[Debian-med-packaging] Bug#1048520: psortb: Fails to build source after successful build
Lucas Nussbaum
lucas at debian.org
Sun Aug 13 20:21:07 BST 2023
Source: psortb
Version: 3.0.6+dfsg-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 psortb
> dpkg-buildpackage: info: source version 3.0.6+dfsg-3
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Étienne Mollier <emollier 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 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> "/usr/bin/perl" -e 'exit 0 unless chdir '\''algorithm-hmm'\''; system '\''make clean'\'' if -f '\''Makefile'\'';' --
> "/usr/bin/perl" "-MExtUtils::Manifest=fullcheck" -e fullcheck
> make[3]: Entering directory '/<<PKGBUILDDIR>>/algorithm-hmm'
> rm -f \
> HMM.bso HMM.def \
> HMM.exp HMM.x \
> HMM.bs ../blib/arch/auto/Algorithm/HMM/extralibs.all \
> ../blib/arch/auto/Algorithm/HMM/extralibs.ld Makefile.aperl \
> *.a *.o \
> *perl.core HMM.base \
> HMM.bs HMM.bso \
> HMM.c HMM.def \
> HMM.exp HMM.o \
> HMM_def.old MYMETA.json \
> MYMETA.yml blibdirs.ts \
> core core.*perl.*.? \
> core.[0-9] core.[0-9][0-9] \
> core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
> core.[0-9][0-9][0-9][0-9][0-9] libHMM.def \
> mon.out perl \
> perl perl.exe \
> perlmain.c pm_to_blib \
> pm_to_blib.ts so_locations \
> tmon.out
> rm -rf \
> blib
> mv Makefile Makefile.old > /dev/null 2>&1
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/algorithm-hmm'
> "/usr/bin/perl" -e 'exit 0 unless chdir '\''bio-tools-psort-svmloc'\''; system '\''make clean'\'' if -f '\''Makefile'\'';' --
> make[3]: Entering directory '/<<PKGBUILDDIR>>/bio-tools-psort-svmloc'
> rm -f \
> SVMLoc.bso SVMLoc.def \
> SVMLoc.exp SVMLoc.x \
> SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/extralibs.all \
> ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/extralibs.ld Makefile.aperl \
> *.a *.o \
> *perl.core MYMETA.json \
> MYMETA.yml SVMLoc.base \
> SVMLoc.bs SVMLoc.bso \
> SVMLoc.c SVMLoc.def \
> SVMLoc.exp SVMLoc.o \
> SVMLoc_def.old blibdirs.ts \
> core core.*perl.*.? \
> core.[0-9] core.[0-9][0-9] \
> core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
> core.[0-9][0-9][0-9][0-9][0-9] libSVMLoc.def \
> mon.out perl \
> perl perl.exe \
> perlmain.c pm_to_blib \
> pm_to_blib.ts so_locations \
> tmon.out
> rm -rf \
> blib
> mv Makefile Makefile.old > /dev/null 2>&1
> Not in MANIFEST: .pc/.quilt_patches
> Not in MANIFEST: .pc/.quilt_series
> Not in MANIFEST: .pc/.version
> Not in MANIFEST: .pc/applied-patches
> Not in MANIFEST: .pc/biosquid_includes.patch/algorithm-hmm/Makefile.PL
> Not in MANIFEST: .pc/fix_build_Algorithm-SVM.patch/bio-tools-psort-svmloc/Makefile.PL
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/bio-tools-psort-svmloc'
> Not in MANIFEST: .pc/fix_hmmer_interface.patch/algorithm-hmm/hmm-binding.cpp
> Not in MANIFEST: .pc/fix_module_path.patch/lib/Bio/Tools/PSort/Module/InputI.pm
> Not in MANIFEST: .pc/path_to_conf.patch/psort/bin/psort
> Not in MANIFEST: .pc/path_to_conf.patch/psort/server/startup.pl
> Not in MANIFEST: .pc/remove-bundled-party-libsvm.patch/bio-tools-psort-svmloc/bindings.h
> "/usr/bin/perl" -e 'exit 0 unless chdir '\''bio-tools-psort-modhmm'\''; system '\''make clean'\'' if -f '\''Makefile'\'';' --
> Not in MANIFEST: .pc/remove-bundled-party-libsvm.patch/bio-tools-psort-svmloc/Makefile.PL
> Not in MANIFEST: .pc/remove-bundled-party-libsvm.patch/bio-tools-psort-svmloc/MANIFEST
> Not in MANIFEST: algorithm-hmm/hmm-binding.cpp
> Not in MANIFEST: algorithm-hmm/hmm.h
> Not in MANIFEST: algorithm-hmm/HMM.xs
> Not in MANIFEST: algorithm-hmm/lib/Algorithm/HMM.pm
> Not in MANIFEST: algorithm-hmm/lib/Algorithm/HMM/Hit.pm
> Not in MANIFEST: algorithm-hmm/lib/Algorithm/HMM/Hit/Domain.pm
> Not in MANIFEST: algorithm-hmm/lib/Algorithm/HMM/Hit/Global.pm
> Not in MANIFEST: algorithm-hmm/lib/Algorithm/HMM/Report.pm
> Not in MANIFEST: algorithm-hmm/Makefile.PL
> Not in MANIFEST: algorithm-hmm/MANIFEST
> Not in MANIFEST: algorithm-hmm/README
> Not in MANIFEST: algorithm-hmm/sample.hmm
> Not in MANIFEST: algorithm-hmm/sample.hmm.1
> Not in MANIFEST: algorithm-hmm/t/hmm.t
> Not in MANIFEST: algorithm-hmm/typemap
> Not in MANIFEST: bio-tools-psort-modhmm/binding.c
> Not in MANIFEST: bio-tools-psort-modhmm/binding.o
> Not in MANIFEST: bio-tools-psort-modhmm/cdriver.c
