Updates of R CRAN packages (#21223)

var/spack/repos/builtin/packages/r-animation/package.py

@@ -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')

var/spack/repos/builtin/packages/r-bookdown/package.py

@@ -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:')

var/spack/repos/builtin/packages/r-brio/package.py

@@ -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')

var/spack/repos/builtin/packages/r-broom/package.py

@@ -7,32 +7,41 @@
 
 
 class RBroom(RPackage):
-    """Convert statistical analysis objects from R into tidy data frames, so
+    """Convert Statistical Objects into Tidy Tibbles
-       that they can more easily be combined, reshaped and otherwise processed
+
-       with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides
+    Summarizes key information about statistical objects in tidy tibbles. This
-       three S3 generics: tidy, which summarizes a model's statistical
+    makes it easy to report results, create plots and consistently work with
-       findings such as coefficients of a regression; augment, which adds
+    large numbers of models at once. Broom provides three verbs that each
-       columns to the original data such as predictions, residuals and cluster
+    provide different types of information about a model. tidy() summarizes
-       assignments; and glance, which provides a one-row summary of
+    information about model components such as coefficients of a regression.
-       model-level statistics."""
+    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'))

var/spack/repos/builtin/packages/r-caret/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-conquer/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-construct/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-corhmm/package.py

@@ -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
+    Fits hidden Markov models of discrete character evolution which allow
-       on different portions of a phylogeny by treating rate classes as hidden
+    different transition rate classes on different portions of a phylogeny.
-       states in a Markov process and various other functions for evaluating
+    Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>."""
-       models of binary character evolution."""
 
     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'))

var/spack/repos/builtin/packages/r-credentials/package.py

@@ -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')

var/spack/repos/builtin/packages/r-devtools/package.py

@@ -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-dt@0.15:', when='@2.3.2:', type=('build', 'run'))
-    depends_on('r-digest@0.6.25:', when='@3.2.0:', 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-ellipsis@0.3.1:', when='@2.3.2:', 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-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'))

var/spack/repos/builtin/packages/r-diffobj/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-fastmap/package.py

@@ -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')

var/spack/repos/builtin/packages/r-fastmatrix/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-future-apply/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-future/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-geiger/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-geomorph/package.py

@@ -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:')

var/spack/repos/builtin/packages/r-geor/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-gert/package.py

@@ -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:')

var/spack/repos/builtin/packages/r-ggally/package.py

@@ -7,26 +7,35 @@
 
 
 class RGgally(RPackage):
-    """The R package 'ggplot2' is a plotting system based on the grammar of
+    """Extension to 'ggplot2'
-       graphics. 'GGally' extends 'ggplot2' by adding several functions to
+
-       reduce the complexity of combining geometric objects with transformed
+    The R package 'ggplot2' is a plotting system based on the grammar of
-       data. Some of these functions include a pairwise plot matrix, a two
+    graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce
-       group pairwise plot matrix, a parallel coordinates plot, a survival
+    the complexity of combining geometric objects with transformed data. Some
-       plot, and several functions to plot networks."""
+    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:')

var/spack/repos/builtin/packages/r-ggpubr/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-ggraph/package.py

@@ -7,18 +7,24 @@
 
 
 class RGgraph(RPackage):
-    """ggraph: An Implementation of Grammar of Graphics for Graphs and
+    """An Implementation of Grammar of Graphics for Graphs and Networks
-       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'))

var/spack/repos/builtin/packages/r-gistr/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-grbase/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-lfe/package.py

@@ -6,13 +6,25 @@
 from spack import *
 
 
-class RLfe(AutotoolsPackage):
+class RLfe(RPackage):
-    """Transforms away factors with many levels prior to doing an OLS"""
+    """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')
 

var/spack/repos/builtin/packages/r-loo/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-magick/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-manipulatewidget/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-metap/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-mlrmbo/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-nanotime/package.py

