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Updates of R CRAN packages (#21223)

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Glenn Johnson 2021-01-24 17:54:25 -06:00 committed by GitHub
parent 88cafacd09
commit cf35661d3c
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GPG key ID: 4AEE18F83AFDEB23
227 changed files with 2196 additions and 686 deletions
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1
var/spack/repos/builtin/packages/r-animation/package.py
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@ -20,6 +20,7 @@ class RAnimation(RPackage):
version('2.6', sha256='90293638920ac436e7e4de76ebfd92e1643ccdb0259b62128f16dd0b13245b0a')
version('2.5', sha256='b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f')
depends_on('r+X', type=('build', 'run'))
depends_on('r@2.14:', type=('build', 'run'))
depends_on('r-magick', when='@2.6:', type=('build', 'run'))
depends_on('imagemagick')

3
var/spack/repos/builtin/packages/r-bookdown/package.py
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@ -20,7 +20,7 @@ class RBookdown(RPackage):
version('0.12', sha256='38eb4c5b877ccd85b16cfe74a48c3bc53de2f276da98e5515f37e7a06e065bb0')
version('0.5', sha256='b7331fd56f64bd2bddc34e2a188fc491f9ff5308f44f7e3151721247f21ca67e')
depends_on('pandoc@1.17.2:')
depends_on('r+X', type=('build', 'run'))
depends_on('r-htmltools@0.3.6:', type=('build', 'run'))
depends_on('r-knitr@1.22:', type=('build', 'run'))
depends_on('r-rmarkdown@1.12:', when='@:0.12', type=('build', 'run'))
@ -30,3 +30,4 @@ class RBookdown(RPackage):
depends_on('r-tinytex@0.12:', when='@0.12:', type=('build', 'run'))
depends_on('r-yaml@2.1.14:', when='@:0.12', type=('build', 'run'))
depends_on('r-yaml@2.1.19:', when='@0.21:', type=('build', 'run'))
depends_on('pandoc@1.17.2:')

20
var/spack/repos/builtin/packages/r-brio/package.py Normal file
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@ -0,0 +1,20 @@
# Copyright 2013-2021 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 RBrio(RPackage):
"""Basic R Input Output
Functions to handle basic input output, these functions always read and
write UTF-8 (8-bit Unicode Transformation Format) files and provide more
explicit control over line endings."""
homepage = "https://github.com/r-lib/brio"
url = "https://cloud.r-project.org/src/contrib/brio_1.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/brio"
version('1.1.0', sha256='6bb3a3b47bea13f1a1e3dcdc8b9f688502643e4b40a481a34aa04a261aabea38')

39
var/spack/repos/builtin/packages/r-broom/package.py
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@ -7,32 +7,41 @@
class RBroom(RPackage):
"""Convert statistical analysis objects from R into tidy data frames, so
that they can more easily be combined, reshaped and otherwise processed
with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides
three S3 generics: tidy, which summarizes a model's statistical
findings such as coefficients of a regression; augment, which adds
columns to the original data such as predictions, residuals and cluster
assignments; and glance, which provides a one-row summary of
model-level statistics."""
"""Convert Statistical Objects into Tidy Tibbles
Summarizes key information about statistical objects in tidy tibbles. This
makes it easy to report results, create plots and consistently work with
large numbers of models at once. Broom provides three verbs that each
provide different types of information about a model. tidy() summarizes
information about model components such as coefficients of a regression.
glance() reports information about an entire model, such as goodness of fit
measures like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence measures."""
homepage = "http://github.com/tidyverse/broom"
url = "https://cloud.r-project.org/src/contrib/broom_0.4.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/broom"
version('0.7.3', sha256='de5650e46ca6884876b63bc401d22bef9eace671147774466406d43324aebc2f')
version('0.5.2', sha256='16af7b446b24bc14461efbda9bea1521cf738c778c5e48fcc7bad45660a4ac62')
version('0.5.1', sha256='da9e6bf7cb8f960b83309cf107743976cc32b54524675f6471982abe3d1aae2e')
version('0.4.2', sha256='9f409413623cf25e7110452e6215353af5114f7044d73af182bd6c10971c5a44')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-plyr', when='@:0.4.2', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-psych', when='@:0.4.2', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-backports', when='@0.5.0:', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-dplyr@1.0.0:', when='@0.7.3:', type=('build', 'run'))
depends_on('r-ellipsis', when='@0.7.3:', type=('build', 'run'))
depends_on('r-generics@0.0.2:', when='@0.5.1:', type=('build', 'run'))
depends_on('r-glue', when='@0.7.3:', type=('build', 'run'))
depends_on('r-purrr', when='@0.5.0:', type=('build', 'run'))
depends_on('r-rlang', when='@0.7.3:', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-tibble', when='@0.5.0:', type=('build', 'run'))
depends_on('r-tibble@3.0.0:', when='@0.7.3:', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-tidyr@1.0.0:', when='@0.7.3:', type=('build', 'run'))
depends_on('r-plyr', when='@:0.4.2', type=('build', 'run'))
depends_on('r-psych', when='@:0.4.2', type=('build', 'run'))
depends_on('r-reshape2', when='@:0.5.2', type=('build', 'run'))
depends_on('r-nlme', when='@:0.5.2', type=('build', 'run'))

14
var/spack/repos/builtin/packages/r-caret/package.py
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@ -7,27 +7,33 @@
class RCaret(RPackage):
"""Misc functions for training and plotting classification and regression
"""Classification and Regression Training
Misc functions for training and plotting classification and regression
models."""
homepage = "https://github.com/topepo/caret/"
url = "https://cloud.r-project.org/src/contrib/caret_6.0-73.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caret"
version('6.0-86', sha256='da4a1c7c3fbf645c5b02871e563a77404622b83623f0d1c5dc1425de7aa4ce37')
version('6.0-84', sha256='a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d')
version('6.0-83', sha256='9bde5e4da1f0b690bfe06c2439c0136504e851a8d360bf56b644f171fe20dcef')
version('6.0-73', sha256='90a0a4a10f1a3b37502cb0ed7d8830063d059a548faabb9cc5d8d34736c7eacb')
version('6.0-70', sha256='21c5bdf7cf07bece38729465366564d8ca104c2466ee9fd800ca1fd88eb82f38')
depends_on('r@2.10:', when='@:6.0-81', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r@3.2.0:', when='@6.0-82:', type=('build', 'run'))
depends_on('r-lattice@0.20:', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-car', when='@:6.0-73', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-modelmetrics@1.1.0:', type=('build', 'run'))
depends_on('r-modelmetrics@1.2.2.2:', when='@6.0-86:', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-recipes@0.1.4:', when='@6.0-83:', type=('build', 'run'))
depends_on('r-recipes@0.1.4:', when='@6.0-83:6.0-84', type=('build', 'run'))
depends_on('r-recipes@0.1.10:', when='@6.0-86:', type=('build', 'run'))
depends_on('r-withr@2.0.0:', when='@6.0-83:', type=('build', 'run'))
depends_on('r-proc', when='@6.0-86:', type=('build', 'run'))
depends_on('r-car', when='@:6.0-73', type=('build', 'run'))

27
var/spack/repos/builtin/packages/r-conquer/package.py Normal file
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@ -0,0 +1,27 @@
# Copyright 2013-2021 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 RConquer(RPackage):
"""Convolution-Type Smoothed Quantile Regression
Fast and accurate convolution-type smoothed quantile regression.
Implemented using Barzilai-Borwein gradient descent with a Huber regression
warm start. Construct confidence intervals for regression coefficients
using multiplier bootstrap."""
homepage = "https://github.com/XiaoouPan/conquer"
url = "https://cloud.r-project.org/src/contrib/conquer_1.0.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/conquer"
version('1.0.2', sha256='542f6154ce1ffec0c1b4dd4e1f5b86545015f4b378c4c66a0840c65c57d674ff')
depends_on('r@3.5.0:', type=('build', 'run'))
depends_on('r-rcpp@1.0.3:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-matrixstats', type=('build', 'run'))
depends_on('r-rcpparmadillo@0.9.850.1.0:', type=('build', 'run'))

1
var/spack/repos/builtin/packages/r-construct/package.py
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@ -23,6 +23,7 @@ class RConstruct(RPackage):
version('1.0.4', sha256='4e585b718a361061bc1432cea46fc65f802fb0ef58e4516d33e1af99bbfe90ce')
version('1.0.3', sha256='b449c133a944ad05a28f84f312ed4ccbc1574c4659aa09c678618d2ae9008310')
depends_on('r+X', type=('build', 'run'))
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
depends_on('r-rstan@2.18.1:', type=('build', 'run'))

16
var/spack/repos/builtin/packages/r-corhmm/package.py
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@ -7,17 +7,17 @@
class RCorhmm(RPackage):
"""corHMM: Analysis of Binary Character Evolution
"""Hidden Markov Models of Character Evolution
Fits a hidden rates model that allows different transition rate classes
on different portions of a phylogeny by treating rate classes as hidden
states in a Markov process and various other functions for evaluating
models of binary character evolution."""
Fits hidden Markov models of discrete character evolution which allow
different transition rate classes on different portions of a phylogeny.
Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>."""
homepage = "https://cloud.r-project.org/package=corHMM"
url = "https://cloud.r-project.org/src/contrib/corHMM_1.22.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/corHMM/"
version('2.6', sha256='726de9707ede8ef447915171a3abe1003a0e42fe8e17eb440442cac9adf8cdcf')
version('1.22', sha256='d262fa1183eab32087afb70f1789fabae6fb49bec01d627974c54a088a48b10d')
depends_on('r-ape', type=('build', 'run'))
@ -25,7 +25,11 @@ class RCorhmm(RPackage):
depends_on('r-gensa', type=('build', 'run'))
depends_on('r-expm', type=('build', 'run'))
depends_on('r-numderiv', type=('build', 'run'))
depends_on('r-nnet', type=('build', 'run'))
depends_on('r-corpcor', type=('build', 'run'))
depends_on('r-mass', when='@2.6:', type=('build', 'run'))
depends_on('r-nnet', type=('build', 'run'))
depends_on('r-phangorn', type=('build', 'run'))
depends_on('r-viridis', when='@2.6:', type=('build', 'run'))
depends_on('r-rmpfr', type=('build', 'run'))
depends_on('r-igraph', when='@2.6:', type=('build', 'run'))
depends_on('r-phytools', when='@2.6:', type=('build', 'run'))

31
var/spack/repos/builtin/packages/r-credentials/package.py Normal file
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@ -0,0 +1,31 @@
# Copyright 2013-2021 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 RCredentials(RPackage):
"""Tools for Managing SSH and Git Credentials
Setup and retrieve HTTPS and SSH credentials for use with 'git' and other
services. For HTTPS remotes the package interfaces the 'git-credential'
utility which 'git' uses to store HTTP usernames and passwords. For SSH
remotes we provide convenient functions to find or generate appropriate SSH
keys. The package both helps the user to setup a local git installation,
and also provides a back-end for git/ssh client libraries to authenticate
with existing user credentials."""
homepage = "https://docs.ropensci.org/credentials"
url = "https://cloud.r-project.org/src/contrib/credentials_1.3.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/credentials"
version('1.3.0', sha256='c119ec26fd97b977c3b0cd1eb8fad3c59b84df6262c3adbf5ee9f3d6c9903ff1')
depends_on('r-openssl@1.3:', type=('build', 'run'))
depends_on('r-sys@2.1:', type=('build', 'run'))
depends_on('r-curl', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-askpass', type=('build', 'run'))
depends_on('git', type='run')

33
var/spack/repos/builtin/packages/r-devtools/package.py
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@ -7,12 +7,15 @@
class RDevtools(RPackage):
"""Collection of package development tools."""
"""Tools to Make Developing R Packages Easier
Collection of package development tools."""
homepage = "https://github.com/hadley/devtools"
url = "https://cloud.r-project.org/src/contrib/devtools_1.12.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/devtools"
version('2.3.2', sha256='e5086106baef6bb925445dfdddb3cd5ff4f8fff96353365b135aba5618d1986d')
version('2.3.0', sha256='4fc375c171335c67bd71df4e0b1b3dff2ae3aa17b3e0566b790ba0808b39dcd0')
version('2.1.0', sha256='c1f75346a90adf0669b5508fe68cc78bd3b114c1303fa7d22bf90991edd9230d')
version('2.0.2', sha256='99a2fa957068254b8ecdb3fc2d50e2950230910ea31c314fc0e7d934e4bd1709')
@ -22,41 +25,55 @@ class RDevtools(RPackage):
depends_on('r@3.0.2:', type=('build', 'run'))
depends_on('r-usethis@1.5.0:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-usethis@1.6.0:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-usethis@1.6.3:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-callr', when='@2.0.0:', type=('build', 'run'))
depends_on('r-callr@3.4.3:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-callr@3.4.4:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-cli', when='@2.0.0:', type=('build', 'run'))
depends_on('r-cli@2.0.2:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-covr@3.5.0:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-crayon@1.3.4:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-covr@3.5.1:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-desc@1.2.0:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-dt@0.13:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-digest', type=('build', 'run'))
depends_on('r-digest@0.6.25:', when='@3.2.0:', type=('build', 'run'))
depends_on('r-dt@0.15:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-ellipsis@0.3.0:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-glue@1.4.0:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-git2r@0.23.0:', type=('build', 'run'))
depends_on('r-git2r@0.26.1:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-ellipsis@0.3.1:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-httr@0.4:', type=('build', 'run'))
depends_on('r-httr@1.4.1:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-httr@1.4.2:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-jsonlite@1.6.1:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-jsonlite@1.7.1:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-memoise@1.0.0:', type=('build', 'run'))
depends_on('r-memoise@1.1.0:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-pkgbuild@1.0.3:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-pkgbuild@1.0.6:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-pkgbuild@1.1.0:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-pkgload@1.0.2:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-pkgload@1.1.0:', when='@2.0.2:', type=('build', 'run'))
depends_on('r-rcmdcheck@1.3.3:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-remotes@2.1.0:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-remotes@2.1.1:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-remotes@2.2.0:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-rlang@0.4.5:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-rlang@0.4.7:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-roxygen2@6.1.1:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-roxygen2@7.1.0:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-roxygen2@7.1.1:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-rstudioapi@0.7.0:', type=('build', 'run'))
depends_on('r-rstudioapi@0.11:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-rversions@2.0.1:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-rversions@2.0.2:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-sessioninfo@1.1.1:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-testthat@2.1.1:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-testthat@2.3.2:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-whisker', when='@:1.9.9', type=('build', 'run'))
depends_on('r-withr', type=('build', 'run'))
depends_on('r-withr@2.1.2:', when='@2.3.0:', type=('build', 'run'))
depends_on('r-withr@2.2.0:', when='@2.3.2:', type=('build', 'run'))
depends_on('r-crayon@1.3.4:', when='@2.3.0', type=('build', 'run'))
depends_on('r-digest', when='@:2.3.0', type=('build', 'run'))
depends_on('r-digest@0.6.25:', when='@2.3.0', type=('build', 'run'))
depends_on('r-glue@1.4.0:', when='@2.3.0', type=('build', 'run'))
depends_on('r-git2r@0.23.0:', when='@:2.3.0', type=('build', 'run'))
depends_on('r-git2r@0.26.1:', when='@2.3.0', type=('build', 'run'))
depends_on('r-whisker', when='@:1.9.9', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-diffobj/package.py Normal file
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@ -0,0 +1,22 @@
# Copyright 2013-2021 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 RDiffobj(RPackage):
"""Diffs for R Objects
Generate a colorized diff of two R objects for an intuitive visualization
of their differences."""
homepage = "https://github.com/brodieG/diffobj"
url = "https://cloud.r-project.org/src/contrib/diffobj_0.3.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/diffobj"
version('0.3.3', sha256='414e5573470b9565b9149a0a61c7e8344fb37f889d23dc4e131acc8aa62e6df4')
depends_on('r@3.1.0:', type=('build', 'run'))
depends_on('r-crayon@1.3.2:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-fastmap/package.py Normal file
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@ -0,0 +1,23 @@
# Copyright 2013-2021 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 RFastmap(RPackage):
"""Fast Implementation of a Key-Value Store
Fast implementation of a key-value store. Environments are commonly used as
key-value stores, but every time a new key is used, it is added to R's
global symbol table, causing a small amount of memory leakage. This can be
problematic in cases where many different keys are used. Fastmap avoids
this memory leak issue by implementing the map using data structures in
C++."""
homepage = "https://r-lib.github.io/fastmap/"
url = "https://cloud.r-project.org/src/contrib/fastmap_1.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/fastmap"
version('1.0.1', sha256='4778b05dfebd356f8df980dfeff3b973a72bca14898f870e5c40c1d84db9faec')