> Not in MANIFEST: bio-tools-psort-modhmm/HMMS/amino_multi.pri
> Not in MANIFEST: bio-tools-psort-modhmm/HMMS/replacement_letter_multi.rpl
> Not in MANIFEST: bio-tools-psort-modhmm/HMMS/S_TMHMM_0.92b.hmg
> Not in MANIFEST: bio-tools-psort-modhmm/lib/Bio/Tools/PSort/ModHMM.pm
> Not in MANIFEST: bio-tools-psort-modhmm/LICENSE
> Not in MANIFEST: bio-tools-psort-modhmm/Makefile.cdriver
> Not in MANIFEST: bio-tools-psort-modhmm/Makefile.PL
> Not in MANIFEST: bio-tools-psort-modhmm/ModHMM.bs
> Not in MANIFEST: bio-tools-psort-modhmm/modhmm.c
> Not in MANIFEST: bio-tools-psort-modhmm/modhmm.o
> Not in MANIFEST: bio-tools-psort-modhmm/modhmm.xs
> Not in MANIFEST: bio-tools-psort-modhmm/modhmm0.92b/funcs.h
> Not in MANIFEST: bio-tools-psort-modhmm/modhmm0.92b/structs.h
> Not in MANIFEST: bio-tools-psort-modhmm/MYMETA.json
> Not in MANIFEST: bio-tools-psort-modhmm/MYMETA.yml
> Not in MANIFEST: bio-tools-psort-modhmm/README
> Not in MANIFEST: bio-tools-psort-modhmm/t/modhmm.t
> Not in MANIFEST: bio-tools-psort-modhmm/typemap
> Not in MANIFEST: bio-tools-psort-svmloc/bindings.h
> Not in MANIFEST: bio-tools-psort-svmloc/Changes
> Not in MANIFEST: bio-tools-psort-svmloc/fre_patterns.txt
> Not in MANIFEST: bio-tools-psort-svmloc/lib/Bio/Tools/PSort/SVMLoc.pm
> Not in MANIFEST: bio-tools-psort-svmloc/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm
> Not in MANIFEST: bio-tools-psort-svmloc/Makefile.PL
> make[3]: Entering directory '/<<PKGBUILDDIR>>/bio-tools-psort-modhmm'
> Not in MANIFEST: bio-tools-psort-svmloc/MANIFEST
> Not in MANIFEST: bio-tools-psort-svmloc/README
> Not in MANIFEST: bio-tools-psort-svmloc/sample.model
> Not in MANIFEST: bio-tools-psort-svmloc/sample.model2
> Not in MANIFEST: bio-tools-psort-svmloc/SVMLoc.xs
> Not in MANIFEST: bio-tools-psort-svmloc/t/svmloc.t
> Not in MANIFEST: bio-tools-psort-svmloc/TODO
> Not in MANIFEST: bio-tools-psort-svmloc/typemap
> rm -f \
> ModHMM.bso ModHMM.def \
> ModHMM.exp ModHMM.x \
> ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/extralibs.all \
> ../blib/arch/auto/Bio/Tools/PSort/ModHMM/extralibs.ld Makefile.aperl \
> *.a *.o \
> *perl.core MYMETA.json \
> MYMETA.yml blibdirs.ts \
> core core.*perl.*.? \
> core.[0-9] core.[0-9][0-9] \
> core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
> core.[0-9][0-9][0-9][0-9][0-9] libModHMM.def \
> modhmm.base modhmm.bs \
> modhmm.bso modhmm.c \
> modhmm.def modhmm.exp \
> modhmm.o modhmm_def.old \
> mon.out perl \
> perl perl.exe \
> perlmain.c pm_to_blib \
> pm_to_blib.ts so_locations \
> tmon.out
> Not in MANIFEST: Changes
> Not in MANIFEST: debian/.debhelper/generated/psortb/dh_installchangelogs.dch.trimmed
> Not in MANIFEST: debian/.debhelper/generated/psortb/installed-by-dh_install
> Not in MANIFEST: debian/.debhelper/generated/psortb/installed-by-dh_installdocs
> Not in MANIFEST: debian/.debhelper/generated/psortb/installed-by-dh_installman
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-build-ids
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-root/DEBIAN/control
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-root/DEBIAN/md5sums
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-root/usr/lib/debug/.build-id/04/155f8f8d35b9f4c3642ebeb91742659598ab02.debug
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-root/usr/lib/debug/.build-id/6c/39bd1b458be0b409d75ccbaf97bd261158c826.debug
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-root/usr/lib/debug/.build-id/ee/41b6c4a93cf329b8be36ec5931c33829322281.debug
> rm -rf \
> blib
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-root/usr/lib/debug/.dwz/x86_64-linux-gnu/psortb.debug
> Not in MANIFEST: debian/.debhelper/psortb/dbgsym-root/usr/share/doc/psortb-dbgsym
> Not in MANIFEST: debian/changelog
> Not in MANIFEST: debian/clean
> Not in MANIFEST: debian/control
> Not in MANIFEST: debian/copyright
> Not in MANIFEST: debian/createmanpages
> Not in MANIFEST: debian/debhelper-build-stamp
> Not in MANIFEST: debian/files
> Not in MANIFEST: debian/install
> Not in MANIFEST: debian/lintian-overrides
> Not in MANIFEST: debian/manpages
> Not in MANIFEST: debian/patches/biosquid_includes.patch
> Not in MANIFEST: debian/patches/fix_build_Algorithm-SVM.patch
> Not in MANIFEST: debian/patches/fix_hmmer_interface.patch
