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:
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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##############################################################################
# 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 RAde4(RPackage):
"""Analysis of Ecological Data : Exploratory and Euclidean Methods in
Environmental Sciences"""
homepage = "http://pbil.univ-lyon1.fr/ADE-4"
url = "https://cran.r-project.org/src/contrib/ade4_1.7-6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ade4"
version('1.7-6', '63401ca369677538c96c3d7b75b3f4a1')
depends_on('r@2.10:')

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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'))

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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 RApe(RPackage):
"""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 DNA sequences, reading and writing nucleotide
sequences as well as importing from BioConductor, 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, dating trees with non-contemporaneous sequences,
translating DNA into AA sequences, and assessing sequence alignments.
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."""
homepage = "http://ape-package.ird.fr/"
url = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
version('4.1', 'a9ed416d6d172d4b9682556cf692d7c2')
depends_on('r@3.2:')

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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 RDeldir(RPackage):
"""Calculates the Delaunay triangulation and the Dirichlet or Voronoi
tessellation (with respect to the entire plane) of a planar point set.
Plots triangulations and tessellations in various ways. Clips
tessellations to sub-windows. Calculates perimeters of tessellations.
Summarises information about the tiles of the tessellation."""
homepage = "https://CRAN.R-project.org/package=deldir"
url = "https://cran.r-project.org/src/contrib/deldir_0.1-14.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/deldir"
version('0.1-14', '6a22b13d962615cd9d51b6eae403409f')
depends_on('r@0.99:')

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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 RExpm(RPackage):
"""Computation of the matrix exponential, logarithm, sqrt, and related
quantities."""
homepage = "http://R-Forge.R-project.org/projects/expm"
url = "https://cran.r-project.org/src/contrib/expm_0.999-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/expm"
version('0.999-2', 'e05fa3f995754af92bd03227625da984')

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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 RGmodels(RPackage):
"""Various R programming tools for model fitting."""
homepage = "http://www.sf.net/projects/r-gregmisc"
url = "https://cran.r-project.org/src/contrib/gmodels_2.16.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/gmodels"
version('2.16.2', 'f13e5feb2a8b9f0cd47fdf25ddc74228')
depends_on('r@1.9:')
depends_on('r-gdata', type=('build', 'run'))

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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 RLearnbayes(RPackage):
"""LearnBayes contains a collection of functions helpful in learning the
basic tenets of Bayesian statistical inference. It contains functions for
summarizing basic one and two parameter posterior distributions and
predictive distributions. It contains MCMC algorithms for summarizing
posterior distributions defined by the user. It also contains functions
for regression models, hierarchical models, Bayesian tests, and
illustrations of Gibbs sampling."""
homepage = "https://CRAN.R-project.org/package=LearnBayes"
url = "https://cran.r-project.org/src/contrib/LearnBayes_2.15.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/LearnBayes"
version('2.15', '213713664707bc79fd6d3a109555ef76')

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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 RPermute(RPackage):
"""A set of restricted permutation designs for freely exchangeable, line
transects (time series), and spatial grid designs plus permutation of
blocks (groups of samples) is provided. 'permute' also allows split-plot
designs, in which the whole-plots or split-plots or both can be
freely-exchangeable or one of the restricted designs. The 'permute'
package is modelled after the permutation schemes of 'Canoco 3.1'
(and later) by Cajo ter Braak."""
homepage = "https://github.com/gavinsimpson/permute"
url = "https://cran.r-project.org/src/contrib/permute_0.9-4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/permute"
version('0.9-4', '569fc2442d72a1e3b7e2d456019674c9')
depends_on('r@2.14:')

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@ -38,5 +38,5 @@ class RRmpfr(RPackage):
version('0.6-1', '55d4ec257bd2a9233bafee9e444d0265')
depends_on('r-gmp@0.5-8:')
depends_on('r-gmp@0.5-8:', type=('build', 'run'))
depends_on('mpfr@3.0.0:')

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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')

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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 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')

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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 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'))

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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 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'))