Run of fresh-releases for salmon

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

debcheckout salmon
cd salmon
new-upstream
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Processing: salmon
Total 1850 (delta 856), reused 1850 (delta 856)

/usr/lib/python3/dist-packages/debian/copyright.py:652: UserWarning: Fixing Format URL
  warnings.warn('Fixing Format URL')
Using upstream branch https://github.com/COMBINE-lab/salmon (guessed)
Total 11492 (delta 45), reused 58 (delta 24), pack-reused 11401
Using version string 0.14.1.
No upstream upstream-revision format specified, trying tag:0.14.1
No upstream upstream-revision format specified, trying tag:salmon-0.14.1
No upstream upstream-revision format specified, trying tag:v0.14.1
Using uscan to look for the upstream tarball.
uscan warn: No files matched excluded pattern as the last matching glob: doc/build/*
uscan warn: No files matched excluded pattern as the last matching glob: include/CollapsedIterativeOptimizer.hpp.bak
uscan warn: No files matched excluded pattern as the last matching glob: src/SalmonQuantify.cpp.bak
uscan warn: No files matched excluded pattern as the last matching glob: include/obsolete
uscan warn: No files matched excluded pattern as the last matching glob: include/tensemble/Tree.h.backup.h
Total 11491 (delta 45), reused 57 (delta 24), pack-reused 11401
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v0.9.0 does not point to a valid object
before-no-fmd does not point to a valid object
v0.9.1 does not point to a valid object
v0.11.2 does not point to a valid object
v0.10.0 does not point to a valid object
v0.7.1 does not point to a valid object
v0.8.1 does not point to a valid object
v0.4.1 does not point to a valid object
v0.4.2 does not point to a valid object
v0.4.0 does not point to a valid object
v0.11.3 does not point to a valid object
v0.6.0 does not point to a valid object
v0.7.0 does not point to a valid object
v0.12.0 does not point to a valid object
v0.5.0 does not point to a valid object
v0.7.2 does not point to a valid object
v0.13.1 does not point to a valid object
v0.3.2 does not point to a valid object
v0.8.0 does not point to a valid object
v0.10.2 does not point to a valid object
v0.11.1 does not point to a valid object
v0.7.0-pre does not point to a valid object
v0.11.0 does not point to a valid object
v0.10.1 does not point to a valid object
v0.5.1 does not point to a valid object
v0.14.0 does not point to a valid object
v0.6.1-pre does not point to a valid object
All changes applied successfully.
v0.9.0 does not point to a valid object
before-no-fmd does not point to a valid object
v0.9.1 does not point to a valid object
v0.11.2 does not point to a valid object
v0.10.0 does not point to a valid object
v0.7.1 does not point to a valid object
v0.8.1 does not point to a valid object
v0.4.1 does not point to a valid object
v0.4.2 does not point to a valid object
v0.4.0 does not point to a valid object
v0.11.3 does not point to a valid object
v0.6.0 does not point to a valid object
v0.7.0 does not point to a valid object
v0.12.0 does not point to a valid object
v0.5.0 does not point to a valid object
v0.7.2 does not point to a valid object
v0.13.1 does not point to a valid object
v0.3.2 does not point to a valid object
v0.8.0 does not point to a valid object
v0.10.2 does not point to a valid object
v0.11.1 does not point to a valid object
v0.7.0-pre does not point to a valid object
v0.11.0 does not point to a valid object
v0.10.1 does not point to a valid object
v0.5.1 does not point to a valid object
v0.14.0 does not point to a valid object
v0.6.1-pre does not point to a valid object
Committing to: /home/janitor/tmp/tmphtd_o5dg/salmon/
modified CMakeLists.txt
modified README.md
added cmake/Modules/FindCereal.cmake
added cmake/Modules/Findlibdivsufsort.cmake
added cmake/Modules/Findlibgff.cmake
added cmake/Modules/Findlibstadenio.cmake
modified current_version.txt
modified debian/changelog