> Not in MANIFEST: debian/patches/fix_module_path.patch
> Not in MANIFEST: debian/patches/path_to_conf.patch
> mv Makefile Makefile.old > /dev/null 2>&1
> Not in MANIFEST: debian/patches/remove-bundled-party-libsvm.patch
> Not in MANIFEST: debian/patches/series
> Not in MANIFEST: debian/psort.1
> Not in MANIFEST: debian/psortb.substvars
> Not in MANIFEST: debian/psortb/DEBIAN/control
> Not in MANIFEST: debian/psortb/DEBIAN/md5sums
> Not in MANIFEST: debian/psortb/usr/bin/psort
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/modhmm/amino_multi.pri
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/modhmm/replacement_letter_multi.rpl
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/modhmm/S_TMHMM_0.92b.hmg
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/motif/archaea/changes
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/motif/archaea/motifs.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/motif/archaea/notes.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/motif/gramneg/motifs.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/motif/grampos/motifs.txt
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/bio-tools-psort-modhmm'
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/omp-motif/omp-motifs.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/profile/archaea/notes.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/profile/archaea/profile_ids
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/profile/archaea/ps_ALL
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/profile/gramneg/profile_ids
> rm -f \
> PSort.bso PSort.def \
> PSort.exp PSort.x \
> blib/arch/auto/Bio/Tools/PSort/extralibs.all \
> blib/arch/auto/Bio/Tools/PSort/extralibs.ld Makefile.aperl \
> *.a *.o \
> *perl.core MYMETA.json \
> MYMETA.yml blibdirs.ts \
> core core.*perl.*.? \
> core.[0-9] core.[0-9][0-9] \
> core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
> core.[0-9][0-9][0-9][0-9][0-9] libPSort.def \
> mon.out perl \
> perl perl.exe \
> perlmain.c pm_to_blib \
> pm_to_blib.ts so_locations \
> tmon.out
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/profile/gramneg/ps_ALL
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/profile/grampos/profile_ids
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/profile/grampos/ps_ALL
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/archaea/notes
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/archaea/sclblast
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/archaea/sclblast+swissprot+some_manual
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/archaea/sclblast.pos
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/archaea/sclblast.pot
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/archaea/sclblast.ptf
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/archaea/sclblast.pto
> rm -rf \
> blib
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/gramneg/sclblast
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/gramneg/sclblast.pos
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/gramneg/sclblast.pot
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/gramneg/sclblast.ptf
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/gramneg/sclblast.pto
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/grampos/sclblast
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/grampos/sclblast.pos
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/grampos/sclblast.pot
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/grampos/sclblast.ptf
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/grampos/sclblast.pto
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/sclblast/makedb.sh
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/archaea/check-sig
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/archaea/model.hmm
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/archaea/model.svm
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/archaea/notes
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/gramneg/check-sig
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/gramneg/model.hmm
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/gramneg/model.svm
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/grampos/check-sig
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/grampos/model.hmm