@@ -7,18 +7,24 @@
 
 
 class RNanotime(RPackage):
-    """Full 64-bit resolution date and time support with resolution up to
+    """Nanosecond-Resolution Time Support for R
-       nanosecond granularity is provided, with easy transition to and from
+
-       the standard 'POSIXct' type."""
+    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'))

var/spack/repos/builtin/packages/r-ncdf4/package.py

@@ -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')

var/spack/repos/builtin/packages/r-network/package.py

@@ -7,14 +7,17 @@
 
 
 class RNetwork(RPackage):
-    """Tools to create and modify network objects. The network class can
+    """Classes for Relational Data
-       represent a range of relational data types, and supports
+
-       arbitrary vertex/edge/graph attributes."""
+    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')

var/spack/repos/builtin/packages/r-nimble/package.py

@@ -6,17 +6,29 @@
 from spack import *
 
 
-class RNimble(AutotoolsPackage):
+class RNimble(RPackage):
-    """A system for writing hierarchical statistical models largely
+    """MCMC, Particle Filtering, and Programmable Hierarchical Modeling
-       compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to
+
-       operate models and do basic R-style math, and compiling both
+    A system for writing hierarchical statistical models largely compatible
-       models and nimbleFunctions via custom- generated C++.
+    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')

var/spack/repos/builtin/packages/r-nlme/package.py

@@ -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')

var/spack/repos/builtin/packages/r-nloptr/package.py

@@ -7,23 +7,27 @@
 
 
 class RNloptr(RPackage):
-    """nloptr is an R interface to NLopt. NLopt is a free/open-source
+    """R Interface to NLopt
-    library for nonlinear optimization, providing a common interface
+
-    for a number of different free optimization routines available
+    Solve optimization problems using an R interface to NLopt. NLopt is a
-    online as well as original implementations of various other
+    free/open-source library for nonlinear optimization, providing a common
-    algorithms. See http://ab-initio.mit.edu/wiki/index.php/NLopt
+    interface for a number of different free optimization routines available
-    _Introduction for more information on the available algorithms.
+    online as well as original implementations of various other algorithms. See
-    During installation on Unix the NLopt code is downloaded and
+    <http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction> for more
-    compiled from the NLopt website."""
+    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

var/spack/repos/builtin/packages/r-nmf/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-nmof/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-nnet/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-np/package.py

@@ -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')

var/spack/repos/builtin/packages/r-npsurv/package.py

@@ -7,13 +7,20 @@
 
 
 class RNpsurv(RPackage):
-    """Contains functions for non-parametric survival analysis of exact and
+    """Nonparametric Survival Analysis
-    interval-censored observations."""
+
+    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'))

var/spack/repos/builtin/packages/r-openssl/package.py

@@ -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')

var/spack/repos/builtin/packages/r-openxlsx/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-optparse/package.py

@@ -7,14 +7,17 @@
 
 
 class ROptparse(RPackage):
-    """A command line parser inspired by Python's 'optparse' library to be used
+    """Command Line Option Parser
-       with Rscript to write "#!" shebang scripts that accept short and long
+
-       flag/options"""
+   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')

var/spack/repos/builtin/packages/r-ordinal/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-paleotree/package.py

@@ -8,14 +8,16 @@
 
 
 class RPaleotree(RPackage):
-    """Provides tools for transforming, a posteriori
+    """Paleontological and Phylogenetic Analyses of Evolution
-       time-scaling, and modifying phylogenies containing
+
-       extinct (i.e. fossil) lineages"""
+    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')
 