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@ -0,0 +1,21 @@
# Copyright 2013-2021 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 RFastmatrix(RPackage):
"""Fast Computation of some Matrices Useful in Statistics
Small set of functions to fast computation of some matrices and operations
useful in statistics."""
homepage = "https://faosorios.github.io/fastmatrix/"
url = "https://cloud.r-project.org/src/contrib/fastmatrix_0.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/fastmatrix"
version('0.3', sha256='d92e789454a129db5f6f5b23e0d2245f3d55ff34b167427af265b9a6331e7c21')
depends_on('r@3.5.0:', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RFutureApply(RPackage):
"""Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(),
"""Apply Function to Elements in Parallel using Futures
Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(),
replicate(), sapply(), tapply(), and vapply() that can be resolved using
any future-supported backend, e.g. parallel on the local machine or
distributed on a compute cluster. These future_*apply() functions come with
@ -19,8 +21,11 @@ class RFutureApply(RPackage):
url = "https://cloud.r-project.org/src/contrib/future.apply_1.3.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/future.apply"
version('1.7.0', sha256='2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db')
version('1.3.0', sha256='6374eca49bb81e05c013509c8e324cf9c5d023f9f8217b29ce7b7e12025ca371')
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r-future@1.13.0:', type=('build', 'run'))
depends_on('r-future@1.17.0:', when='@1.7.0:', type=('build', 'run'))
depends_on('r-globals@0.12.4:', type=('build', 'run'))
depends_on('r-globals@0.12.5:', when='@1.7.0:', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RFuture(RPackage):
"""The purpose of this package is to provide a lightweight and unified
"""Unified Parallel and Distributed Processing in R for Everyone
The purpose of this package is to provide a lightweight and unified
Future API for sequential and parallel processing of R expression via
futures. The simplest way to evaluate an expression in parallel is to use
'x %<-% { expression }' with 'plan(multiprocess)'. This package implements
@ -26,8 +28,12 @@ class RFuture(RPackage):
url = "https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/future"
version('1.21.0', sha256='909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d')
version('1.14.0', sha256='0a535010d97a01b21aaf9d863603e44359335e273019c1e1980bbb5b2917dbcb')
depends_on('r-digest', type=('build', 'run'))
depends_on('r-globals@0.12.4:', type=('build', 'run'))
depends_on('r-globals@0.13.1:', when='@1.21.0:', type=('build', 'run'))
depends_on('r-listenv@0.7.0:', type=('build', 'run'))
depends_on('r-listenv@0.8.0:', when='@1.21.0:', type=('build', 'run'))
depends_on('r-parallelly@1.21.0:', when='@1.21.0:', type=('build', 'run'))

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@ -7,18 +7,23 @@
class RGeiger(RPackage):
"""Methods for fitting macroevolutionary models to phylogenetic trees."""
"""Analysis of Evolutionary Diversification
Methods for fitting macroevolutionary models to phylogenetic trees Pennell
(2014) <doi:10.1093/bioinformatics/btu181>."""
homepage = "https://cloud.r-project.org/package=geiger"
url = "https://cloud.r-project.org/src/contrib/geiger_2.0.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/geiger"
version('2.0.7', sha256='d200736c4ad7ed4bc55a13e7d0126ddc7fed88e245cd5706d4692aaa437e9596')
version('2.0.6.2', sha256='9153047b608d652821251206d1450bb3f517c8884379f498a695315574ae001d')
version('2.0.6.1', sha256='2a95e20a3a90c096343b014344dd97e699e954da99c151c17fc6c245c77dba0b')
version('2.0.6', sha256='e13b2c526378eaf9356b00bbe21b3c2c956327f8062fed638ccc1f49591c3eff')
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r-ape@3.0-6:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-mvtnorm', type=('build', 'run'))
depends_on('r-subplex', type=('build', 'run'))
depends_on('r-desolve@1.7:', type=('build', 'run'))
@ -27,4 +32,4 @@ class RGeiger(RPackage):
depends_on('r-coda', type=('build', 'run'))
depends_on('r-ncbit', type=('build', 'run'))
depends_on('r-colorspace', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-phytools@0.7.31:', when='@2.0.7:', type=('build', 'run'))

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@ -24,6 +24,7 @@ class RGeomorph(RPackage):
version('3.0.7', sha256='68f8942e1a5bc3f0298c9f5b8f69c4702c8e12ecb2275d740fda4d04d66d38e1')
version('3.0.5', sha256='7a3a587b253770a5e7e70536234dee13e6a073f1fdf1d644ae4f11d2eb95b104')
depends_on('r+X', type=('build', 'run'))
depends_on('r@3.1.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@3.3.2:', type=('build', 'run'))
depends_on('r-rrpp', type=('build', 'run'), when='@3.0.7:')

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@ -20,7 +20,8 @@ class RGeor(RPackage):
version('1.8-1', sha256='990647804590b925a50f72897b24bbabd331cebef0be1696a60528b2f79d6fd3')
version('1.7-5.2.1', sha256='3895e49c005a5745738d190ccaad43bb0aa49c74465d4d0b4dd88c5850ed63b9')
depends_on('r+X@2.10:', type=('build', 'run'))
depends_on('r+X', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-sp', type=('build', 'run'))
depends_on('r-splancs', type=('build', 'run'))

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@ -0,0 +1,31 @@
# Copyright 2013-2021 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 RGert(RPackage):
"""Simple Git Client for R
Simple git client for R based on 'libgit2' with support for SSH and HTTPS
remotes. All functions in 'gert' use basic R data types (such as vectors
and data-frames) for their arguments and return values. User credentials
are shared with command line 'git' through the git-credential store and ssh
keys stored on disk or ssh-agent. On Linux, a somewhat recent version of
'libgit2' is required; we provide a 'PPA' for older Ubuntu 'LTS'
versions."""
homepage = "https://docs.ropensci.org/gert/"
url = "https://cloud.r-project.org/src/contrib/gert_1.0.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/gert"
version('1.0.2', sha256='36687ab98291d50a35752fcb2e734a926a6b845345c18d36e3f48823f68304d3')
depends_on('r-askpass', type=('build', 'run'))
depends_on('r-credentials@1.2.1:', type=('build', 'run'))
depends_on('r-openssl@1.4.1:', type=('build', 'run'))
depends_on('r-rstudioapi@0.11:', type=('build', 'run'))
depends_on('r-zip@2.1.0:', type=('build', 'run'))
depends_on('libgit2@0.26:')

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@ -7,26 +7,35 @@
class RGgally(RPackage):
"""The R package 'ggplot2' is a plotting system based on the grammar of
graphics. 'GGally' extends 'ggplot2' by adding several functions to
reduce the complexity of combining geometric objects with transformed
data. Some of these functions include a pairwise plot matrix, a two
group pairwise plot matrix, a parallel coordinates plot, a survival
plot, and several functions to plot networks."""
"""Extension to 'ggplot2'
The R package 'ggplot2' is a plotting system based on the grammar of
graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce
the complexity of combining geometric objects with transformed data. Some
of these functions include a pairwise plot matrix, a two group pairwise
plot matrix, a parallel coordinates plot, a survival plot, and several
functions to plot networks."""
homepage = "https://cloud.r-project.org/package=GGally"
url = "https://cloud.r-project.org/src/contrib/GGally_1.3.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/GGally"
version('2.1.0', sha256='7ffb86b8a4e79543cf7e6bb1e3684d738ecd8e0ba89e8ef38991898b18dd6c53')
version('1.4.0', sha256='9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe')
version('1.3.2', sha256='f4143f45254fed794be991180aeffe459f6756bfa08acad963707d8e843cfd0a')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-ggplot2@2.2.0:', type=('build', 'run'))
depends_on('r-ggplot2@3.3.0:', when='@2.1.0:', type=('build', 'run'))
depends_on('r-dplyr@1.0.0:', when='@2.1.0:', type=('build', 'run'))
depends_on('r-forcats', when='@2.1.0:', type=('build', 'run'))
depends_on('r-gtable@0.2.0:', type=('build', 'run'))
depends_on('r-lifecycle', when='@2.1.0:', type=('build', 'run'))
depends_on('r-plyr@1.8.3:', type=('build', 'run'))
depends_on('r-progress', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-reshape@0.8.5:', type=('build', 'run'))
depends_on('r-rlang', when='@1.4.0:', type=('build', 'run'))
depends_on('r-scales@1.1.0:', when='@2.1.0:', type=('build', 'run'))
depends_on('r-tidyr', when='@2.1.0:', type=('build', 'run'))
depends_on('openssl', when='@1.4.0:')

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@ -7,12 +7,21 @@
class RGgpubr(RPackage):
"""ggpubr: 'ggplot2' Based Publication Ready Plots"""
"""'ggplot2' Based Publication Ready Plots
The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some
formatting before we can send them for publication. Furthermore, to
customize a 'ggplot', the syntax is opaque and this raises the level of
difficulty for researchers with no advanced R programming skills. 'ggpubr'
provides some easy-to-use functions for creating and customizing 'ggplot2'-
based publication ready plots."""
homepage = "http://www.sthda.com/english/rpkgs/ggpubr"
url = "https://cloud.r-project.org/src/contrib/ggpubr_0.1.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ggpubr"
version('0.4.0', sha256='abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675')
version('0.2.2', sha256='1c93dc6d1f08680dd00a10b6842445700d1fccb11f18599fbdf51e70c6b6b364')
version('0.2.1', sha256='611e650da9bd15d7157fdcdc4e926fee3b88df3aba87410fdb1c8a7294d98d28')
version('0.2', sha256='06c3075d8c452840662f5d041c3d966494b87254a52a858c849b9e1e96647766')
@ -20,11 +29,10 @@ class RGgpubr(RPackage):
depends_on('r@3.1.0:', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-ggrepel', type=('build', 'run'))
depends_on('r-ggsci', type=('build', 'run'))
depends_on('r-plyr', when='@:0.1.2', type=('build', 'run'))
depends_on('r-tidyr', when='@0.2:', type=('build', 'run'))
depends_on('r-plyr', when='@:0.1.2', type=('build', 'run'))
depends_on('r-purrr', when='@0.2:', type=('build', 'run'))
depends_on('r-dplyr@0.7.1:', when='@0.2:', type=('build', 'run'))
depends_on('r-cowplot', when='@0.2:', type=('build', 'run'))
@ -34,3 +42,6 @@ class RGgpubr(RPackage):
depends_on('r-glue', when='@0.2:', type=('build', 'run'))
depends_on('r-polynom', when='@0.2:', type=('build', 'run'))
depends_on('r-rlang', when='@0.2.2:', type=('build', 'run'))
depends_on('r-rstatix@0.6.0:', when='@0.4.0:', type=('build', 'run'))
depends_on('r-tibble', when='@0.4.0:', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))

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@ -7,18 +7,24 @@
class RGgraph(RPackage):
"""ggraph: An Implementation of Grammar of Graphics for Graphs and
Networks"""
"""An Implementation of Grammar of Graphics for Graphs and Networks
The grammar of graphics as implemented in ggplot2 is a poor fit for graph
and network visualizations due to its reliance on tabular data input.
ggraph is an extension of the ggplot2 API tailored to graph visualizations
and provides the same flexible approach to building up plots layer by
layer."""
homepage = "https://github.com/thomasp85/ggraph"
url = "https://cloud.r-project.org/src/contrib/ggraph_2.0.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ggraph"
version('2.0.4', sha256='9c6092d9a98b7b116f9c765ba44de7a34ceff2f584e776ef7a2082ad1d717dc8')
version('2.0.0', sha256='4307efe85bfc6a0496797f6b86d6b174ba196538c51b1a6b6af55de0d4e04762')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-ggplot2@3.0.0:', type=('build', 'run'))
depends_on('r-rcpp@0.12.2', type=('build', 'run'))
depends_on('r-rcpp@0.12.2:', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-ggforce@0.3.1:', type=('build', 'run'))
depends_on('r-igraph@1.0.0:', type=('build', 'run'))
@ -31,3 +37,4 @@ class RGgraph(RPackage):
depends_on('r-rlang', type=('build', 'run'))
depends_on('r-tidygraph', type=('build', 'run'))
depends_on('r-graphlayouts@0.5.0:', type=('build', 'run'))
depends_on('r-withr', when='@2.0.4:', type=('build', 'run'))

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@ -30,6 +30,7 @@ class RGistr(RPackage):
version('0.4.0', sha256='51771a257379a17552d0c88ada72ca6263954bbe896997f8a66cde3bf0b83ce0')
version('0.3.6', sha256='ab22523b79510ec03be336e1d4600ec8a3a65afe57c5843621a4cf8f966b52e5')
depends_on('r+X', type=('build', 'run'))
depends_on('r-jsonlite@1.4:', type=('build', 'run'))
depends_on('r-crul', when='@0.9.0:', type=('build', 'run'))
depends_on('r-httr@1.2.0:', type=('build', 'run'))

