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update CRAN R packages (#28786)

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9
var/spack/repos/builtin/packages/r-abind/package.py
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@ -7,14 +7,15 @@
class RAbind(RPackage):
"""Combine multidimensional arrays into a single array. This is a
"""
Combine Multidimensional Arrays.
Combine multidimensional arrays into a single array. This is a
generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and
higher-dimensional arrays. Also provides functions 'adrop', 'asub', and
'afill' for manipulating, extracting and replacing data in arrays."""
homepage = "https://cloud.r-project.org/package=abind"
url = "https://cloud.r-project.org/src/contrib/abind_1.4-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/abind"
cran = "abind"
version('1.4-5', sha256='3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c')
version('1.4-3', sha256='b6c255878c1ab81701ae701f34546e88be115629b984ac4272e311fa3c0ea6ce')

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var/spack/repos/builtin/packages/r-acepack/package.py
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@ -7,10 +7,24 @@
class RAcepack(RPackage):
"""ACE and AVAS for Selecting Multiple Regression Transformations."""
"""ACE and AVAS for Selecting Multiple Regression Transformations.
homepage = "https://cloud.r-project.org/package=acepack"
url = "https://cloud.r-project.org/src/contrib/acepack_1.4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/acepack"
Two nonparametric methods for multiple regression transform selection are
provided. The first, Alternative Conditional Expectations (ACE), is an
algorithm to find the fixed point of maximal correlation, i.e. it finds a
set of transformed response variables that maximizes R^2 using smoothing
functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal
Transformations for Multiple Regression and Correlation". Journal of the
American Statistical Association. 80:580-598.
<doi:10.1080/01621459.1985.10478157>]. Also included is the Additivity
Variance Stabilization (AVAS) method which works better than ACE when
correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations
for Regression via Additivity and Variance Stabilization". Journal of the
American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>]. A good introduction to these two
methods is in chapter 16 of Frank Harrel's "Regression Modeling Strategies"
in the Springer Series in Statistics."""
cran = "acepack"
version('1.4.1', sha256='82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9')

12
var/spack/repos/builtin/packages/r-ada/package.py
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@ -7,12 +7,14 @@
class RAda(RPackage):
"""Performs discrete, real, and gentle boost under both exponential
and logistic loss on a given data set."""
"""The R Package Ada for Stochastic Boosting.
homepage = "https://cloud.r-project.org/package=ada"
url = "https://cloud.r-project.org/src/contrib/ada_2.0-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ada"
Performs discrete, real, and gentle boost under both exponential and
logistic loss on a given data set. The package ada provides a
straightforward, well-documented, and broad boosting routine for
classification, ideally suited for small to moderate-sized data sets."""
cran = "ada"
version('2.0-5', sha256='d900172059eebeef30c27944fc29737a231fc4f92e3c2661868383fbd9016ac0')

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var/spack/repos/builtin/packages/r-adabag/package.py
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@ -7,17 +7,37 @@
class RAdabag(RPackage):
"""Applies Multiclass AdaBoost.M1, SAMME and Bagging."""
"""Applies Multiclass AdaBoost.M1, SAMME and Bagging.
homepage = "https://cloud.r-project.org/package=adabag"
url = "https://cloud.r-project.org/src/contrib/adabag_4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/adabag"
It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's
Bagging algorithm using classification trees as individual classifiers.
Once these classifiers have been trained, they can be used to predict on
new data. Also, cross validation estimation of the error can be done. Since
version 2.0 the function margins() is available to calculate the margins
for these classifiers. Also a higher flexibility is achieved giving access
to the rpart.control() argument of 'rpart'. Four important new features
were introduced on version 3.0, AdaBoost-SAMME (Zhu et al., 2009) is
implemented and a new function errorevol() shows the error of the ensembles
as a function of the number of iterations. In addition, the ensembles can
be pruned using the option 'newmfinal' in the predict.bagging() and
predict.boosting() functions and the posterior probability of each class
for observations can be obtained. Version 3.1 modifies the relative
importance measure to take into account the gain of the Gini index given by
a variable in each tree and the weights of these trees. Version 4.0
includes the margin-based ordered aggregation for Bagging pruning (Guo and
Boukir, 2013) and a function to auto prune the 'rpart' tree. Moreover,
three new plots are also available importanceplot(), plot.errorevol() and
plot.margins(). Version 4.1 allows to predict on unlabeled data. Version
4.2 includes the parallel computation option for some of the functions."""
cran = "adabag"
version('4.2', sha256='47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81')
version('4.1', sha256='ff938c36122cdf58a71a59a6bf79a3c7816966ee7cc4907c4a0a3c0732e3d028')
depends_on('r-rpart', type=('build', 'run'))
depends_on('r-mlbench', when='@:4.1', type=('build', 'run'))
depends_on('r-caret', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-doparallel', type=('build', 'run'))
depends_on('r-mlbench', type=('build', 'run'), when='@:4.1')

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var/spack/repos/builtin/packages/r-ade4/package.py
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@ -8,7 +8,7 @@
class RAde4(RPackage):
"""Analysis of Ecological Data : Exploratory and Euclidean Methods in
Environmental Sciences
Environmental Sciences.
Tools for multivariate data analysis. Several methods are provided for the
analysis (i.e., ordination) of one-table (e.g., principal component
@ -17,10 +17,9 @@ class RAde4(RPackage):
STATIS, multiple coinertia analysis). The philosophy of the package is
described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>."""
homepage = "https://pbil.univ-lyon1.fr/ADE-4"
url = "https://cloud.r-project.org/src/contrib/ade4_1.7-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ade4"
cran = "ade4"
version('1.7-18', sha256='ecb6f4c42c60f39702aa96f454bb536a333049c9608ee2b6bdf8795e059cc525')
version('1.7-16', sha256='9bd7a25ff4fe30a32fd8f6b71909f4c638a0e2f002fc8303c0a4795423385590')
version('1.7-13', sha256='f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b')
version('1.7-11', sha256='4ccd799ae99bd625840b866a697c4a48adb751660470bf0d6cf9207b1927a572')
@ -28,6 +27,7 @@ class RAde4(RPackage):
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-pixmap', when='@1.7-16:', type=('build', 'run'))
depends_on('r-sp', when='@1.7-16:', type=('build', 'run'))
depends_on('r-progress', when='@1.7-16:', type=('build', 'run'))
depends_on('r-pixmap', type=('build', 'run'), when='@1.7-16:')
depends_on('r-sp', type=('build', 'run'), when='@1.7-16:')
depends_on('r-progress', type=('build', 'run'), when='@1.7-16')

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var/spack/repos/builtin/packages/r-adegenet/package.py
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@ -7,22 +7,21 @@
class RAdegenet(RPackage):
"""Exploratory Analysis of Genetic and Genomic Data
"""Exploratory Analysis of Genetic and Genomic Data.
Toolset for the exploration of genetic and genomic data. Adegenet
provides formal (S4) classes for storing and handling various genetic
data, including genetic markers with varying ploidy and hierarchical
population structure ('genind' class), alleles counts by populations
('genpop'), and genome-wide SNP data ('genlight'). It also implements
original multivariate methods (DAPC, sPCA), graphics, statistical tests,
simulation tools, distance and similarity measures, and several spatial
methods. A range of both empirical and simulated datasets is also provided
to illustrate various methods."""
Toolset for the exploration of genetic and genomic data. Adegenet provides
formal (S4) classes for storing and handling various genetic data,
including genetic markers with varying ploidy and hierarchical population
structure ('genind' class), alleles counts by populations ('genpop'), and
genome-wide SNP data ('genlight'). It also implements original multivariate
methods (DAPC, sPCA), graphics, statistical tests, simulation tools,
distance and similarity measures, and several spatial methods. A range of
both empirical and simulated datasets is also provided to illustrate
various methods."""
homepage = "https://github.com/thibautjombart/adegenet/wiki"
url = "https://cloud.r-project.org/src/contrib/adegenet_2.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/adegenet"
cran = "adegenet"
version('2.1.5', sha256='e4eee8c41dae6cb0841db74ec6f9adb2580873f3e313471f37df58324c1857f2')
version('2.1.3', sha256='0790114ecb22642683b5be1f4b3a6a49856e06dc2f9e21b9cba4390c2257f6c6')
version('2.1.1', sha256='3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a')
version('2.1.0', sha256='7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a')
@ -36,8 +35,9 @@ class RAdegenet(RPackage):
depends_on('r-shiny', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-seqinr', type=('build', 'run'))
depends_on('r-spdep', type=('build', 'run'))
depends_on('r-boot', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-dplyr@0.4.1:', type=('build', 'run'))
depends_on('r-vegan', type=('build', 'run'))
depends_on('r-spdep', type=('build', 'run'), when='@:2.1.3')

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var/spack/repos/builtin/packages/r-adegraphics/package.py
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@ -7,17 +7,15 @@
class RAdegraphics(RPackage):
"""adegraphics: An S4 Lattice-Based Package for the Representation of
Multivariate Data.
"""An S4 Lattice-Based Package for the Representation of Multivariate Data.
Graphical functionalities for the representation of multivariate data.
It is a complete re-implementation of the functions available in the 'ade4'
Graphical functionalities for the representation of multivariate data. It
is a complete re-implementation of the functions available in the 'ade4'
package."""
homepage = "https://pbil.univ-lyon1.fr/ADE-4"
url = "https://cloud.r-project.org/src/contrib/adegraphics_1.0-15.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/adegraphics"
cran = "adegraphics"
version('1.0-16', sha256='7ba59ce9aeefe1c25b4b118d08ef458ffd34115412c147cc428629e72a82ec3a')
version('1.0-15', sha256='87bbcd072e9a898955f5ede4315e82365086a50a2887bf5bd2e94bbb4d3f678a')
depends_on('r@3.0.2:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-adephylo/package.py
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@ -7,14 +7,12 @@
class RAdephylo(RPackage):
"""adephylo: Exploratory Analyses for the Phylogenetic Comparative Method.
"""Exploratory Analyses for the Phylogenetic Comparative Method.
Multivariate tools to analyze comparative data, i.e. a phylogeny and
some traits measured for each taxa."""
Multivariate tools to analyze comparative data, i.e. a phylogeny and some
traits measured for each taxa."""
homepage = "https://cloud.r-project.org/package=adephylo"
url = "https://cloud.r-project.org/src/contrib/adephylo_1.1-11.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/adephylo"
cran = "adephylo"
version('1.1-11', sha256='154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a')

