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commit 2d77e58e660a50ab8aad4ea18e95d7cdba84f404 Author: Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +Source: https://cran.r-project.org/web/packages/adegenet/ + +Files: * +Copyright: 2013-2016 Thibaut Jombart <[email protected]>, + 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 <[email protected]> +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 + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-adegenet.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
