[Debian-med-packaging] Bug#1044789: gemma: Fails to build source after successful build

[Lucas Nussbaum]

Source: gemma
Version: 0.98.5+dfsg-2
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 gemma
> dpkg-buildpackage: info: source version 0.98.5+dfsg-2
> 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 clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -vf ./src/*.o
> removed './src/bslmm.o'
> removed './src/bslmmdap.o'
> removed './src/debug.o'
> removed './src/fastblas.o'
> removed './src/gemma.o'
> removed './src/gemma_io.o'
> removed './src/gzstream.o'
> removed './src/lapack.o'
> removed './src/ldr.o'
> removed './src/lm.o'
> removed './src/lmm.o'
> removed './src/logistic.o'
> removed './src/main.o'
> removed './src/mathfunc.o'
> removed './src/mvlmm.o'
> removed './src/param.o'
> removed './src/prdt.o'
> removed './src/varcov.o'
> removed './src/vc.o'
> rm -vf ./src/*~
> rm -vf ./test/src/*.o
> removed './test/src/unittests-main.o'
> removed './test/src/unittests-math.o'
> rm -vf ./bin/gemma
> removed './bin/gemma'
> rm -vf ./bin/unittests-gemma
> removed './bin/unittests-gemma'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> 	rm -f debian/gemma-doc.debhelper.log debian/gemma.debhelper.log
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> 	rm -f debian/debhelper-build-stamp
> 	rm -rf debian/.debhelper/
> 	rm -f -- debian/gemma.substvars debian/gemma-doc.substvars debian/files
> 	rm -fr -- debian/gemma/ debian/tmp/ debian/gemma-doc/
> 	find .  \( \( \
> 		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
> 	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
> 		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
> 		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
> 		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
> 		\) -exec rm -f {} + \) -o \
> 		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
> rm -f *.log
> rm -rf test/output/
> rm -f bin/gemma
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building gemma using existing ./gemma_0.98.5+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: info: local changes detected, the modified files are:
>  gemma-0.98.5+dfsg/output/BXD.cXX.txt
>  gemma-0.98.5+dfsg/output/BXD.log.txt
>  gemma-0.98.5+dfsg/output/BXDLMM.assoc.txt
>  gemma-0.98.5+dfsg/output/BXDLMM.log.txt
>  gemma-0.98.5+dfsg/output/BXDLMM9.assoc.txt
>  gemma-0.98.5+dfsg/output/BXDLMM9.log.txt
>  gemma-0.98.5+dfsg/output/mouse_hs1940_CD8_lm.assoc.txt
>  gemma-0.98.5+dfsg/output/mouse_hs1940_CD8_lm.log.txt
>  gemma-0.98.5+dfsg/output/mouse_hs1940_loco.assoc.txt
>  gemma-0.98.5+dfsg/output/mouse_hs1940_loco.cXX.txt
>  gemma-0.98.5+dfsg/output/mouse_hs1940_loco.log.txt
>  gemma-0.98.5+dfsg/output/plink_lmm1_cov.assoc.txt
>  gemma-0.98.5+dfsg/output/plink_lmm1_cov.log.txt
>  gemma-0.98.5+dfsg/output/testPlinkStandardRelatednessMatrixK.log.txt
>  gemma-0.98.5+dfsg/output/testPlinkStandardRelatednessMatrixK.sXX.txt
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/gemma_0.98.5+dfsg-2.diff.39Lmds
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> 
> 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/gemma_0.98.5+dfsg-2_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.