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var/spack/repos/builtin/packages/r-adespatial/package.py
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@ -7,7 +7,7 @@
class RAdespatial(RPackage):
"""adespatial: Multivariate Multiscale Spatial Analysis.
"""Multivariate Multiscale Spatial Analysis.
Tools for the multiscale spatial analysis of multivariate data. Several
methods are based on the use of a spatial weighting matrix and its
@ -15,10 +15,9 @@ class RAdespatial(RPackage):
approaches are described in the review Dray et al (2012)
<doi:10.1890/11-1183.1>."""
homepage = "https://cloud.r-project.org/package=adespatial"
url = "https://cloud.r-project.org/src/contrib/adespatial_0.3-8.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/adespatial"
cran = "adespatial"
version('0.3-14', sha256='a2ef7549c1ed7a23651716c633b25eaff468af8ccbf2e9fcd164e485984cbfbf')
version('0.3-8', sha256='e3fd3209ce3f0a862a0794187e8c884f1697c87c96e569a2f51f252e00022906')
depends_on('r-ade4@1.7-13:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-adgoftest/package.py
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@ -7,11 +7,11 @@
class RAdgoftest(RPackage):
"""Anderson-Darling GoF test with p-value calculation based on Marsaglia's
2004 paper 'Evaluating the Anderson-Darling Distribution'"""
"""Anderson-Darling GoF test.
homepage = "https://cloud.r-project.org/package=ADGofTest"
url = "https://cloud.r-project.org/src/contrib/ADGofTest_0.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ADGofTest"
Anderson-Darling GoF test with p-value calculation based on Marsaglia's
2004 paper 'Evaluating the Anderson-Darling Distribution'."""
cran = "ADGofTest"
version('0.3', sha256='9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846')

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var/spack/repos/builtin/packages/r-aer/package.py
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@ -7,16 +7,13 @@
class RAer(RPackage):
"""Applied Econometrics with R
"""Applied Econometrics with R.
Functions, data sets, examples, demos, and vignettes
for the book Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2."""
Functions, data sets, examples, demos, and vignettes for the book Christian
Kleiber and Achim Zeileis (2008), Applied Econometrics with R,
Springer-Verlag, New York. ISBN 978-0-387-77316-2."""
homepage = "https://cloud.r-project.org/package=AER"
url = "https://cloud.r-project.org/src/contrib/AER_1.2-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/AER"
cran = "AER"
version('1.2-9', sha256='3b79390b14766419fc1e8912689bc462d4beb01aff9dad26d628aed69d04540d')
version('1.2-7', sha256='3aee5c606313710c2dca6c1e9b2c20a145aa33f2a3ecc5cfcec66c8e91838a93')

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var/spack/repos/builtin/packages/r-afex/package.py
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@ -7,24 +7,21 @@
class RAfex(RPackage):
"""Analysis of Factorial Experiments
"""Analysis of Factorial Experiments.
Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed (i.e., split-plot)
ANOVAs for data in long format (i.e., one observation per row),
automatically aggregating multiple observations per individual and cell
of the design. mixed() fits mixed models using lme4::lmer() and computes
automatically aggregating multiple observations per individual and cell of
the design. mixed() fits mixed models using lme4::lmer() and computes
p-values for all fixed effects using either Kenward-Roger or Satterthwaite
approximation for degrees of freedom (LMM only), parametric bootstrap
(LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
afex_plot() provides a high-level interface for interaction or one-way
plots using ggplot2, combining raw data and model estimates. afex uses
type 3 sums of squares as default (imitating commercial statistical
software).
"""
approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs
and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex_plot()
provides a high-level interface for interaction or one-way plots using
ggplot2, combining raw data and model estimates. afex uses type 3 sums of
squares as default (imitating commercial statistical software)."""
homepage = "https://github.com/singmann/afex"
cran = "afex"
version('1.0-1', sha256='6febc34b87a1109f5cbcd213c08d2b7b3e9cf99065fa41c19bc88ac99fb104cc')

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var/spack/repos/builtin/packages/r-als/package.py
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@ -7,17 +7,17 @@
class RAls(RPackage):
"""Alternating least squares is often used to resolve components
contributing to data with a bilinear structure; the basic
technique may be extended to alternating constrained least squares.
Commonly applied constraints include unimodality, non-negativity,
and normalization of components. Several data matrices may be
decomposed simultaneously by assuming that one of the two matrices
in the bilinear decomposition is shared between datasets."""
"""Multivariate Curve Resolution Alternating Least Squares (MCR-ALS).
homepage = "https://cloud.r-project.org/package=ALS"
url = "https://cloud.r-project.org/src/contrib/ALS_0.0.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ALS"
Alternating least squares is often used to resolve components contributing
to data with a bilinear structure; the basic technique may be extended to
alternating constrained least squares. Commonly applied constraints
include unimodality, non-negativity, and normalization of components.
Several data matrices may be decomposed simultaneously by assuming that one
of the two matrices in the bilinear decomposition is shared between
datasets."""
cran = "ALS"
version('0.0.6', sha256='ca90d27115ae9e476967f521bf6935723e410a3bf92477e7570e14bfd3b099eb')

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var/spack/repos/builtin/packages/r-amap/package.py
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@ -7,18 +7,16 @@
class RAmap(RPackage):
"""Another Multidimensional Analysis Package
"""Another Multidimensional Analysis Package.
Tools for Clustering and Principal Component Analysis (With robust methods,
and parallelized functions)."""
homepage = "https://cran.r-project.org/web/packages/amap/index.html"
url = "https://cloud.r-project.org/src/contrib/amap_0.8-16.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/amap/"
cran = "amap"
version('0.8-18', sha256='7afbbdd681a201121374821b733c9000ca1046a2353ee386507604c2c759ec7e')
version('0.8-17', sha256='6b8473d1d35a9cbc611661882c8f681162e8f913f911ccd51629200ae72289c6')
version('0.8-16', sha256='d3775ad7f660581f7d2f070e426be95ae0d6743622943e6f5491988e5217d4e2')
depends_on('r@2.10.0:', when='@:0.8-16', type=('build', 'run'))
depends_on('r@3.6.0:', when='@0.8-17:', type=('build', 'run'))
depends_on('r@2.10.0:', type=('build', 'run'))
depends_on('r@3.6.0:', type=('build', 'run'), when='@0.8-17:')

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var/spack/repos/builtin/packages/r-amelia/package.py
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@ -7,18 +7,27 @@
class RAmelia(RPackage):
"""Amelia: A Program for Missing Data
"""A Program for Missing Data.
Amelia II "multiply imputes" missing data in a single
cross-section (such as a survey), from a time series (like
variables collected for each year in a country), or from a
time-series-cross-sectional data set (such as collected by
years for each of several countries)."""
A tool that "multiply imputes" missing data in a single cross-section (such
as a survey), from a time series (like variables collected for each year in
a country), or from a time-series-cross-sectional data set (such as
collected by years for each of several countries). Amelia II implements our
bootstrapping-based algorithm that gives essentially the same answers as
the standard IP or EMis approaches, is usually considerably faster than
existing approaches and can handle many more variables. Unlike Amelia I
and other statistically rigorous imputation software, it virtually never
crashes (but please let us know if you find to the contrary!). The program
also generalizes existing approaches by allowing for trends in time series
across observations within a cross-sectional unit, as well as priors that
allow experts to incorporate beliefs they have about the values of missing
cells in their data. Amelia II also includes useful diagnostics of the fit
of multiple imputation models. The program works from the R command line
or via a graphical user interface that does not require users to know R."""
homepage = "https://gking.harvard.edu/amelia"
url = "https://cloud.r-project.org/src/contrib/Amelia_1.7.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/Amelia"
cran = "Amelia"
version('1.8.0', sha256='3ec1d5a68dac601b354227916aa8ec72fa1216b603dd887aae2b24cb69b5995e')
version('1.7.6', sha256='63c08d374aaf78af46c34dc78da719b3085e58d9fabdc76c6460d5193a621bea')
depends_on('r@3.0.2:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-animation/package.py
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@ -7,23 +7,25 @@
class RAnimation(RPackage):
"""Provides functions for animations in statistics, covering topics
in probability theory, mathematical statistics, multivariate statistics,
"""A Gallery of Animations in Statistics and Utilities to Create
Animations.
Provides functions for animations in statistics, covering topics in
probability theory, mathematical statistics, multivariate statistics,
non-parametric statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions maybe helpful in teaching statistics and data analysis."""
computational statistics, data mining and machine learning. These
functions maybe helpful in teaching statistics and data analysis."""
homepage = "https://cloud.r-project.org/package=animation"
url = "https://cloud.r-project.org/src/contrib/animation_2.5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/animation"
cran = "animation"
version('2.7', sha256='88418f1b04ec785963bad492f30eb48b05914e9e5d88c7eef705d949cbd7e469')
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('r-magick', type=('build', 'run'), when='@2.6:')
depends_on('imagemagick')
depends_on('ffmpeg')
depends_on('swftools')
depends_on('texlive')
depends_on('swftools')
depends_on('ffmpeg')

