Packages/r adegenet (#4354)
* 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:
parent
7055be82b9
commit
794dc50995
38
var/spack/repos/builtin/packages/r-ade4/package.py
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38
var/spack/repos/builtin/packages/r-ade4/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
|
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# Produced at the Lawrence Livermore National Laboratory.
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#
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||||
# 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
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##############################################################################
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from spack import *
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class RAde4(RPackage):
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"""Analysis of Ecological Data : Exploratory and Euclidean Methods in
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Environmental Sciences"""
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homepage = "http://pbil.univ-lyon1.fr/ADE-4"
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url = "https://cran.r-project.org/src/contrib/ade4_1.7-6.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/ade4"
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version('1.7-6', '63401ca369677538c96c3d7b75b3f4a1')
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depends_on('r@2.10:')
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55
var/spack/repos/builtin/packages/r-adegenet/package.py
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55
var/spack/repos/builtin/packages/r-adegenet/package.py
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@ -0,0 +1,55 @@
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##############################################################################
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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
|
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class RAdegenet(RPackage):
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"""Toolset for the exploration of genetic and genomic data. Adegenet
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provides formal (S4) classes for storing and handling various genetic
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data, including genetic markers with varying ploidy and hierarchical
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population structure ('genind' class), alleles counts by populations
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('genpop'), and genome-wide SNP data ('genlight'). It also implements
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original multivariate methods (DAPC, sPCA), graphics, statistical tests,
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simulation tools, distance and similarity measures, and several spatial
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methods. A range of both empirical and simulated datasets is also provided
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to illustrate various methods."""
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homepage = "https://github.com/thibautjombart/adegenet/wiki"
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url = "https://cran.r-project.org/src/contrib/adegenet_2.0.1.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/adegenet"
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version('2.0.1', 'ecb1220ce7c9affaba2987bc7f38adda')
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depends_on('r@2.14:')
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depends_on('r-ade4', type=('build', 'run'))
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depends_on('r-igraph', type=('build', 'run'))
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depends_on('r-ape', type=('build', 'run'))
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depends_on('r-shiny', type=('build', 'run'))
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depends_on('r-ggplot2', type=('build', 'run'))
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depends_on('r-seqinr', type=('build', 'run'))
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depends_on('r-spdep', type=('build', 'run'))
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depends_on('r-reshape2', type=('build', 'run'))
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depends_on('r-dplyr@0.4.1:', type=('build', 'run'))
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depends_on('r-vegan', type=('build', 'run'))
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51
var/spack/repos/builtin/packages/r-ape/package.py
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51
var/spack/repos/builtin/packages/r-ape/package.py
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@ -0,0 +1,51 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
|
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# LLNL-CODE-647188
|
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#
|
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# For details, see https://github.com/llnl/spack
|
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# 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.
|
||||
#
|
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# This program is distributed in the hope that it will be useful, but
|
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
|
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# 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
|
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class RApe(RPackage):
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"""Functions for reading, writing, plotting, and manipulating phylogenetic
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trees, analyses of comparative data in a phylogenetic framework, ancestral
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character analyses, analyses of diversification and macroevolution,
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computing distances from DNA sequences, reading and writing nucleotide
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sequences as well as importing from BioConductor, and several tools such
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as Mantel's test, generalized skyline plots, graphical exploration of
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phylogenetic data (alex, trex, kronoviz), estimation of absolute
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evolutionary rates and clock-like trees using mean path lengths and
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penalized likelihood, dating trees with non-contemporaneous sequences,
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translating DNA into AA sequences, and assessing sequence alignments.
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Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
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triangle methods, and several methods handling incomplete distance
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matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
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functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
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whose results are returned into R."""
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homepage = "http://ape-package.ird.fr/"
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url = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
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version('4.1', 'a9ed416d6d172d4b9682556cf692d7c2')
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depends_on('r@3.2:')
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41
var/spack/repos/builtin/packages/r-deldir/package.py
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41
var/spack/repos/builtin/packages/r-deldir/package.py
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@ -0,0 +1,41 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
|
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# LLNL-CODE-647188
|
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#
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# 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.
|
||||
#
|
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# This program is distributed in the hope that it will be useful, but
|
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# 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
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##############################################################################
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from spack import *
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class RDeldir(RPackage):
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"""Calculates the Delaunay triangulation and the Dirichlet or Voronoi
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tessellation (with respect to the entire plane) of a planar point set.
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Plots triangulations and tessellations in various ways. Clips
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tessellations to sub-windows. Calculates perimeters of tessellations.
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Summarises information about the tiles of the tessellation."""
