[med-svn] [r-cran-ape] 01/01: Initial commit.

Sat May 3 13:02:15 UTC 2014

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bob.dybian-guest pushed a commit to branch master
in repository r-cran-ape.

commit 2c87ae2242ffb9be1621263a3bbc89e0088d8f5d
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Sat May 3 14:57:26 2014 +0200

    Initial commit.
---
 debian/changelog         |  6 ++++++
 debian/compat            |  1 +
 debian/control           | 33 +++++++++++++++++++++++++++++++++
 debian/copyright         | 34 ++++++++++++++++++++++++++++++++++
 debian/rules             |  6 ++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 15 +++++++++++++++
 debian/watch             |  2 ++
 8 files changed, 98 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..b557ad4
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+r-cran-ape (3.1-1-1) unstable; urgency=low
+
+  * Initial Debian Release. (Closes: #746208)
+
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Sun, 13 Apr 2014 17:00:00 +0200
+ 
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..7b97598
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: r-cran-ape
+Section: gnu-r
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
+Build-Depends: debhelper (>= 9.0.0),
+ r-base-dev (>= 3.0.0),
+ cdbs
+Standards-Version: 3.9.5
+Homepage: http://cran.r-project.org/web/packages/ape/index.html
+
+Package: r-cran-ape
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${R:Depends},
+ r-cran-nlme (>= 3.1.117),
+ r-cran-lattice (>= 0.20-29)
+Description: GNU R package for Analyses of Phylogenetics and Evolution
+ This package provides functions for reading, writing, plotting, and
+ manipulating phylogenetic trees, analyses of comparative data in a
+ phylogenetic framework, ancestral character analyses, analyses of
+ diversification and macroevolution, computing distances from allelic
+ and nucleotide data, reading and writing nucleotide sequences, and
+ several tools such as Mantel's test, generalized skyline plots,
+ graphical exploration of phylogenetic data (alex, trex, kronoviz),
+ estimation of absolute evolutionary rates and clock-like trees using
+ mean path lengths and penalized likelihood. Phylogeny estimation can
+ be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and
+ several methods handling incomplete distance matrices (NJ*, BIONJ*,
+ MVR*, and the corresponding triangle method). Some functions call
+ external applications (PhyML, Clustal, T-Coffee, Muscle) whose
+ results are returned into R.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..04b38ff
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,34 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ape
+Upstream-Contact: Emmanuel Paradis <Emmanuel.Paradis at ird.fr>
+Source: http://cran.r-project.org/src/contrib/
+
+Files: *
+Copyright: 2004-2014 Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Damien de Vienne.
+License: GPL-2+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE.  See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
+
+Files: debian/*
+Copyright: 2014 Dylan Aïssi <bob.dybian at gmail.com>
+License: GPL-2+
+ Same as r-cran-ape itelf
+
diff --git a/debian/rules b/debian/rules
new file mode 100644
index 0000000..9c30f79
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# debian/rules file for the Debian/GNU Linux r-cran-ape package
+
+include /usr/share/R/debian/r-cran.mk
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..7533b3d
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,15 @@
+Archive: CRAN
+Contact: Emmanuel Paradis <Emmanuel.Paradis at ird.fr>
+Name: ape
+Reference:
+  Author: Emmanuel Paradis, Julien Claude and Korbinian Strimmer
+  Title: "APE: Analyses of Phylogenetics and Evolution in R language"
+  Journal: Bioinformatics
+  Volume: 20
+  Number: 2
+  Pages: 289-290
+  Year: 2004
+  DOI: 10.1093/bioinformatics/btg412
+  URL: http://bioinformatics.oxfordjournals.org/content/20/2/289
+  eprint: http://bioinformatics.oxfordjournals.org/content/20/2/289.full.pdf+html
+
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..1a24beb
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://cran.r-project.org/src/contrib/ape_([-\d.]*)\.tar\.gz

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