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var/spack/repos/builtin/packages/r-anytime/package.py
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@ -7,16 +7,14 @@
class RAnytime(RPackage):
"""Anything to 'POSIXct' or 'Date' Converter
"""Anything to 'POSIXct' or 'Date' Converter.
Convert input in any one of character, integer, numeric,
factor, or ordered type into 'POSIXct' (or 'Date') objects,
using one of a number of predefined formats, and relying on
Boost facilities for date and time parsing."""
Convert input in any one of character, integer, numeric, factor, or ordered
type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time
parsing."""
homepage = "https://dirk.eddelbuettel.com/code/anytime.html"
url = "https://cloud.r-project.org/src/contrib/anytime_0.3.9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/anytime"
cran = "anytime"
version('0.3.9', sha256='1096c15249ac70997a8a41c37eeb2a6d38530621abeae05d3dcd96a8acc7574a')

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class RAod(RPackage):
"""Provides a set of functions to analyse overdispersed counts or
proportions. Most of the methods are already available elsewhere but are
scattered in different packages. The proposed functions should be
considered as complements to more sophisticated methods such as generalized
estimating equations (GEE) or generalized linear mixed effect models
(GLMM)."""
"""Analysis of Overdispersed Data.
homepage = "https://cloud.r-project.org/package=aod"
url = "https://cloud.r-project.org/src/contrib/aod_1.3.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/aod"
Provides a set of functions to analyse overdispersed counts or proportions.
Most of the methods are already available elsewhere but are scattered in
different packages. The proposed functions should be considered as
complements to more sophisticated methods such as generalized estimating
equations (GEE) or generalized linear mixed effect models (GLMM)."""
cran = "aod"
version('1.3.1', sha256='052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc')

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class RApe(RPackage):
"""Analyses of Phylogenetics and Evolution
"""Analyses of Phylogenetics and Evolution.
Functions for reading, writing, plotting, and manipulating phylogenetic
trees, analyses of comparative data in a phylogenetic framework, ancestral
character analyses, analyses of diversification and macroevolution,
computing distances from DNA sequences, reading and writing nucleotide
sequences as well as importing from BioConductor, and several tools such
as Mantel's test, generalized skyline plots, graphical exploration of
sequences as well as importing from BioConductor, and several tools such as
Mantel's test, generalized skyline plots, graphical exploration of
phylogenetic data (alex, trex, kronoviz), estimation of absolute
evolutionary rates and clock-like trees using mean path lengths and
penalized likelihood, dating trees with non-contemporaneous sequences,
translating DNA into AA sequences, and assessing sequence alignments.
Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
triangle methods, and several methods handling incomplete distance
matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
whose results are returned into R."""
triangle methods, and several methods handling incomplete distance matrices
(NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions
call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results
are returned into R."""
homepage = "http://ape-package.ird.fr/"
url = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ape"
cran = "ape"
version('5.6-1', sha256='25401e036576eed1200e15bf68879ccd85611303a3508b989e15164cd4c0f7f7')
version('5.4-1', sha256='f0316c8e74ce900053e8b3e8c9322b9d10e7730f3be2150365f74630bee7eee4')
version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23')
version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415')

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class RArgparse(RPackage):
"""Command Line Optional and Positional Argument Parser
"""Command Line Optional and Positional Argument Parser.
A command line parser to be used with Rscript to write "#!" shebang scripts
that gracefully accept positional and optional arguments and automatically
generate usage."""
homepage = "https://github.com/trevorld/argparse"
url = "https://cloud.r-project.org/src/contrib/argparse_1.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/argparse"
cran = "argparse"
version('2.1.3', sha256='aeda31a54a8d7a0a511cfbf7c5868637e129922671d43938165867437fb6a66e')
version('2.0.3', sha256='d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0')
version('2.0.1', sha256='949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab')
version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b')
depends_on('r-proto@1:', when='@1.0.0:1.9.9', type=('build', 'run'))
depends_on('r-getopt', when='@1.0.0:1.9.9', type=('build', 'run'))
depends_on('r-r6', when='@2.0.0:', type=('build', 'run'))
depends_on('r-r6', type=('build', 'run'), when='@2.0.0:')
depends_on('r-findpython', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('python@3.2:', type=('build', 'run'))
depends_on('r-proto@1:', type=('build', 'run'), when='@1.0.0:1.9.9')
depends_on('r-getopt', type=('build', 'run'), when='@1.0.0:1.9.9')

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class RAsh(RPackage):
"""David Scott's ASH routines ported from S-PLUS to R."""
"""David Scott's ASH Routines.
David Scott's ASH routines ported from S-PLUS to R."""
cran = 'ash'

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@ -7,7 +7,9 @@
class RAskpass(RPackage):
"""Cross-platform utilities for prompting the user for credentials or a
"""Safe Password Entry for R, Git, and SSH.
Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a protected
key. Includes native programs for MacOS and Windows, hence no 'tcltk' is
required. Password entry can be invoked in two different ways: directly
@ -16,9 +18,7 @@ class RAskpass(RPackage):
environment variables. Thereby the user can be prompted for credentials or
a passphrase if needed when R calls out to git or ssh."""
homepage = "https://github.com/jeroen/askpass#readme"
url = "https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/askpass"
cran = "askpass"
version('1.1', sha256='db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f')

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class RAssertiveBase(RPackage):
"""assertive.base: A Lightweight Core of the 'assertive' Package
"""A Lightweight Core of the 'assertive' Package.
A minimal set of predicates and assertions used by the assertive package.
This is mainly for use by other package developers who want to include run-time
testing features in their own packages. End-users will usually want to use
assertive directly."""
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.base"
url = "https://cloud.r-project.org/src/contrib/assertive.base_0.0-7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.base"
cran = "assertive.base"
version('0.0-9', sha256='4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e')
version('0.0-7', sha256='f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7')
version('0.0-1', sha256='6a5fb06ad912f01cd8aaf2aa7c8ca03b8ebbb1c5eb2be47fa145930f15f4d258')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@0.0-9:')

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class RAssertiveCode(RPackage):
"""assertive.code: Assertions to Check Properties of Code
"""Assertions to Check Properties of Code.
A set of predicates and assertions for checking the
properties of code. This is mainly for use by other package
developers who want to include run-time testing features in
their own packages. End-users will usually want to use
assertive directly."""
A set of predicates and assertions for checking the properties of code.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.code"
url = "https://cloud.r-project.org/src/contrib/assertive.code_0.0-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.code"
cran = "assertive.code"
version('0.0-3', sha256='ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2')

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var/spack/repos/builtin/packages/r-assertive-data-uk/package.py
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class RAssertiveDataUk(RPackage):
"""assertive.data.uk: Assertions to Check Properties of Strings
"""Assertions to Check Properties of Strings.
A set of predicates and assertions for checking the
properties of UK-specific complex data types. This is
mainly for use by other package developers who want to
include run-time testing features in their own packages.
End-users will usually want to use assertive directly."""
A set of predicates and assertions for checking the properties of
UK-specific complex data types. This is mainly for use by other package
developers who want to include run-time testing features in their own
packages. End-users will usually want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.data.uk"
url = "https://cloud.r-project.org/src/contrib/assertive.data.uk_0.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.data.uk"
cran = "assertive.data.uk"
version('0.0-2', sha256='ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb')

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class RAssertiveDataUs(RPackage):
"""assertive.data.us: Assertions to Check Properties of Strings
"""Assertions to Check Properties of Strings.
A set of predicates and assertions for checking the
properties of US-specific complex data types. This is
mainly for use by other package developers who want to
include run-time testing features in their own packages.
End-users will usually want to use assertive directly."""
A set of predicates and assertions for checking the properties of
US-specific complex data types. This is mainly for use by other package
developers who want to include run-time testing features in their own
packages. End-users will usually want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.data.us"
url = "https://cloud.r-project.org/src/contrib/assertive.data.us_0.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.data.us"
cran = "assertive.data.us"
version('0.0-2', sha256='180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad')

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var/spack/repos/builtin/packages/r-assertive-data/package.py
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class RAssertiveData(RPackage):
"""assertive.data: Assertions to Check Properties of Data
"""Assertions to Check Properties of Data.
A set of predicates and assertions for checking the
properties of (country independent) complex data types.
This is mainly for use by other package developers who want
to include run-time testing features in their own packages.
End-users will usually want to use assertive directly."""
A set of predicates and assertions for checking the properties of (country
independent) complex data types. This is mainly for use by other package
developers who want to include run-time testing features in their own
packages. End-users will usually want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.data"
url = "https://cloud.r-project.org/src/contrib/assertive.data_0.0-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.data"
cran = "assertive.data"
version('0.0-3', sha256='5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01')

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var/spack/repos/builtin/packages/r-assertive-datetimes/package.py
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class RAssertiveDatetimes(RPackage):
"""assertive.datetimes: Assertions to Check Properties of Dates and Times
"""Assertions to Check Properties of Dates and Times.
A set of predicates and assertions for checking the properties of
dates and times. This is mainly for use by other package developers
who want to include run-time testing features in their own packages.
End-users will usually want to use assertive directly."""
A set of predicates and assertions for checking the properties of dates and
times. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.datetimes"
url = "https://cloud.r-project.org/src/contrib/assertive.datetimes_0.0-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.datetimes"
cran = "assertive.datetimes"
version('0.0-3', sha256='014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94')

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class RAssertiveFiles(RPackage):
"""assertive.files: Assertions to Check Properties of Files
"""Assertions to Check Properties of Files.
A set of predicates and assertions for checking the
properties of files and connections. This is mainly for use
by other package developers who want to include run-time
testing features in their own packages. End-users will
A set of predicates and assertions for checking the properties of files and
connections. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.files"
url = "https://cloud.r-project.org/src/contrib/assertive.files_0.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.files"
cran = "assertive.files"
version('0.0-2', sha256='be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a')

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var/spack/repos/builtin/packages/r-assertive-matrices/package.py
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class RAssertiveMatrices(RPackage):
"""assertive.matrices: Assertions to Check Properties of
Matrices
"""Assertions to Check Properties of Matrices.
A set of predicates and assertions for checking the
properties of matrices. This is mainly for use by other
package developers who want to include run-time testing
features in their own packages. End-users will usually want
to use assertive directly."""
A set of predicates and assertions for checking the properties of matrices.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.matrices"
url = "https://cloud.r-project.org/src/contrib/assertive.matrices_0.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.matrices"
cran = "assertive.matrices"
version('0.0-2', sha256='3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b')