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@ -31,6 +31,7 @@ class RGrbase(RPackage):
version('1.8-6.7', sha256='aaafc7e1b521de60e1a57c0175ac64d4283850c3273bd14774cf24dabc743388')
version('1.8-3.4', sha256='d35f94c2fb7cbd4ce3991570424dfe6723a849658da32e13df29f53b6ea2cc2c')
depends_on('r+X', type=('build', 'run'))
depends_on('r@3.0.2:', type=('build', 'run'))
depends_on('r@3.6.0:', when='@1.8-6.7:', type=('build', 'run'))
depends_on('r-graph', type=('build', 'run'))

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@ -6,13 +6,25 @@
from spack import *
class RLfe(AutotoolsPackage):
"""Transforms away factors with many levels prior to doing an OLS"""
class RLfe(RPackage):
"""Linear Group Fixed Effects
Transforms away factors with many levels prior to doing an OLS. Useful for
estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure
control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024>
Includes support for instrumental variables, conditional F statistics for
weak instruments, robust and multi-way clustered standard errors, as well
as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>).
WARNING: This package is NOT under active development anymore, no further
improvements are to be expected, and the package is at risk of being
removed from CRAN."""
homepage = "https://cloud.r-project.org/package=lfe"
url = "https://cloud.r-project.org/src/contrib/lfe_2.8-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/lfe"
version('2.8-6', sha256='bf5fd362e9722e871a5236f30da562c489ae6506b667609b9465eefa8f101612')
version('2.8-5', sha256='fd80c573d334594db933ff38f67bd4c9f899aaf648c3bd68f19477a0059723c2')
version('2.8-4', sha256='ee5f6e312214aa73e285ae84a6bdf49ba10e830f1a68ffded2fea2e532f2cd6a')

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@ -28,6 +28,7 @@ class RLoo(RPackage):
version('2.3.1', sha256='d98de21b71d9d9386131ae5ba4da051362c3ad39e0305af4f33d830f299ae08b')
version('2.1.0', sha256='1bf4a1ef85d151577ff96d4cf2a29c9ef24370b0b1eb08c70dcf45884350e87d')
depends_on('r+X', type=('build', 'run'))
depends_on('r@3.1.2:', type=('build', 'run'))
depends_on('r-checkmate', type=('build', 'run'))
depends_on('r-matrixstats@0.52:', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RMagick(RPackage):
"""Bindings to 'ImageMagick': the most comprehensive open-source image
"""Advanced Graphics and Image-Processing in R
Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg,
tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur,
etc). All operations are vectorized via the Magick++ STL meaning they
@ -22,8 +24,10 @@ class RMagick(RPackage):
url = "https://cloud.r-project.org/src/contrib/magick_2.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/magick"
version('2.6.0', sha256='66585336e3ff18793ae9e2726af67a6672622f270468670ab5fe5e013bc48ecc')
version('2.1', sha256='ef4fb8fc1c5a9cfcc36b22485a0e17d622f61e55803b1e7423fd15f0550de7df')
depends_on('r+X', type=('build', 'run'))
depends_on('r-rcpp@0.12.12:', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-curl', type=('build', 'run'))

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@ -28,6 +28,7 @@ class RManipulatewidget(RPackage):
version('0.5.0', sha256='2599e25f78bb0d748705160e1dfe62a673f5bb388ac5f415f3d649d2511737c8')
version('0.4.0', sha256='65cc7d28c2b2efc81fda35da019ac6e6058580cf0fdf5e31458cc96386c0c599')
depends_on('r+X', type=('build', 'run'))
depends_on('r-shiny@1.0.3:', type=('build', 'run'))
depends_on('r-miniui', type=('build', 'run'))
depends_on('r-htmltools', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RMetap(RPackage):
"""The canonical way to perform meta-analysis involves using effect sizes.
"""Meta-Analysis of Significance Values
The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington,
Fisher, Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets
@ -17,7 +19,12 @@ class RMetap(RPackage):
url = "https://cloud.r-project.org/src/contrib/metap_1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/metap"
version('1.4', sha256='5fac23d823d0ad4eebc3f97620364e25f7b41f8d0c3579f6c09ec059940b85a5')
version('1.1', sha256='20120428672d39dc15829c7e66850fc4350a34df290d48cef0b1cc78d13f7b82')
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-rdpack', type=('build', 'run'))
depends_on('r-rdpack@0.7:', when='@1.4:', type=('build', 'run'))
depends_on('r-tfisher', when='@1.4:', type=('build', 'run'))
depends_on('r-mutoss', when='@1.4:', type=('build', 'run'))
depends_on('r-mathjaxr@0.8-3:', when='@1.4:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-mlrmbo/package.py
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@ -31,6 +31,7 @@ class RMlrmbo(RPackage):
version('1.1.1', sha256='e87d9912a9b4a968364584205b8ef6f7fea0b5aa043c8d31331a7b7be02dd7e4')
version('1.1.0', sha256='6ae82731a566333f06085ea2ce23ff2a1007029db46eea57d06194850350a8a0')
depends_on('r+X', type=('build', 'run'))
depends_on('r-mlr@2.10:', type=('build', 'run'))
depends_on('r-paramhelpers@1.10:', type=('build', 'run'))
depends_on('r-smoof@1.5.1:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-nanotime/package.py
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@ -7,18 +7,24 @@
class RNanotime(RPackage):
"""Full 64-bit resolution date and time support with resolution up to
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type."""
"""Nanosecond-Resolution Time Support for R
Full 64-bit resolution date and time support with resolution up to
nanosecond granularity is provided, with easy transition to and from the
standard 'POSIXct' type."""
homepage = "https://cloud.r-project.org/package=nanotime"
url = "https://cloud.r-project.org/src/contrib/nanotime_0.2.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/nanotime"
version('0.3.2', sha256='9ef53c3bca01b605a9519190117988e170e63865327007c90b05d31fe7f22b1d')
version('0.2.4', sha256='2dfb7e7435fec59634b87563a215467e7793e2711e302749c0533901c74eb184')
version('0.2.3', sha256='7d6df69a4223ae154f610b650e24ece38ce4aa706edfa38bec27d15473229f5d')
version('0.2.0', sha256='9ce420707dc4f0cb4241763579b849d842904a3aa0d88de8ffef334d08fa188d')
depends_on('r-bit64', type=('build', 'run'))
depends_on('r-rcppcctz@0.2.3:', type=('build', 'run'))
depends_on('r-rcppcctz@0.2.9:', when='@0.3.2:', type=('build', 'run'))
depends_on('r-zoo', type=('build', 'run'))
depends_on('r-rcpp', when='@0.3.2:', type=('build', 'run'))
depends_on('r-rcppdate', when='@0.3.2:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-ncdf4/package.py
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@ -7,7 +7,9 @@
class RNcdf4(RPackage):
"""Provides a high-level R interface to data files written using Unidata's
"""Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
Provides a high-level R interface to data files written using Unidata's
netCDF library (version 4 or earlier), which are binary data files that are
portable across platforms and include metadata information in addition to
the data sets. Using this package, netCDF files (either version 4 or
@ -26,6 +28,7 @@ class RNcdf4(RPackage):
url = "https://cloud.r-project.org/src/contrib/ncdf4_1.15.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ncdf4"
version('1.17', sha256='db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6')
version('1.16.1', sha256='0dde2d6d1e8474f4abd15a61af8a2f7de564f13da00f1a01d7a479ab88587a20')
version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253')
version('1.15', sha256='d58298f4317c6c80a041a70216126492fd09ba8ecde9da09d5145ae26f324d4d')

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var/spack/repos/builtin/packages/r-network/package.py
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@ -7,14 +7,17 @@
class RNetwork(RPackage):
"""Tools to create and modify network objects. The network class can
represent a range of relational data types, and supports
arbitrary vertex/edge/graph attributes."""
"""Classes for Relational Data
Tools to create and modify network objects. The network class can represent
a range of relational data types, and supports arbitrary vertex/edge/graph
attributes."""
homepage = "https://statnet.org"
url = "https://cloud.r-project.org/src/contrib/network_1.13.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/network"
version('1.16.1', sha256='eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1')
version('1.15', sha256='5cbe5c0369e5f8363e33a86f14fd33ce8727166106381627ecd13b7452e14cb3')
version('1.14-377', sha256='013c02f8d97f1f87f2c421760534df9353d2a8c2277f20b46b59fb79822d3e46')
version('1.13.0', sha256='7a04ea89261cdf32ccb52222810699d5fca59a849053e306b5ec9dd5c1184f87')

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@ -6,17 +6,29 @@
from spack import *
class RNimble(AutotoolsPackage):
"""A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to
operate models and do basic R-style math, and compiling both
models and nimbleFunctions via custom- generated C++.
"""
class RNimble(RPackage):
"""MCMC, Particle Filtering, and Programmable Hierarchical Modeling
A system for writing hierarchical statistical models largely compatible
with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do
basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte
Carlo Expectation Maximization, and some other tools. The nimbleFunction
system makes it easy to do things like implement new MCMC samplers from R,
customize the assignment of samplers to different parts of a model from R,
and compile the new samplers automatically via C++ alongside the samplers
'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it
extensible: New distributions and functions can be added, including as
calls to external compiled code. Although most people think of MCMC as the
main goal of the 'BUGS'/'JAGS' language for writing models, one can use
'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as
well. A full User Manual is available at <https://r-nimble.org>."""
homepage = "https://cloud.r-project.org/package=nimble"
url = "https://cloud.r-project.org/src/contrib/nimble_0.9.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/nimble"
version('0.10.1', sha256='11e248fda442f233c3590640efd9381c9b4b2e6fb66dce45a3391db03b70e702')
version('0.9.1', sha256='ad5e8a171193cb0172e68bf61c4f94432c45c131a150101ad1c5c7318c335757')
version('0.9.0', sha256='ebc28fadf933143eea73900cacaf96ff81cb3c2d607405016062b7e93afa5611')
@ -24,4 +36,4 @@ class RNimble(AutotoolsPackage):
depends_on('r-igraph', type=('build', 'run'))
depends_on('r-coda', type=('build', 'run'))
depends_on('r-r6', type=('build', 'run'))
depends_on('automake')
depends_on('gmake', type='build')

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var/spack/repos/builtin/packages/r-nlme/package.py
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@ -7,12 +7,15 @@
class RNlme(RPackage):
"""Fit and compare Gaussian linear and nonlinear mixed-effects models."""
"""Fit and compare Gaussian linear and nonlinear mixed-effects models
Fit and compare Gaussian linear and nonlinear mixed-effects models."""
homepage = "https://cloud.r-project.org/package=nlme"
url = "https://cloud.r-project.org/src/contrib/nlme_3.1-130.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/nlme"
version('3.1-151', sha256='a2c626bad68bf582663005170d1b9d844a10dca8efb13597f15ffb4b1fe886ca')
version('3.1-141', sha256='910046260a03d8f776ac7b0766b5adee91556829d0d8a70165b2c695ce038056')
version('3.1-139', sha256='0460fc69d85122177e7ef01bad665d56bcaf63d31bdbfdbdfdcba2c082085739')
version('3.1-131', sha256='79daa167eb9bc7d8dba506da4b24b5250665b051d4e0a51dfccbb0087fdb564c')

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@ -7,23 +7,27 @@
class RNloptr(RPackage):
"""nloptr is an R interface to NLopt. NLopt is a free/open-source
library for nonlinear optimization, providing a common interface
for a number of different free optimization routines available
online as well as original implementations of various other
algorithms. See http://ab-initio.mit.edu/wiki/index.php/NLopt
_Introduction for more information on the available algorithms.
During installation on Unix the NLopt code is downloaded and
compiled from the NLopt website."""
"""R Interface to NLopt
Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms. See
<http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction> for more
information on the available algorithms. During installation of nloptr on
Unix-based systems, the installer checks whether the NLopt library is
installed on the system. If the NLopt library cannot be found, the code is
compiled using the NLopt source included in the nloptr package."""
homepage = "https://cloud.r-project.org/package=nloptr"
url = "https://cloud.r-project.org/src/contrib/nloptr_1.0.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/nloptr"
version('1.2.2.2', sha256='e80ea9619ac18f4bfe44812198b40b9ae5c0ddf3f9cc91778f9ccc82168d1372')
version('1.2.1', sha256='1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97')
version('1.0.4', sha256='84225b993cb1ef7854edda9629858662cc8592b0d1344baadea4177486ece1eb')
depends_on('nlopt')
depends_on('nlopt@2.4.0:')
def configure_args(self):
include_flags = self.spec['nlopt'].headers.include_flags

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var/spack/repos/builtin/packages/r-nmf/package.py
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@ -7,17 +7,20 @@
class RNmf(RPackage):
"""Provides a framework to perform Non-negative Matrix Factorization (NMF).
"""Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
Provides a framework to perform Non-negative Matrix Factorization (NMF).
The package implements a set of already published algorithms and seeding
methods, and provides a framework to test, develop and plug new/custom
algorithms. Most of the built-in algorithms have been optimized in C++, and
the main interface function provides an easy way of performing parallel
computations on multicore machines.."""
computations on multicore machines."""
homepage = "http://renozao.github.io/NMF"
url = "https://cloud.r-project.org/src/contrib/NMF_0.21.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF"
version('0.23.0', sha256='0f0cca01b37bf46fce90d2e951df609d3d377908aa607825083fd0c47cc24753')
version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3')
depends_on('r@3.0.0:', type=('build', 'run'))
@ -34,3 +37,5 @@ class RNmf(RPackage):
depends_on('r-doparallel', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-biocmanager', when='@0.23.0', type=('build', 'run'))
depends_on('r-biobase', when='@0.23.0', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RNmof(RPackage):
"""Functions, examples and data from the book "Numerical Methods and
"""Numerical Methods and Optimization in Finance
Functions, examples and data from the book "Numerical Methods and
Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2011),
ISBN 978-0123756626. The package provides implementations of several
optimisation heuristics, such as Differential Evolution, Genetic Algorithms
@ -19,6 +21,7 @@ class RNmof(RPackage):
url = "https://cloud.r-project.org/src/contrib/NMOF_1.6-0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/NMOF"
version('2.2-2', sha256='e64472f89023f0d779a35df753747d750174ce89644a9142312a1d2dc6f24642')
version('1.6-0', sha256='5484cd43c28aaf23d560c2dde8bcd8dd440a205d2214eb50e02fe0bb42ec2755')
depends_on('r@2.14:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-nnet/package.py
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@ -7,13 +7,17 @@
class RNnet(RPackage):
"""Software for feed-forward neural networks with a single hidden layer,
"""Feed-Forward Neural Networks and Multinomial Log-Linear Models
Software for feed-forward neural networks with a single hidden layer,
and for multinomial log-linear models."""
homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
url = "https://cloud.r-project.org/src/contrib/nnet_7.3-12.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/nnet"
version('7.3-14', sha256='5d1b9e9764d74d16c651f18f949aa4e9e2995ba64633cbfa2c6a7355ae30f4af')
version('7.3-12', sha256='2723523e8581cc0e2215435ac773033577a16087a3f41d111757dd96b8c5559d')
depends_on('r@2.14:', type=('build', 'run'))
depends_on('r@3.0.0:', when='@7.3-14:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-np/package.py
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@ -7,7 +7,9 @@
class RNp(RPackage):
"""This package provides a variety of nonparametric (and semiparametric)
"""Nonparametric Kernel Smoothing Methods for Mixed Data Types
This package provides a variety of nonparametric (and semiparametric)
kernel methods that seamlessly handle a mix of continuous, unordered, and
ordered factor data types. We would like to gratefully acknowledge support
from the Natural Sciences and Engineering Research Council of Canada
@ -19,6 +21,7 @@ class RNp(RPackage):
url = "https://cloud.r-project.org/src/contrib/np_0.60-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/np"
version('0.60-10', sha256='a27b4bbca8b83a289c98920c1c8f5e9979ba9772086893252a4297dd2698081a')
version('0.60-9', sha256='fe31a8985f0b1a576a7775022b7131093b1c9a8337734136d5fcad85fa6592fc')
version('0.60-8', sha256='924c342feb2a862fa3871a45db5f8434dbbfb900cfc40c001a0872108a3a069e')
version('0.60-2', sha256='25d667fc1056899516584b9d5d933377e6f4694d8e5e868dd047db572b69417f')