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homepage = "https://CRAN.R-project.org/package=deldir"
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url = "https://cran.r-project.org/src/contrib/deldir_0.1-14.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/deldir"
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version('0.1-14', '6a22b13d962615cd9d51b6eae403409f')
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depends_on('r@0.99:')
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36
var/spack/repos/builtin/packages/r-expm/package.py
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36
var/spack/repos/builtin/packages/r-expm/package.py
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@ -0,0 +1,36 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
|
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# Produced at the Lawrence Livermore National Laboratory.
|
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#
|
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# This file is part of Spack.
|
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# 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.
|
||||
#
|
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# This program is distributed in the hope that it will be useful, but
|
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# 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
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##############################################################################
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from spack import *
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class RExpm(RPackage):
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"""Computation of the matrix exponential, logarithm, sqrt, and related
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quantities."""
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homepage = "http://R-Forge.R-project.org/projects/expm"
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url = "https://cran.r-project.org/src/contrib/expm_0.999-2.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/expm"
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version('0.999-2', 'e05fa3f995754af92bd03227625da984')
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38
var/spack/repos/builtin/packages/r-gmodels/package.py
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38
var/spack/repos/builtin/packages/r-gmodels/package.py
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@ -0,0 +1,38 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
|
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# Produced at the Lawrence Livermore National Laboratory.
|
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#
|
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# This file is part of Spack.
|
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
|
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# LLNL-CODE-647188
|
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#
|
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# For details, see https://github.com/llnl/spack
|
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# Please also see the LICENSE file for our notice and the LGPL.
|
||||
#
|
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# This program is free software; you can redistribute it and/or modify
|
||||
# it under the terms of the GNU Lesser General Public License (as
|
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# published by the Free Software Foundation) version 2.1, February 1999.
|
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#
|
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# This program is distributed in the hope that it will be useful, but
|
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
|
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# 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
|
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class RGmodels(RPackage):
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"""Various R programming tools for model fitting."""
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homepage = "http://www.sf.net/projects/r-gregmisc"
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url = "https://cran.r-project.org/src/contrib/gmodels_2.16.2.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/gmodels"
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version('2.16.2', 'f13e5feb2a8b9f0cd47fdf25ddc74228')
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depends_on('r@1.9:')
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depends_on('r-gdata', type=('build', 'run'))
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41
var/spack/repos/builtin/packages/r-learnbayes/package.py
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41
var/spack/repos/builtin/packages/r-learnbayes/package.py
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@ -0,0 +1,41 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
|
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# Produced at the Lawrence Livermore National Laboratory.
|
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#
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# This file is part of Spack.
|
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
|
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# LLNL-CODE-647188
|
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#
|
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# 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
|
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# published by the Free Software Foundation) version 2.1, February 1999.
|
||||
#
|
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# This program is distributed in the hope that it will be useful, but
|
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# 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
|
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##############################################################################
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from spack import *
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class RLearnbayes(RPackage):
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"""LearnBayes contains a collection of functions helpful in learning the
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basic tenets of Bayesian statistical inference. It contains functions for
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summarizing basic one and two parameter posterior distributions and
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predictive distributions. It contains MCMC algorithms for summarizing
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posterior distributions defined by the user. It also contains functions
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for regression models, hierarchical models, Bayesian tests, and
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illustrations of Gibbs sampling."""
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homepage = "https://CRAN.R-project.org/package=LearnBayes"
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url = "https://cran.r-project.org/src/contrib/LearnBayes_2.15.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/LearnBayes"
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version('2.15', '213713664707bc79fd6d3a109555ef76')
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43
var/spack/repos/builtin/packages/r-permute/package.py
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43
var/spack/repos/builtin/packages/r-permute/package.py
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@ -0,0 +1,43 @@
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##############################################################################
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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
|
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##############################################################################
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from spack import *
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class RPermute(RPackage):
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"""A set of restricted permutation designs for freely exchangeable, line
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transects (time series), and spatial grid designs plus permutation of
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blocks (groups of samples) is provided. 'permute' also allows split-plot
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designs, in which the whole-plots or split-plots or both can be
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freely-exchangeable or one of the restricted designs. The 'permute'
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package is modelled after the permutation schemes of 'Canoco 3.1'
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(and later) by Cajo ter Braak."""
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homepage = "https://github.com/gavinsimpson/permute"
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url = "https://cran.r-project.org/src/contrib/permute_0.9-4.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/permute"
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version('0.9-4', '569fc2442d72a1e3b7e2d456019674c9')
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depends_on('r@2.14:')
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@ -38,5 +38,5 @@ class RRmpfr(RPackage):
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version('0.6-1', '55d4ec257bd2a9233bafee9e444d0265')
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depends_on('r-gmp@0.5-8:')
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depends_on('r-gmp@0.5-8:', type=('build', 'run'))
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depends_on('mpfr@3.0.0:')
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37
var/spack/repos/builtin/packages/r-segmented/package.py
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37
var/spack/repos/builtin/packages/r-segmented/package.py
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@ -0,0 +1,37 @@
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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 RSegmented(RPackage):
|
||||
"""Given a regression model, segmented 'updates' the model by adding
|
||||
one or more segmented (i.e., piecewise-linear) relationships. Several
|
||||
variables with multiple breakpoints are allowed."""