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/signal/grampos/model.svm
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Cellwall/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Cellwall/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Cytoplasmic/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Cytoplasmic/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Extracellular/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Extracellular/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Membrane/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/Membrane/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/archaea/notes.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Cytoplasmic/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Cytoplasmic/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Extracellular/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Extracellular/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Innermembrane/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Innermembrane/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Outermembrane/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Outermembrane/SVM_MODEL.txt
> mv Makefile Makefile.old > /dev/null 2>&1
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Periplasmic/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/gramneg/Periplasmic/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Cellwall/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Cellwall/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Cytoplasmic/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Cytoplasmic/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Extracellular/fre_patterns.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Extracellular/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Membrane/fre_patterns.txt
> "/usr/bin/perl" -e 'chdir '\''algorithm-hmm'\''; system '\''make -f Makefile.old realclean'\'' if -f '\''Makefile.old'\'';' --
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/analysis/subloc/grampos/Membrane/SVM_MODEL.txt
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/output/bayesian/archaea/bayes.model
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/output/bayesian/gramneg/bayes-rpc.model
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/output/bayesian/gramneg/bayes.model
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/output/bayesian/grampos/bayes-rpc.model
> Not in MANIFEST: debian/psortb/usr/lib/psort/conf/output/bayesian/grampos/bayes.model
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Hit.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Hit/Domain.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Hit/Global.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Report.pm
> make[3]: Entering directory '/<<PKGBUILDDIR>>/algorithm-hmm'
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Algorithm/HMM/autosplit.ix
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Algorithm/HMM/HMM.so
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Bio/Tools/PSort/ModHMM/autosplit.ix
> rm -f \
> HMM.bso HMM.def \
> HMM.exp HMM.x \
> HMM.bs ../blib/arch/auto/Algorithm/HMM/extralibs.all \
> ../blib/arch/auto/Algorithm/HMM/extralibs.ld Makefile.aperl \
> *.a *.o \
> *perl.core HMM.base \
> HMM.bs HMM.bso \
> HMM.c HMM.def \
> HMM.exp HMM.o \
> HMM_def.old MYMETA.json \
> MYMETA.yml blibdirs.ts \
> core core.*perl.*.? \
> core.[0-9] core.[0-9][0-9] \
> core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
> core.[0-9][0-9][0-9][0-9][0-9] libHMM.def \
> mon.out perl \
> perl perl.exe \
> perlmain.c pm_to_blib \
> pm_to_blib.ts so_locations \
> tmon.out
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Bio/Tools/PSort/ModHMM/ModHMM.so
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Bio/Tools/PSort/SVMLoc/autosplit.ix
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Motif.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Motif/Match.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Motif/Pattern.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Constants.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Install.pm
> rm -rf \
> blib
