[med-svn] [r-cran-adegenet] 01/12: Inject r-cran-adegenet
Andreas Tille
tille at debian.org
Mon Oct 2 17:04:33 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-adegenet.
commit 2d77e58e660a50ab8aad4ea18e95d7cdba84f404
Author: Andreas Tille <tille at debian.org>
Date: Wed Mar 23 10:59:13 2016 +0000
Inject r-cran-adegenet
---
debian/README.test | 9 +++++++++
debian/changelog | 8 ++++++++
debian/compat | 1 +
debian/control | 49 ++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 32 ++++++++++++++++++++++++++++++
debian/docs | 3 +++
debian/rules | 3 +++
debian/source/format | 1 +
debian/tests/control | 3 +++
debian/tests/run-unit-test | 12 ++++++++++++
debian/watch | 3 +++
11 files changed, 124 insertions(+)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..8d70ca3
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+cd tests
+LC_ALL=C R --no-save < testthat.R
+
+in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..b37dc91
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,8 @@
+r-cran-adegenet (2.0.1-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #???)
+ TODO: r-cran-shiny,
+ svn://anonscm.debian.org/debian-science/packages/R/r-cran-spdep/trunk/
+ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-dplyr/trunk/
+
+ -- Andreas Tille <tille at debian.org> Tue, 22 Mar 2016 21:32:09 +0100
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..b7ddac3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,49 @@
+Source: r-cran-adegenet
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cdbs,
+ r-base-dev,
+ r-cran-ade4,
+ r-cran-mass,
+ r-cran-igraph,
+ r-cran-ape,
+ r-cran-ggplot2,
+ r-cran-seqinr,
+ r-cran-boot,
+ r-cran-reshape2,
+ r-cran-vegan,
+# r-cran-shiny,
+# r-cran-spdep,
+# r-cran-dplyr
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-adegenet/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-adegenet/trunk/
+Homepage: https://cran.r-project.org/web/packages/adegenet/
+
+Package: r-cran-adegenet
+Architecture: any
+Depends: ${misc:Depends},
+ ${shlibs:Depends},
+ ${R:Depends}
+ r-cran-ade4,
+ r-cran-mass,
+ r-cran-igraph,
+ r-cran-ape,
+ r-cran-ggplot2,
+ r-cran-seqinr,
+ r-cran-boot,
+ r-cran-reshape2,
+ r-cran-vegan,
+Description: GNU R exploratory analysis of genetic and genomic data
+ Toolset for the exploration of genetic and genomic data. Adegenet
+ provides formal (S4) classes for storing and handling various genetic
+ data, including genetic markers with varying ploidy and hierarchical
+ population structure ('genind' class), alleles counts by populations
+ ('genpop'), and genome-wide SNP data ('genlight'). It also implements
+ original multivariate methods (DAPC, sPCA), graphics, statistical tests,
+ simulation tools, distance and similarity measures, and several spatial
+ methods. A range of both empirical and simulated datasets is also
+ provided to illustrate various methods.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..df7f247
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,32 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Thibaut Jombart <thibautjombart at gmail.com>
+Source: https://cran.r-project.org/web/packages/adegenet/
+
+Files: *
+Copyright: 2013-2016 Thibaut Jombart <thibautjombart at gmail.com>,
+ Zhian N. Kamvar, Roman Lustrik, Caitlin Collins,
+ Marie-Pauline Beugin, Brian Knaus, Peter Solymos,
+ Klaus Schliep, Ismail Ahmed, Anne Cori, Federico Calboli
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+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 program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in `/usr/share/common-licenses/GPL-2'.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..960011c
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+tests
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..2fbba2d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,3 @@
+#!/usr/bin/make -f
+
+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/tests/control b/debian/tests/control
new file mode 100644
index 0000000..b044b0c
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-testthat
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..b1aa7d1
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,12 @@
+#!/bin/sh -e
+
+oname=adegenet
+pkg=r-cran-`echo $oname | tr [A-Z] [a-z]`
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+LC_ALL=C R --no-save < testthat.R
+rm -fr $ADTTMP/*
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e57c72a
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+http://cran.r-project.org/src/contrib/adegenet_([-0-9\.]*).tar.gz
+
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