|
||||
|
||||
homepage = "https://CRAN.R-project.org/package=segmented"
|
||||
url = "https://cran.r-project.org/src/contrib/segmented_0.5-1.4.tar.gz"
|
||||
list_url = "https://cran.r-project.org/src/contrib/Archive/segmented"
|
||||
|
||||
version('0.5-1.4', 'f9d76ea9e22ef5f40aa126b697351cae')
|
42
var/spack/repos/builtin/packages/r-seqinr/package.py
Normal file
42
var/spack/repos/builtin/packages/r-seqinr/package.py
Normal file
@ -0,0 +1,42 @@
|
||||
##############################################################################
|
||||
# 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 RSeqinr(RPackage):
|
||||
"""Exploratory data analysis and data visualization for biological
|
||||
sequence (DNA and protein) data. Includes also utilities for sequence
|
||||
data management under the ACNUC system."""
|
||||
|
||||
homepage = "http://seqinr.r-forge.r-project.org"
|
||||
url = "https://cran.r-project.org/src/contrib/seqinr_3.3-6.tar.gz"
|
||||
list_url = "https://cran.r-project.org/src/contrib/Archive/seqinr"
|
||||
|
||||
version('3.3-6', '73023d627e72021b723245665e1ad055')
|
||||
|
||||
depends_on('r@2.10:')
|
||||
depends_on('r-ade4', type=('build', 'run'))
|
||||
depends_on('r-segmented', type=('build', 'run'))
|
||||
depends_on('zlib')
|
56
var/spack/repos/builtin/packages/r-spdep/package.py
Normal file
56
var/spack/repos/builtin/packages/r-spdep/package.py
Normal file
@ -0,0 +1,56 @@
|
||||
##############################################################################
|
||||
# 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 RSpdep(RPackage):
|
||||
"""A collection of functions to create spatial weights matrix objects from
|
||||
polygon contiguities, from point patterns by distance and tessellations,
|
||||
for summarizing these objects, and for permitting their use in spatial
|
||||
data analysis, including regional aggregation by minimum spanning tree;
|
||||
a collection of tests for spatial autocorrelation, including global
|
||||
Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic,
|
||||
Empirical Bayes estimates and AssunasReis Index, Getis/Ord G and
|
||||
multicoloured join count statistics, local Moran's I and Getis/Ord G,
|
||||
saddlepoint approximations and exact tests for global and local Moran's I;
|
||||
and functions for estimating spatial simultaneous autoregressive (SAR) lag
|
||||
and error models, impact measures for lag models, weighted and unweighted
|
||||
SAR and CAR spatial regression models, semi-parametric and Moran
|
||||
eigenvector spatial filtering, GM SAR error models, and generalized spatial
|
||||
two stage least squares models."""
|
||||
|
||||
homepage = "https://r-forge.r-project.org/projects/spdep"
|
||||
url = "https://cran.r-project.org/src/contrib/spdep_0.6-13.tar.gz"
|
||||
list_url = "https://cran.r-project.org/src/contrib/Archive/spdep"
|
||||
|
||||
version('0.6-13', 'bfc68b3016b4894b152ecec4b86f85d1')
|
||||
|
||||
depends_on('r@3.0:')
|
||||
depends_on('r-sp@1.0:', type=('build', 'run'))
|
||||
depends_on('r-learnbayes', type=('build', 'run'))
|
||||
depends_on('r-deldir', type=('build', 'run'))
|
||||
depends_on('r-coda', type=('build', 'run'))
|
||||
depends_on('r-gmodels', type=('build', 'run'))
|
||||
depends_on('r-expm', type=('build', 'run'))
|
39
var/spack/repos/builtin/packages/r-vegan/package.py
Normal file
39
var/spack/repos/builtin/packages/r-vegan/package.py
Normal file
@ -0,0 +1,39 @@
|
||||
##############################################################################
|
||||
# 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 RVegan(RPackage):
|
||||
"""Ordination methods, diversity analysis and other functions for
|
||||
community and vegetation ecologists."""
|
||||
|
||||
homepage = "https://github.com/vegandevs/vegan"
|
||||
url = "https://cran.r-project.org/src/contrib/vegan_2.4-3.tar.gz"
|
||||
list_url = "https://cran.r-project.org/src/contrib/Archive/vegan"
|
||||
|
||||
version('2.4-3', 'db17d4c4b9a4d421246abd5b36b00fec')
|
||||
|
||||
depends_on('r@3.0:')
|
||||
depends_on('r-permute@0.9-0:', type=('build', 'run'))
|
Loading…
Reference in New Issue
Block a user