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/ModHMM.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/AnalysisI.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Bayesian.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/HMMTOP.pm
> mv Makefile Makefile.old > /dev/null 2>&1
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/InputI.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/ModHMM.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Motif.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Null.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/OMPMotif.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/OutputI.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Profile.pm
> make[3]: [Makefile.old:547: clean] Error 1 (ignored)
> rm -f \
> Makefile Makefile.old \
> HMM.o hmm-binding.o
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Rules.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SCLBlast.pm
> rm -rf \
>
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Signal.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SVMLoc.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SVMLocApache.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/ModuleI.pm
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/algorithm-hmm'
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Pathway.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Profile.pm
> "/usr/bin/perl" -e 'chdir '\''algorithm-hmm'\''; system '\''make -f Makefile realclean'\'' if -f '\''Makefile'\'';' --
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Profile/Match.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter.pm
> "/usr/bin/perl" -e 'chdir '\''bio-tools-psort-svmloc'\''; system '\''make -f Makefile.old realclean'\'' if -f '\''Makefile.old'\'';' --
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/html.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/long.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/normal.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/terse.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Result.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/SVMLoc.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/SVMLoc/DataSet.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/XMLRPC/Client.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP/Helix.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP/Report.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlast.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlast/Hit.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlast/Report.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlastLocal.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Signal.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Signal/Report.pm
> Not in MANIFEST: debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/SVMLoc.pm
> Not in MANIFEST: debian/psortb/usr/share/doc/psortb/changelog.Debian.gz
> Not in MANIFEST: debian/psortb/usr/share/doc/psortb/changelog.gz
> Not in MANIFEST: debian/psortb/usr/share/doc/psortb/copyright
> make[3]: Entering directory '/<<PKGBUILDDIR>>/bio-tools-psort-svmloc'
> Not in MANIFEST: debian/psortb/usr/share/lintian/overrides/psortb
> Not in MANIFEST: debian/psortb/usr/share/man/man1/psort.1.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Algorithm::HMM.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit.3pm.gz
> rm -f \
> SVMLoc.bso SVMLoc.def \
> SVMLoc.exp SVMLoc.x \
> SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/extralibs.all \
> ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/extralibs.ld Makefile.aperl \
> *.a *.o \
> *perl.core MYMETA.json \
> MYMETA.yml SVMLoc.base \
> SVMLoc.bs SVMLoc.bso \
> SVMLoc.c SVMLoc.def \
> SVMLoc.exp SVMLoc.o \
> SVMLoc_def.old blibdirs.ts \
> core core.*perl.*.? \
> core.[0-9] core.[0-9][0-9] \
> core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
> core.[0-9][0-9][0-9][0-9][0-9] libSVMLoc.def \
> mon.out perl \
> perl perl.exe \
> perlmain.c pm_to_blib \
> pm_to_blib.ts so_locations \
> tmon.out
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Domain.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Global.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Algorithm::HMM::Report.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::Motif.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Match.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Pattern.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModHMM.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::AnalysisI.3pm.gz