var/spack/repos/builtin/packages/r-parallelmap/package.py

@@ -7,17 +7,20 @@
 
 
 class RParallelmap(RPackage):
-    """Unified parallelization framework for multiple back-end, designed for
+    """Unified Interface to Parallelization Back-Ends
-       internal package and interactive usage. The main operation is a parallel
+
-       "map" over lists. Supports local, multicore, mpi and BatchJobs mode.
+    Unified parallelization framework for multiple back-end, designed for
-       Allows "tagging" of the parallel operation with a level name that can be
+    internal package and interactive usage. The main operation is a parallel
-       later selected by the user to switch on parallel execution for exactly
+    "map" over lists. Supports local, multicore, mpi and BatchJobs mode.
-       this operation."""
+    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')
 

var/spack/repos/builtin/packages/r-paramhelpers/package.py

@@ -7,21 +7,24 @@
 
 
 class RParamhelpers(RPackage):
-    """Functions for parameter descriptions and operations in black-box
+    """Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
-       optimization, tuning and machine learning. Parameters can be described
+
-       (type, constraints, defaults, etc.), combined to parameter sets and can
+   Functions for parameter descriptions and operations in black-box
-       in general be programmed on. A useful OptPath object (archive) to log
+   optimization, tuning and machine learning. Parameters can be described
-       function evaluations is also provided."""
+   (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'))

var/spack/repos/builtin/packages/r-party/package.py

@@ -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')

var/spack/repos/builtin/packages/r-partykit/package.py

@@ -8,27 +8,33 @@
 
 
 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@3.5.0:', when='@1.2-11:', type=('build', 'run'))
-    depends_on('r-formula@1.2-1:', 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'))

var/spack/repos/builtin/packages/r-patchwork/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-pbapply/package.py

@@ -7,13 +7,19 @@
 
 
 class RPbapply(RPackage):
-    """A lightweight package that adds progress bar to vectorized R
+    """Adding Progress Bar to '*apply' Functions
-    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')

var/spack/repos/builtin/packages/r-pbdzmq/package.py

@@ -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:')

var/spack/repos/builtin/packages/r-pbkrtest/package.py

@@ -7,22 +7,36 @@
 
 
 class RPbkrtest(RPackage):
-    """Test in mixed effects models. Attention is on mixed effects models as
+    """Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for
-    implemented in the 'lme4' package. This package implements a parametric
+    Test in Mixed Models
-    bootstrap test and a Kenward Roger modification of F-tests for linear mixed
+
-    effects models and a parametric bootstrap test for generalized linear mixed
+    Test in mixed effects models. Attention is on mixed effects models as
-    models."""
+    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'))

var/spack/repos/builtin/packages/r-phytools/package.py

@@ -7,28 +7,49 @@
 
 
 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'))

var/spack/repos/builtin/packages/r-picante/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-pillar/package.py

@@ -7,13 +7,16 @@
 
 
 class RPillar(RPackage):
-    """Provides a 'pillar' generic designed for formatting columns of data
+    """Coloured Formatting for Columns
-       using the full range of colours provided by modern terminals."""
+
+    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'))

var/spack/repos/builtin/packages/r-pkgconfig/package.py

@@ -7,13 +7,15 @@
 
 
 class RPkgconfig(RPackage):
-    """Set configuration options on a per-package basis. Options set by a
+    """Private Configuration for 'R' Packages
-     given package only apply to that package,
+
-     other packages are unaffected."""
+    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')

var/spack/repos/builtin/packages/r-pkgmaker/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-plot3d/package.py

@@ -7,15 +7,19 @@
 
 
 class RPlot3d(RPackage):
-    """Functions for viewing 2-D and 3-D data, including perspective plots,
+    """Plotting Multi-Dimensional Data
-       slice plots, surface plots, scatter plots, etc. Includes data sets from
+
-       oceanography."""
+    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'))

var/spack/repos/builtin/packages/r-plotly/package.py

@@ -7,13 +7,17 @@
 
 
 class RPlotly(RPackage):
-    """Easily translate 'ggplot2' graphs to an interactive web-based version
+    """Create Interactive Web Graphics via 'plotly.js'
-    and/or create custom web-based visualizations directly from R."""
+
+    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'))

var/spack/repos/builtin/packages/r-plotrix/package.py

@@ -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')

var/spack/repos/builtin/packages/r-pls/package.py

@@ -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')

var/spack/repos/builtin/packages/r-plyr/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-polspline/package.py