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var/spack/repos/builtin/packages/r-assertive-models/package.py
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class RAssertiveModels(RPackage):
"""assertive.models: Assertions to Check Properties of Models
"""Assertions to Check Properties of Models.
A set of predicates and assertions for checking the
properties of models. This is mainly for use by other
package developers who want to include run-time testing
features in their own packages. End-users will usually want
to use assertive directly."""
A set of predicates and assertions for checking the properties of models.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.models"
url = "https://cloud.r-project.org/src/contrib/assertive.models_0.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.models"
cran = "assertive.models"
version('0.0-2', sha256='b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e')

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class RAssertiveNumbers(RPackage):
"""assertive.numbers: Assertions to Check Properties of Numbers
"""Assertions to Check Properties of Numbers.
A set of predicates and assertions for checking the
properties of numbers. This is mainly for use by other
package developers who want to include run-time testing
features in their own packages. End-users will usually want
to use assertive directly."""
A set of predicates and assertions for checking the properties of numbers.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.numbers"
url = "https://cloud.r-project.org/src/contrib/assertive.numbers_0.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.numbers"
cran = "assertive.numbers"
version('0.0-2', sha256='bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349')

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class RAssertiveProperties(RPackage):
"""assertive.properties: Assertions to Check Properties of
Variables
"""Assertions to Check Properties of Variables.
A set of predicates and assertions for checking the
properties of variables, such as length, names and
attributes. This is mainly for use by other package
developers who want to include run-time testing features in
their own packages. End-users will usually want to use
assertive directly."""
A set of predicates and assertions for checking the properties of
variables, such as length, names and attributes. This is mainly for use by
other package developers who want to include run-time testing features in
their own packages. End-users will usually want to use assertive
directly."""
homepage = "https://bitbucket.org/richierocks/assertive.properties"
url = "https://cloud.r-project.org/src/contrib/assertive.properties_0.0-4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.properties"
cran = "assertive.properties"
version('0.0-4', sha256='5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b')

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var/spack/repos/builtin/packages/r-assertive-reflection/package.py
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class RAssertiveReflection(RPackage):
"""assertive.reflection: Assertions for Checking the State of R
"""Assertions for Checking the State of R.
A set of predicates and assertions for checking the state
and capabilities of R, the operating system it is running
on, and the IDE being used. This is mainly for use by other
package developers who want to include run-time testing
features in their own packages. End-users will usually want
to use assertive directly."""
A set of predicates and assertions for checking the state and capabilities
of R, the operating system it is running on, and the IDE being used. This
is mainly for use by other package developers who want to include run-time
testing features in their own packages. End-users will usually want to use
assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.reflection"
url = "https://cloud.r-project.org/src/contrib/assertive.reflection_0.0-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.reflection"
cran = "assertive.reflection"
version('0.0-5', sha256='c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd')

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class RAssertiveSets(RPackage):
"""assertive.sets: Assertions to Check Properties of Sets
"""Assertions to Check Properties of Sets.
A set of predicates and assertions for checking the
properties of sets. This is mainly for use by other package
developers who want to include run-time testing features in
their own packages. End-users will usually want to use
assertive directly."""
A set of predicates and assertions for checking the properties of sets.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.sets"
url = "https://cloud.r-project.org/src/contrib/assertive.sets_0.0-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.sets"
cran = "assertive.sets"
version('0.0-3', sha256='876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3')

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@ -7,17 +7,14 @@
class RAssertiveStrings(RPackage):
"""assertive.strings: Assertions to Check Properties of Strings
"""Assertions to Check Properties of Strings.
A set of predicates and assertions for checking the
properties of strings. This is mainly for use by other
package developers who want to include run-time testing
features in their own packages. End-users will usually want
to use assertive directly."""
A set of predicates and assertions for checking the properties of strings.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.strings"
url = "https://cloud.r-project.org/src/contrib/assertive.strings_0.0-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.strings"
cran = "assertive.strings"
version('0.0-3', sha256='d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258')

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class RAssertiveTypes(RPackage):
"""assertive.types: Assertions to Check Types of Variables
"""Assertions to Check Types of Variables.
A set of predicates and assertions for checking the types
of variables. This is mainly for use by other package
developers who want to include run-time testing features in
their own packages. End-users will usually want to use
assertive directly."""
A set of predicates and assertions for checking the types of variables.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
homepage = "https://bitbucket.org/richierocks/assertive.types"
url = "https://cloud.r-project.org/src/contrib/assertive.types_0.0-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.types"
cran = "assertive.types"
version('0.0-3', sha256='ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f')

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var/spack/repos/builtin/packages/r-assertive/package.py
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class RAssertive(RPackage):
"""assertive: Readable Check Functions to Ensure Code Integrity
"""Readable Check Functions to Ensure Code Integrity.
Lots of predicates (is_* functions) to check the state of your
variables, and assertions (assert_* functions) to throw errors if
they aren't in the right form."""
Lots of predicates (is_* functions) to check the state of your variables,
and assertions (assert_* functions) to throw errors if they aren't in the
right form."""
homepage = "https://bitbucket.org/richierocks/assertive"
url = "https://cloud.r-project.org/src/contrib/assertive_0.3-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive"
cran = "assertive"
version('0.3-6', sha256='c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a')

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class RAssertthat(RPackage):
"""assertthat is an extension to stopifnot() that makes it easy to declare
the pre and post conditions that you code should satisfy, while also
producing friendly error messages so that your users know what they've done
wrong."""
"""Easy Pre and Post Assertions.
homepage = "https://cloud.r-project.org/package=assertthat"
url = "https://cloud.r-project.org/src/contrib/assertthat_0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertthat"
An extension to stopifnot() that makes it easy to declare the pre and post
conditions that you code should satisfy, while also producing friendly
error messages so that your users know what's gone wrong."""
cran = "assertthat"
version('0.2.1', sha256='85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f')
version('0.2.0', sha256='d73ef79b1e75293ed889a99571b237a95829c099f7da094d4763f83ea6fde5f2')

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@ -7,7 +7,7 @@
class RBackports(RPackage):
"""Reimplementations of Functions Introduced Since R-3.0.0
"""Reimplementations of Functions Introduced Since R-3.0.0.
Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
@ -16,9 +16,9 @@ class RBackports(RPackage):
functions or arguments by selectively importing specific backports to
support older installations."""
homepage = "https://github.com/r-lib/backports"
cran = "backports"
version('1.4.1', sha256='845c3c59fbb05e5a892c4231b955a0afdd331d82b7cc815bcff0672023242474')
version('1.4.0', sha256='e7611565d24a852ad8b08579a7c67ad9121c1bda148bade98c7bec686e8dabbf')
version('1.2.1', sha256='a2834bbd57e305e5d8010322f1906ea1789b3b5ba5eca77c5ff4248aceb7c2d5')
version('1.1.4', sha256='ee4b5efef22fa7ef27d7983ffcd31db52f81e1fbb7189c6e89ee09b69349ff03')

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@ -7,13 +7,13 @@
class RBase64(RPackage):
"""Compatibility wrapper to replace the orphaned package by Romain
Francois. New applications should use the 'openssl' or 'base64enc'
package instead."""
"""Base64 Encoder and Decoder.
homepage = "https://cloud.r-project.org/package=base64"
url = "https://cloud.r-project.org/src/contrib/base64_2.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/base64"
Compatibility wrapper to replace the orphaned package by Romain Francois.
New applications should use the 'openssl' or 'base64enc' package
instead."""
cran = "base64"
version('2.0', sha256='8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1')

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@ -7,12 +7,12 @@
class RBase64enc(RPackage):
"""This package provides tools for handling base64 encoding. It is more
"""Tools for base64 encoding.
This package provides tools for handling base64 encoding. It is more
flexible than the orphaned base64 package."""
homepage = "https://www.rforge.net/base64enc"
url = "https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/base64enc"
cran = "base64enc"
version('0.1-3', sha256='6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d')

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@ -7,7 +7,7 @@
class RBayesm(RPackage):
"""Bayesian Inference for Marketing/Micro-Econometrics
"""Bayesian Inference for Marketing/Micro-Econometrics.
Covers many important models used in marketing and micro-econometrics
applications. The package includes: Bayes Regression (univariate or
@ -29,9 +29,7 @@ class RBayesm(RPackage):
2005) and Bayesian Non- and Semi-Parametric Methods and Applications
(Princeton U Press 2014)."""
homepage = "https://cloud.r-project.org/package=bayesm"
url = "https://cloud.r-project.org/src/contrib/bayesm_3.1-0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bayesm"
cran = "bayesm"
version('3.1-4', sha256='061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94')
version('3.1-3', sha256='51e4827eca8cd4cf3626f3c2282543df7c392b3ffb843f4bfb386fe104642a10')

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@ -7,7 +7,7 @@
class RBayesplot(RPackage):
"""Plotting for Bayesian Models:
"""Plotting for Bayesian Models.
Plotting functions for posterior analysis, MCMC diagnostics, prior and
posterior predictive checks, and other visualizations to support the
@ -18,7 +18,6 @@ class RBayesplot(RPackage):
R packages for Bayesian modeling, particularly (but not exclusively)
packages interfacing with 'Stan'."""
homepage = "https://mc-stan.org/bayesplot/"
cran = "bayesplot"
version('1.8.1', sha256='d8d74201ea91fa5438714686ca22a947ec9375b6c12b0cfef010c57104b1aa2a')

