Run of fresh-releases for mummer

Try this locally (using silver-platter):

debian-svp new-upstream mummer 
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Processing: mummer
Total 998 (delta 375), reused 924 (delta 327)

Total 179 (delta 35), reused 177 (delta 34)
Using upstream branch http://mummer.cvs.sourceforge.net/mummer/ (from configuration)
Upstream branch http://mummer.cvs.sourceforge.net/mummer/ inaccessible; ignoring. Branch does not exist: Not a branch: "http://mummer.cvs.sourceforge.net/mummer/".
Using version string 4.0.0~beta2.
Using uscan to look for the upstream tarball.
All changes applied successfully.
Committing to: /home/janitor/tmp/tmpco31bbyh/mummer/
added .gitignore
added .gitmod
added .travis.yml
deleted INSTALL
added INSTALL.md
deleted LICENSE
added LICENSE.md
added MANUAL.md
deleted Makefile
added Makefile.am
added Makefile.orig
added OBSOLETE.md
deleted README
added README.md
added configs
added configs/debug.config
added configs/default.config
added configs/sanitize.config
added configure.ac
modified debian/changelog
added examples
added examples/Readme.md
added examples/align.pl
added examples/align.py
added examples/align.rb
added examples/align_cpp
added examples/align_cpp/Makefile
added examples/align_cpp/Readme.md
added examples/align_cpp/align.cpp
added include
added include/compactsufsort
added include/compactsufsort/compactsufsort.hpp
added include/compactsufsort/compactsufsort_imp.hpp
added include/compactsufsort/const_iterator_traits.hpp
added include/compactsufsort/divsufsort_private.h
added include/compactsufsort/said_traits.hpp
added include/compactsufsort/sssort_imp.hpp
added include/compactsufsort/trsort_imp.hpp
added include/jellyfish
added include/jellyfish/circular_buffer.hpp
added include/jellyfish/cooperative_pool2.hpp
added include/jellyfish/cpp_array.hpp
added include/jellyfish/divisor.hpp
added include/jellyfish/stream_manager.hpp
added include/jellyfish/whole_sequence_parser.hpp
added include/mt_skip_list
added include/mt_skip_list/common.hpp
added include/mt_skip_list/set.hpp
added include/mummer
added include/mummer/48bit_index.hpp
added include/mummer/48bit_iterator.hpp
added include/mummer/const_iterator_traits.hpp
added include/mummer/delta.hh
added include/mummer/dset.hpp
added include/mummer/fasta.hpp
added include/mummer/mgaps.hh
added include/mummer/nucmer.hpp
added include/mummer/openmp_qsort.hpp
added include/mummer/postnuc.hh
added include/mummer/redirect_to_pager.hpp
added include/mummer/sparseSA.hpp
added include/mummer/sparseSA_imp.hpp
added include/mummer/sw_align.hh
added include/mummer/sw_alignscore.hh
added include/mummer/tigrinc.hh
added include/mummer/timer.hpp
added include/mummer/translate.hh
added include/thread_pipe
added include/thread_pipe/circular_buffer.hpp
added include/thread_pipe/cooperative_pool2.hpp
added include/thread_pipe/divisor.hpp
added include/thread_pipe/traits.hpp
added include/thread_pipe.hpp
added m4
added m4/ax_openmp.m4
added m4/m4-ax_perl_ext.m4
added m4/m4-ax_pkg_swig.m4
added m4/m4-ax_python_devel.m4
added m4/m4-ax_ruby_ext.m4
added m4/m4-ax_swig_enable_cxx.m4
added mummer.pc.in
modified scripts/dnadiff.pl
deleted scripts/exact-tandems.csh
added scripts/exact-tandems.sh
modified scripts/mapview.pl
modified scripts/mummerplot.pl
deleted scripts/nucmer.pl
modified scripts/nucmer2xfig.pl
added scripts/nucmer_ori.pl
modified scripts/promer.pl
deleted scripts/run-mummer1.csh
added scripts/run-mummer1.sh
deleted scripts/run-mummer3.csh
added scripts/run-mummer3.sh
