From ff529e6dc110fdfe106706bfc2c8104c56d54c01 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 27 Jul 2020 15:08:48 -0500 Subject: 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 --- .../builtin/packages/r-adegraphics/package.py | 29 ++++++++++++++++++ .../repos/builtin/packages/r-adephylo/package.py | 24 +++++++++++++++ .../repos/builtin/packages/r-adespatial/package.py | 32 ++++++++++++++++++++ .../repos/builtin/packages/r-phylobase/package.py | 26 ++++++++++++++++ var/spack/repos/builtin/packages/r-rncl/package.py | 26 ++++++++++++++++ .../repos/builtin/packages/r-rnexml/package.py | 35 ++++++++++++++++++++++ 6 files changed, 172 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-adegraphics/package.py create mode 100644 var/spack/repos/builtin/packages/r-adephylo/package.py create mode 100644 var/spack/repos/builtin/packages/r-adespatial/package.py create mode 100644 var/spack/repos/builtin/packages/r-phylobase/package.py create mode 100644 var/spack/repos/builtin/packages/r-rncl/package.py create mode 100644 var/spack/repos/builtin/packages/r-rnexml/package.py 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) + .""" + + 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')) -- cgit v1.2.3-60-g2f50