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@ -7,12 +7,12 @@
class RBbmisc(RPackage):
"""Miscellaneous helper functions for and from B. Bischl and some other
guys, mainly for package development."""
"""Miscellaneous Helper Functions for B. Bischl.
homepage = "https://github.com/berndbischl/BBmisc"
url = "https://cloud.r-project.org/src/contrib/BBmisc_1.11.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BBmisc"
Miscellaneous helper functions for and from B. Bischl and some other guys,
mainly for package development."""
cran = "BBmisc"
version('1.11', sha256='1ea48c281825349d8642a661bb447e23bfd651db3599bf72593bfebe17b101d2')

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@ -7,11 +7,11 @@
class RBeanplot(RPackage):
"""Plots univariate comparison graphs, an alternative to
"""Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot).
Plots univariate comparison graphs, an alternative to
boxplot/stripchart/violin plot."""
homepage = "https://cloud.r-project.org/package=beanplot"
url = "https://cloud.r-project.org/src/contrib/beanplot_1.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/beanplot"
cran = "beanplot"
version('1.2', sha256='49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372')

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@ -7,10 +7,12 @@
class RBeeswarm(RPackage):
"""beeswarm: The Bee Swarm Plot, an Alternative to Stripchart"""
"""The Bee Swarm Plot, an Alternative to Stripchart.
homepage = "https://www.cbs.dtu.dk/~eklund/beeswarm/"
url = "https://cloud.r-project.org/src/contrib/beeswarm_0.2.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/beeswarm"
The bee swarm plot is a one-dimensional scatter plot like "stripchart", but
with closely-packed, non-overlapping points."""
cran = "beeswarm"
version('0.4.0', sha256='51f4339bf4080a2be84bb49a844c636625657fbed994abeaa42aead916c3d504')
version('0.2.3', sha256='0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843')

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var/spack/repos/builtin/packages/r-bfast/package.py
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@ -7,17 +7,37 @@
class RBfast(RPackage):
"""bfast: Breaks For Additive Season and Trend (BFAST)"""
"""Breaks for Additive Season and Trend.
homepage = "https://cloud.r-project.org/package=bfast"
url = "https://cloud.r-project.org/src/contrib/bfast_1.5.7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bfast"
Decomposition of time series into trend, seasonal, and remainder components
with methods for detecting and characterizing abrupt changes within the
trend and seasonal components. 'BFAST' can be used to analyze different
types of satellite image time series and can be applied to other
disciplines dealing with seasonal or non-seasonal time series, such as
hydrology, climatology, and econometrics. The algorithm can be extended to
label detected changes with information on the parameters of the fitted
piecewise linear models. 'BFAST' monitoring functionality is described in
Verbesselt et al. (2010) <doi:10.1016/j.rse.2009.08.014>. 'BFAST monitor'
provides functionality to detect disturbance in near real-time based on
'BFAST'- type models, and is described in Verbesselt et al. (2012)
<doi:10.1016/j.rse.2012.02.022>. 'BFAST Lite' approach is a flexible
approach that handles missing data without interpolation, and will be
described in an upcoming paper. Furthermore, different models can now be
used to fit the time series data and detect structural changes (breaks)."""
cran = "bfast"
version('1.6.1', sha256='aaf479af1924691cbec8c67c68005c00d97cead51b2b44863c18acd4cea453ee')
version('1.5.7', sha256='01585fe8944d05ebdb13795214077bc1365f0c0372e2a1f7edb914356dace558')
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r-strucchange', type=('build', 'run'))
depends_on('r@3.0.0:', type=('build', 'run'), when='@1.6.1:')
depends_on('r-strucchangercpp', type=('build', 'run'), when='@1.6.1:')
depends_on('r-zoo', type=('build', 'run'))
depends_on('r-forecast', type=('build', 'run'))
depends_on('r-sp', type=('build', 'run'))
depends_on('r-raster', type=('build', 'run'))
depends_on('r-rcpp@0.12.7:', type=('build', 'run'), when='@1.6.1:')
depends_on('r-rdpack@0.7:', type=('build', 'run'), when='@1.6.1:')
depends_on('r-strucchange', type=('build', 'run'), when='@:1.5.7')
depends_on('r-sp', type=('build', 'run'), when='@:1.5.7')
depends_on('r-raster', type=('build', 'run'), when='@:1.5.7')

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@ -7,13 +7,13 @@
class RBglr(RPackage):
"""BGLR: Bayesian Generalized Linear Regression"""
"""Bayesian Generalized Linear Regression."""
homepage = "https://cloud.r-project.org/package=BGLR"
url = "https://cloud.r-project.org/src/contrib/BGLR_1.0.8.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BGLR"
cran = "BGLR"
version('1.0.9', sha256='440a96f9f502e0d6ecc8c00720d1ccdbab5ee8223e1def6c930edaa9a9de9099')
version('1.0.8', sha256='5e969590d80b2f272c02a43b487ab1ffa13af386e0342993e6ac484fc82c9b95')
depends_on('r@3.5.0:', type=('build', 'run'))
depends_on('r-truncnorm', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'), when='@1.0.9:')

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@ -24,9 +24,9 @@ class RBh(RPackage):
'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit'
'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'."""
homepage = "https://cloud.r-project.org/package=BH"
cran = "BH"
version('1.78.0-0', sha256='3b9e9d07682013e0c06a396dda176b405eab99a7273eca6c40d1b4c4110e8cb3')
version('1.75.0-0', sha256='ae4c10992607dd697663f60675a46a5770851da159330bb63c4a68890bdd6f5a')
version('1.72.0-3', sha256='888ec1a3316bb69e1ba749b08ba7e0903ebc4742e3a185de8d148c13cddac8ab')
version('1.69.0-1', sha256='a0fd4364b7e368f09c56dec030823f52c16da0787580af7e4615eddeb99baca2')

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@ -7,15 +7,15 @@
class RBiasedurn(RPackage):
"""Statistical models of biased sampling in the form of univariate and
multivariate noncentral hypergeometric distributions, including
Wallenius' noncentral hypergeometric distribution and Fisher's
noncentral hypergeometric distribution (also called extended
hypergeometric distribution). See vignette("UrnTheory") for
explanation of these distributions."""
"""Biased Urn Model Distributions.
homepage = "https://www.agner.org/random/"
url = "https://cloud.r-project.org/src/contrib/BiasedUrn_1.07.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BiasedUrn/"
Statistical models of biased sampling in the form of univariate and
multivariate noncentral hypergeometric distributions, including Wallenius'
noncentral hypergeometric distribution and Fisher's noncentral
hypergeometric distribution (also called extended hypergeometric
distribution). See vignette("UrnTheory") for explanation of these
distributions."""
cran = "BiasedUrn"
version('1.07', sha256='2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e')

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var/spack/repos/builtin/packages/r-bibtex/package.py
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@ -7,13 +7,11 @@
class RBibtex(RPackage):
"""Bibtex Parser
"""Bibtex Parser.
Utility to parse a bibtex file."""
homepage = "https://cloud.r-project.org/package=bibtex"
url = "https://cloud.r-project.org/src/contrib/bibtex_0.4.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bibtex/"
cran = "bibtex"
version('0.4.2.3', sha256='7bad194920b412781ac9754ad41058d52d3cd7186e1851c2bce3640490e9bc6d')
version('0.4.2', sha256='1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372')

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@ -7,14 +7,23 @@
class RBigalgebra(RPackage):
"""This package provides arithmetic functions for R matrix
and big.matrix objects."""
"""'BLAS' and 'LAPACK' Routines for Native R Matrices and 'big.matrix'
Objects.
homepage = "https://r-forge.r-project.org/R/?group_id=556"
url = "https://cloud.r-project.org/src/contrib/Archive/bigalgebra/bigalgebra_0.8.4.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bigalgebra"
Provides arithmetic functions for R matrix and 'big.matrix' objects as well
as functions for QR factorization, Cholesky factorization, General
eigenvalue, and Singular value decomposition (SVD). A method matrix
multiplication and an arithmetic method -for matrix addition, matrix
difference- allows for mixed type operation -a matrix class object and a
big.matrix class object- and pure type operation for two big.matrix class
objects."""
cran = "bigalgebra"
version('1.0.1', sha256='ff7e261d0aa0e0f498e926d923ac62fc5cb783fa1f74bb2ff76a09167388a9d2')
version('1.0.0', sha256='f186b603bd660be0cc5b7a52c943e23e92fef264f0bc96a8858e38df6cfc4085')
version('0.8.4.2', sha256='29962468cbfa6416f8628563d5ed8c9f76089190311ff1c618f099ee8d9eea75')
depends_on('r-bigmemory@4.0.0:', type=('build', 'run'))
depends_on('r-bh', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'), when='@1.0.0:')

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@ -7,11 +7,11 @@
class RBigmemorySri(RPackage):
"""This package provides a shared resource interface
for the bigmemory and synchronicity packages."""
"""A shared resource interface for Bigmemory Project packages.
homepage = "https://cloud.r-project.org/web/packages/bigmemory.sri/index.html"
url = "https://cloud.r-project.org/src/contrib/bigmemory.sri_0.1.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bigmemory.sri"
This package provides a shared resource interface for the bigmemory and
synchronicity packages."""
cran = "bigmemory.sri"
version('0.1.3', sha256='55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155')

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class RBigmemory(RPackage):
"""Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use
memory-mapped files. Packages 'biganalytics', 'bigtabulate',
'synchronicity', and 'bigalgebra' provide advanced functionality."""
"""Manage Massive Matrices with Shared Memory and Memory-Mapped.
homepage = "https://cloud.r-project.org/web/packages/bigmemory/index.html"
url = "https://cloud.r-project.org/src/contrib/bigmemory_4.5.36.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bigmemory"
Files Create, store, access, and manipulate massive matrices. Matrices are
allocated to shared memory and may use memory-mapped files. Packages
'biganalytics', 'bigtabulate', 'synchronicity', and 'bigalgebra' provide
advanced functionality."""
cran = "bigmemory"
version('4.5.36', sha256='18c67fbe6344b2f8223456c4f19ceebcf6c1166255eab81311001fd67a45ef0e')