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@ -7,13 +7,20 @@
class RNpsurv(RPackage):
"""Contains functions for non-parametric survival analysis of exact and
interval-censored observations."""
"""Nonparametric Survival Analysis
Non-parametric survival analysis of exact and interval-censored
observations. The methods implemented are developed by Wang (2007)
<doi:10.1111/j.1467-9868.2007.00583.x>, Wang (2008)
<doi:10.1016/j.csda.2007.10.018>, Wang and Taylor (2013)
<doi:10.1007/s11222-012-9341-9> and Wang and Fani (2018)
<doi:10.1007/s11222-017-9724-z>."""
homepage = "https://www.stat.auckland.ac.nz/~yongwang"
url = "https://cloud.r-project.org/src/contrib/npsurv_0.4-0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/npsurv"
version('0.5-0', sha256='bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6')
version('0.4-0', sha256='404cf7135dc40a04e9b81224a543307057a8278e11109ba1fcaa28e87c6204f3')
depends_on('r-lsei', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-openssl/package.py
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@ -7,7 +7,9 @@
class ROpenssl(RPackage):
"""Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey
"""Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey
parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521.
Cryptographic signatures can either be created and verified manually or via
x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric
@ -22,6 +24,7 @@ class ROpenssl(RPackage):
url = "https://cloud.r-project.org/src/contrib/openssl_0.9.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/openssl"
version('1.4.3', sha256='342001df8ecff5df2cdf757f123d35ea4b449751045f708b91f27c1be0d48269')
version('1.4.1', sha256='f7fbecc75254fc43297a95a4338c674ab9ba2ec056b59e027d16d23122161fc6')
version('1.3', sha256='1c83f4d529adc1f5ec40e477c690a8d5b0a42422f3e542f1fc39062dcfaca4bf')
version('0.9.7', sha256='697d9e86f99270163744538dc3dc4d19d00af89a8570a1d304b110e1d2650e9d')

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@ -7,7 +7,9 @@
class ROpenxlsx(RPackage):
"""Simplifies the creation of Excel .xlsx files by providing a high level
"""Read, Write and Edit xlsx Files
Simplifies the creation of Excel .xlsx files by providing a high level
interface to writing, styling and editing worksheets. Through the use of
'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect'
packages with the added benefit of removing the dependency on Java."""
@ -16,8 +18,10 @@ class ROpenxlsx(RPackage):
url = "https://cloud.r-project.org/src/contrib/openxlsx_4.1.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/openxlsx"
version('4.2.3', sha256='cdef89d826e50bef772af3e5eae935ca0316626a6e22f55f7631eac733b5e46f')
version('4.1.0.1', sha256='8b7011debe14714de035ef42797c8caa923162d5dc3cc3c2a299fc10eff3d4d1')
depends_on('r@3.3.0:', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-zip', type=('build', 'run'))
depends_on('r-stringi', when='@4.2.3:', type=('build', 'run'))

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@ -7,14 +7,17 @@
class ROptparse(RPackage):
"""A command line parser inspired by Python's 'optparse' library to be used
with Rscript to write "#!" shebang scripts that accept short and long
flag/options"""
"""Command Line Option Parser
A command line parser inspired by Python's 'optparse' library to be used
with Rscript to write "#!" shebang scripts that accept short and long
flag/options"""
homepage = "https://cloud.r-project.org/package=optparse"
url = "https://cloud.r-project.org/src/contrib/optparse_1.6.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/optparse"
version('1.6.6', sha256='51779d497146e9354b1153713d939e81551e08948c2b00e4b117b1377c0b60d0')
version('1.6.2', sha256='b5a5a49ae05005f20359868329b73daac83d50f5e088981dcf5c41399534377f')
version('1.6.1', sha256='819be3eff54cb7f3f18703eed9714fc655290ab8e169f87605433d069b597e13')
version('1.6.0', sha256='10e816bb8f5b08d52cfd3a0028903a8c62ef9cf7bfd85f9dae8af442e82bfbb4')

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@ -7,7 +7,9 @@
class ROrdinal(RPackage):
"""Implementation of cumulative link (mixed) models also known as ordered
"""Regression Models for Ordinal Data
Implementation of cumulative link (mixed) models also known as ordered
regression models, proportional odds models, proportional hazards models
for grouped survival times and ordered logit/probit/... models. Estimation
is via maximum likelihood and mixed models are fitted with the Laplace
@ -23,6 +25,7 @@ class ROrdinal(RPackage):
url = "https://cloud.r-project.org/src/contrib/ordinal_2019.4-25.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ordinal"
version('2019.12-10', sha256='7a41e7b7e852a8fa3e911f8859d36e5709ccec5ca42ee3de14a813b7aaac7725')
version('2019.4-25', sha256='2812ad7a123cae5dbe053d1fe5f2d9935afc799314077eac185c844e3c9d79df')
depends_on('r@2.13.0:', type=('build', 'run'))

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@ -8,14 +8,16 @@
class RPaleotree(RPackage):
"""Provides tools for transforming, a posteriori
time-scaling, and modifying phylogenies containing
extinct (i.e. fossil) lineages"""
"""Paleontological and Phylogenetic Analyses of Evolution
Provides tools for transforming, a posteriori time-scaling, and modifying
phylogenies containing extinct (i.e. fossil) lineages"""
homepage = "https://github.com/dwbapst/paleotree"
url = "https://cloud.r-project.org/src/contrib/paleotree_3.1.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/paleotree"
version('3.3.25', sha256='aa64b9120075581229439227a12db776d052b03eb5f9721692a16a9402ac8712')
version('3.3.0', sha256='f8f6b0228dd5290b251cad3a8626689442b5aa793d8f072c8c2c7813a063df90')
version('3.1.3', sha256='4c1cc8a5e171cbbbd88f78914f86d5e6d144ae573816fbeeff2ab54a814ec614')

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@ -7,17 +7,20 @@
class RParallelmap(RPackage):
"""Unified parallelization framework for multiple back-end, designed for
internal package and interactive usage. The main operation is a parallel
"map" over lists. Supports local, multicore, mpi and BatchJobs mode.
Allows "tagging" of the parallel operation with a level name that can be
later selected by the user to switch on parallel execution for exactly
this operation."""
"""Unified Interface to Parallelization Back-Ends
Unified parallelization framework for multiple back-end, designed for
internal package and interactive usage. The main operation is a parallel
"map" over lists. Supports local, multicore, mpi and BatchJobs mode.
Allows "tagging" of the parallel operation with a level name that can be
later selected by the user to switch on parallel execution for exactly this
operation."""
homepage = "https://github.com/berndbischl/parallelMap"
url = "https://cloud.r-project.org/src/contrib/parallelMap_1.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/parallelMap"
version('1.5.0', sha256='4afa727f4786279718cc799e45e91859a46f5cbc1ee652b0f47ae3b9f9d45e4e')
version('1.4', sha256='fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b')
version('1.3', sha256='a52d93572c1b85281e41d8e3c2db97dda5fce96c222e04171b4489ec5000cd08')

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class RParamhelpers(RPackage):
"""Functions for parameter descriptions and operations in black-box
optimization, tuning and machine learning. Parameters can be described
(type, constraints, defaults, etc.), combined to parameter sets and can
in general be programmed on. A useful OptPath object (archive) to log
function evaluations is also provided."""
"""Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
Functions for parameter descriptions and operations in black-box
optimization, tuning and machine learning. Parameters can be described
(type, constraints, defaults, etc.), combined to parameter sets and can in
general be programmed on. A useful OptPath object (archive) to log function
evaluations is also provided."""
homepage = "https://github.com/berndbischl/ParamHelpers"
url = "https://cloud.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ParamHelpers"
version('1.14', sha256='b17652d0a69de3241a69f20be4ad1bfe02c413328a17f3c1ac7b73886a6ba2eb')
version('1.12', sha256='b54db9e6608ba530345c380c757a60cb2b78ab08992a890b1a41914ce7abcc14')
version('1.11', sha256='1614f4c0842cf822befc01228ab7263417f3423dd6a1dc24347b14f8491637a0')
version('1.10', sha256='80629ba62e93b0b706bf2e451578b94fbb9c5b95ff109ecfb5b011bfe0a0fa5b')
depends_on('r-backports', when='@1.11:', type=('build', 'run'))
depends_on('r-bbmisc@1.10:', type=('build', 'run'))
depends_on('r-checkmate@1.8.2:', type=('build', 'run'))
depends_on('r-backports', when='@1.11:', type=('build', 'run'))
depends_on('r-fastmatch', when='@1.11:', type=('build', 'run'))

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@ -7,12 +7,30 @@
class RParty(RPackage):
"""A computational toolbox for recursive partitioning."""
"""A Laboratory for Recursive Partytioning
A computational toolbox for recursive partitioning. The core of the package
is ctree(), an implementation of conditional inference trees which embed
tree-structured regression models into a well defined theory of
conditional inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including nominal,
ordinal, numeric, censored as well as multivariate response variables and
arbitrary measurement scales of the covariates. Based on conditional
inference trees, cforest() provides an implementation of Breiman's random
forests. The function mob() implements an algorithm for recursive
partitioning based on parametric models (e.g. linear models, GLMs or
survival regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in Hothorn et al.
(2006) <doi:10.1198/106186006X133933>, Zeileis et al. (2008)
<doi:10.1198/106186008X319331> and Strobl et al. (2007)
<doi:10.1186/1471-2105-8-25>."""
homepage = "https://cloud.r-project.org/package=party"
url = "https://cloud.r-project.org/src/contrib/party_1.1-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/party"
version('1.3-5', sha256='1c3a35d3fe56498361542b3782de2326561c14a8fa1b76f3c9f13beb1fd51364')
version('1.3-3', sha256='9f72eea02d43a4cee105790ae7185b0478deb6011ab049cc9d31a0df3abf7ce9')
version('1.3-2', sha256='9f350fa21114151c49bccc3d5f8536dbc5a608cfd88f60461c9805a4c630510b')
version('1.1-2', sha256='c3632b4b02dc12ec949e2ee5b24004e4a4768b0bc9737432e9a85acbc2ed0e74')

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class RPartykit(RPackage):
"""A toolkit with infrastructure for representing, summarizing, and
"""A Toolkit for Recursive Partytioning
A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and
improved reimplementations of conditional inference trees (ctree()) and
model-based recursive partitioning (mob()) from the 'party' package are
provided based on the new infrastructure."""
provided based on the new infrastructure. A description of this package was
published by Hothorn and Zeileis (2015)
<https://jmlr.org/papers/v16/hothorn15a.html>."""
homepage = "http://partykit.r-forge.r-project.org/partykit"
url = "https://cloud.r-project.org/src/contrib/partykit_1.1-1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/partykit"
version('1.2-11', sha256='3a83332d782a235cfb5ba60cc8f1c51d46ca5477b22979a614f514d1c951c602')
version('1.2-5', sha256='f48e30790f93fa5d03e68e8ce71ce33d009d107d46d45d85da2016b38b27629c')
version('1.2-3', sha256='56749b246e283f94ac2ad2cdcfc0a477e05cd44b5e8f6e462c26f4dff818da35')
version('1.1-1', sha256='d9f4762690cd85ee4e3dc44f5a14069d10a1900afdfbcdc284d2a94b4a8e8332')
depends_on('r@3.1.0:', type=('build', 'run'))
depends_on('r-survival', type=('build', 'run'))
depends_on('r-formula@1.2-1:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@1.2-11:', type=('build', 'run'))
depends_on('r-libcoin@1.0-0:', when='@1.2-0:', type=('build', 'run'))
depends_on('r-mvtnorm', when='@1.2-0:', type=('build', 'run'))
depends_on('r-survival', type=('build', 'run'))
depends_on('r-formula@1.2-1:', type=('build', 'run'))
depends_on('r-inum@1.0-0:', when='@1.2-0:', type=('build', 'run'))
depends_on('r-rpart@4.1-11:', when='@1.2-0:', type=('build', 'run'))

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@ -0,0 +1,26 @@
# Copyright 2013-2021 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 RPatchwork(RPackage):
"""The Composer of Plots
The 'ggplot2' package provides a strong API for sequentially building up a
plot, but does not concern itself with composition of multiple plots.
'patchwork' is a package that expands the API to allow for arbitrarily
complex composition of plots by, among others, providing mathematical
operators for combining multiple plots. Other packages that try to address
this need (but with a different approach) are 'gridExtra' and 'cowplot'."""
homepage = "https://patchwork.data-imaginist.com/"
url = "https://cloud.r-project.org/src/contrib/patchwork_1.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/patchwork"
version('1.1.1', sha256='cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481')
depends_on('r-ggplot2@3.0.0:', type=('build', 'run'))
depends_on('r-gtable', type=('build', 'run'))

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class RPbapply(RPackage):
"""A lightweight package that adds progress bar to vectorized R
apply functions."""
"""Adding Progress Bar to '*apply' Functions
A lightweight package that adds progress bar to vectorized R functions
('*apply'). The implementation can easily be added to functions where
showing the progress is useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time) can be set through
options. Supports several parallel processing backends."""
homepage = "https://cloud.r-project.org/package=pbapply"
url = "https://cloud.r-project.org/src/contrib/pbapply_1.3-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pbapply"
version('1.4-3', sha256='8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21')
version('1.4-1', sha256='b3633349181db944e1dfc4422b4728a6562e454117a232cbb51633906cd27cad')
version('1.3-4', sha256='cdfdaf9b8aecbe48daac858aecaf65a766b74a363d1eb7cd6ebf27c0549f6552')
version('1.3-3', sha256='7379b21d1176db5769f5cac858dd12c975736e80a600870180cec9625cf51047')

