[med-svn] [r-cran-ape] branch debian/jessie-backports updated (5ea2c9e -> bef70bf)

[Andreas Tille]

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-ape.

      from  5ea2c9e   Rebuild for jessie-backports
      adds  bd01c59   Add autopkgtest
      adds  3b7b29e   Imported Upstream version 4.0
      adds  485ea02   Merge tag 'upstream/4.0'
      adds  932f829   Update d/changelog
      adds  9c921ba   Update debian/*
      adds  91b7372   Canonical homepage for CRAN
      adds  32a3053   Update watch file
      adds  860b061   Convert to dh-r
      adds  e392dd0   Bump debhelper to 10
      adds  badaf97   Upload to unstable
       new  90e39f7   Merge tag 'debian/4.0-1' into debian/jessie-backports
       new  bef70bf   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                |  14 +-
 MD5                        | 126 +++++++-------
 NAMESPACE                  |  39 ++++-
 R/CDF.birth.death.R        |   6 +-
 R/DNA.R                    | 202 ++++++++++++++++------
 R/MPR.R                    |   2 +-
 R/SDM.R                    |   2 +-
 R/SlowinskiGuyer.R         |  25 +--
 R/ace.R                    |   6 +-
 R/as.phylo.R               |   2 +-
 R/checkValidPhylo.R        |   9 +-
 R/chronoMPL.R              |   2 +-
 R/clustal.R                |  35 +++-
 R/coalescent.intervals.R   |   2 +-
 R/dist.topo.R              | 124 +++++++------
 R/is.binary.tree.R         |  37 ++--
 R/is.ultrametric.R         |  45 +++--
 R/ltt.plot.R               |   6 +-
 R/makeLabel.R              |   6 +-
 R/multi2di.R               |  54 +++++-
 R/node.dating.R            | 277 +++++++++++++++++++++++++++++
 R/pic.R                    |   2 +-
 R/plot.phylo.R             |  29 +++-
 R/plot.phyloExtra.R        |  32 +++-
 R/read.GenBank.R           |  80 ++++-----
 R/read.dna.R               |  16 +-
 R/read.gff.R               |  22 +++
 R/reconstruct.R            | 421 ++++++++++++++++++++++++++++++++++++++-------
 R/reorder.phylo.R          |  37 +++-
 R/root.R                   | 103 ++++++++---
 R/rtt.R                    |  16 +-
 R/summary.phylo.R          | 116 ++++++++++---
 R/write.dna.R              |   2 +-
 R/yule.R                   |   2 +-
 build/vignette.rds         | Bin 192 -> 194 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2190 bytes
 data/landplants.newick.rda | Bin 575 -> 0 bytes
 data/opsin.newick.rda      | Bin 445 -> 0 bytes
 debian/README.source       |  10 +-
 debian/README.test         |   8 +
 debian/changelog           |  23 +++
 debian/compat              |   2 +-
 debian/control             |  49 +++---
 debian/copyright           |   6 +-
 debian/docs                |   2 +
 debian/examples            |   1 +
 debian/rules               |   3 +-
 debian/tests/control       |   5 +
 debian/tests/run-unit-test |  19 ++
 debian/upstream/metadata   |  10 ++
 debian/watch               |   4 +-
 inst/doc/MoranI.pdf        | Bin 238263 -> 238589 bytes
 man/AAbin.Rd               |   3 +-
 man/all.equal.DNAbin.Rd    |  65 +++++++
 man/alview.Rd              |   2 +-
 man/ape-internal.Rd        |   6 +
 man/ape-package.Rd         |   4 +
 man/boot.phylo.Rd          |   9 +-
 man/c.phylo.Rd             |  23 +--
 man/checkAlignment.Rd      |   2 +-
 man/clustal.Rd             |  31 +++-
 man/dist.topo.Rd           |  21 ++-
 man/image.DNAbin.Rd        |   5 +-
 man/is.binary.tree.Rd      |  40 +++--
 man/is.ultrametric.Rd      |  39 +++--
 man/landplants.Rd          |  36 ----
 man/mixedFontLabel.Rd      |   2 +-
 man/multi2di.Rd            |  25 ++-
 man/node.dating.Rd         | 107 ++++++++++++
 man/opsin.Rd               |  35 ----
 man/plot.phyloExtra.Rd     |   2 +-
 man/plotTreeTime.Rd        |  44 +++++
 man/read.GenBank.Rd        |  62 +++----
 man/read.dna.Rd            |   4 +-
 man/read.gff.Rd            |  46 +++++
 man/reconstruct.Rd         |  85 ++++++---
 man/reorder.phylo.Rd       |   8 +-
 man/root.Rd                |  64 +++++--
 man/summary.phylo.Rd       |  20 ++-
 src/ape.c                  |   8 +-
 src/dist_dna.c             | 126 +++++++++-----
 src/read_dna.c             |  26 +--
 82 files changed, 2222 insertions(+), 769 deletions(-)
 create mode 100644 R/node.dating.R
 create mode 100644 R/read.gff.R
 delete mode 100644 data/landplants.newick.rda
 delete mode 100644 data/opsin.newick.rda
 create mode 100644 debian/README.test
 create mode 100644 debian/docs
 create mode 100644 debian/examples
 create mode 100644 debian/tests/control
 create mode 100644 debian/tests/run-unit-test
 create mode 100644 man/all.equal.DNAbin.Rd
 delete mode 100644 man/landplants.Rd
 create mode 100644 man/node.dating.Rd
 delete mode 100644 man/opsin.Rd
 create mode 100644 man/plotTreeTime.Rd
 create mode 100644 man/read.gff.Rd

-- 
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