> rm -rf \
> blib
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::InputI.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Motif.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Null.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OMPMotif.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OutputI.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Profile.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModuleI.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Pathway.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile::Match.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc::DataSet.3pm.gz
> mv Makefile Makefile.old > /dev/null 2>&1
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::Run::HMMTOP.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::Signal.3pm.gz
> Not in MANIFEST: debian/psortb/usr/share/man/man3/Bio::Tools::SVMLoc.3pm.gz
> Not in MANIFEST: debian/rules
> Not in MANIFEST: debian/salsa-ci.yml
> Not in MANIFEST: debian/source/format
> Not in MANIFEST: debian/tests/pkg-perl/use-name
> Not in MANIFEST: debian/upstream/metadata
> Not in MANIFEST: debian/watch
> Not in MANIFEST: INSTALL
> Not in MANIFEST: lib/Bio/Tools/Motif.pm
> Not in MANIFEST: lib/Bio/Tools/Motif/Match.pm
> Not in MANIFEST: lib/Bio/Tools/Motif/Pattern.pm
> Not in MANIFEST: lib/Bio/Tools/PSort.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Constants.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Install.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/AnalysisI.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/Bayesian.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/HMMTOP.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/InputI.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/ModHMM.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/Motif.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/Null.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/OMPMotif.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/OutputI.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/Profile.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/Rules.pm
> make[3]: [Makefile.old:532: clean] Error 1 (ignored)
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/SCLBlast.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/Signal.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/SVMLoc.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Module/SVMLocApache.pm
> rm -f \
> Makefile Makefile.old \
> SVMLoc.o
> Not in MANIFEST: lib/Bio/Tools/PSort/ModuleI.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Pathway.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Profile.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Profile/Match.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Report.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Report/Formatter.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Report/Formatter/html.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Report/Formatter/long.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Report/Formatter/normal.pm
> rm -rf \
>
> Not in MANIFEST: lib/Bio/Tools/PSort/Report/Formatter/terse.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/Report/Result.pm
> Not in MANIFEST: lib/Bio/Tools/PSort/XMLRPC/Client.pm
> Not in MANIFEST: lib/Bio/Tools/Run/HMMTOP.pm
> Not in MANIFEST: lib/Bio/Tools/Run/HMMTOP/Helix.pm
> Not in MANIFEST: lib/Bio/Tools/Run/HMMTOP/Report.pm
> Not in MANIFEST: lib/Bio/Tools/Run/SCLBlast.pm
> Not in MANIFEST: lib/Bio/Tools/Run/SCLBlast/Hit.pm
> Not in MANIFEST: lib/Bio/Tools/Run/SCLBlast/Report.pm
> Not in MANIFEST: lib/Bio/Tools/Run/SCLBlastLocal.pm
> Not in MANIFEST: lib/Bio/Tools/Signal.pm
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/bio-tools-psort-svmloc'
> Not in MANIFEST: lib/Bio/Tools/Signal/Report.pm
> Not in MANIFEST: lib/Bio/Tools/SVMLoc.pm
> Not in MANIFEST: LICENSE
> Not in MANIFEST: Makefile.PL
> Not in MANIFEST: MANIFEST
> Not in MANIFEST: psort/bin/check-sig
> Not in MANIFEST: psort/bin/psort
> Not in MANIFEST: psort/bin/psort.tmpt