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@ -8,7 +8,9 @@
class RPbdzmq(RPackage):
"""'ZeroMQ' is a well-known library for high-performance asynchronous
"""Programming with Big Data -- Interface to 'ZeroMQ'
'ZeroMQ' is a well-known library for high-performance asynchronous
messaging in scalable, distributed applications. This package provides
high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus
on interactive client/server programming frameworks. For convenience, a
@ -20,11 +22,13 @@ class RPbdzmq(RPackage):
url = "https://cloud.r-project.org/src/contrib/pbdZMQ_0.2-4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pbdZMQ"
version('0.3-4', sha256='07794bd6858e093f8b6b879ddd5ab0195449b47a41b70cab2f60603f0a53b129')
version('0.3-3', sha256='ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca')
version('0.3-2', sha256='ece2a2881c662f77126e4801ba4e01c991331842b0d636ce5a2b591b9de3fc37')
version('0.2-4', sha256='bfacac88b0d4156c70cf63fc4cb9969a950693996901a4fa3dcd59949ec065f6')
depends_on('r@3.0.0:', when='@:0.2-5', type=('build', 'run'))
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@0.3-4:', type=('build', 'run'))
depends_on('r-r6', when='@:0.2-6', type=('build', 'run'))
depends_on('libzmq@4.0.4:')

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class RPbkrtest(RPackage):
"""Test in mixed effects models. Attention is on mixed effects models as
implemented in the 'lme4' package. This package implements a parametric
bootstrap test and a Kenward Roger modification of F-tests for linear mixed
effects models and a parametric bootstrap test for generalized linear mixed
models."""
"""Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for
Test in Mixed Models
Test in mixed effects models. Attention is on mixed effects models as
implemented in the 'lme4' package. For linear mixed models, this package
implements (1) a parametric bootstrap test, (2) a Kenward-Roger-typ
modification of F-tests for linear mixed effects models and (3) a
Satterthwaite-type modification of F-tests for linear mixed effects models.
The package also implements a parametric bootstrap test for generalized
linear mixed models. The facilities of the package are documented in the
paper by Halehoh and Hojsgaard, (2012, <doi:10.18637/jss.v059.i09>).
Please see 'citation("pbkrtest")' for citation details."""
homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/"
url = "https://cloud.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pbkrtest"
version('0.5-0.1', sha256='f56525488c6efe4a5cbf849bf9a82747041478605b166c29bad54e464e46f469')
version('0.4-7', sha256='5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea')
version('0.4-6', sha256='9d28b8916fea3ffec8d5958bb8c531279b1e273f21fdbeb2fcad6d7e300a9c01')
version('0.4-4', sha256='a685392ef3fca0ddc2254f6cc9bba6bc22b298fa823359fc4515e64e753abd31')
depends_on('r@3.0.2:', when='@:0.4-5', type=('build', 'run'))
depends_on('r@3.0.2:', type=('build', 'run'))
depends_on('r@3.2.3:', when='@0.4-6:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@0.5-0.1:', type=('build', 'run'))
depends_on('r-lme4@1.1.10:', type=('build', 'run'))
depends_on('r-matrix@1.2.3:', type=('build', 'run'))
depends_on('r-broom', when='@0.5-0.1:', type=('build', 'run'))
depends_on('r-dplyr', when='@0.5-0.1:', type=('build', 'run'))
depends_on('r-magrittr', when='@0.5-0.1:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-matrix@1.2.3:', type=('build', 'run'))
depends_on('r-numderiv', when='@0.5-0.1:', type=('build', 'run'))
depends_on('r-knitr', when='@0.5-0.1:', type=('build', 'run'))

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class RPhytools(RPackage):
"""Phylogenetic Tools for Comparative Biology (and Other Things)"""
"""Phylogenetic Tools for Comparative Biology (and Other Things)
A wide range of functions for phylogenetic analysis. Functionality is
concentrated in phylogenetic comparative biology, but also includes
numerous methods for visualizing, manipulating, reading or writing, and
even inferring phylogenetic trees and data. Included among the functions in
phylogenetic comparative biology are various for ancestral state
reconstruction, model-fitting, simulation of phylogenies and data, and
multivariate analysis. There are a broad range of plotting methods for
phylogenies and comparative data which include, but are not restricted to,
methods for mapping trait evolution on trees, for projecting trees into
phenotypic space or a geographic map, and for visualizing correlated
speciation between trees. Finally, there are a number of functions for
reading, writing, analyzing, inferring, simulating, and manipulating
phylogenetic trees and comparative data not covered by other packages. For
instance, there are functions for randomly or non-randomly attaching
species or clades to a phylogeny, for estimating supertrees or consensus
phylogenies from a set, for simulating trees and phylogenetic data under a
range of models, and for a wide variety of other manipulations and analyses
that phylogenetic biologists might find useful in their research."""
homepage = "http://github.com/liamrevell/phytools"
url = "https://cloud.r-project.org/src/contrib/phytools_0.6-60.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/phytools/"
version('0.7-70', sha256='e3432c3b006e5cc6f1292bebd81ebc20044edf1f56c3d27a3497f738eb99f0d3')
version('0.6-99', sha256='2ef532cba77c5f73803bd34582bef05709705311a0b50e42316e69944567390f')
version('0.6-60', sha256='55cad759510d247ebbf03a53a46caddadd3bf87584ccf7fcd6dd06d44516b377')
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r-animation', type=('build', 'run'))
depends_on('r@3.5.0:', when='@0.7-70:', type=('build', 'run'))
depends_on('r-ape@4.0:', type=('build', 'run'))
depends_on('r-maps', type=('build', 'run'))
depends_on('r-clustergeneration', type=('build', 'run'))
depends_on('r-coda', type=('build', 'run'))
depends_on('r-combinat', type=('build', 'run'))
depends_on('r-expm', type=('build', 'run'))
depends_on('r-gtools', when='@0.6-99:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-maps', type=('build', 'run'))
depends_on('r-mnormt', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-numderiv', type=('build', 'run'))
depends_on('r-phangorn@2.3.1:', type=('build', 'run'))
depends_on('r-plotrix', type=('build', 'run'))
depends_on('r-scatterplot3d', type=('build', 'run'))
depends_on('r-gtools', when='@0.6-99:', type=('build', 'run'))
depends_on('r-animation', when='@:0.6-99', type=('build', 'run'))

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@ -7,17 +7,27 @@
class RPicante(RPackage):
"""R tools for integrating phylogenies and ecology"""
"""R tools for integrating phylogenies and ecology
Functions for phylocom integration, community analyses, null-models, traits
and evolution. Implements numerous ecophylogenetic approaches including
measures of community phylogenetic and trait diversity, phylogenetic
signal, estimation of trait values for unobserved taxa, null models for
community and phylogeny randomizations, and utility functions for data
input/output and phylogeny plotting. A full description of package
functionality and methods are provided by Kembel et al. (2010)
<doi:10.1093/bioinformatics/btq166>."""
homepage = "https://cloud.r-project.org/package=picante"
url = "https://cloud.r-project.org/src/contrib/picante_1.6-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/picante"
version('1.8.2', sha256='56565ca7f7c37f49c961372a816724967c21a4f5025cd69b8b671122bfdc4aa7')
version('1.8', sha256='81a6308dbb53c9cdab30c1f9ac727abee76314351823b3a2142c21ed8e1498ad')
version('1.7', sha256='75e4d73080db67e776562a1d58685438461cbde39af46900c7838da56aef0a62')
version('1.6-2', sha256='4db3a5a0fe5e4e9197c96245195843294fbb8d0a324edcde70c6ab01276ab7ff')
version('1.6-1', sha256='2708315b26737857a6729fd67bde06bc939930035c5b09a8bba472a593f24000')
depends_on('r-ape', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-vegan', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))

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@ -7,13 +7,16 @@
class RPillar(RPackage):
"""Provides a 'pillar' generic designed for formatting columns of data
using the full range of colours provided by modern terminals."""
"""Coloured Formatting for Columns
Provides a 'pillar' generic designed for formatting columns of data using
the full range of colours provided by modern terminals."""
homepage = "https://cloud.r-project.org/package=pillar"
url = "https://cloud.r-project.org/src/contrib/pillar_1.3.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pillar"
version('1.4.7', sha256='cdedb2b2a4854e917f43b0c6379efefda9d7ff4e58dec2a3159a80ee8288f298')
version('1.4.2', sha256='bababb76b6db06dc32ccd947dbad6c164a1749ff5b558c6783ad03570f010825')
version('1.4.1', sha256='f571ca7a3ef0927747510b972da31a26da24b9da68990fe1bbc9d4ae58028c55')
version('1.3.1', sha256='b338b55f956dd7134f379d39bb94dfb25e13cf27999d6a6e6dc9f292755acbf6')
@ -28,7 +31,10 @@ class RPillar(RPackage):
depends_on('r-cli', type=('build', 'run'))
depends_on('r-crayon@1.3.4:', type=('build', 'run'))
depends_on('r-ellipsis', when='@1.4.7:', type=('build', 'run'))
depends_on('r-fansi', type=('build', 'run'))
depends_on('r-lifecycle', when='@1.4.7:', type=('build', 'run'))
depends_on('r-rlang@0.3.0:', type=('build', 'run'))
depends_on('r-utf8@1.1.0:', type=('build', 'run'))
depends_on('r-vctrs', when='@1.4.0:', type=('build', 'run'))
depends_on('r-vctrs@0.2.0:', when='@1.4.7:', type=('build', 'run'))

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@ -7,13 +7,15 @@
class RPkgconfig(RPackage):
"""Set configuration options on a per-package basis. Options set by a
given package only apply to that package,
other packages are unaffected."""
"""Private Configuration for 'R' Packages
Set configuration options on a per-package basis. Options set by a given
package only apply to that package, other packages are unaffected."""
homepage = "https://cloud.r-project.org/package=pkgconfig"
url = "https://cloud.r-project.org/src/contrib/pkgconfig_2.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgconfig"
version('2.0.3', sha256='330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850')
version('2.0.2', sha256='25997754d1adbe7a251e3bf9879bb52dced27dd8b84767d558f0f644ca8d69ca')
version('2.0.1', sha256='ab02b2a4b639ba94dcba882a059fe9cddae5498a4309841f764b62ec46ba5a40')

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@ -7,7 +7,9 @@
class RPkgmaker(RPackage):
"""This package provides some low-level utilities to use for package
"""Development Utilities for R Packages
This package provides some low-level utilities to use for package
development. It currently provides managers for multiple package specific
options and registries, vignette, unit test and bibtex related utilities.
It serves as a base package for packages like NMF, RcppOctave, doRNG, and
@ -19,15 +21,17 @@ class RPkgmaker(RPackage):
url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.27.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker"
version('0.32.2', sha256='ce45b22def771a9c90a414093823e6befe7e23489c500eeccee5154b44d3ef91')
version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-registry', type=('build', 'run'))
depends_on('r-codetools', type=('build', 'run'))
depends_on('r-digest', type=('build', 'run'))
depends_on('r-stringi', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-xtable', type=('build', 'run'))
depends_on('r-withr', type=('build', 'run'))
depends_on('r-bibtex@0.4:', type=('build', 'run'))
depends_on('r-assertthat', when='@0.32.2:', type=('build', 'run'))
depends_on('r-stringi', when='@:0.27', type=('build', 'run'))
depends_on('r-magrittr', when='@:0.27', type=('build', 'run'))
depends_on('r-bibtex@0.4:', when='@:0.27', type=('build', 'run'))

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@ -7,15 +7,19 @@
class RPlot3d(RPackage):
"""Functions for viewing 2-D and 3-D data, including perspective plots,
slice plots, surface plots, scatter plots, etc. Includes data sets from
oceanography."""
"""Plotting Multi-Dimensional Data
Functions for viewing 2-D and 3-D data, including perspective plots, slice
plots, surface plots, scatter plots, etc. Includes data sets from
oceanography."""
homepage = "https://cloud.r-project.org/package=plot3D"
url = "https://cloud.r-project.org/src/contrib/plot3D_1.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/plot3D"
version('1.3', sha256='b9e4ec2789e34ad249318900e186868650e1a33466b385cb492a45466db3dfc9')
version('1.1.1', sha256='f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632')
depends_on('r+X', type=('build', 'run'))
depends_on('r@2.15:', type=('build', 'run'))
depends_on('r-misc3d', type=('build', 'run'))

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@ -7,13 +7,17 @@
class RPlotly(RPackage):
"""Easily translate 'ggplot2' graphs to an interactive web-based version
and/or create custom web-based visualizations directly from R."""
"""Create Interactive Web Graphics via 'plotly.js'
Create interactive web graphics from 'ggplot2' graphs and/or a custom
interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by
the grammar of graphics."""
homepage = "https://cloud.r-project.org/package=plotly"
url = "https://cloud.r-project.org/src/contrib/plotly_4.7.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/plotly"
version('4.9.3', sha256='d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120')
version('4.9.0', sha256='f761148338231f210fd7fe2f8325ffe9cfdaaaeddd7b933b65c44ebb4f85e2cf')
version('4.8.0', sha256='78f90282c831bbbb675ed4811fb506a98dd05e37251fabd42ebc263c80bae8a6')
version('4.7.1', sha256='7cd4b040f9bfd9356a8a2aba59ccf318cae6b5d94ded7463e2e823c10fa74972')
@ -24,24 +28,26 @@ class RPlotly(RPackage):
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r-ggplot2@3.0.0:', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-base64enc', type=('build', 'run'))
depends_on('r-htmltools@0.3.6:', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-htmlwidgets@1.3:', type=('build', 'run'))
depends_on('r-data-table', type=('build', 'run'))
depends_on('r-hexbin', type=('build', 'run'))
depends_on('r-purrr', type=('build', 'run'))
depends_on('r-crosstalk', when='@4.6.0:', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-httr@1.3.0:', when='@4.9.3:', type=('build', 'run'))
depends_on('r-jsonlite@1.6:', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-digest', type=('build', 'run'))
depends_on('r-viridislite', type=('build', 'run'))
depends_on('r-base64enc', type=('build', 'run'))
depends_on('r-htmltools@0.3.6:', type=('build', 'run'))
depends_on('r-htmlwidgets@1.3:', type=('build', 'run'))
depends_on('r-htmlwidgets@1.5.2.9001:', when='@4.9.3:', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-rcolorbrewer', when='@4.6.0:', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-vctrs', when='@4.9.3:', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'))
depends_on('r-lazyeval@0.2.0:', type=('build', 'run'))
depends_on('r-rcolorbrewer', when='@4.6.0:', type=('build', 'run'))
depends_on('r-data-table', when='@4.7.0:', type=('build', 'run'))
depends_on('r-rlang', when='@4.8.0:', type=('build', 'run'))
depends_on('r-crosstalk', when='@4.6.0:', type=('build', 'run'))
depends_on('r-purrr', type=('build', 'run'))
depends_on('r-data-table', when='@4.7.0:', type=('build', 'run'))
depends_on('r-promises', when='@4.8.0:', type=('build', 'run'))
depends_on('r-hexbin', when='@:4.9.0', type=('build', 'run'))