@@ -7,15 +7,17 @@
 
 
 class RPolspline(RPackage):
-    """Routines for the polynomial spline fitting routines hazard regression,
+    """Polynomial Spline Routines
-       hazard estimation with flexible tails, logspline, lspec, polyclass,
+
-       and polymars, by C. Kooperberg and co-authors.
+    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')

var/spack/repos/builtin/packages/r-popgenome/package.py

@@ -7,16 +7,23 @@
 
 
 class RPopgenome(RPackage):
-    """PopGenome is an efficient Swiss army knife for population genetics data
+    """An Efficient Swiss Army Knife for Population Genomic Analyses
-       analysis, able to process individual loci, large sets of loci, or whole
+
-       genomes."""
+    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')

var/spack/repos/builtin/packages/r-powerlaw/package.py

@@ -7,18 +7,22 @@
 
 
 class RPowerlaw(RPackage):
-    """An implementation of maximum likelihood estimators for a variety of
+    """Analysis of Heavy Tailed Distributions
-       heavy tailed distributions, including both the discrete and continuous
+
-       power law distributions. Additionally, a goodness-of-fit based approach
+    An implementation of maximum likelihood estimators for a variety of heavy
-       is used to estimate the lower cut-off for the scaling region."""
+    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'))

var/spack/repos/builtin/packages/r-prabclus/package.py

@@ -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')

var/spack/repos/builtin/packages/r-pracma/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-prettyunits/package.py

@@ -7,15 +7,18 @@
 
 
 class RPrettyunits(RPackage):
-    """Pretty, human readable formatting of quantities. Time intervals:
+    """Pretty, Human Readable Formatting of Quantities
-       1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about
+
-       a month ago. Bytes: 1337 -> 1.34 kB."""
+    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-magrittr', when='@:1.0.2', type=('build', 'run'))
-    depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-assertthat', when='@:1.0.2', type=('build', 'run'))

var/spack/repos/builtin/packages/r-prodlim/package.py

@@ -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')

var/spack/repos/builtin/packages/r-proj/package.py

@@ -7,21 +7,17 @@
 
 
 class RProj(RPackage):
-    """A wrapper around the generic coordinate transformation software 'PROJ'
+    """Generic Coordinate System Transformations Using 'PROJ'
-    that transforms geospatial coordinates from one coordinate reference system
+
-    ('CRS') to another. This includes cartographic projections as well as
+    Currently non-operational, a harmless wrapper to allow package 'reproj' to
-    geodetic transformations. Version 6.0.0 or higher is required. The
+    install and function while relying on the 'proj4' package."""
-    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/>."""
 
     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('r@3.0.2:', when='@0.4.0:', type=('build', 'run'))
-    depends_on('proj@6:')

var/spack/repos/builtin/packages/r-proj4/package.py

@@ -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@4.4.6:5')
-    depends_on('proj@:5')

var/spack/repos/builtin/packages/r-promises/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-proxy/package.py

@@ -7,16 +7,18 @@
 
 
 class RProxy(RPackage):
-    """Provides an extensible framework for the efficient calculation of
+    """Distance and Similarity Measures
-       auto- and cross-proximities, along with implementations of the most
+
-       popular ones."""
+    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'))

var/spack/repos/builtin/packages/r-ps/package.py

@@ -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')

