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Packages/r adegenet (#4354)

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* Add mpi support to R

* Add multiple precision math routines to R

* Updated the URL to match the version

* Remove duplicate packages

* Add packages for r-ergm and it's dependents

* Fixed depends-on types

* Correct flake8 errors

* Correct Build type

* r-adegenet and dependent packages
This commit is contained in:
Tom Merrick
2017-05-25 14:42:49 -05:00
committed by Adam J. Stewart
parent 7055be82b9
commit 794dc50995
13 changed files with 518 additions and 1 deletions
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var/spack/repos/builtin/packages/r-adegenet/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# 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 terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RAdegenet(RPackage):
"""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."""
homepage = "https://github.com/thibautjombart/adegenet/wiki"
url = "https://cran.r-project.org/src/contrib/adegenet_2.0.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/adegenet"
version('2.0.1', 'ecb1220ce7c9affaba2987bc7f38adda')
depends_on('r@2.14:')
depends_on('r-ade4', type=('build', 'run'))
depends_on('r-igraph', type=('build', 'run'))
depends_on('r-ape', type=('build', 'run'))
depends_on('r-shiny', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-seqinr', type=('build', 'run'))
depends_on('r-spdep', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-dplyr@0.4.1:', type=('build', 'run'))
depends_on('r-vegan', type=('build', 'run'))