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r-adespatial: added new package (#17700)

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

- r-adegraphics
- r-adephylo
- r-phylobase
- r-rncl
- r-rnexml
This commit is contained in:
Glenn Johnson 2020-07-27 15:08:48 -05:00 committed by GitHub
parent 1c0abaa6eb
commit ff529e6dc1
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6 changed files with 172 additions and 0 deletions
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# 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'))

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# 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'))

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# 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'))

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# 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'))

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# 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'))

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# 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'))