs.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/pcadata/freqs.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/pcadata/means.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/pcadata/scales.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/EmpiricalCodonModels/codon-data/pcadata/startfacs.csv has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testAlignmentStatistics.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testBinaryDollo.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testLatentLiability.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testLikelihood.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testMCMC.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testMSSD.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testMVOU.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testMarkovJumps.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testMixedModel.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testNormalModelEllipticalSliceSampler.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testPosteriorIBD.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testSequenceSimulator.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testSimplePathSampling.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testTruncatedNormal15dimension.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/TestXML/testUniformizedMarkovJumps.xml has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/examples/test.sh has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to release/Linux/BEASTv1.10.4/images/beast.png: binary file contents changed
> dpkg-source: error: add release/Linux/BEASTv1.10.4/images/beast.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to release/Linux/BEASTv1.10.4/images/beauti.png: binary file contents changed
> dpkg-source: error: add release/Linux/BEASTv1.10.4/images/beauti.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to release/Linux/BEASTv1.10.4/images/utility.png: binary file contents changed
> dpkg-source: error: add release/Linux/BEASTv1.10.4/images/utility.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to release/Linux/BEASTv1.10.4/lib/beast.jar: binary file contents changed
> dpkg-source: error: add release/Linux/BEASTv1.10.4/lib/beast.jar in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to release/Linux/BEASTv1.10.4/lib/beauti.jar: binary file contents changed
> dpkg-source: error: add release/Linux/BEASTv1.10.4/lib/beauti.jar in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/native/Makefile.OSX has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/native/Makefile.amd64 has no final newline (either original or modified version)
> dpkg-source: warning: file beast-mcmc-1.10.4+dfsg/release/Linux/BEASTv1.10.4/native/Makefile.ia64 has no final newline (either original or modified version)
> 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/beast-mcmc_1.10.4+dfsg-5_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.