[med-svn] [genometools] branch debian/jessie-backports updated (c285929 -> 331e1fb)
Sascha Steinbiss
satta at debian.org
Fri Jul 29 23:56:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch debian/jessie-backports
in repository genometools.
from c285929 backport for jessie
adds 793e425 use pkg-config for shared lib detection
adds f132b41 add spelling fixes
adds 3f28322 remove external library code
adds a131c3a Imported Upstream version 1.5.8+ds
adds 854ac1f Merge tag 'upstream/1.5.8+ds'
adds 7c738e7 change uscan target, use xz compression
adds a38c8bd adjust patches
adds c79eeb8 update d/changelog
adds 0cd9f9f work on reproducibility issues
adds 478bb5e dch -r
adds 4b6989a add gbp.conf to force use of pristine-tar
adds c327047 remove unneeded maintainer scripts
adds 5dfef4c update upstream metadata
adds f5192cf update spelling patch
adds 4169931 update patch header
adds b7d0164 enable full hardening
adds 8f09e6b3 add override for pedantic Lintian msg
adds 51805de reproducibility and housekeeping
adds e70b033 fix more dates in manuals
adds 6479bdb update email addresses
adds 369ee1e update d/changelog
adds ce6f539 bump Standards-Version
adds a84e526 Imported Upstream version 1.5.9+ds
adds 6928fbb Merge tag 'upstream/1.5.9+ds'
adds f73a143 new upstream release
adds 5b2cdb3 dch -r
adds 0eb6393 use fixed date
new 46ed24f Merge tag 'debian/1.5.9+ds-2' into debian/jessie-backports
new 4e1d2dc backports version bump
new 331e1fb add ldconfig trigger
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.github/ISSUE_TEMPLATE.md | 19 +
.github/PULL_REQUEST_TEMPLATE.md | 12 +
.gitignore | 1 +
CHANGELOG | 16 +
INSTALL | 25 +-
LICENSE | 33 +-
Makefile | 425 +-
VERSION | 2 +-
debian/changelog | 58 +
debian/control | 4 +-
debian/copyright | 1 +
debian/gbp.conf | 2 +
debian/libgenometools0.postinst | 37 -
debian/libgenometools0.postrm | 38 -
debian/libgenometools0.triggers | 1 +
debian/patches/adding_soname | 14 +-
debian/patches/gtdoc-traverse-sorted | 40 +
debian/patches/ignore-m32-m64.patch | 27 +
debian/patches/libbam-fix | 27 +-
debian/patches/manual_fixed_dates.patch | 170 +
debian/patches/remove_png_timestamps | 12 +-
debian/patches/series | 5 +-
debian/patches/spelling | 224 +-
debian/patches/split-manuals | 17 +-
debian/patches/use-mx32 | 2 +-
debian/patches/use-pkgconfig | 53 +
debian/rules | 9 +-
debian/source.lintian-overrides | 2 +
debian/strip-nondeterminism/pdflatex | 6 +-
debian/tests/build-lib | 2 +-
debian/tests/python-lib | 2 +-
debian/upstream/metadata | 10 +-
debian/watch | 5 +-
doc/devguide/devguide.tex | 27 +-
doc/manuals/annotationsketch.tex | 6 +
doc/manuals/genomediff.tex | 1 +
doc/manuals/hop.tex | 1 +
doc/manuals/ltrdigest.tex | 1 +
doc/manuals/ltrharvest.tex | 1 +
doc/manuals/mgth.tex | 1 +
doc/manuals/packedindex.tex | 1 +
doc/manuals/readjoiner.tex | 1 +
doc/manuals/repfind.tex | 1 +
doc/manuals/tagerator.tex | 1 +
doc/manuals/tallymer.tex | 1 +
doc/manuals/uniquesub.tex | 1 +
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gtdata/doc/fingerprint.lua | 2 +-
gtdata/modules/external/des56.lua | 1 +
gtdata/modules/external/md5.lua | 21 +-
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gtdata/modules/gtdoclib/classes_latex.lp | 3 +-
gtdata/modules/gtdoclib/docvisitorlatex.lua | 31 +-
gtdata/modules/gtdoclib/footer.lp | 2 +-
.../gtdoclib/libgenometools_header_latex.lp | 3 +-
gtdata/modules/gtdoclib/method_latex.lp | 5 +-
gtdata/modules/gtdoclib/module_latex.lp | 2 +-
gtdata/modules/gtdoclib/modules_latex.lp | 1 +
gtdata/modules/gtdoclib/sole_function_latex.lp | 3 +-
gtdata/spec/output_drivers/tabular | 72 +
gtdata/spec/speclib.lua | 14 +
gtpython/tests/test_version.py | 4 +-
gtscripts/gtdoc.lua | 16 +-
scripts/collect-mappings.rb | 26 +
scripts/coverage-MEM.rb | 97 +
scripts/esq-in-bytes.sh | 5 +-
scripts/gen-intsets.rb | 28 +-
scripts/gen-randseq.rb | 42 +-
scripts/sim-read-mapping.sh | 87 +
src/core/compact_ulong_store.h | 2 +-
src/core/encseq.c | 13 +-
src/core/encseq_col.c | 26 +-
src/core/error_api.h | 2 +-
src/core/fa.h | 2 +-
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src/core/seq_iterator_api.h | 2 +-
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src/extended/affinealign.h | 81 +-
src/extended/alignment.c | 63 +-
src/extended/cds_check_visitor.c | 29 +-
src/extended/compressed_bitsequence.c | 6 +-
src/extended/compressed_bitsequence.h | 6 +-
src/extended/condenseq.c | 26 +-
src/extended/condenseq.h | 15 +-
src/extended/condenseq_creator.c | 6 +-
src/extended/condenseq_rep.h | 34 +-
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src/extended/diagonalbandalign.h | 85 +-
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src/extended/diagonalbandalign_affinegapcost.h | 94 +-
src/extended/editscript.c | 150 +-
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src/extended/rcr.c | 33 +-
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src/extended/reconstructalignment.h | 87 +-
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src/extended/samfile_iterator.c | 2 +-
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