> Not in MANIFEST: psort/conf/analysis/modhmm/amino_multi.pri
> Not in MANIFEST: psort/conf/analysis/modhmm/replacement_letter_multi.rpl
> Not in MANIFEST: psort/conf/analysis/modhmm/S_TMHMM_0.92b.hmg
> "/usr/bin/perl" -e 'chdir '\''bio-tools-psort-svmloc'\''; system '\''make -f Makefile realclean'\'' if -f '\''Makefile'\'';' --
> Not in MANIFEST: psort/conf/analysis/motif/archaea/changes
> Not in MANIFEST: psort/conf/analysis/motif/archaea/motifs.txt
> Not in MANIFEST: psort/conf/analysis/motif/archaea/notes.txt
> Not in MANIFEST: psort/conf/analysis/motif/gramneg/motifs.txt
> Not in MANIFEST: psort/conf/analysis/motif/grampos/motifs.txt
> Not in MANIFEST: psort/conf/analysis/omp-motif/omp-motifs.txt
> Not in MANIFEST: psort/conf/analysis/profile/archaea/notes.txt
> Not in MANIFEST: psort/conf/analysis/profile/archaea/profile_ids
> Not in MANIFEST: psort/conf/analysis/profile/archaea/ps_ALL
> Not in MANIFEST: psort/conf/analysis/profile/gramneg/profile_ids
> Not in MANIFEST: psort/conf/analysis/profile/gramneg/ps_ALL
> Not in MANIFEST: psort/conf/analysis/profile/grampos/profile_ids
> Not in MANIFEST: psort/conf/analysis/profile/grampos/ps_ALL
> Not in MANIFEST: psort/conf/analysis/sclblast/archaea/notes
> Not in MANIFEST: psort/conf/analysis/sclblast/archaea/sclblast
> Not in MANIFEST: psort/conf/analysis/sclblast/archaea/sclblast+swissprot+some_manual
> Not in MANIFEST: psort/conf/analysis/sclblast/archaea/sclblast.pos
> Not in MANIFEST: psort/conf/analysis/sclblast/archaea/sclblast.pot
> Not in MANIFEST: psort/conf/analysis/sclblast/archaea/sclblast.ptf
> Not in MANIFEST: psort/conf/analysis/sclblast/archaea/sclblast.pto
> Not in MANIFEST: psort/conf/analysis/sclblast/gramneg/sclblast
> Not in MANIFEST: psort/conf/analysis/sclblast/gramneg/sclblast.pos
> "/usr/bin/perl" -e 'chdir '\''bio-tools-psort-modhmm'\''; system '\''make -f Makefile.old realclean'\'' if -f '\''Makefile.old'\'';' --
> Not in MANIFEST: psort/conf/analysis/sclblast/gramneg/sclblast.pot
> Not in MANIFEST: psort/conf/analysis/sclblast/gramneg/sclblast.ptf
> Not in MANIFEST: psort/conf/analysis/sclblast/gramneg/sclblast.pto
> Not in MANIFEST: psort/conf/analysis/sclblast/grampos/sclblast
> Not in MANIFEST: psort/conf/analysis/sclblast/grampos/sclblast.pos
> Not in MANIFEST: psort/conf/analysis/sclblast/grampos/sclblast.pot
> Not in MANIFEST: psort/conf/analysis/sclblast/grampos/sclblast.ptf
> Not in MANIFEST: psort/conf/analysis/sclblast/grampos/sclblast.pto
> Not in MANIFEST: psort/conf/analysis/sclblast/makedb.sh
> Not in MANIFEST: psort/conf/analysis/signal/archaea/check-sig
> Not in MANIFEST: psort/conf/analysis/signal/archaea/model.hmm
> Not in MANIFEST: psort/conf/analysis/signal/archaea/model.svm
> Not in MANIFEST: psort/conf/analysis/signal/archaea/notes
> Not in MANIFEST: psort/conf/analysis/signal/gramneg/check-sig
> Not in MANIFEST: psort/conf/analysis/signal/gramneg/model.hmm
> Not in MANIFEST: psort/conf/analysis/signal/gramneg/model.svm
> Not in MANIFEST: psort/conf/analysis/signal/grampos/check-sig
> Not in MANIFEST: psort/conf/analysis/signal/grampos/model.hmm
> Not in MANIFEST: psort/conf/analysis/signal/grampos/model.svm
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Cellwall/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Cellwall/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Cytoplasmic/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Cytoplasmic/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Extracellular/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Extracellular/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Membrane/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/Membrane/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/archaea/notes.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Cytoplasmic/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Cytoplasmic/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Extracellular/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Extracellular/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Innermembrane/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Innermembrane/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Outermembrane/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Outermembrane/SVM_MODEL.txt
