This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-cran-phylobase.
commit 6bf89adf00abf1d87f6c3ee748cdedad5ef18555 Merge: 71b6f0e 7b6b9ef Author: Andreas Tille <[email protected]> Date: Mon Oct 2 22:34:10 2017 +0200 Updated version 0.8.4 from 'upstream/0.8.4' with Debian dir 055534cc9379f72dc03dc2728899da803d089e62 DESCRIPTION | 37 ++ MD5 | 145 +++++ NAMESPACE | 97 ++++ NEWS.md | 298 ++++++++++ R/MRCA-methods.R | 73 +++ R/RcppExports.R | 79 +++ R/addData-methods.R | 98 ++++ R/ancestors.R | 234 ++++++++ R/checkdata.R | 318 +++++++++++ R/edgeLength-methods.R | 310 ++++++++++ R/extractTree.R | 37 ++ R/formatData.R | 213 +++++++ R/getNode-methods.R | 206 +++++++ R/internal-constructors.R | 87 +++ R/labels-methods.R | 298 ++++++++++ R/multiphylo4-class.R | 53 ++ R/nodeId-methods.R | 100 ++++ R/oldclasses-class.R | 13 + R/pdata.R | 149 +++++ R/phylo4-accessors.R | 177 ++++++ R/phylo4-class.R | 35 ++ R/phylo4-methods.R | 178 ++++++ R/phylo4d-accessors.R | 82 +++ R/phylo4d-class.R | 39 ++ R/phylo4d-methods.R | 414 ++++++++++++++ R/phylobase-package.R | 137 +++++ R/phylobase.options.R | 54 ++ R/phylomats-class.R | 136 +++++ R/print-methods.R | 126 +++++ R/readNCL.R | 435 ++++++++++++++ R/reorder-methods.R | 149 +++++ R/root-methods.R | 64 +++ R/setAs-methods.R | 321 +++++++++++ R/shortestPath-methods.R | 67 +++ R/subset-methods.R | 429 ++++++++++++++ R/summary-methods.R | 251 +++++++++ R/tbind.R | 44 ++ R/tdata-methods.R | 212 +++++++ R/treePlot.R | 784 ++++++++++++++++++++++++++ R/treestruc.R | 87 +++ R/zzz.R | 16 + build/vignette.rds | Bin 0 -> 233 bytes data/geospiza.rda | Bin 0 -> 1541 bytes data/geospiza_raw.rda | Bin 0 -> 1212 bytes data/owls4.rda | Bin 0 -> 345 bytes inst/doc/phylobase.Rnw | 674 ++++++++++++++++++++++ inst/doc/phylobase.pdf | Bin 0 -> 203197 bytes inst/nexmlfiles/comp_analysis.xml | 135 +++++ inst/nexusfiles/ExContData.Rdata | Bin 0 -> 4596 bytes inst/nexusfiles/MultiLineTrees.nex | 89 +++ inst/nexusfiles/NastyLabels.nex | 56 ++ inst/nexusfiles/NastyLabels2.nex | 52 ++ inst/nexusfiles/co1.nex | 13 + inst/nexusfiles/minNex.nex | 56 ++ inst/nexusfiles/minSeq.nex | 12 + inst/nexusfiles/newick.tre | 1 + inst/nexusfiles/noStateLabels.nex | 36 ++ inst/nexusfiles/shorebird_underscore.nex | 321 +++++++++++ inst/nexusfiles/testSubsetTaxa.nex | 26 + inst/nexusfiles/test_min.nex | 20 + inst/nexusfiles/treeRoundingError.nex | 35 ++ inst/nexusfiles/treeWithContinuousData.nex | 365 ++++++++++++ inst/nexusfiles/treeWithDiscAndContData.nex | 413 ++++++++++++++ inst/nexusfiles/treeWithDiscreteData.nex | 354 ++++++++++++ inst/nexusfiles/treeWithPolyExcludedData.nex | 465 +++++++++++++++ inst/nexusfiles/treeWithSpecialCharacters.nex | 35 ++ inst/nexusfiles/treeWithUnderscoreLabels.nex | 354 ++++++++++++ man/MRCA.Rd | 