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

13 files changed, 518 insertions, 1 deletions

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'))