[med-svn] [r-cran-phangorn] branch debian/jessie-backports updated (f12497c -> 3647fc8)
Andreas Tille
tille at debian.org
Sat Jun 10 05:30:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/jessie-backports
in repository r-cran-phangorn.
from f12497c Rebuild for jessie-backports
adds 6c56854 New upstream version 2.1.1
adds 30344e5 Merge tag 'upstream/2.1.1'
adds 617d906 New upstream version
adds 87efbe3 Convert to dh-r
adds 76570a4 debhelper 10
adds 8b5cae8 Canonical homepage for CRAN, Update copyright
adds f60abeb d/watch: version=4
adds ee011e6 Upload to unstable
new d546c68 Merge tag 'debian/2.1.1-1' into debian/jessie-backports
new 3647fc8 Rebuild for jessie-backports
The 2 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 | 17 +
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, 2721 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
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