added src/essaMEM
added src/essaMEM/fasta.cpp
added src/essaMEM/mummer.cpp
added src/essaMEM/sparseSA.cpp
added src/essaMEM/sssort_compact.cc
modified src/kurtz/libbasedir/Mkprotodef.sh
deleted src/kurtz/libbasedir/protodef.h
modified src/kurtz/streesrc/Mkstreeproto.sh
modified src/kurtz/streesrc/depthtab.c
modified src/kurtz/streesrc/stree.c
deleted src/kurtz/streesrc/streefiledoc.c
added src/kurtz/streesrc/streefiledoc_c
deleted src/kurtz/streesrc/streeproto.h
modified src/tigr/annotate.cc
modified src/tigr/combineMUMs.cc
modified src/tigr/delta-filter.cc
modified src/tigr/delta.cc
deleted src/tigr/delta.hh
modified src/tigr/gaps.cc
modified src/tigr/mgaps.cc
added src/tigr/mgaps_main.cc
modified src/tigr/postnuc.cc
added src/tigr/postnuc_main.cc
modified src/tigr/postpro.cc
modified src/tigr/prenuc.cc
modified src/tigr/prepro.cc
modified src/tigr/repeat-match.cc
modified src/tigr/show-aligns.cc
modified src/tigr/show-coords.cc
modified src/tigr/show-diff.cc
modified src/tigr/show-snps.cc
modified src/tigr/show-tiling.cc
modified src/tigr/sw_align.cc
deleted src/tigr/sw_align.hh
deleted src/tigr/sw_alignscore.hh
modified src/tigr/tigrinc.cc
deleted src/tigr/tigrinc.hh
modified src/tigr/translate.cc
deleted src/tigr/translate.hh
added src/umd
added src/umd/nucmer.cc
added src/umd/nucmer_cmdline.yaggo
added src/umd/nucmer_main.cc
added swig
added swig/INSTALL.md
added swig/Makefile.am
added swig/README.md
added swig/mummer.i
added swig/nucmer.i
added swig/perl5
added swig/perl5/test_nucmer.pl
added swig/python
added swig/python/test_nucmer.py
added swig/ruby
added swig/ruby/test_nucmer.rb
added tests
added tests/Makefile.am
added tests/batch.sh
added tests/check_LCP.cc
added tests/check_LCP_cmdline.yaggo
added tests/check_cigar.cc
added tests/check_cigar_cmdline.yaggo
added tests/data_seed
added tests/delta-filter.sh
added tests/generate_sequences.cc
added tests/generate_sequences_cmdline.yaggo
added tests/genome.sh
added tests/mummer.sh
added tests/nucmer.sh
added tests/sam.sh
added tests/save_load.sh
added tests/test.mums
added tests/test_md5
added tests/test_sequence_align.cc
added tests/testsh.in
added tests/ufasta_src
added tests/ufasta_src/Makefile.am
added tests/ufasta_src/common.hpp
added tests/ufasta_src/dsort.cc
added tests/ufasta_src/dsort_cmdline.yaggo
added tests/ufasta_src/sort.cc
added tests/ufasta_src/sort_cmdline.yaggo
added tests/ufasta_src/ufasta.cc
added unittests
added unittests/Makefile.am
added unittests/gtest
added unittests/gtest/gtest.h
added unittests/gtest/src
added unittests/gtest/src/gtest-all.cc
added unittests/gtest/src/gtest_main.cc
added unittests/gtest/test.hpp
added unittests/test_cooperative_pool2.cc
added unittests/test_nucmer.cc
added unittests/test_qsort.cc
added unittests/test_sparse_sa.cc
added unittests/test_whole_sequence_parser.cc
added yaggo.mk
Committed revision 102.
Worker failed: An error (1) occurred refreshing quilt patches: None

Applying patch debian/patches/hardening.patch
can't find file to patch at input line 7
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|Author: Andreas Tille <tille@debian.org>
|Last-Update: Mon, 13 Apr 2015 22:29:27 +0200
|Description: Propagate hardening options
|
|--- a/Makefile
|+++ b/Makefile
--------------------------
No file to patch.  Skipping patch.
1 out of 1 hunk ignored
patching file src/tigr/Makefile
Patch debian/patches/hardening.patch does not apply (enforce with -f)

Elapsed time: 0:26:15.021967

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