47 ++ man/addData-methods.Rd | 79 +++ man/ancestors.Rd | 110 ++++ man/checkPhylo4.Rd | 59 ++ man/edgeLength-methods.Rd | 150 +++++ man/edges-accessors.Rd | 73 +++ man/extractTree.Rd | 45 ++ man/formatData.Rd | 88 +++ man/geospiza.Rd | 29 + man/getNode-methods.Rd | 104 ++++ man/labels-methods.Rd | 165 ++++++ man/multiPhylo-class.Rd | 21 + man/nTips-methods.Rd | 41 ++ man/nodeId-methods.Rd | 46 ++ man/owls4.Rd | 22 + man/pdata-class.Rd | 26 + man/pdata.Rd | 33 ++ man/phylo4-class.Rd | 26 + man/phylo4-methods.Rd | 119 ++++ man/phylo4d-accessors.Rd | 77 +++ man/phylo4d-class.Rd | 33 ++ man/phylo4d-methods.Rd | 290 ++++++++++ man/phyloXXYY.Rd | 50 ++ man/phylobase-package.Rd | 73 +++ man/phylobase.options.Rd | 39 ++ man/phylobubbles.Rd | 61 ++ man/phylomat-class.Rd | 59 ++ man/plotOneTree.Rd | 66 +++ man/print-methods.Rd | 101 ++++ man/readNexus.Rd | 180 ++++++ man/reorder-methods.Rd | 58 ++ man/root-methods.Rd | 47 ++ man/setAs-methods.Rd | 69 +++ man/shortestPath-methods.Rd | 40 ++ man/subset-methods.Rd | 184 ++++++ man/summary-methods.Rd | 100 ++++ man/tdata-methods.Rd | 114 ++++ man/tip.data.plot.Rd | 48 ++ man/treePlot-methods.Rd | 117 ++++ man/treeStructure-methods.Rd | 59 ++ src/Makevars | 2 + src/Makevars.win | 6 + src/RcppExports.cpp | 222 ++++++++ src/ancestors.c | 53 ++ src/checkPhylo4.cpp | 415 ++++++++++++++ src/descendants.c | 53 ++ src/phyloXX.c | 97 ++++ src/phylobase_init.c | 74 +++ src/reorderBinary.c | 66 +++ src/reorderRobust.c | 62 ++ tests/misctests.R | 112 ++++ tests/phylo4dtests.R | 29 + tests/phylosubtest.R | 16 + tests/phylotorture.R | 129 +++++ tests/plottest.R | 54 ++ tests/roundtrip.R | 41 ++ tests/test-all.R | 3 + tests/testprune.R | 20 + tests/testthat/test.badnex.R | 15 + tests/testthat/test.checkdata.R | 70 +++ tests/testthat/test.class-phylo4.R | 119 ++++ tests/testthat/test.class-phylo4d.R | 317 +++++++++++ tests/testthat/test.formatData.R | 480 ++++++++++++++++ tests/testthat/test.methods-oldclasses.R | 8 + tests/testthat/test.methods-phylo4.R | 641 +++++++++++++++++++++ tests/testthat/test.pdata.R | 21 + tests/testthat/test.phylo4.R | 11 + tests/testthat/test.phylobase.options.R | 32 ++ tests/testthat/test.prune.R | 18 + tests/testthat/test.readNCL.R | 585 +++++++++++++++++++ tests/testthat/test.setAs-Methods.R | 183 ++++++ tests/testthat/test.subset.R | 133 +++++ tests/testthat/test.tbind.R | 8 + tests/testthat/test.treePlot.R | 42 ++ tests/testthat/test.treestruc.R | 30 + tests/testthat/test.treewalk.R | 275 +++++++++ vignettes/auto/developer.el | 19 + vignettes/auto/phylobase.el | 21 + vignettes/phylobase.Rnw | 674 ++++++++++++++++++++++ 146 files changed, 18898 insertions(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-phylobase.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
