[med-svn] [r-cran-rncl] 07/10: Update upstream source from tag 'upstream/0.8.2'
Andreas Tille
tille at debian.org
Wed Nov 29 19:40:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-rncl.
commit b01263ad53e04614bdd80450693c64ecf18e8aac
Merge: 9935806 ea566f8
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 29 20:34:53 2017 +0100
Update upstream source from tag 'upstream/0.8.2'
Update to upstream version '0.8.2'
with Debian dir f3ae383f773b357d92df839fecdd024f9eadb13f
DESCRIPTION | 33 +
LICENSE | 2 +
MD5 | 87 +
NAMESPACE | 11 +
NEWS.md | 75 +
R/RcppExports.R | 15 +
R/collapse_singles.R | 38 +
R/rncl-package.R | 22 +
R/rncl.R | 319 ++
README.md | 43 +
cleanup | 65 +
inst/newick_bad/Gudrun.nex | 149 +
inst/newick_bad/bad_newick.tre | 1 +
inst/newick_good/Gudrun.tre | 1 +
inst/newick_good/missing_edge_lengths.tre | 1 +
inst/newick_good/simpleTree.tre | 1 +
inst/newick_good/singleton_tree.tre | 1 +
inst/newick_good/singleton_with_edge_length.tre | 1 +
inst/newick_good/test_sing.tre | 1 +
inst/newick_good/tree1.tre | 1 +
inst/newick_good/tree2.tre | 1 +
inst/nexusfiles/MultiLineTrees.nex | 89 +
inst/nexusfiles/badnex.nex | 101 +
inst/nexusfiles/co1.nex | 13 +
inst/nexusfiles/multiLines.rds | Bin 0 -> 1547 bytes
inst/nexusfiles/newick.tre | 1 +
inst/nexusfiles/test_empty.nex | 14 +
inst/nexusfiles/test_subset_alltaxa.nex | 23 +
inst/nexusfiles/test_subset_taxa.nex | 27 +
inst/nexusfiles/test_underscores.nex | 42 +
inst/nexusfiles/treeWithDiscreteData.nex | 354 ++
inst/nexusfiles/treeWithUnderscoreLabels.nex | 354 ++
man/read_nexus_phylo.Rd | 50 +
man/rncl.Rd | 169 +
src/GetNCL.cpp | 424 ++
src/Makevars | 2 +
src/Makevars.win | 6 +
src/RcppExports.cpp | 44 +
src/collapse_singles.cpp | 128 +
src/ncl/ncl.h | 97 +
src/ncl/nxsallocatematrix.h | 253 ++
src/ncl/nxsassumptionsblock.h | 391 ++
src/ncl/nxsblock.h | 363 ++
src/ncl/nxscdiscretematrix.h | 113 +
src/ncl/nxscharactersblock.h | 1972 ++++++++
src/ncl/nxscxxdiscretematrix.h | 264 ++
src/ncl/nxsdatablock.h | 69 +
src/ncl/nxsdefs.h | 108 +
src/ncl/nxsdiscretedatum.h | 58 +
src/ncl/nxsdiscretematrix.h | 90 +
src/ncl/nxsdistancedatum.h | 42 +
src/ncl/nxsdistancesblock.h | 197 +
src/ncl/nxsemptyblock.h | 77 +
src/ncl/nxsexception.h | 97 +
src/ncl/nxsindent.h | 56 +
src/ncl/nxsmultiformat.h | 260 ++
src/ncl/nxspublicblocks.h | 731 +++
src/ncl/nxsreader.h | 612 +++
src/ncl/nxssetreader.h | 104 +
src/ncl/nxsstring.h | 742 +++
src/ncl/nxstaxaassociationblock.h | 139 +
src/ncl/nxstaxablock.h | 484 ++
src/ncl/nxstoken.h | 876 ++++
src/ncl/nxstreesblock.h | 1000 ++++
src/ncl/nxsunalignedblock.h | 332 ++
src/ncl/nxsutilcopy.h | 264 ++
src/nxsassumptionsblock.cpp | 2807 ++++++++++++
src/nxsblock.cpp | 644 +++
src/nxscharactersblock.cpp | 5518 +++++++++++++++++++++++
src/nxscxxdiscretematrix.cpp | 511 +++
src/nxsdatablock.cpp | 63 +
src/nxsdistancedatum.cpp | 36 +
src/nxsdistancesblock.cpp | 714 +++
src/nxsemptyblock.cpp | 158 +
src/nxsexception.cpp | 106 +
src/nxsmultiformat.cpp | 1606 +++++++
src/nxspublicblocks.cpp | 811 ++++
src/nxsreader.cpp | 1396 ++++++
src/nxssetreader.cpp | 536 +++
src/nxsstring.cpp | 1041 +++++
src/nxstaxaassociationblock.cpp | 237 +
src/nxstaxablock.cpp | 633 +++
src/nxstoken.cpp | 1106 +++++
src/nxstreesblock.cpp | 2146 +++++++++
src/nxsunalignedblock.cpp | 915 ++++
tests/test-all.R | 3 +
tests/testthat/test.badnex.R | 14 +
tests/testthat/test.rncl.R | 307 ++
88 files changed, 33808 insertions(+)
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