Run of fresh-snapshots for hhsuite

Try this locally (using the lintian-brush package):

debcheckout hhsuite
cd hhsuite
new-upstream --snapshot
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Processing: hhsuite
Total 1429 (delta 729), reused 1254 (delta 582)
Total 23 (delta 5), reused 17 (delta 3)
Total 0 (delta 0), reused 0 (delta 0)
Using upstream branch https://github.com/soedinglab/hh-suite.git (guessed)
Total 8216 (delta 70), reused 87 (delta 52), pack-reused 8082
Using version string 3.2.0+git20190826.745d58a.
Exporting upstream branch revision b'git-v1:745d58afd70c0ed378c3b55553962ca95c442251' to create the tarball
Total 8216 (delta 70), reused 87 (delta 52), pack-reused 8082
All changes applied successfully.
Committing to: /home/janitor/tmp/tmpul6_rj2w/hhsuite/
added .gitattributes
added .gitignore
modified CMakeLists.txt
modified README.md
modified debian/changelog
added lib
added lib/ffindex
added lib/ffindex/.gitignore
added lib/ffindex/CMakeLists.txt
added lib/ffindex/LICENSE
added lib/ffindex/README.md
added lib/ffindex/src
added lib/ffindex/src/CMakeLists.txt
added lib/ffindex/src/ext
added lib/ffindex/src/ext/CMakeLists.txt
added lib/ffindex/src/ext/fmemopen.c
added lib/ffindex/src/ext/fmemopen.h
added lib/ffindex/src/ffindex.c
added lib/ffindex/src/ffindex.h
added lib/ffindex/src/ffindex_apply_mpi.c
added lib/ffindex/src/ffindex_build.c
added lib/ffindex/src/ffindex_from_fasta.c
added lib/ffindex/src/ffindex_from_fasta_with_split.c
added lib/ffindex/src/ffindex_get.c
added lib/ffindex/src/ffindex_modify.c
added lib/ffindex/src/ffindex_order.c
added lib/ffindex/src/ffindex_reduce.c
added lib/ffindex/src/ffindex_unpack.c
added lib/ffindex/src/ffutil.c
added lib/ffindex/src/ffutil.h
added lib/ffindex/src/mpq
added lib/ffindex/src/mpq/CMakeLists.txt
added lib/ffindex/src/mpq/mpq.c
added lib/ffindex/src/mpq/mpq.h
added scripts/hhpred
added scripts/hhpred/.gitignore
added scripts/hhpred/README
added scripts/hhpred/bin
added scripts/hhpred/bin/repair_pdb.pl
added scripts/hhpred/dependencies
added scripts/hhpred/dependencies/HHPaths.pm
added scripts/hhpred/dependencies/Makefile
added scripts/hhpred/dependencies/hhmakemodel.pl
added scripts/hhpred/dependencies/modeller_cuser
added scripts/hhpred/dependencies/modeller_cuser/buildall.sh
added scripts/hhpred/dependencies/modeller_cuser/cuser_form.c
added scripts/hhpred/dependencies/modeller_cuser/cuser_form.h
added scripts/hhpred/dependencies/modeller_cuser/cuser_form.i
added scripts/hhpred/dependencies/modeller_cuser/cuser_form52.c
added scripts/hhpred/dependencies/modeller_cuser/cuser_form52.h
added scripts/hhpred/dependencies/modeller_cuser/cuser_form52.i
added scripts/hhpred/dependencies/modeller_cuser/cuser_form52_wrap.c
added scripts/hhpred/dependencies/modeller_cuser/cuser_form54.c
added scripts/hhpred/dependencies/modeller_cuser/cuser_form54.h
added scripts/hhpred/dependencies/modeller_cuser/cuser_form54.i
added scripts/hhpred/dependencies/modeller_cuser/cuser_form54_wrap.c
added scripts/hhpred/dependencies/modeller_cuser/cuser_form56.c
added scripts/hhpred/dependencies/modeller_cuser/cuser_form56.h
added scripts/hhpred/dependencies/modeller_cuser/cuser_form56.i
added scripts/hhpred/dependencies/modeller_cuser/cuser_form56_wrap.c
added scripts/hhpred/dependencies/modeller_cuser/cuser_form_wrap.c
added scripts/hhpred/dependencies/patch_modeller_h_missing_files.patch
added scripts/hhpred/dependencies/patch_probcons_main_cc_missing_cstring.patch
added scripts/hhpred/example
added scripts/hhpred/example/test.a3m
added scripts/hhpred/hhpred.pl
added scripts/hhpred/lib
added scripts/hhpred/lib/Class
added scripts/hhpred/lib/Class/Singleton.pm
added scripts/hhpred/lib/FastaFile.pm
added scripts/hhpred/lib/FixOccupancy.pm
added scripts/hhpred/lib/PDBResolution.pm
added scripts/hhpred/lib/PdbFile.pm
added scripts/hhpred/lib/PirFile.pm
added scripts/hhpred/lib/QualityAssessModel.pm
added scripts/hhpred/lib/Template.pm