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@ -7,12 +7,12 @@
class RBindr(RPackage):
"""Provides a simple interface for creating active bindings where the
bound function accepts additional arguments."""
"""Parametrized Active Bindings.
homepage = "https://github.com/krlmlr/bindr"
url = "https://cloud.r-project.org/src/contrib/bindr_0.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bindr"
Provides a simple interface for creating active bindings where the bound
function accepts additional arguments."""
cran = "bindr"
version('0.1.1', sha256='7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0')
version('0.1', sha256='cca166612eeafd6e1c961b34aaf177f9b47f8b4bc37520e277b9920eaa8b2535')

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class RBindrcpp(RPackage):
"""Provides an easy way to fill an environment with active bindings that
call a C++ function."""
"""An 'Rcpp' Interface to Active Bindings.
homepage = "https://github.com/krlmlr/bindrcpp"
url = "https://cloud.r-project.org/src/contrib/bindrcpp_0.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bindrcpp"
Provides an easy way to fill an environment with active bindings that call
a C++ function."""
cran = "bindrcpp"
version('0.2.2', sha256='48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467')
version('0.2', sha256='d0efa1313cb8148880f7902a4267de1dcedae916f28d9a0ef5911f44bf103450')

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@ -7,7 +7,7 @@
class RBio3d(RPackage):
"""Biological Structure Analysis
"""Biological Structure Analysis.
Utilities to process, organize and explore protein structure, sequence and
dynamics data. Features include the ability to read and write structure,
@ -22,10 +22,9 @@ class RBio3d(RPackage):
to work with biological sequence and structural data. Please refer to the
URLs below for more information."""
homepage = "http://thegrantlab.org/bio3d/"
url = "https://cloud.r-project.org/src/contrib/bio3d_2.3-4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bio3d"
cran = "bio3d"
version('2.4-2', sha256='91415766cda0f96557e6bc568dbce8d44254a9460f2e2d0beed0ce14ffad6ccb')
version('2.4-1', sha256='679fbd87fe9fb82a65427d281d3b68906509e411270cd87d2deb95d404333c1f')
version('2.3-4', sha256='f9b39ab242cbedafcd98c1732cb1f5c0dd9ef66e28be39695e3420dd93e2bafe')

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var/spack/repos/builtin/packages/r-biocmanager/package.py
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@ -7,10 +7,11 @@
class RBiocmanager(RPackage):
"""BiocManager: Access the Bioconductor Project Package Repository"""
"""Access the Bioconductor Project Package Repository.
homepage = "https://cloud.r-project.org/package=BiocManager"
url = "https://cloud.r-project.org/src/contrib/BiocManager_1.30.10.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BiocManager"
A convenient tool to install and update Bioconductor packages."""
cran = "BiocManager"
version('1.30.16', sha256='75a754a55192ef6aa6ac9b054fd5381ff03fe6bb8b2e033eb8143da930ef3855')
version('1.30.10', sha256='f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e')

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var/spack/repos/builtin/packages/r-biom-utils/package.py
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class RBiomUtils(RPackage):
"""Provides utilities to facilitate import, export and computation with
the BIOM (Biological Observation Matrix) format (https://biom-format.org/).
"""
"""Utilities for the BIOM (Biological Observation Matrix) Format.
homepage = "https://github.com/braithwaite/BIOM.utils/"
url = "https://cloud.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/biom/"
Provides utilities to facilitate import, export and computation with the
BIOM (Biological Observation Matrix) format (https://biom-format.org/)."""
cran = "BIOM.utils"
version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375')

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@ -7,7 +7,9 @@
class RBiomartr(RPackage):
"""Perform large scale genomic data retrieval and functional annotation
"""Genomic Data Retrieval.
Perform large scale genomic data retrieval and functional annotation
retrieval. This package aims to provide users with a standardized way to
automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and
metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',
@ -19,9 +21,7 @@ class RBiomartr(RPackage):
Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as
'ENSEMBL' and 'ENSEMBLGENOMES' with only one command."""
homepage = "https://docs.ropensci.org/biomartr"
url = "https://cloud.r-project.org/src/contrib/biomartr_0.9.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/biomartr"
cran = "biomartr"
version('0.9.2', sha256='d88085696e9c5614828602254c33f2cdd3bbfeebc2f21a705eee3cb961097c89')

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class RBit(RPackage):
"""Classes and Methods for Fast Memory-Efficient Boolean Selections
"""Classes and Methods for Fast Memory-Efficient Boolean Selections.
Provided are classes for boolean and skewed boolean vectors, fast boolean
methods, fast unique and non-unique integer sorting, fast set operations on
sorted and unsorted sets of integers, and foundations for ff (range index,
compression, chunked processing)."""
homepage = "https://cloud.r-project.org/package=bit"
url = "https://cloud.r-project.org/src/contrib/bit_1.1-12.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bit"
cran = "bit"
version('4.0.4', sha256='e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168')
version('1.1-14', sha256='5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254')

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var/spack/repos/builtin/packages/r-bit64/package.py
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@ -7,7 +7,7 @@
class RBit64(RPackage):
"""A S3 Class for Vectors of 64bit Integers
"""A S3 Class for Vectors of 64bit Integers.
Package 'bit64' provides serializable S3 atomic 64bit (signed) integers.
These are useful for handling database keys and exact counting in +-2^63.
@ -21,13 +21,11 @@ class RBit64(RPackage):
active data exploration and manipulation and optionally leverage
caching."""
homepage = "https://cloud.r-project.org/package=bit64"
url = "https://cloud.r-project.org/src/contrib/bit64_0.9-7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bit64"
cran = "bit64"
version('4.0.5', sha256='25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578')
version('0.9-7', sha256='7b9aaa7f971198728c3629f9ba1a1b24d53db5c7e459498b0fdf86bbd3dff61f')
depends_on('r@3.0.1:', type=('build', 'run'))
depends_on('r-bit@1.1-12:', when='@:9.9-7', type=('build', 'run'))
depends_on('r-bit@4.0.0:', when='@4.0.5:', type=('build', 'run'))
depends_on('r-bit@1.1-12:', type=('build', 'run'))
depends_on('r-bit@4.0.0:', type=('build', 'run'), when='@4.0.5:')

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var/spack/repos/builtin/packages/r-bitops/package.py
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@ -8,10 +8,11 @@
class RBitops(RPackage):
"""Functions for bitwise operations on integer vectors."""
"""Bitwise Operations.
homepage = "https://cloud.r-project.org/package=bitops"
url = "https://cloud.r-project.org/src/contrib/bitops_1.0-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bitops"
Functions for bitwise operations on integer vectors."""
cran = "bitops"
version('1.0-7', sha256='e9b5fc92c39f94a10cd0e13f3d6e2a9c17b75ea01467077a51d47a5f708517c4')
version('1.0-6', sha256='9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c')

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var/spack/repos/builtin/packages/r-blavaan/package.py
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@ -7,30 +7,37 @@
class RBlavaan(RPackage):
"""Bayesian Latent Variable Analysis:
"""Bayesian Latent Variable Analysis.
Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve
models."""
Fit a variety of Bayesian latent variable models, including confirmatory factor
analysis, structural equation models, and latent growth curve models.
References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al.
(2021) <doi:10.18637/jss.v100.i06>."""
cran = "blavaan"
version('0.4-1', sha256='afb077d72f84ef0b6f45ef2ccb8335358042943c32a3472a9ca239ebca1c4aa4')
version('0.3-18', sha256='373960a22fc741c765e2ad2e0d99c1d4b2162f5f2a230ef314778ef8f433e865')
version('0.3-15', sha256='f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f')
depends_on('r@3.5.0:', type=('build', 'run'))
depends_on('r-lavaan@0.6-5:', type=('build', 'run'))
depends_on('r-lavaan@0.6-7:', type=('build', 'run'), when='@0.3-18:')
depends_on('r-lavaan@0.6-10:', type=('build', 'run'), when='@0.4-1:')
depends_on('r-rcpp@0.12.15:', type=('build', 'run'))
depends_on('r-rcppparallel@5.0.1:', type=('build', 'run'))
depends_on('r-mcmcpack', type=('build', 'run'))
depends_on('r-coda', type=('build', 'run'))
depends_on('r-mnormt', type=('build', 'run'))
depends_on('r-nonnest2@0.5-5:', type=('build', 'run'))
depends_on('r-loo@2.0:', type=('build', 'run'))
depends_on('r-rstan@2.19.2:', type=('build', 'run'))
depends_on('r-rstan@2.21.2:', type=('build', 'run'), when='@0.3-18:')
depends_on('r-rstantools@1.5.0:', type=('build', 'run'))
depends_on('r-rcppparallel@5.0.1:', type=('build', 'run'))
depends_on('r-bayesplot', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-future-apply', type=('build', 'run'))
depends_on('r-tmvnsim', type=('build', 'run'), when='@0.3-18:')
depends_on('r-stanheaders@2.18.1:', type=('build', 'run'))
depends_on('r-bh@1.69.0:', type=('build', 'run'))
depends_on('r-rcppeigen@0.3.3.4.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-blob/package.py
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@ -7,14 +7,13 @@
class RBlob(RPackage):
"""A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
"""A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS').
R's raw vector is useful for storing a single binary object.
What if you want to put a vector of them in a data frame? The blob
package provides the blob object, a list of raw vectors, suitable
for use as a column in data frame."""
R's raw vector is useful for storing a single binary object. What if you
want to put a vector of them in a data frame? The blob package provides the
blob object, a list of raw vectors, suitable for use as a column in data
frame."""
homepage = "https://blob.tidyverse.org"
cran = "blob"
version('1.2.2', sha256='4976053c65994c769a4c22b4553bea0bd9c623b3b991dbaf023d2a164770c7fa')
@ -22,8 +21,9 @@ class RBlob(RPackage):
version('1.2.0', sha256='1af1cfa28607bc0e2f1f01598a00a7d5d1385ef160a9e79e568f30f56538e023')
version('1.1.0', sha256='16d6603df3ddba177f0ac4d9469c938f89131c4bf8834345db838defd9ffea16')
depends_on('r-tibble', when='@:1.1.0', type=('build', 'run'))
depends_on('r-prettyunits', when='@1.2.0', type=('build', 'run'))
depends_on('r-rlang', when='@1.2.0:', type=('build', 'run'))
depends_on('r-vctrs@0.2.0:', when='@1.2.0:', type=('build', 'run'))
depends_on('r-vctrs@0.2.1:', when='@1.2.1:', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'), when='@1.2.0:')
depends_on('r-vctrs@0.2.0:', type=('build', 'run'), when='@1.2.0:')
depends_on('r-vctrs@0.2.1:', type=('build', 'run'), when='@1.2.1:')
depends_on('r-prettyunits', type=('build', 'run'), when='@1.2.0')
depends_on('r-tibble', type=('build', 'run'), when='@:1.1.0')