> make[3]: Entering directory '/<<PKGBUILDDIR>>/bio-tools-psort-modhmm'
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Periplasmic/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/gramneg/Periplasmic/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Cellwall/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Cellwall/SVM_MODEL.txt
> rm -f \
> ModHMM.bso ModHMM.def \
> ModHMM.exp ModHMM.x \
> ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/extralibs.all \
> ../blib/arch/auto/Bio/Tools/PSort/ModHMM/extralibs.ld Makefile.aperl \
> *.a *.o \
> *perl.core MYMETA.json \
> MYMETA.yml blibdirs.ts \
> core core.*perl.*.? \
> core.[0-9] core.[0-9][0-9] \
> core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
> core.[0-9][0-9][0-9][0-9][0-9] libModHMM.def \
> modhmm.base modhmm.bs \
> modhmm.bso modhmm.c \
> modhmm.def modhmm.exp \
> modhmm.o modhmm_def.old \
> mon.out perl \
> perl perl.exe \
> perlmain.c pm_to_blib \
> pm_to_blib.ts so_locations \
> tmon.out
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Cytoplasmic/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Cytoplasmic/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Extracellular/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Extracellular/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Membrane/fre_patterns.txt
> Not in MANIFEST: psort/conf/analysis/subloc/grampos/Membrane/SVM_MODEL.txt
> Not in MANIFEST: psort/conf/output/bayesian/archaea/bayes.model
> Not in MANIFEST: psort/conf/output/bayesian/gramneg/bayes-rpc.model
> Not in MANIFEST: psort/conf/output/bayesian/gramneg/bayes.model
> Not in MANIFEST: psort/conf/output/bayesian/grampos/bayes-rpc.model
> Not in MANIFEST: psort/conf/output/bayesian/grampos/bayes.model
> rm -rf \
> blib
> Not in MANIFEST: psort/server/rpc/classify.base
> Not in MANIFEST: psort/server/rpc/classify.code
> Not in MANIFEST: psort/server/rpc/classify.help
> Not in MANIFEST: psort/server/rpc/classify.xpl
> Not in MANIFEST: psort/server/startup.pl
> Not in MANIFEST: psort/server/www/results.pl
> Not in MANIFEST: psort/server/www/submit.html
> Not in MANIFEST: README
> Not in MANIFEST: t/psort.t
> Not in MANIFEST: t/sclblast.pl
> Not in MANIFEST: USAGE
> mv Makefile Makefile.old > /dev/null 2>&1
> make[3]: [Makefile.old:530: clean] Error 1 (ignored)
> rm -f \
> Makefile Makefile.old \
> modhmm.o binding.o
> rm -rf \
>
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/bio-tools-psort-modhmm'
> "/usr/bin/perl" -e 'chdir '\''bio-tools-psort-modhmm'\''; system '\''make -f Makefile realclean'\'' if -f '\''Makefile'\'';' --
> rm -f \
> Makefile Makefile.old
> rm -rf \
> Bio-Tools-PSort-3
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> if [ -x psort/bin/psort.debsave ] ; then \
> mv psort/bin/psort.debsave psort/bin/psort ; \
> fi
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_clean
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building psortb using existing ./psortb_3.0.6+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file psort/conf/analysis/motif/archaea/changes.bak, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file psort/conf/analysis/motif/archaea/motifs.txt.bak, use --include-removal to override
> dpkg-source: error: cannot represent change to psort/conf/analysis/sclblast/archaea/sclblast.pos: binary file contents changed
> dpkg-source: error: add psort/conf/analysis/sclblast/archaea/sclblast.pos in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to psort/conf/analysis/sclblast/archaea/sclblast.pot: binary file contents changed
> dpkg-source: error: add psort/conf/analysis/sclblast/archaea/sclblast.pot in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to psort/conf/analysis/sclblast/archaea/sclblast.ptf: binary file contents changed
> dpkg-source: error: add psort/conf/analysis/sclblast/archaea/sclblast.ptf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to psort/conf/analysis/sclblast/archaea/sclblast.pto: binary file contents changed
> dpkg-source: error: add psort/conf/analysis/sclblast/archaea/sclblast.pto in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> 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/psortb_3.0.6+dfsg-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.
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