Source: gemma Version: 0.98.5+dfsg-2 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-sab-20230813 ftbfs-source-after-build User: [email protected] 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 <[email protected]> > 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.