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var/spack/repos/builtin/packages/r-blockmodeling/package.py
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@ -7,21 +7,21 @@
class RBlockmodeling(RPackage):
"""Generalized and Classical Blockmodeling of Valued Networks
"""Generalized and Classical Blockmodeling of Valued Networks.
This is primarily meant as an implementation of generalized blockmodeling
for valued networks."""
homepage = "https://cloud.r-project.org/package=blockmodeling"
url = "https://cloud.r-project.org/src/contrib/blockmodeling_0.3.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/blockmodeling/"
cran = "blockmodeling"
version('1.0.5', sha256='18c227bb52f28aff4dae8929563474e3e006e238438c823b67dc6baa897f88ed')
version('1.0.0', sha256='f10c41fff56dc7dc46dffbceacb8ff905eca06578d610a5a590fb408f0149cfc')
version('0.3.4', sha256='a269c83669dd5294cff0adddab36bc023db6a276a06b74b1fa94b7e407486987')
version('0.3.1', sha256='39e8360400cec6baa920d5589d4e779568bdf2954f7331be0e3cadf22a217d31')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-doparallel', when='@:0.3.4', type=('build', 'run'))
depends_on('r-dorng', when='@:0.3.4', type=('build', 'run'))
depends_on('r-foreach', when='@:0.3.4', type=('build', 'run'))
depends_on('r-doparallel', type=('build', 'run'), when='@:0.3.4')
depends_on('r-dorng', type=('build', 'run'), when='@:0.3.4')
depends_on('r-foreach', type=('build', 'run'), when='@:0.3.4')

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var/spack/repos/builtin/packages/r-bmp/package.py
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@ -7,12 +7,12 @@
class RBmp(RPackage):
"""Reads Windows BMP format images. Currently limited to 8 bit greyscale
"""Read Windows Bitmap (BMP) Images.
Reads Windows BMP format images. Currently limited to 8 bit greyscale
images and 24,32 bit (A)RGB images. Pure R implementation without external
dependencies."""
homepage = "https://cloud.r-project.org/package=bmp"
url = "https://cloud.r-project.org/src/contrib/bmp_0.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bmp"
cran = "bmp"
version('0.3', sha256='bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649')

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var/spack/repos/builtin/packages/r-bookdown/package.py
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@ -7,15 +7,14 @@
class RBookdown(RPackage):
"""Authoring Books and Technical Documents with R Markdown
"""Authoring Books and Technical Documents with R Markdown.
Output formats and utilities for authoring books and technical
documents with R Markdown."""
Output formats and utilities for authoring books and technical documents
with R Markdown."""
homepage = "https://cloud.r-project.org/package=bookdown"
url = "https://cloud.r-project.org/src/contrib/bookdown_0.5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bookdown"
cran = "bookdown"
version('0.24', sha256='8bead2a20542d05f643fe77a949689a17b0ae9ff23efbb918ddab47597db1be3')
version('0.21', sha256='47c0fa7a65da83753c2f445e0e972913f9203460f1daae3ab255d0d4b30eba76')
version('0.12', sha256='38eb4c5b877ccd85b16cfe74a48c3bc53de2f276da98e5515f37e7a06e065bb0')
version('0.5', sha256='b7331fd56f64bd2bddc34e2a188fc491f9ff5308f44f7e3151721247f21ca67e')
@ -23,11 +22,15 @@ class RBookdown(RPackage):
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'))
depends_on('r-rmarkdown@2.4:', when='@0.21:', type=('build', 'run'))
depends_on('r-xfun@0.6:', when='@:0.12', type=('build', 'run'))
depends_on('r-xfun@0.13:', when='@0.21:', type=('build', 'run'))
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('r-knitr@1.31:', type=('build', 'run'), when='@0.24:')
depends_on('r-rmarkdown@1.12:', type=('build', 'run'))
depends_on('r-rmarkdown@2.4:', type=('build', 'run'), when='@0.21:')
depends_on('r-rmarkdown@2.9:', type=('build', 'run'), when='@0.24:')
depends_on('r-jquerylib', type=('build', 'run'), when='@0.24:')
depends_on('r-xfun@0.6:', type=('build', 'run'))
depends_on('r-xfun@0.13:', type=('build', 'run'), when='@0.21:')
depends_on('r-xfun@0.22:', type=('build', 'run'), when='@0.24:')
depends_on('r-tinytex@0.12:', type=('build', 'run'), when='@0.12:')
depends_on('r-yaml@2.1.14:', type=('build', 'run'))
depends_on('r-yaml@2.1.19:', type=('build', 'run'), when='@0.21:')
depends_on('pandoc@1.17.2:')

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var/spack/repos/builtin/packages/r-boot/package.py
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@ -7,15 +7,13 @@
class RBoot(RPackage):
"""Bootstrap Functions (Originally by Angelo Canty for S)
"""Bootstrap Functions (Originally by Angelo Canty for S).
Functions and datasets for bootstrapping from the book "Bootstrap
Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997,
CUP), originally written by Angelo Canty for S."""
Functions and datasets for bootstrapping from the book "Bootstrap Methods
and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP),
originally written by Angelo Canty for S."""
homepage = "https://cloud.r-project.org/package=boot"
url = "https://cloud.r-project.org/src/contrib/boot_1.3-18.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/boot"
cran = "boot"
version('1.3-28', sha256='9f7158fd2714659f590c3955651893dc24bd8f39196bc5a4cc35b0b031744a32')
version('1.3-25', sha256='464835fcb453072346ce49e4ae318e04c9dba682349be49db616623b6088fbbe')

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var/spack/repos/builtin/packages/r-boruta/package.py
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@ -7,15 +7,13 @@
class RBoruta(RPackage):
"""An all relevant feature selection wrapper algorithm. It finds
relevant features by comparing original attributes' importance
with importance achievable at random, estimated using their
permuted copies (shadows).
"""
"""Wrapper Algorithm for All Relevant Feature Selection.
homepage = "https://cloud.r-project.org/package=Boruta"
url = "https://cloud.r-project.org/src/contrib/Boruta_7.0.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/Boruta"
An all relevant feature selection wrapper algorithm. It finds relevant
features by comparing original attributes' importance with importance
achievable at random, estimated using their permuted copies (shadows)."""
cran = "Boruta"
version('7.0.0', sha256='6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78')
version('6.0.0', sha256='1c9a7aabe09f040e147f6c614f5fe1d0b951d3b0f0024161fbb4c31da8fae8de')

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var/spack/repos/builtin/packages/r-brew/package.py
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@ -7,12 +7,12 @@
class RBrew(RPackage):
"""brew implements a templating framework for mixing text and R code for
"""Templating Framework for Report Generation.
Brew implements a templating framework for mixing text and R code for
report generation. brew template syntax is similar to PHP, Ruby's erb
module, Java Server Pages, and Python's psp module."""
homepage = "https://cloud.r-project.org/package=brew"
url = "https://cloud.r-project.org/src/contrib/brew_1.0-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/brew"
cran = "brew"
version('1.0-6', sha256='d70d1a9a01cf4a923b4f11e4374ffd887ad3ff964f35c6f9dc0f29c8d657f0ed')

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var/spack/repos/builtin/packages/r-bridgesampling/package.py
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@ -7,7 +7,7 @@
class RBridgesampling(RPackage):
"""Bridge Sampling for Marginal Likelihoods and Bayes Factors:
"""Bridge Sampling for Marginal Likelihoods and Bayes Factors.
Provides functions for estimating marginal likelihoods, Bayes factors,
posterior model probabilities, and normalizing constants in general, via
@ -15,7 +15,6 @@ class RBridgesampling(RPackage):
<http://www3.stat.sinica.edu.tw/statistica/j6n4/j6n43/j6n43.htm>). Gronau,
Singmann, & Wagenmakers (2020) <doi:10.18637/jss.v092.i10>."""
homepage = "https://github.com/quentingronau/bridgesampling"
cran = "bridgesampling"
version('1.1-2', sha256='54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b')

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var/spack/repos/builtin/packages/r-brio/package.py
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@ -7,13 +7,12 @@
class RBrio(RPackage):
"""Basic R Input Output
"""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"
cran = "brio"
version('1.1.3', sha256='eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6')

