[med-svn] [r-cran-phangorn] branch master updated (a174223 -> ee011e6)
Andreas Tille
tille at debian.org
Wed Dec 7 08:46:52 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-cran-phangorn.
from a174223 Upload to unstable
new 6c56854 New upstream version 2.1.1
new 30344e5 Merge tag 'upstream/2.1.1'
new 617d906 New upstream version
new 87efbe3 Convert to dh-r
new 76570a4 debhelper 10
new 8b5cae8 Canonical homepage for CRAN, Update copyright
new f60abeb d/watch: version=4
new ee011e6 Upload to unstable
The 8 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:
DESCRIPTION | 22 +-
MD5 | 124 ++--
NAMESPACE | 26 +-
NEWS | 36 +
R/Densi.R | 231 ------
R/RcppExports.R | 11 +
R/ancestral_pml.R | 32 +-
R/bootstrap.R | 55 +-
R/distSeq.R | 97 +--
R/distTree.R | 104 ++-
R/fitch.R | 3 +-
R/networx.R | 120 +++-
R/parsimony.R | 46 +-
R/phyDat.R | 388 ++++++-----
R/phylo.R | 36 +-
R/sankoff.R | 2 -
R/simSeq.R | 17 +-
R/superTree.R | 135 ++++
R/treeManipulation.R | 65 +-
R/treedist.R | 154 +++-
R/zzz.R | 5 +
README.md | 6 +-
build/vignette.rds | Bin 375 -> 376 bytes
debian/changelog | 11 +
debian/compat | 2 +-
debian/control | 16 +-
debian/copyright | 14 +-
debian/docs | 1 -
debian/rules | 7 +-
debian/watch | 2 +-
inst/doc/Ancestral.pdf | Bin 260891 -> 245485 bytes
inst/doc/IntertwiningTreesAndNetworks.html | 6 +-
inst/doc/Networx.Rmd | 2 +-
inst/doc/Networx.html | 16 +-
inst/doc/Trees.pdf | Bin 167890 -> 167906 bytes
inst/doc/phangorn-specials.pdf | Bin 180115 -> 179955 bytes
man/SOWH.test.Rd | 2 +-
man/ancestral.pml.Rd | 2 +-
man/as.splits.Rd | 9 +-
man/densiTree.Rd | 7 +-
man/dist.p.Rd | 2 +-
man/hadamard.Rd | 14 +-
man/maxCladeCred.Rd | 2 +-
man/midpoint.Rd | 2 +-
man/modelTest.Rd | 4 +-
man/nni.Rd | 2 +-
man/parsimony.Rd | 5 +-
man/phyDat.Rd | 19 +-
man/plot.networx.Rd | 2 +-
man/pml.Rd | 4 +-
man/pml.fit.Rd | 31 +-
man/simSeq.Rd | 5 +-
man/superTree.Rd | 22 +-
man/treedist.Rd | 20 +-
src/RcppExports.cpp | 30 +
src/dist.c | 9 +-
src/fitch.c | 18 +-
src/ml.c | 51 +-
src/phangorn.c | 25 +-
src/phangorn_help.cpp | 48 ++
src/sankoff.c | 11 +-
src/sprdist.c | 1047 ++++++++++++++++++++++++++++
tests/testthat/test_dist_tree.R | 22 +
tests/testthat/test_distances.R | 22 +-
tests/testthat/test_hadamard.R | 21 +
tests/testthat/test_parsimony.R | 34 +-
tests/testthat/test_phyDat.R | 78 ++-
tests/testthat/test_pml.R | 93 ++-
tests/testthat/test_splits.R | 39 ++
tests/testthat/test_superTree.R | 26 +
tests/testthat/test_treeManipulation.R | 31 +-
tests/testthat/test_treedist.R | 27 +
vignettes/Networx.Rmd | 2 +-
vignettes/phangorn.bib | 79 +++
74 files changed, 2715 insertions(+), 944 deletions(-)
create mode 100644 R/RcppExports.R
create mode 100644 R/superTree.R
create mode 100644 src/RcppExports.cpp
create mode 100644 src/phangorn_help.cpp
create mode 100644 src/sprdist.c
create mode 100644 tests/testthat/test_dist_tree.R
create mode 100644 tests/testthat/test_hadamard.R
create mode 100644 tests/testthat/test_superTree.R
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-phangorn.git
More information about the debian-med-commit
mailing list