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@ -7,12 +7,15 @@
class RPlotrix(RPackage):
"""Lots of plots, various labeling, axis and color scaling functions."""
"""Various Plotting Functions
Lots of plots, various labeling, axis and color scaling functions."""
homepage = "https://cloud.r-project.org/package=plotrix"
url = "https://cloud.r-project.org/src/contrib/plotrix_3.6-4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/plotrix"
version('3.7-8', sha256='8ccd1f7e656413b9956cea614c986ce9cc61366deba356afb38cee6672a59480')
version('3.7-6', sha256='83d5f7574592953288b4fe39c4c0dd7670d097598ad7f6bddbb0687a32954e46')
version('3.7-5', sha256='b22f3f9d93961d23ad46e41597d1e45d2665ced04dcad8c40f6806a67cded14c')
version('3.6-4', sha256='883b7d0a00c1b2b418f9167c72ed9e86eca3c9865d34158a7a6ad0b9bf95bff3')

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@ -7,7 +7,9 @@
class RPls(RPackage):
"""Multivariate regression methods Partial Least Squares Regression (PLSR),
"""Partial Least Squares and Principal Component Regression
Multivariate regression methods Partial Least Squares Regression (PLSR),
Principal Component Regression (PCR) and Canonical Powered Partial Least
Squares (CPPLS)."""
@ -15,6 +17,7 @@ class RPls(RPackage):
url = "https://cloud.r-project.org/src/contrib/pls_2.6-0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pls"
version('2.7-3', sha256='8f1d960ab74f05fdd11c4c7a3d30ff9e263fc658f5690b67278ca7c045d0742c')
version('2.7-1', sha256='f8fd817fc2aa046970c49a9a481489a3a2aef8b6f09293fb1f0218f00bfd834b')
version('2.7-0', sha256='5ddc1249a14d69a7a39cc4ae81595ac8c0fbb1e46c911af67907baddeac35875')
version('2.6-0', sha256='3d8708fb7f45863d3861fd231e06955e6750bcbe717e1ccfcc6d66d0cb4d4596')

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@ -7,7 +7,9 @@
class RPlyr(RPackage):
"""A set of tools that solves a common set of problems: you need to break a
"""Tools for Splitting, Applying and Combining Data
A set of tools that solves a common set of problems: you need to break a
big problem down into manageable pieces, operate on each piece and then put
all the pieces back together. For example, you might want to fit a model to
each spatial location or time point in your study, summarise data by panels
@ -19,6 +21,7 @@ class RPlyr(RPackage):
url = "https://cloud.r-project.org/src/contrib/plyr_1.8.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/plyr"
version('1.8.6', sha256='ea55d26f155443e9774769531daa5d4c20a0697bb53abd832e891b126c935287')
version('1.8.4', sha256='60b522d75961007658c9806f8394db27989f1154727cb0bb970062c96ec9eac5')
depends_on('r@3.1.0:', type=('build', 'run'))

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@ -7,15 +7,17 @@
class RPolspline(RPackage):
"""Routines for the polynomial spline fitting routines hazard regression,
hazard estimation with flexible tails, logspline, lspec, polyclass,
and polymars, by C. Kooperberg and co-authors.
"""
"""Polynomial Spline Routines
Routines for the polynomial spline fitting routines hazard regression,
hazard estimation with flexible tails, logspline, lspec, polyclass, and
polymars, by C. Kooperberg and co-authors."""
homepage = "https://cloud.r-project.org/package=polspline"
url = "https://cloud.r-project.org/src/contrib/polspline_1.1.18.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/polspline"
version('1.1.19', sha256='953e3c4d007c3ef86ac2af3c71b272a99e8e35b194bdd58575785558c6711f66')
version('1.1.18', sha256='df250ee144bfff154249ba50308f46863107ef3efb2333ad908e599ed0eb0102')
version('1.1.17', sha256='d67b269d01105d4a6ea774737e921e66e065a859d1931ae38a70f88b6fb7ee30')
version('1.1.16', sha256='aa3b5a1560008a1a401a65a25f19a27ba6f0a6ea185b6d093acd40e4e2818934')

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@ -7,16 +7,23 @@
class RPopgenome(RPackage):
"""PopGenome is an efficient Swiss army knife for population genetics data
analysis, able to process individual loci, large sets of loci, or whole
genomes."""
"""An Efficient Swiss Army Knife for Population Genomic Analyses
Provides efficient tools for population genomics data analysis, able to
process individual loci, large sets of loci, or whole genomes. PopGenome
<DOI:10.1093/molbev/msu136> not only implements a wide range of population
genetics statistics, but also facilitates the easy implementation of new
algorithms by other researchers. PopGenome is optimized for speed via the
seamless integration of C code."""
homepage = "https://popgenome.weebly.com"
url = "https://cloud.r-project.org/src/contrib/PopGenome_2.6.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/PopGenome"
version('2.7.5', sha256='d627b8ac87b4db6038d7349b2df20648d2fcfd48e2dafcd7f4731d1b607cbc75')
version('2.7.1', sha256='a84903b151528fa026ccaba42ada22cd89babbc1824afd40269b7204e488a5fa')
version('2.6.1', sha256='7a2922ed505fa801117a153e479d246bcf4854b91c6ab0241acc620a9d779b1c')
depends_on('r@2.14.2:', type=('build', 'run'))
depends_on('r-ff', type=('build', 'run'))
depends_on('zlib')

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@ -7,18 +7,22 @@
class RPowerlaw(RPackage):
"""An implementation of maximum likelihood estimators for a variety of
heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach
is used to estimate the lower cut-off for the scaling region."""
"""Analysis of Heavy Tailed Distributions
An implementation of maximum likelihood estimators for a variety of heavy
tailed distributions, including both the discrete and continuous power law
distributions. Additionally, a goodness-of-fit based approach is used to
estimate the lower cut-off for the scaling region."""
homepage = "https://github.com/csgillespie/poweRlaw"
url = "https://cloud.r-project.org/src/contrib/poweRlaw_0.70.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/poweRlaw"
version('0.70.6', sha256='efc091449c5c6494c1c13c85a8eb95625d1c55ffffebe86c7ea16e4abbafa191')
version('0.70.2', sha256='240f1454389b1a00ad483fb63e5b53243cc9367f21a3e7253ab2c293673459ab')
version('0.70.1', sha256='15b1b8dadeb550c01b9f1308cfa64720be6fbf56afb80f6a096987d6a0055913')
depends_on('r@3.1.0:', when='@:0.70.1', type=('build', 'run'))
depends_on('r@3.4.0:', when='@0.70.2:', type=('build', 'run'))
depends_on('r-vgam', type=('build', 'run'))
depends_on('r-pracma', when='@0.70.6:', type=('build', 'run'))
depends_on('r-vgam', when='@:0.70.2', type=('build', 'run'))

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@ -8,12 +8,20 @@
class RPrabclus(RPackage):
"""prabclus: Functions for Clustering of Presence-Absence, Abundance and
Multilocus Genetic Data"""
Multilocus Genetic Data
Distance-based parametric bootstrap tests for clustering with spatial
neighborhood information. Some distance measures, Clustering of
presence-absence, abundance and multilocus genetic data for species
delimitation, nearest neighbor based noise detection. Genetic distances
between communities. Tests whether various distance-based regressions are
equal. Try package?prabclus for on overview."""
homepage = "http://www.homepages.ucl.ac.uk/~ucakche"
url = "https://cloud.r-project.org/src/contrib/prabclus_2.2-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/prabclus"
version('2.3-2', sha256='f421bcbcb557281e0de4a06b15f9a496adb5c640e883c0f7bb12051efc69e441')
version('2.3-1', sha256='ef3294767d43bc3f72478fdaf0d1f13c8de18881bf9040c9f1add68af808b3c0')
version('2.2-7.1', sha256='2c5bf3bbb0d225e04c53bb0e11e9c2a6809f0e46d95b8f6dc14b9dd6a2452975')
version('2.2-6', sha256='41792980e40ba18204fab92d85120dcd468860e2204e52fb42636c6f7aee5a62')

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@ -0,0 +1,23 @@
# Copyright 2013-2021 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 RPracma(RPackage):
"""Practical Numerical Math Functions
Provides a large number of functions from numerical analysis and linear
algebra, numerical optimization, differential equations, time series, plus
some well-known special mathematical functions. Uses 'MATLAB' function
names where appropriate to simplify porting."""
homepage = "https://cloud.r-project.org/package=pracma"
url = "https://cloud.r-project.org/src/contrib/pracma_2.2.9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/pracma"
version('2.2.9', sha256='0cea0ff5e88643df121e07b9aebfe57084c61e11801680039752f371fe87bf1e')
depends_on('r@3.1.0:', type=('build', 'run'))

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@ -7,15 +7,18 @@
class RPrettyunits(RPackage):
"""Pretty, human readable formatting of quantities. Time intervals:
1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about
a month ago. Bytes: 1337 -> 1.34 kB."""
"""Pretty, Human Readable Formatting of Quantities
Pretty, human readable formatting of quantities. Time intervals: 1337000 ->
15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes:
1337 -> 1.34 kB."""
homepage = "https://cloud.r-project.org/package=prettyunits"
url = "https://cloud.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/prettyunits"
version('1.1.1', sha256='9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5')
version('1.0.2', sha256='35a4980586c20650538ae1e4fed4d80fdde3f212b98546fc3c7d9469a1207f5c')
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-assertthat', type=('build', 'run'))
depends_on('r-magrittr', when='@:1.0.2', type=('build', 'run'))
depends_on('r-assertthat', when='@:1.0.2', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RProdlim(RPackage):
"""Product-Limit Estimation for Censored Event History Analysis. Fast and
"""Product-Limit Estimation for Censored Event History Analysis
Product-Limit Estimation for Censored Event History Analysis. Fast and
user friendly implementation of nonparametric estimators for censored event
history (survival) analysis. Kaplan-Meier and Aalen-Johansen method."""
@ -15,6 +17,7 @@ class RProdlim(RPackage):
url = "https://cloud.r-project.org/src/contrib/prodlim_1.5.9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/prodlim"
version('2019.11.13', sha256='6809924f503a14681de84730489cdaf9240d7951c64f5b98ca37dc1ce7809b0f')
version('2018.04.18', sha256='4b22b54fdf712439309be0ff74f63cde9080464667b00e19823372ac0fc254ab')
version('1.6.1', sha256='3f2665257118a3db8682731a500b1ae4d669af344672dc2037f987bee3cca154')
version('1.5.9', sha256='853644886c57102e7f6dd26b6e03e54bf3f9e126f54c76f8d63a3324811f7b42')

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@ -7,21 +7,17 @@
class RProj(RPackage):
"""A wrapper around the generic coordinate transformation software 'PROJ'
that transforms geospatial coordinates from one coordinate reference system
('CRS') to another. This includes cartographic projections as well as
geodetic transformations. Version 6.0.0 or higher is required. The
intention is for this package to be used by user-packages such as 'reproj',
and that the older 'PROJ.4' and version 5 pathways be provided by the
legacy package. The 'PROJ' library is available from
<https://proj.org/>."""
"""Generic Coordinate System Transformations Using 'PROJ'
Currently non-operational, a harmless wrapper to allow package 'reproj' to
install and function while relying on the 'proj4' package."""
homepage = "https://github.com/hypertidy/PROJ"
url = "https://cloud.r-project.org/src/contrib/PROJ_0.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/PROJ"
version('0.4.0', sha256='dde90cfeca83864e61a7422e1573d2d55bb0377c32b9a8f550f47b8631121ce7')
version('0.1.0', sha256='5186f221335e8092bbcd4d82bd323ee7e752c7c9cf83d3f94e4567e0b407aa6f')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('proj@6:')
depends_on('r@3.0.2:', when='@0.4.0:', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RProj4(RPackage):
"""A simple interface to lat/long projection and datum transformation of
"""A simple interface to the PROJ.4 cartographic projections library
A simple interface to lat/long projection and datum transformation of
the PROJ.4 cartographic projections library. It allows transformation of
geographic coordinates from one projection and/or datum to another."""
@ -15,8 +17,8 @@ class RProj4(RPackage):
url = "https://cloud.r-project.org/src/contrib/proj4_1.0-8.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/proj4"
version('1.0-10', sha256='5f396f172a17cfa9821a390f11ff7d3bff3c92ccf585572116dec459c621d1d0')
version('1.0-8.1', sha256='a3a2a8f0014fd79fa34b5957440fd38299d8e97f1a802a61a068a6c6cda10a7e')
depends_on('r@2.0.0:', type=('build', 'run'))
depends_on('proj@:5')
depends_on('proj@4.4.6:5')

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@ -7,7 +7,9 @@
class RPromises(RPackage):
"""Provides fundamental abstractions for doing asynchronous programming in
"""Abstractions for Promise-Based Asynchronous Programming
Provides fundamental abstractions for doing asynchronous programming in
R using promises. Asynchronous programming is useful for allowing a single
R process to orchestrate multiple tasks in the background while also
attending to something else. Semantics are similar to 'JavaScript'
@ -17,6 +19,7 @@ class RPromises(RPackage):
url = "https://cloud.r-project.org/src/contrib/promises_1.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/promises"
version('1.1.1', sha256='3718c6eb2c3362cbe89389e613118f783f9977dbf24757f85026e661199c5800')
version('1.0.1', sha256='c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558')
depends_on('r-r6', type=('build', 'run'))

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@ -7,16 +7,18 @@
class RProxy(RPackage):
"""Provides an extensible framework for the efficient calculation of
auto- and cross-proximities, along with implementations of the most
popular ones."""
"""Distance and Similarity Measures
Provides an extensible framework for the efficient calculation of auto- and
cross-proximities, along with implementations of the most popular ones."""
homepage = "https://cloud.r-project.org/package=proxy"
url = "https://cloud.r-project.org/src/contrib/proxy_0.4-19.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/proxy"
version('0.4-24', sha256='8cff9bf036475941a7c44ba9bb5e2f6d4777d49ab3daaeb52d23f4b2af6d9c7c')
version('0.4-23', sha256='9dd4eb0978f40e4fcb55c8a8a26266d32eff9c63ac9dfe70cf1f664ca9c3669d')
version('0.4-19', sha256='6b27e275018366e6024382704da9a9757c8878535dbcd7d450824b70e2e34d51')
depends_on('r@3.3.2:', when='@:0.4-20', type=('build', 'run'))
depends_on('r@3.3.2:', type=('build', 'run'))
depends_on('r@3.4.0:', when='@0.4-21:', type=('build', 'run'))