added scripts/hhpred/lib/TemplateList.pm
added scripts/hhpred/lib/TemplateListStruct.pm
added scripts/hhpred/lib/TemplateStruct.pm
added scripts/hhpred/lib/aminoAcid.pm
added scripts/hhpred/lib/checkTemplates.pm
added scripts/hhpred/lib/config.pm
added scripts/hhpred/lib/distanceTree.pm
added scripts/hhpred/lib/filterAlignments.pm
added scripts/hhpred/lib/modeller.pm
added scripts/hhpred/lib/multiTemplateMDN.pm
added scripts/hhpred/lib/predTMscore.pm
added scripts/hhpred/lib/selectTemplatesHeuristic.pm
added scripts/hhpred/lib/simpleTree.pm
added scripts/hhpred/lib/singleRankingNet.pm
added scripts/hhpred/lib/utilities.pm
added scripts/hhpred/share
added scripts/hhpred/share/distancethreshold
added scripts/hhpred/share/distancethreshold/comp_simple_distancethreshold_5.5_alpha_0.3_beta_1.5.csv
added scripts/hhpred/share/distancethreshold/contact_simple_distancethreshold_11.6.csv
added scripts/hhpred/share/distancethreshold/css_simple_distancethreshold_5.5_alpha_0.3_beta_1.5.csv
added scripts/hhpred/share/neural-net
added scripts/hhpred/share/neural-net/MDNWeightsLayer1CACAminP.dat
added scripts/hhpred/share/neural-net/MDNWeightsLayer1NOminP.dat
added scripts/hhpred/share/neural-net/MDNWeightsLayer1SCMCminP.dat
added scripts/hhpred/share/neural-net/MDNWeightsLayer1SCSCminP.dat
added scripts/hhpred/share/neural-net/MDNWeightsLayer2CACAminP.dat
added scripts/hhpred/share/neural-net/MDNWeightsLayer2NOminP.dat
added scripts/hhpred/share/neural-net/MDNWeightsLayer2SCMCminP.dat
added scripts/hhpred/share/neural-net/MDNWeightsLayer2SCSCminP.dat
added scripts/hhpred/share/neural-net/onhold
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1CACA.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1CACAalternative.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1CACAdiff.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1CACAnew.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1NO.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1NOalternative.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1NOalternative7.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1NOdiff.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1SCMC.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1SCMCdiff.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1SCSC.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer1SCSCdiff.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2CACA.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2CACAalternative.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2CACAdiff.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2CACAnew.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2NO.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2NOalternative.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2NOalternative7.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2NOdiff.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2SCMC.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2SCMCdiff.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2SCSC.dat
added scripts/hhpred/share/neural-net/onhold/MDNWeightsLayer2SCSCdiff.dat
modified src/CMakeLists.txt
modified src/a3m_database_filter.cpp
modified src/a3m_database_reduce.cpp
modified src/a3m_extract.cpp
modified src/a3m_reduce.cpp
modified src/cs/getopt_pp.cc
modified src/ffindexdatabase.cpp
modified src/hhviterbialgorithm.cpp
Committed revision 127.
Worker failed: An error occurred refreshing quilt patch drop-fmemopen.h.patch: 

Applying patch debian/patches/drop-fmemopen.h.patch
patching file src/hhfunc.cpp
patching file src/hhprefilter.cpp
patching file src/cs/cstranslate_app.h
patching file src/CMakeLists.txt
Hunk #1 FAILED at 118.
1 out of 1 hunk FAILED -- rejects in file src/CMakeLists.txt
Patch debian/patches/drop-fmemopen.h.patch does not apply (enforce with -f)

Elapsed time: 0:03:02.576378

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