modified doc/source/alevin.rst
modified doc/source/conf.py
modified doc/source/library_type.rst
modified doc/source/salmon.rst
modified doc/steps_to_prepare_release.md
modified docker/Dockerfile
modified docker/build_test.sh
added include/AlevinHash.hpp
modified include/AlevinOpts.hpp
modified include/AlevinUtils.hpp
modified include/AlignmentGroup.hpp
modified include/AlignmentLibrary.hpp
modified include/BAMQueue.tpp
added include/BAMUtils.hpp
modified include/BarcodeGroup.hpp
modified include/CollapsedCellOptimizer.hpp
modified include/DedupUMI.hpp
modified include/EquivalenceClassBuilder.hpp
modified include/GZipWriter.hpp
modified include/Graph.hpp
added include/MappingStatistics.hpp
modified include/ReadExperiment.hpp
modified include/SalmonConfig.hpp
modified include/SalmonDefaults.hpp
modified include/SalmonIndex.hpp
modified include/SalmonOpts.hpp
modified include/SalmonUtils.hpp
modified include/Sampler.hpp
modified include/Transcript.hpp
modified include/WhiteList.hpp
deleted include/ksw2pp
deleted include/ksw2pp/KSW2Aligner.hpp
deleted include/ksw2pp/kalloc.h
deleted include/ksw2pp/ksw2.h
deleted include/metro
deleted include/metro/metrohash.h
deleted include/metro/metrohash128.h
deleted include/metro/metrohash128crc.h
deleted include/metro/metrohash64.h
deleted include/metro/platform.h
deleted include/metro/testvector.h
deleted include/tsl
deleted include/tsl/array_growth_policy.h
deleted include/tsl/array_hash.h
deleted include/tsl/array_map.h
deleted include/tsl/array_set.h
deleted include/tsl/bhopscotch_map.h
deleted include/tsl/bhopscotch_set.h
deleted include/tsl/hopscotch_growth_policy.h
deleted include/tsl/hopscotch_hash.h
deleted include/tsl/hopscotch_map.h
deleted include/tsl/hopscotch_set.h
deleted include/tsl/robin_growth_policy.h
deleted include/tsl/robin_hash.h
deleted include/tsl/robin_map.h
deleted include/tsl/robin_set.h
modified scripts/fetchRapMap.sh
added scripts/merge_into_master.sh
modified src/Alevin.cpp
added src/AlevinHash.cpp
modified src/AlevinUtils.cpp
modified src/AlignmentModel.cpp
added src/BAMUtils.cpp
modified src/BuildSalmonIndex.cpp
modified src/CMakeLists.txt
modified src/CollapsedCellOptimizer.cpp
modified src/CollapsedEMOptimizer.cpp
modified src/CollapsedGibbsSampler.cpp
modified src/DedupUMI.cpp
modified src/FastxParser.cpp
modified src/GZipWriter.cpp
modified src/Graph.cpp
modified src/ProgramOptionsGenerator.cpp
modified src/Salmon.cpp
modified src/SalmonAlevin.cpp
modified src/SalmonQuantMerge.cpp
modified src/SalmonQuantify.cpp
modified src/SalmonQuantifyAlignments.cpp
modified src/SalmonUtils.cpp
modified src/WhiteList.cpp
deleted src/ksw2pp
deleted src/ksw2pp/KSW2Aligner.cpp
deleted src/ksw2pp/kalloc.c
deleted src/ksw2pp/ksw2_dispatch.c
deleted src/ksw2pp/ksw2_extd.c
deleted src/ksw2pp/ksw2_extd2_sse.c
deleted src/ksw2pp/ksw2_extf2_sse.c
deleted src/ksw2pp/ksw2_exts2_sse.c
deleted src/ksw2pp/ksw2_extz.c
deleted src/ksw2pp/ksw2_extz2_sse.c
deleted src/ksw2pp/ksw2_gg.c
deleted src/ksw2pp/ksw2_gg2.c
deleted src/ksw2pp/ksw2_gg2_sse.c
deleted src/metro
deleted src/metro/metrohash128.cpp
deleted src/metro/metrohash128crc.cpp
deleted src/metro/metrohash64.cpp
modified tests/alevin_test_data.tar.gz
modified tests/basic_alevin_test.sh
Committed revision 90.
Worker failed: An error (1) occurred refreshing quilt patches: None

Applying patch debian/patches/use_debian_packaged_libs.patch
patching file CMakeLists.txt
Hunk #1 FAILED at 477.
Hunk #2 FAILED at 498.
Hunk #3 FAILED at 527.
Hunk #4 FAILED at 623.
Hunk #5 FAILED at 647.
Hunk #6 FAILED at 661.
Hunk #7 succeeded at 609 with fuzz 2 (offset -71 lines).
6 out of 7 hunks FAILED -- rejects in file CMakeLists.txt
patching file src/CMakeLists.txt
Hunk #3 FAILED at 199.
Hunk #4 FAILED at 209.
Hunk #5 FAILED at 234.
3 out of 5 hunks FAILED -- rejects in file src/CMakeLists.txt
Patch debian/patches/use_debian_packaged_libs.patch does not apply (enforce with -f)

Elapsed time: 0:02:41.117145

Full worker log