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@ -7,12 +7,16 @@
class RPs(RPackage):
"""Manipulate processes on Windows, Linux and MacOS"""
"""List, Query, Manipulate System Processes
List, query and manipulate all system processes, on 'Windows', 'Linux' and
'macOS'."""
homepage = "https://github.com/r-lib/ps"
url = "https://cloud.r-project.org/src/contrib/ps_1.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ps"
version('1.5.0', sha256='7461a196f55557feda569a9791ad851c884f9a2dd71671655ed17cb048fafe96')
version('1.3.0', sha256='289193d0ccd2db0b6fe8702e8c5711e935219b17f90f01a6e9684982413e98d1')
version('1.2.1', sha256='bd7207164e6557a9e4213c4b00dc5dc23d7705ab290569765998640b16a3beff')
version('1.1.0', sha256='5d5240d5bf1d48c721b3fdf47cfc9dbf878e388ea1f057b764db05bffdc4a9fe')

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@ -7,33 +7,34 @@
class RPsych(RPackage):
"""A general purpose toolbox for personality, psychometric theory and
experimental psychology. Functions are primarily for multivariate
analysis and scale construction using factor analysis, principal
component analysis, cluster analysis and reliability analysis, although
others provide basic descriptive statistics. Item Response Theory is
done using factor analysis of tetrachoric and polychoric correlations.
Functions for analyzing data at multiple levels include within and
between group statistics, including correlations and factor analysis.
Functions for simulating and testing particular item and test structures
are included. Several functions serve as a useful front end for
structural equation modeling. Graphical displays of path diagrams,
factor analysis and structural equation models are created using basic
graphics. Some of the functions are written to support a book on
psychometric theory as well as publications in personality research.
For more information, see the <http://personality-project.org/r> web
page."""
"""Procedures for Psychological, Psychometric, and Personality Research
A general purpose toolbox for personality, psychometric theory and
experimental psychology. Functions are primarily for multivariate analysis
and scale construction using factor analysis, principal component analysis,
cluster analysis and reliability analysis, although others provide basic
descriptive statistics. Item Response Theory is done using factor analysis
of tetrachoric and polychoric correlations. Functions for analyzing data
at multiple levels include within and between group statistics, including
correlations and factor analysis. Functions for simulating and testing
particular item and test structures are included. Several functions serve
as a useful front end for structural equation modeling. Graphical displays
of path diagrams, factor analysis and structural equation models are
created using basic graphics. Some of the functions are written to support
a book on psychometric theory as well as publications in personality
research. For more information, see the <http://personality-project.org/r>
web page."""
homepage = "http://personality-project.org/r/psych"
url = "https://cloud.r-project.org/src/contrib/psych_1.7.8.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/psych"
version('2.0.12', sha256='8a71d4a1d8bc8c96703f9b4515cfb497e1947c6e017cb08270a7cfb36ce1ad4c')
version('1.8.12', sha256='6e175e049bc1ee5b79a9e51ccafb22b962b4e6c839ce5c9cfa1ad83967037743')
version('1.8.10', sha256='e8901ddab14729bfccbd82a8824fbb6523c10c2cd8fb7199b1ca56a7ffcb6e58')
version('1.7.8', sha256='f328ea602e22b0e7e5f310a8d19f305d8e0a3a86040cdfb64863b68b56d55135')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-mnormt', type=('build', 'run'))
depends_on('r-foreign', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-foreign', when='@:1.8.12', type=('build', 'run'))

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class RPtw(RPackage):
"""Parametric Time Warping aligns patterns, i.e. it aims to put
corresponding features at the same locations. The algorithm
searches for an optimal polynomial describing the warping. It is
possible to align one sample to a reference, several samples to
the same reference, or several samples to several references.
One can choose between calculating individual warpings, or one
global warping for a set of samples and one reference. Two
optimization criteria are implemented: RMS (Root Mean Square
error) and WCC (Weighted Cross Correlation). Both warping of
peak profiles and of peak lists are supported."""
"""Parametric Time Warping
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding
features at the same locations. The algorithm searches for an optimal
polynomial describing the warping. It is possible to align one sample to a
reference, several samples to the same reference, or several samples to
several references. One can choose between calculating individual warpings,
or one global warping for a set of samples and one reference. Two
optimization criteria are implemented: RMS (Root Mean Square error) and WCC
(Weighted Cross Correlation). Both warping of peak profiles and of peak
lists are supported. A vignette for the latter is contained in the inst/doc
directory of the source package - the vignette source can be found on the
package github site."""
homepage = "https://cloud.r-project.org/package=ptw"
url = "https://cloud.r-project.org/src/contrib/ptw_1.9-12.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ptw"
version('1.9-15', sha256='22fa003f280bc000f46bca88d69bf332b29bc68435115ba8044533b70bfb7b46')
version('1.9-13', sha256='7855e74a167db3d3eba9df9d9c3daa25d7cf487cbcfe8b095f16d96eba862f46')
version('1.9-12', sha256='cdb1752e04e661e379f11867b0a17e2177e9ee647c54bbcc37d39d6b8c062b84')

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class RQtl(RPackage):
"""qtl: Tools for Analyzing QTL Experiments"""
"""Tools for Analyzing QTL Experiments
Analysis of experimental crosses to identify genes (called quantitative
trait loci, QTLs) contributing to variation in quantitative traits. Broman
et al. (2003) <doi:10.1093/bioinformatics/btg112>."""
homepage = "http://rqtl.org"
url = "https://cloud.r-project.org/src/contrib/qtl_1.44-9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/qtl"
version('1.47-9', sha256='6ba4e7b40d946b3ab68d54624599284b1d352c86fb50d31b134826be758ece41')
version('1.44-9', sha256='315063f0c3fbb95cd2169eb4109ade0339e8f3c28670b38c3167214b9bdf950e')
depends_on('r@2.14.0:', type=('build', 'run'))

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@ -7,13 +7,16 @@
class RQuadprog(RPackage):
"""This package contains routines and documentation for solving
quadratic programming problems."""
"""Functions to Solve Quadratic Programming Problems
This package contains routines and documentation for solving quadratic
programming problems."""
homepage = "https://cloud.r-project.org/package=quadprog"
url = "https://cloud.r-project.org/src/contrib/quadprog_1.5-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/quadprog"
version('1.5-8', sha256='22128dd6b08d3516c44ff89276719ad4fe46b36b23fdd585274fa3a93e7a49cd')
version('1.5-7', sha256='1af41e57df6f2d08ee8b72a1a5ada137beadb36c7ec9ab9bdb7c05226e8ae76d')
version('1.5-6', sha256='1443e5ffdf884b13dd454e4f6aa260fce6ec47e6845d85b62238c206ce57dcba')
version('1.5-5', sha256='d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349')

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@ -7,13 +7,16 @@
class RQuantmod(RPackage):
"""Specify, build, trade, and analyse quantitative financial trading
"""Quantitative Financial Modelling Framework
Specify, build, trade, and analyse quantitative financial trading
strategies."""
homepage = "http://www.quantmod.com/"
url = "https://cloud.r-project.org/src/contrib/quantmod_0.4-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/quantmod"
version('0.4.18', sha256='aa40448e93a1facf399213ac691784007731e869ad243fe762381ab099cd6c35')
version('0.4-15', sha256='7ef2e798d4d8e4d2af0a5b2b9fecebec30568087afbd24bfd923cdeb8b53df53')
version('0.4-14', sha256='d95b1acf73328d675bbad18a93fa3c40faf58959e0401458ad21cf6b9f9254b3')
version('0.4-10', sha256='030040aa567adaba1ea4a1f05eb45712dbdaabbabca72733e7fb2984051f688b')

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@ -7,17 +7,19 @@
class RQuantreg(RPackage):
"""Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation
penalized) models for conditional quantiles of a univariate response
and several methods for handling censored survival data. Portfolio
selection methods based on expected shortfall risk are also
included."""
"""Quantile Regression
Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation
penalized) models for conditional quantiles of a univariate response and
several methods for handling censored survival data. Portfolio selection
methods based on expected shortfall risk are also now included."""
homepage = "https://cloud.r-project.org/package=quantreg"
url = "https://cloud.r-project.org/src/contrib/quantreg_5.29.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/quantreg"
version('5.82', sha256='eac34e1e34d00a24ed7cb6981af258a3afc561843c00501de3206b4540548c07')
version('5.51', sha256='df1330d245f66ee6d924b209bd4c15d44ff8cce52667959ec0d299975428bdb1')
version('5.42.1', sha256='4cc2b0883c52694e58fcfde83e30e4a54be9f4d9cbcf6138f6498cc8e0b3ccab')
version('5.40', sha256='86e310a235009ab85635dfb8803c175f80a35892e237db2525c4ef37a98936eb')
@ -28,3 +30,4 @@ class RQuantreg(RPackage):
depends_on('r-sparsem', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-matrixmodels', type=('build', 'run'))
depends_on('r-conquer', when='@5.82:', type=('build', 'run'))

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class RRMethodss3(RPackage):
"""Methods that simplify the setup of S3 generic functions and
"""S3 Methods Simplified
Methods that simplify the setup of S3 generic functions and
S3 methods. Major effort has been made in making definition of
methods as simple as possible with a minimum of maintenance for
package developers. For example, generic functions are created
@ -21,6 +23,7 @@ class RRMethodss3(RPackage):
url = "https://cloud.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/R.methodsS3"
version('1.8.1', sha256='8a98fb81bcfa78193450f855f614f6f64e6c65daf115f301d97d1f474f5e619b')
version('1.7.1', sha256='44b840399266cd27f8f9157777b4d9d85ab7bd31bfdc143b3fc45079a2d8e687')
depends_on('r@2.13.0:', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RROo(RPackage):
"""Methods and classes for object-oriented programming in R with
"""R Object-Oriented Programming with or without References
Methods and classes for object-oriented programming in R with
or without references. Large effort has been made on making
definition of methods as simple as possible with a minimum of
maintenance for package developers. The package has been developed
@ -19,9 +21,11 @@ class RROo(RPackage):
url = "https://cloud.r-project.org/src/contrib/R.oo_1.21.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/R.oo"
version('1.24.0', sha256='37a1dab8dd668ceba69a1ba36c0c60e9809e29b74bd56d1e8ed519e19c8e3bb6')
version('1.23.0', sha256='f5124ce3dbb0a62e8ef1bfce2de2d1dc2f776e8c48fd8cac358f7f5feb592ea1')
version('1.22.0', sha256='c0862e4608fb2b8f91ec4494d46c2f3ba7bc44999f9aa3d7b9625d3792e7dd4c')
version('1.21.0', sha256='645ceec2f815ed39650ca72db87fb4ece7357857875a4ec73e18bfaf647f431c')
depends_on('r@2.13.0:', type=('build', 'run'))
depends_on('r-r-methodss3@1.7.1:', type=('build', 'run'))
depends_on('r-r-methodss3@1.8.0:', when='@1.24.0:', type=('build', 'run'))

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class RRUtils(RPackage):
"""Utility functions useful when programming and
"""Various Programming Utilities
Utility functions useful when programming and
developing R packages."""
homepage = "https://github.com/HenrikBengtsson/R.utils"
url = "https://cloud.r-project.org/src/contrib/R.utils_2.5.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/R.utils"
version('2.10.1', sha256='957a4f51998c79403a50f6a46266e6553bbf08757b26bf80603a423bceb45abf')
version('2.9.0', sha256='b2aacc5a55d3ea86c41ac576d2583e446af145f4cb1103ad7b6f95b09ab09ff0')
version('2.5.0', sha256='1ae1a0f0c6a4972bb2369a2dbccd29ade87d747255ff9cb5a0bd784a5be1039f')
depends_on('r@2.14.0:', type=('build', 'run'))
depends_on('r-r-oo@1.22.0:', type=('build', 'run'))
depends_on('r-r-oo@1.23.0:', when='@2.10.1:', type=('build', 'run'))
depends_on('r-r-methodss3@1.7.1:', type=('build', 'run'))
depends_on('r-r-methodss3@1.8.0:', when='@2.10.1:', type=('build', 'run'))

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@ -7,7 +7,9 @@
class RR6(RPackage):
"""The R6 package allows the creation of classes with reference semantics,
"""Encapsulated Classes with Reference Semantics
The R6 package allows the creation of classes with reference semantics,
similar to R's built-in reference classes. Compared to reference classes,
R6 classes are simpler and lighter-weight, and they are not built on S4
classes so they do not require the methods package. These classes allow
@ -18,6 +20,7 @@ class RR6(RPackage):
url = "https://cloud.r-project.org/src/contrib/R6_2.2.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/R6"
version('2.5.0', sha256='aec1af9626ec532cb883b544bf9eff4cb2d89c343c7ce0fa31761ec5a7882e02')
version('2.4.0', sha256='70be110174fbf5f5304049b186a6f9c05b77bfaec6d8caf980fcef5da6e0abce')
version('2.2.2', sha256='087756f471884c3b3ead80215a7cc5636a78b8a956e91675acfe2896426eae8f')
version('2.2.0', sha256='7d7bddc4303fafa99954182ccad938166d681499d4e9ae7001d21b0fd60d25c7')

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class RRandomfields(RPackage):
"""Methods for the inference on and the simulation of Gaussian fields
are provided, as well as methods for the simulation of extreme
value random fields."""
"""Simulation and Analysis of Random Fields
Methods for the inference on and the simulation of Gaussian fields are
provided, as well as methods for the simulation of extreme value random
fields. Main geostatistical parts are based on the books by Christian
Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre
Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie
<doi:10.1002/9781119115151>. For the extreme value random fields see
Oesting, Schlather, Schillings (2019) <doi.org/10.1002/sta4.228> and
Schlather (2002) <doi.org/10.1023/A:1020977924878>."""
homepage = "https://cloud.r-project.org/package=RandomFields"
url = "https://cloud.r-project.org/src/contrib/RandomFields_3.1.50.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFields"
version('3.3.8', sha256='8a08e2fdae428e354a29fb6818ae781cc56235a6849a0d29574dc756f73199d0')
version('3.3.6', sha256='51b7bfb4e5bd7fd0ce1207c77f428508a6cd3dfc9de01545a8724dfd9c050213')
version('3.3.4', sha256='a340d4f3ba7950d62acdfa19b9724c82e439d7b1a9f73340124038b7c90c73d4')
version('3.1.50', sha256='2d6a07c3a716ce20f9c685deb59e8fcc64fd52c8a50b0f04baf451b6b928e848')
depends_on('r@3.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@3.3.8:', type=('build', 'run'))
depends_on('r-sp', type=('build', 'run'))
depends_on('r-randomfieldsutils@0.5.1:', type=('build', 'run'))

