r-adespatial: added new package (#17700)

This PR adds the r-adesaptial package and several other new packages as
dependencies.

- r-adegraphics
- r-adephylo
- r-phylobase
- r-rncl
- r-rnexml

6 files changed, 172 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-adegraphics/package.py b/var/spack/repos/builtin/packages/r-adegraphics/package.py
new file mode 100644
index 0000000000..d007d6cb97
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-adegraphics/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAdegraphics(RPackage):
+    """adegraphics: An S4 Lattice-Based Package for the Representation of
+    Multivariate Data.
+
+    Graphical functionalities for the representation of multivariate data.
+    It is a complete re-implementation of the functions available in the 'ade4'
+    package."""
+
+    homepage = "http://pbil.univ-lyon1.fr/ADE-4"
+    url      = "https://cloud.r-project.org/src/contrib/adegraphics_1.0-15.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/adegraphics"
+
+    version('1.0-15', sha256='87bbcd072e9a898955f5ede4315e82365086a50a2887bf5bd2e94bbb4d3f678a')
+
+    depends_on('r@3.0.2:', type=('build', 'run'))
+    depends_on('r-ade4@1.7-13:', type=('build', 'run'))
+    depends_on('r-kernsmooth', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-latticeextra', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-sp@1.1-1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-adephylo/package.py b/var/spack/repos/builtin/packages/r-adephylo/package.py
new file mode 100644
index 0000000000..3527a2fb6f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-adephylo/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAdephylo(RPackage):
+    """adephylo: Exploratory Analyses for the Phylogenetic Comparative Method.
+
+    Multivariate tools to analyze comparative data, i.e. a phylogeny and
+    some traits measured for each taxa."""
+
+    homepage = "https://cloud.r-project.org/package=adephylo"
+    url      = "https://cloud.r-project.org/src/contrib/adephylo_1.1-11.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/adephylo"
+
+    version('1.1-11', sha256='154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a')
+
+    depends_on('r-ade4@1.7-10:', type=('build', 'run'))
+    depends_on('r-phylobase', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-adegenet', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-adespatial/package.py b/var/spack/repos/builtin/packages/r-adespatial/package.py
new file mode 100644
index 0000000000..aeaaae67f5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-adespatial/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAdespatial(RPackage):
+    """adespatial: Multivariate Multiscale Spatial Analysis.
+
+    Tools for the multiscale spatial analysis of multivariate data. Several
+    methods are based on the use of a spatial weighting matrix and its
+    eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several
+    approaches are described in the review Dray et al (2012)
+    <doi:10.1890/11-1183.1>."""
+
+    homepage = "https://cloud.r-project.org/package=adespatial"
+    url      = "https://cloud.r-project.org/src/contrib/adespatial_0.3-8.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/adespatial"
+
+    version('0.3-8', sha256='e3fd3209ce3f0a862a0794187e8c884f1697c87c96e569a2f51f252e00022906')
+
+    depends_on('r-ade4@1.7-13:', type=('build', 'run'))
+    depends_on('r-adegraphics', type=('build', 'run'))
+    depends_on('r-adephylo', type=('build', 'run'))
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('r-spdep', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-shiny', type=('build', 'run'))
+    depends_on('r-vegan', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-phylobase/package.py b/var/spack/repos/builtin/packages/r-phylobase/package.py
new file mode 100644
index 0000000000..7cfe791b3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phylobase/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPhylobase(RPackage):
+    """phylobase: Base Package for Phylogenetic Structures and Comparative
+    Data.
+
+    Provides a base S4 class for comparative methods, incorporating one or
+    more trees and trait data."""
+
+    homepage = "https://github.com/fmichonneau/phylobase"
+    url      = "https://cloud.r-project.org/src/contrib/phylobase_0.8.10.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/phylobase"
+
+    version('0.8.10', sha256='5a44380ff49bab333a56f6f96157324ade8afb4af0730e013194c4badb0bf94b')
+
+    depends_on('r-ade4', type=('build', 'run'))
+    depends_on('r-ape@3.0:', type=('build', 'run'))
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('r-rncl@0.6.0:', type=('build', 'run'))
+    depends_on('r-rnexml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rncl/package.py b/var/spack/repos/builtin/packages/r-rncl/package.py
new file mode 100644
index 0000000000..4501e1c2f3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rncl/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRncl(RPackage):
+    """rncl: An Interface to the Nexus Class Library.
+
+    An interface to the Nexus Class Library which allows parsing of NEXUS,
+    Newick and other phylogenetic tree file formats. It provides elements of
+    the file that can be used to build phylogenetic objects such as ape's
+    'phylo' or phylobase's 'phylo4(d)'. This functionality is demonstrated with
+    'read_newick_phylo()' and 'read_nexus_phylo()'."""
+
+    homepage = "https://github.com/fmichonneau/rncl"
+    url      = "https://cloud.r-project.org/src/contrib/rncl_0.8.4.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/rncl"
+
+    version('0.8.4', sha256='6b19d0dd9bb08ecf99766be5ad684bcd1894d1cd9291230bdd709dbd3396496b')
+
+    depends_on('r@3.1.1:', type=('build', 'run'))
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('r-progress@1.1.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rnexml/package.py b/var/spack/repos/builtin/packages/r-rnexml/package.py
new file mode 100644
index 0000000000..bffab45a28
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rnexml/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRnexml(RPackage):
+    """RNeXML: Semantically Rich I/O for the 'NeXML' Format.
+
+    Provides access to phyloinformatic data in 'NeXML' format. The package
+    should add new functionality to R such as the possibility to manipulate
+    'NeXML' objects in more various and refined way and compatibility with
+    'ape' objects."""
+
+    homepage = "https://github.com/ropensci/RNeXML"
+    url      = "https://cloud.r-project.org/src/contrib/RNeXML_2.4.5.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/RNeXML"
+
+    version('2.4.5', sha256='2b667ecb6400e4c0c125ca73a98cde81330cde3a85b764261f77159e702754f3')
+
+    depends_on('r@3.0.0:', type=('build', 'run'))
+    depends_on('r-ape@3.1:', type=('build', 'run'))
+    depends_on('r-xml@3.95:', type=('build', 'run'))
+    depends_on('r-plyr@1.8:', type=('build', 'run'))
+    depends_on('r-reshape2@1.2.2:', type=('build', 'run'))
+    depends_on('r-httr@0.3:', type=('build', 'run'))
+    depends_on('r-uuid@0.1-1:', type=('build', 'run'))
+    depends_on('r-dplyr@0.5.0:', type=('build', 'run'))
+    depends_on('r-lazyeval@0.1.0:', type=('build', 'run'))
+    depends_on('r-tidyr@0.3.1:', type=('build', 'run'))
+    depends_on('r-stringr@1.0:', type=('build', 'run'))
+    depends_on('r-stringi', type=('build', 'run'))
+    depends_on('r-xml2', type=('build', 'run'))