var/spack/repos/builtin/packages/r-psych/package.py

@@ -7,33 +7,34 @@
 
 
 class RPsych(RPackage):
-    """A general purpose toolbox for personality, psychometric theory and
+    """Procedures for Psychological, Psychometric, and Personality Research
-       experimental psychology. Functions are primarily for multivariate
+
-       analysis and scale construction using factor analysis, principal
+    A general purpose toolbox for personality, psychometric theory and
-       component analysis, cluster analysis and reliability analysis, although
+    experimental psychology. Functions are primarily for multivariate analysis
-       others provide basic descriptive statistics. Item Response Theory is
+    and scale construction using factor analysis, principal component analysis,
-       done using factor analysis of tetrachoric and polychoric correlations.
+    cluster analysis and reliability analysis, although others provide basic
-       Functions for analyzing data at multiple levels include within and
+    descriptive statistics. Item Response Theory is done using factor analysis
-       between group statistics, including correlations and factor analysis.
+    of tetrachoric and polychoric correlations.  Functions for analyzing data
-       Functions for simulating and testing particular item and test structures
+    at multiple levels include within and between group statistics, including
-       are included. Several functions serve as a useful front end for
+    correlations and factor analysis.  Functions for simulating and testing
-       structural equation modeling. Graphical displays of path diagrams,
+    particular item and test structures are included. Several functions serve
-       factor analysis and structural equation models are created using basic
+    as a useful front end for structural equation modeling. Graphical displays
-       graphics. Some of the functions are written to support a book on
+    of path diagrams, factor analysis and structural equation models are
-       psychometric theory as well as publications in personality research.
+    created using basic graphics. Some of the functions are written to support
-       For more information, see the <http://personality-project.org/r> web
+    a book on psychometric theory as well as publications in personality
-       page."""
+    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'))

var/spack/repos/builtin/packages/r-ptw/package.py

@@ -7,21 +7,25 @@
 
 
 class RPtw(RPackage):
-    """Parametric Time Warping aligns patterns, i.e. it aims to put
+    """Parametric Time Warping
-    corresponding features at the same locations. The algorithm
+
-    searches for an optimal polynomial describing the warping. It is
+    Parametric Time Warping aligns patterns, i.e. it aims to put corresponding
-    possible to align one sample to a reference, several samples to
+    features at the same locations. The algorithm searches for an optimal
-    the same reference, or several samples to several references.
+    polynomial describing the warping. It is possible to align one sample to a
-    One can choose between calculating individual warpings, or one
+    reference, several samples to the same reference, or several samples to
-    global warping for a set of samples and one reference. Two
+    several references. One can choose between calculating individual warpings,
-    optimization criteria are implemented: RMS (Root Mean Square
+    or one global warping for a set of samples and one reference. Two
-    error) and WCC (Weighted Cross Correlation). Both warping of
+    optimization criteria are implemented: RMS (Root Mean Square error) and WCC
-    peak profiles and of peak lists are supported."""
+    (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')
 

var/spack/repos/builtin/packages/r-qtl/package.py

@@ -7,12 +7,17 @@
 
 
 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'))

var/spack/repos/builtin/packages/r-quadprog/package.py

@@ -7,13 +7,16 @@
 
 
 class RQuadprog(RPackage):
-    """This package contains routines and documentation for solving
+    """Functions to Solve Quadratic Programming Problems
-       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')

var/spack/repos/builtin/packages/r-quantmod/package.py

@@ -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')

var/spack/repos/builtin/packages/r-quantreg/package.py

@@ -7,17 +7,19 @@
 
 
 class RQuantreg(RPackage):
-    """Estimation and inference methods for models of conditional quantiles:
+    """Quantile Regression
-        Linear and nonlinear parametric and non-parametric (total variation
+
-        penalized) models for conditional quantiles of a univariate response
+    Estimation and inference methods for models of conditional quantiles:
-        and several methods for handling censored survival data. Portfolio
+    Linear and nonlinear parametric and non-parametric (total variation
-        selection methods based on expected shortfall risk are also
+    penalized) models  for conditional quantiles of a univariate response and
-        included."""
+    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'))

var/spack/repos/builtin/packages/r-r-methodss3/package.py

@@ -7,7 +7,9 @@
 
 
 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'))

var/spack/repos/builtin/packages/r-r-oo/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-r-utils/package.py