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@ -7,13 +7,20 @@
class RRanger(RPackage):
"""A fast implementation of Random Forests, particularly suited for high
dimensional data."""
"""A Fast Implementation of Random Forests
A fast implementation of Random Forests, particularly suited for high
dimensional data. Ensembles of classification, regression, survival and
probability prediction trees are supported. Data from genome-wide
association studies can be analyzed efficiently. In addition to data
frames, datasets of class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix'
(R package 'Matrix') can be directly analyzed."""
homepage = "https://cloud.r-project.org/package=ranger"
url = "https://cloud.r-project.org/src/contrib/ranger_0.8.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ranger"
version('0.12.1', sha256='fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef')
version('0.11.2', sha256='13ac8a9433fdd92f62f66de44abc52477dcbb436b2045c1947951a266bffbeeb')
version('0.11.1', sha256='999fb114602e27601ff0fe8ab461c39d667c6f5e8434e7feb3d21c7caf0dcffb')
version('0.8.0', sha256='7f0fdee2f2d553a0aec56c2a4a4ff9dd972e1c7284118d9ea570749e0eaaabb9')
@ -23,6 +30,6 @@ class RRanger(RPackage):
version('0.4.0', sha256='d9f5761c3b07357aa586270cf7cbc97fc3db56ba731b6d0f3baf296f635f2be5')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-rcpp@0.11.2:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-rcppeigen', type=('build', 'run'))

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@ -7,18 +7,24 @@
class RRaster(RPackage):
"""Reading, writing, manipulating, analyzing and modeling of gridded
spatial data. The package implements basic and high-level functions.
Processing of very large files is supported."""
"""Geographic Data Analysis and Modeling
Reading, writing, manipulating, analyzing and modeling of spatial data. The
package implements basic and high-level functions for raster data and for
vector data operations such as intersections. See the manual and tutorials
on <https://rspatial.org/> to get started."""
homepage = "https://cloud.r-project.org/package=raster"
url = "https://cloud.r-project.org/src/contrib/raster_2.5-8.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/raster"
version('3.4-5', sha256='c6620d790b3aba1b64aec31325f726e63f26a14a1b48c1a0f9167a0b1a64e4a5')
version('2.9-23', sha256='90aaec9e3b1e3e6015d9993ea7491e008f2f71990f8abb8610f979c4e28b38af')
version('2.9-22', sha256='8107d95f1aa85cea801c8101c6aa391becfef4b5b915d9bc7a323531fee26128')
version('2.5-8', sha256='47992abd783450513fbce3770298cc257030bf0eb77e42aa3a4b3924b16264cc')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@3.4-5:', type=('build', 'run'))
depends_on('r-sp@1.2-0:', type=('build', 'run'))
depends_on('r-sp@1.4.1:', when='@3.4-5:', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))

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@ -0,0 +1,23 @@
# Copyright 2013-2021 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 RRbibutils(RPackage):
"""Convert Between Bibliography Formats
Converts between a number of bibliography formats, including 'BibTeX',
'BibLaTeX' and 'Bibentry'. Includes a port of the 'bibutils' utilities by
Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in 'bibutils'."""
homepage = "https://geobosh.github.io/rbibutils/"
url = "https://cloud.r-project.org/src/contrib/rbibutils_2.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/rbibutils"
version('2.0', sha256='03d13abee321decb88bc4e7c9f27276d62a4a880fa72bb6b86be91885010cfed')
depends_on('r@2.10:', type=('build', 'run'))

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class RRbokeh(RPackage):
"""R interface for creating plots in Bokeh. Bokeh by Continuum
Analytics."""
"""R Interface for Bokeh
A native R plotting library that provides a flexible declarative interface
for creating interactive web-based graphics, backed by the Bokeh
visualization library <https://bokeh.pydata.org/>."""
homepage = "https://hafen.github.io/rbokeh"
url = "https://cloud.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/rbokeh"
version('0.5.1', sha256='48eba3b238cea2b9aa408d8a48c663564292e76f2ab3f603bc671315a4a75a88')
version('0.5.0', sha256='499c3224a7dcaeb4bb60fd645b3ef528a20e59437747a073713941b80cbcebd2')
depends_on('r+X', type=('build', 'run'))
depends_on('r-htmlwidgets@0.5:', type=('build', 'run'))
depends_on('r-maps', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))

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class RRcpp(RPackage):
"""The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects
can be mapped back and forth to C++ equivalents which facilitates both
writing of new code as well as easier integration of third-party libraries.
Documentation about 'Rcpp' is provided by several vignettes included in
this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the
paper by Eddelbuettel and Francois (2011, JSS), and the book by
Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these
last two."""
"""Seamless R and C++ Integration
The 'Rcpp' package provides R functions as well as C++ classes which; offer
a seamless integration of R and C++. Many R data types and objects can be;
mapped back and forth to C++ equivalents which facilitates both writing of
new; code as well as easier integration of third-party libraries.
Documentation; about 'Rcpp' is provided by several vignettes included in
this package, via the; 'Rcpp Gallery' site at <https://gallery.rcpp.org>,
the paper by Eddelbuettel and; Francois (2011,
<doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,;
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta
(2018,; <doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for
details."""
homepage = "http://dirk.eddelbuettel.com/code/rcpp.html"
url = "https://cloud.r-project.org/src/contrib/Rcpp_0.12.13.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/Rcpp"
version('1.0.6', sha256='c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012')
version('1.0.4.6', sha256='45af675ddbbe155e671453b2e84fe32250bb98d4ccb4342b61c1e25cff10b302')
version('1.0.2', sha256='ad9338d6fc89dd116a3e2c5ecef1956e4be63b6c6aa1b21b2e5f249d65a5129c')
version('1.0.0', sha256='b7378bf0dda17ef72aa3f2a318a9cb5667bef50b601dc1096431e17426e18bc2')

5
var/spack/repos/builtin/packages/r-rcppannoy/package.py
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@ -7,7 +7,9 @@
class RRcppannoy(RPackage):
"""'Annoy' is a small C++ library for Approximate Nearest Neighbors written
"""'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors
'Annoy' is a small C++ library for Approximate Nearest Neighbors written
for efficient memory usage as well an ability to load from / save to disk.
This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
@ -19,6 +21,7 @@ class RRcppannoy(RPackage):
url = "https://cloud.r-project.org/src/contrib/RcppAnnoy_0.0.12.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppAnnoy"
version('0.0.18', sha256='e4e7ddf071109b47b4fdf285db6d2155618ed73da829c30d8e64fc778e63c858')
version('0.0.12', sha256='8f736cbbb4a32c80cb08ba4e81df633846d725f27867e983af2012966eac0eac')
depends_on('r@3.1:', type=('build', 'run'))

16
var/spack/repos/builtin/packages/r-rcpparmadillo/package.py
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@ -7,13 +7,25 @@
class RRcpparmadillo(RPackage):
"""'Rcpp' Integration for the 'Armadillo' Templated Linear
Algebra Library."""
"""'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
'Armadillo' is a templated C++ linear algebra library (by Conrad;
Sanderson) that aims towards a good balance between speed and ease of; use.
Integer, floating point and complex numbers are supported, as; well as a
subset of trigonometric and statistics functions. Various; matrix
decompositions are provided through optional integration with; LAPACK and
ATLAS libraries. The 'RcppArmadillo' package includes the; header files
from the templated 'Armadillo' library. Thus users do; not need to install
'Armadillo' itself in order to use; 'RcppArmadillo'. From release 7.800.0
on, 'Armadillo' is licensed; under Apache License 2; previous releases were
under licensed as MPL; 2.0 from version 3.800.0 onwards and LGPL-3 prior to
that"""
homepage = "https://cloud.r-project.org/package=RcppArmadillo"
url = "https://cloud.r-project.org/src/contrib/RcppArmadillo_0.8.100.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppArmadillo"
version('0.10.1.2.2', sha256='38323703fcf2b61f46f2984aafdd3ddf17c3c993d1d27a8f0f4ba5012b99d069')
version('0.9.600.4.0', sha256='2057b7aa965a4c821dd734276d8e6a01cd59a1b52536b65cb815fa7e8c114f1e')
version('0.9.400.3.0', sha256='56936d501fe8e6f8796ae1a6badb9294d7dad98a0b557c3b3ce6bd4ecaad13b0')
version('0.8.100.1.0', sha256='97ca929b34d84d99d7cadc3612b544632cdd0c43ed962933a3d47caa27854fa7')

6
var/spack/repos/builtin/packages/r-rcppeigen/package.py
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@ -7,7 +7,9 @@
class RRcppeigen(RPackage):
"""R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template
"""'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template
library for linear algebra: matrices, vectors, numerical solvers and
related algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices, and
@ -25,12 +27,12 @@ class RRcppeigen(RPackage):
url = "https://cloud.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppEigen"
version('0.3.3.9.1', sha256='8a0486249b778a4275a1168fc89fc7fc49c2bb031cb14b50a50089acae7fe962')
version('0.3.3.5.0', sha256='e5c6af17770c5f57b7cf2fba04ad1a519901b446e8138bfff221952458207f05')
version('0.3.3.4.0', sha256='11020c567b299b1eac95e8a4d57abf0315931286907823dc7b66c44d0dd6dad4')
version('0.3.3.3.1', sha256='14fdd2cb764d0a822e11b8f09dcf1c3c8580d416f053404732064d8f2b176f24')
version('0.3.2.9.0', sha256='25affba9065e3c12d67b1934d1ce97a928a4011a7738f7b90f0e9830409ec93b')
version('0.3.2.8.1', sha256='ceccb8785531c5c23f9232b594e5372c214a114a08ec759115e946badd08d681')
depends_on('r@2.15.1:', type=('build', 'run'))
depends_on('r-matrix@1.1-0:', type=('build', 'run'))
depends_on('r-rcpp@0.11.0:', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-rcpphnsw/package.py
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@ -7,13 +7,19 @@
class RRcpphnsw(RPackage):
"""RcppHNSW: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate
NearestNeighbors"""
"""'Rcpp' Bindings for 'hnswlib', a Library for Approximate
NearestNeighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This ;
package provides a minimal R interface by relying on the 'Rcpp' package.
See ; <https://github.com/nmslib/hnswlib> for more on 'hnswlib'. 'hnswlib'
is ; released under Version 2.0 of the Apache License."""
homepage = "https://cloud.r-project.org/package=RcppHNSW"
url = "https://cloud.r-project.org/src/contrib/RcppHNSW_0.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppHNSW"
version('0.3.0', sha256='a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007')
version('0.1.0', sha256='75a54c30953845dec685764c7b3b4cd7315197c91aef4ab3b4eb0a6293010a95')
depends_on('r-rcpp@0.11.3:', type=('build', 'run'))

5
var/spack/repos/builtin/packages/r-rcppprogress/package.py
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@ -7,7 +7,9 @@
class RRcppprogress(RPackage):
"""Allows to display a progress bar in the R console for long running
"""An Interruptible Progress Bar with OpenMP Support for C++ in R Packages
Allows to display a progress bar in the R console for long running
computations taking place in c++ code, and support for interrupting
those computations even in multithreaded code, typically using OpenMP."""
@ -15,6 +17,7 @@ class RRcppprogress(RPackage):
url = "https://cloud.r-project.org/src/contrib/RcppProgress_0.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppProgress"
version('0.4.2', sha256='b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48')
version('0.4.1', sha256='11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a')
version('0.4', sha256='706e14360dbc5976db05c2ac6692c3279c0f8c95e72bf9d4becd9e1348025e3e')
version('0.3', sha256='3de5dc47cc2f9e839f92355c463289531e8c13806e54c7438f63c7c34378261d')

4
var/spack/repos/builtin/packages/r-rda/package.py
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@ -14,7 +14,9 @@ class RRda(RPackage):
url = "https://cloud.r-project.org/src/contrib/rda_1.0.2-1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/rda"
version('1.0.2-2.1', sha256='6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8')
# Note: Package 'rda' was removed from the CRAN repository.
# The latest archived version is below
version('1.0.2-2.1', sha256='eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')
version('1.0.2-2', sha256='52ee41249b860af81dc692eee38cd4f8f26d3fbe34cb274f4e118de0013b58bc')
version('1.0.2-1', sha256='e5b96610ec9e82f12efe5dbb9a3ec9ecba9aaddfad1d6ab3f8c37d15fc2b42b7')

8
var/spack/repos/builtin/packages/r-rdpack/package.py
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@ -7,7 +7,9 @@
class RRdpack(RPackage):
"""Functions for manipulation of R documentation objects, including
"""Update and Manipulate Rd Documentation Objects
Functions for manipulation of R documentation objects, including
functions reprompt() and ereprompt() for updating 'Rd' documentation for
functions, methods and classes; 'Rd' macros for citations and import of
references from 'bibtex' files for use in 'Rd' files and 'roxygen2'
@ -19,8 +21,10 @@ class RRdpack(RPackage):
url = "https://cloud.r-project.org/src/contrib/Rdpack_0.11-0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/Rdpack"
version('2.1', sha256='26e094fe3c077fb2a99e95c5bd94015a5f993a4a5f5d217829b4872ff004bfce')
version('0.11-0', sha256='8fb449c80fbe931cdce51f728fb03a1978009ccce66fd6b9edacdc6ff4118d85')
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r-bibtex@0.4.0:', type=('build', 'run'))
depends_on('r-gbrd', type=('build', 'run'))
depends_on('r-rbibutils@1.3:', when='@2.1:', type=('build', 'run'))
depends_on('r-bibtex@0.4.0:', when='@:0.11-0', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-readr/package.py
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@ -7,25 +7,31 @@
class RReadr(RPackage):
"""The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to
flexibly parse many types of data found in the wild, while still cleanly
failing when data unexpectedly changes."""
"""Read Rectangular Text Data
The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly
parse many types of data found in the wild, while still cleanly failing
when data unexpectedly changes."""
homepage = "https://cloud.r-project.org/package=readr"
url = "https://cloud.r-project.org/src/contrib/readr_1.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/readr"
version('1.4.0', sha256='02b1188aab8b2bc3f3d2bba5b946bd299610e87f3f7660c88b60b444093c46b9')
version('1.3.1', sha256='33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3')
version('1.1.1', sha256='1a29b99009a06f2cee18d08bc6201fd4985b6d45c76cefca65084dcc1a2f7cb3')
depends_on('r@3.0.2:', when='@:1.2.1', type=('build', 'run'))
depends_on('r@3.1:', when='@1.3.0:', type=('build', 'run'))
depends_on('r-rcpp@0.12.0.5:', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'))
depends_on('r-hms@0.4.1:', type=('build', 'run'))
depends_on('r-r6', type=('build', 'run'))
depends_on('r-bh', type=('build', 'run'))
depends_on('r-cli', when='@1.4.0:', type=('build', 'run'))
depends_on('r-clipr', when='@1.2.0:', type=('build', 'run'))
depends_on('r-crayon', when='@1.3.1:', type=('build', 'run'))
depends_on('gmake', type='build')
depends_on('r-hms@0.4.1:', type=('build', 'run'))
depends_on('r-rlang', when='@1.4.0:', type=('build', 'run'))
depends_on('r-r6', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'))
depends_on('r-lifecycle', when='@1.4.0:', type=('build', 'run'))
depends_on('r-bh', type=('build', 'run'))
depends_on('r-cpp11', when='@1.4.0:', type=('build', 'run'))
depends_on('r-rcpp@0.12.0.5:', when='@:1.3.1', type=('build', 'run'))

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