From 794dc5099567b075237a12474eedfdd5ffaa357b Mon Sep 17 00:00:00 2001 From: Tom Merrick Date: Thu, 25 May 2017 14:42:49 -0500 Subject: 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 --- var/spack/repos/builtin/packages/r-ade4/package.py | 38 +++++++++++++++ .../repos/builtin/packages/r-adegenet/package.py | 55 +++++++++++++++++++++ var/spack/repos/builtin/packages/r-ape/package.py | 51 ++++++++++++++++++++ .../repos/builtin/packages/r-deldir/package.py | 41 ++++++++++++++++ var/spack/repos/builtin/packages/r-expm/package.py | 36 ++++++++++++++ .../repos/builtin/packages/r-gmodels/package.py | 38 +++++++++++++++ .../repos/builtin/packages/r-learnbayes/package.py | 41 ++++++++++++++++ .../repos/builtin/packages/r-permute/package.py | 43 +++++++++++++++++ .../repos/builtin/packages/r-rmpfr/package.py | 2 +- .../repos/builtin/packages/r-segmented/package.py | 37 ++++++++++++++ .../repos/builtin/packages/r-seqinr/package.py | 42 ++++++++++++++++ .../repos/builtin/packages/r-spdep/package.py | 56 ++++++++++++++++++++++ .../repos/builtin/packages/r-vegan/package.py | 39 +++++++++++++++ 13 files changed, 518 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin/packages/r-ade4/package.py create mode 100644 var/spack/repos/builtin/packages/r-adegenet/package.py create mode 100644 var/spack/repos/builtin/packages/r-ape/package.py create mode 100644 var/spack/repos/builtin/packages/r-deldir/package.py create mode 100644 var/spack/repos/builtin/packages/r-expm/package.py create mode 100644 var/spack/repos/builtin/packages/r-gmodels/package.py create mode 100644 var/spack/repos/builtin/packages/r-learnbayes/package.py create mode 100644 var/spack/repos/builtin/packages/r-permute/package.py create mode 100644 var/spack/repos/builtin/packages/r-segmented/package.py create mode 100644 var/spack/repos/builtin/packages/r-seqinr/package.py create mode 100644 var/spack/repos/builtin/packages/r-spdep/package.py create mode 100644 var/spack/repos/builtin/packages/r-vegan/package.py diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py new file mode 100644 index 0000000000..e7bc51d3af --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ade4/package.py @@ -0,0 +1,38 @@ +############################################################################## +# 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:') diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py new file mode 100644 index 0000000000..368d546e1d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-adegenet/package.py @@ -0,0 +1,55 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/r-ape/package.py b/var/spack/repos/builtin/packages/r-ape/package.py new file mode 100644 index 0000000000..0476a6da29 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ape/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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:') diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py new file mode 100644 index 0000000000..4a08be58bb --- /dev/null +++ b/var/spack/repos/builtin/packages/r-deldir/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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:') diff --git a/var/spack/repos/builtin/packages/r-expm/package.py b/var/spack/repos/builtin/packages/r-expm/package.py new file mode 100644 index 0000000000..ba129a3071 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-expm/package.py @@ -0,0 +1,36 @@ +############################################################################## +# 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') diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py new file mode 100644 index 0000000000..2afb9273ce --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gmodels/package.py @@ -0,0 +1,38 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py new file mode 100644 index 0000000000..85a9e122bc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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') diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py new file mode 100644 index 0000000000..739e001b3b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-permute/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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:') diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py index cbf9b3d3c2..c9a957ae0d 100644 --- a/var/spack/repos/builtin/packages/r-rmpfr/package.py +++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py @@ -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:') diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py new file mode 100644 index 0000000000..53bac60ca9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-segmented/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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') diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py new file mode 100644 index 0000000000..e77914b726 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-seqinr/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py new file mode 100644 index 0000000000..d229876ff3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spdep/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py new file mode 100644 index 0000000000..4892193e59 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vegan/package.py @@ -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')) -- cgit v1.2.3-70-g09d2