@@ -7,16 +7,21 @@
 
 
 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'))

var/spack/repos/builtin/packages/r-r6/package.py

@@ -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')

var/spack/repos/builtin/packages/r-randomfields/package.py

@@ -7,18 +7,27 @@
 
 
 class RRandomfields(RPackage):
-    """Methods for the inference on and the simulation of Gaussian fields
+    """Simulation and Analysis of Random Fields
-       are provided, as well as methods for the simulation of extreme
+
-       value 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'))

var/spack/repos/builtin/packages/r-ranger/package.py

@@ -7,13 +7,20 @@
 
 
 class RRanger(RPackage):
-    """A fast implementation of Random Forests, particularly suited for high
+    """A Fast Implementation of Random Forests
-    dimensional data."""
+
+    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'))

var/spack/repos/builtin/packages/r-raster/package.py

@@ -7,18 +7,24 @@
 
 
 class RRaster(RPackage):
-    """Reading, writing, manipulating, analyzing and modeling of gridded
+    """Geographic Data Analysis and Modeling
-    spatial data. The package implements basic and high-level functions.
+
-    Processing of very large files is supported."""
+    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'))

var/spack/repos/builtin/packages/r-rbibutils/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-rbokeh/package.py

@@ -8,15 +8,20 @@
 
 
 class RRbokeh(RPackage):
-    """R interface for creating plots in Bokeh. Bokeh by Continuum
+    """R Interface for Bokeh
-    Analytics."""
+
+    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'))

var/spack/repos/builtin/packages/r-rcpp/package.py

@@ -7,20 +7,25 @@
 
 
 class RRcpp(RPackage):
-    """The 'Rcpp' package provides R functions as well as C++ classes which
+    """Seamless R and C++ Integration
-    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
+    The 'Rcpp' package provides R functions as well as C++ classes which; offer
-    writing of new code as well as easier integration of third-party libraries.
+    a seamless integration of R and C++. Many R data types and objects can be;
-    Documentation about 'Rcpp' is provided by several vignettes included in
+    mapped back and forth to C++ equivalents which facilitates both writing of
-    this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the
+    new; code as well as easier integration of third-party libraries.
-    paper by Eddelbuettel and Francois (2011, JSS), and the book by
+    Documentation; about 'Rcpp' is provided by several vignettes included in
-    Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these
+    this package, via the; 'Rcpp Gallery' site at <https://gallery.rcpp.org>,
-    last two."""
+    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')

var/spack/repos/builtin/packages/r-rcppannoy/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-rcpparmadillo/package.py

@@ -7,13 +7,25 @@
 
 
 class RRcpparmadillo(RPackage):
-    """'Rcpp' Integration for the 'Armadillo' Templated Linear
+    """'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
-    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')

var/spack/repos/builtin/packages/r-rcppeigen/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-rcpphnsw/package.py

@@ -7,13 +7,19 @@
 
 
 class RRcpphnsw(RPackage):
-    """RcppHNSW: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate
+    """'Rcpp' Bindings for 'hnswlib', a Library for Approximate
-       NearestNeighbors"""
+       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'))

var/spack/repos/builtin/packages/r-rcppprogress/package.py

@@ -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')

var/spack/repos/builtin/packages/r-rda/package.py

@@ -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')
 

var/spack/repos/builtin/packages/r-rdpack/package.py

@@ -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'))

var/spack/repos/builtin/packages/r-readr/package.py

@@ -7,25 +7,31 @@
 
 
 class RReadr(RPackage):
-    """The goal of 'readr' is to provide a fast and friendly way to read
+    """Read Rectangular Text Data
-       rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to
+
-       flexibly parse many types of data found in the wild, while still cleanly
+    The goal of 'readr' is to provide a fast and friendly way to read
-       failing when data unexpectedly changes."""
+    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-cli', when='@1.4.0:', 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-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'))