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var/spack/repos/builtin/packages/r-brms/package.py
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@ -7,7 +7,7 @@
class RBrms(RPackage):
"""Bayesian Regression Models using 'Stan':
"""Bayesian Regression Models using 'Stan'.
Fit Bayesian generalized (non-)linear multivariate multilevel models using
'Stan' for full Bayesian inference. A wide range of distributions and link
@ -25,7 +25,6 @@ class RBrms(RPackage):
<doi:10.18637/jss.v080.i01>; Burkner (2018) <doi:10.32614/RJ-2018-017>;
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>."""
homepage = "https://github.com/paul-buerkner/brms"
cran = "brms"
version('2.16.3', sha256='68302b10b5264f72d163d01c17792c002306cf37f0ee778dcec4c7e118f923e1')
@ -37,13 +36,12 @@ class RBrms(RPackage):
depends_on('r-rstan@2.19.2:', type=('build', 'run'))
depends_on('r-ggplot2@2.0.0:', type=('build', 'run'))
depends_on('r-loo@2.3.1:', type=('build', 'run'))
depends_on('r-posterior@1.0.0:', when='@2.16:', type=('build', 'run'))
depends_on('r-posterior@1.0.0:', type=('build', 'run'), when='@2.16:')
depends_on('r-matrix@1.1.1:', type=('build', 'run'))
depends_on('r-mgcv@1.8-13:', type=('build', 'run'))
depends_on('r-rstantools@2.1.1:', type=('build', 'run'))
depends_on('r-bayesplot@1.5.0:', type=('build', 'run'))
depends_on('r-shinystan@2.4.0:', type=('build', 'run'))
depends_on('r-projpred@2.0.0:', when='@:2.16.1', type=('build', 'run'))
depends_on('r-bridgesampling@0.3-0:', type=('build', 'run'))
depends_on('r-glue@1.3.0:', type=('build', 'run'))
depends_on('r-future@1.19.0:', type=('build', 'run'))
@ -53,3 +51,5 @@ class RBrms(RPackage):
depends_on('r-coda', type=('build', 'run'))
depends_on('r-abind', type=('build', 'run'))
depends_on('r-backports', type=('build', 'run'))
depends_on('r-projpred@2.0.0:', type=('build', 'run'), when='@:2.16.1')

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var/spack/repos/builtin/packages/r-brobdingnag/package.py
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@ -7,13 +7,12 @@
class RBrobdingnag(RPackage):
"""Very Large Numbers in R:
"""Very Large Numbers in R.
Handles very large numbers in R. Real numbers are held using their natural
logarithms, plus a logical flag indicating sign. The package includes a
vignette that gives a step-by-step introduction to using S4 methods."""
homepage = "https://github.com/RobinHankin/Brobdingnag.git"
cran = "Brobdingnag"
version('1.2-6', sha256='19eccaed830ce9d93b70642f6f126ac66722a98bbd48586899cc613dd9966ad4')

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var/spack/repos/builtin/packages/r-broom/package.py
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@ -7,7 +7,7 @@
class RBroom(RPackage):
"""Convert Statistical Objects into Tidy Tibbles
"""Convert Statistical Objects into Tidy Tibbles.
Summarizes key information about statistical objects in tidy tibbles. This
makes it easy to report results, create plots and consistently work with
@ -18,9 +18,10 @@ class RBroom(RPackage):
measures like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence measures."""
homepage = "https://github.com/tidyverse/broom"
cran = "broom"
version('0.7.12', sha256='04fac12b2546689603a474fb92a0572f4241ae87b51b21b0808814a489227bd9')
version('0.7.11', sha256='9e3999d2635ac72e8f4c3a81decd50ee5d464c001c155375b5a970a629ba2e19')
version('0.7.10', sha256='129fd5a53abef7f42b7efac6c64ebd71269b136aa648846d640562357927464f')
version('0.7.9', sha256='1d5695f97b378b2b77fb8f64a4a54b72b278913d4adf9d61a7ca4f38a1c7c5fc')
version('0.7.3', sha256='de5650e46ca6884876b63bc401d22bef9eace671147774466406d43324aebc2f')
@ -29,22 +30,22 @@ class RBroom(RPackage):
version('0.4.2', sha256='9f409413623cf25e7110452e6215353af5114f7044d73af182bd6c10971c5a44')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-backports', when='@0.5.0:', type=('build', 'run'))
depends_on('r-backports', type=('build', 'run'), when='@0.5.0:')
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-dplyr@1.0.0:', type=('build', 'run'), when='@0.7.3:')
depends_on('r-ellipsis', type=('build', 'run'), when='@0.7.3:')
depends_on('r-generics@0.0.2:', type=('build', 'run'), when='@0.5.1:')
depends_on('r-glue', type=('build', 'run'), when='@0.7.3:')
depends_on('r-purrr', type=('build', 'run'), when='@0.5.0:')
depends_on('r-rlang', type=('build', 'run'), when='@0.7.3:')
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-tibble', type=('build', 'run'), when='@0.5.0:')
depends_on('r-tibble@3.0.0:', type=('build', 'run'), when='@0.7.3:')
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-tidyr@1.0.0:', when='@0.7.3:', type=('build', 'run'))
depends_on('r-ggplot2', when='@0.7.10:', type=('build', 'run'))
depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@0.7.3:')
depends_on('r-ggplot2', type=('build', 'run'), when='@0.7.10:')
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'))
depends_on('r-plyr', type=('build', 'run'), when='@:0.4.2')
depends_on('r-psych', type=('build', 'run'), when='@:0.4.2')
depends_on('r-reshape2', type=('build', 'run'), when='@:0.5.2')
depends_on('r-nlme', type=('build', 'run'), when='@:0.5.2')

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@ -0,0 +1,26 @@
# Copyright 2013-2022 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 RBslib(RPackage):
"""Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'.
Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via
'Bootstrap' 'Sass'. Supports both 'Bootstrap' 3 and 4 as well as their
various 'Bootswatch' themes. An interactive widget is also provided for
previewing themes in real time."""
cran = "bslib"
version('0.3.1', sha256='5f5cb56e5cab9039a24cd9d70d73b69c2cab5b2f5f37afc15f71dae0339d9849')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-htmltools@0.5.2:', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-sass@0.4.0:', type=('build', 'run'))
depends_on('r-jquerylib@0.1.3:', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'))

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@ -8,15 +8,14 @@
class RC50(RPackage):
"""C5.0 Decision Trees and Rule-Based Models
"""C5.0 Decision Trees and Rule-Based Models.
C5.0 decision trees and rule-based models for pattern recognition that
extend the work of Quinlan (1993, ISBN:1-55860-238-0)."""
homepage = "https://cloud.r-project.org/package=C50"
url = "https://cloud.r-project.org/src/contrib/C50_0.1.0-24.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/C50"
cran = "C50"
version('0.1.5', sha256='f0c17b4830371832ca64f5fcc702351a394ee90b384e0865307de9447f3f16d7')
version('0.1.3.1', sha256='0b151ba8deef50ab2e2ad8469d87f54f0c6ab862f5c790ed8bb16cb3b8027546')
version('0.1.2', sha256='8f459856e0309274bee24462b7145db4eba1d71031c236db39000a5375bdfaba')
version('0.1.1', sha256='03bc1fc2f64bcd5c680568a24902deafab1965074a66f8802bc4cd0335bd01df')
@ -24,5 +23,6 @@ class RC50(RPackage):
depends_on('r@2.10.0:', type=('build', 'run'))
depends_on('r-partykit', type=('build', 'run'))
depends_on('r-cubist@0.2.1:', when='@:0.1.2', type=('build', 'run'))
depends_on('r-cubist@0.2.3:', when='@0.1.3.1:', type=('build', 'run'))
depends_on('r-cubist@0.2.1:', type=('build', 'run'))
depends_on('r-cubist@0.2.3:', type=('build', 'run'), when='@0.1.3.1:')
depends_on('r-cubist@0.3.0:', type=('build', 'run'), when='@0.1.5:')

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var/spack/repos/builtin/packages/r-ca/package.py
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@ -8,14 +8,12 @@
class RCa(RPackage):
"""Simple, Multiple and Joint Correspondence Analysis
"""Simple, Multiple and Joint Correspondence Analysis.
Computation and visualization of simple, multiple and joint
correspondence analysis."""
Computation and visualization of simple, multiple and joint correspondence
analysis."""
homepage = "http://www.carme-n.org/?sec=ca"
url = "https://cloud.r-project.org/src/contrib/ca_0.71.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ca"
cran = "ca"
version('0.71.1', sha256='040c2fc94c356075f116cc7cd880530b3c9e02206c0035182c03a525ee99b424')

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@ -0,0 +1,21 @@
# Copyright 2013-2022 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 RCachem(RPackage):
"""Cache R Objects with Automatic Pruning.
Key-value stores with automatic pruning. Caches can limit either their
total size or the age of the oldest object (or both), automatically pruning
objects to maintain the constraints."""
cran = "cachem"
version('1.0.6', sha256='9a9452f7bcf3f79436c418b3c3290449fb8fd338714d9b992153754d112f1864')
depends_on('r-rlang', type=('build', 'run'))
depends_on('r-fastmap', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-cairo/package.py
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@ -9,7 +9,7 @@
class RCairo(RPackage):
"""R graphics device using cairo graphics library for creating high-quality
bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11
and Win32) output
and Win32) output.
R graphics device using cairographics library that can be used to create
high-quality vector (PDF, PostScript and SVG) and bitmap output
@ -23,10 +23,9 @@ class RCairo(RPackage):
support or anti-aliasing. Backends are modular such that any subset of
backends is supported."""
homepage = "https://cloud.r-project.org/package=Cairo"
url = "https://cloud.r-project.org/src/contrib/Cairo_1.5-9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/Cairo"
cran = "Cairo"
version('1.5-14', sha256='067751face3b5771e72f9fb49bfeefb3a7bbecc060b672ab4393cb5935204c7b')
version('1.5-12.2', sha256='dd524105c83b82b5c3b3ee2583ef90d4cafa54b0c29817dac48b425b79f90f92')
version('1.5-10', sha256='7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5')
version('1.5-9', sha256='2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4')

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var/spack/repos/builtin/packages/r-callr/package.py
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@ -7,13 +7,12 @@
class RCallr(RPackage):
"""Call R from R
"""Call R from R.
It is sometimes useful to perform a computation in a separate R process,
without affecting the current R process at all. This packages does exactly
that."""
homepage = "https://github.com/MangoTheCat/callr"
cran = "callr"
version('3.7.0', sha256='d67255148595c6d0ba4c4d241bc9f6b5e00cafe25fdc13e38c10acc38653360a')
@ -24,6 +23,6 @@ class RCallr(RPackage):
version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7')
version('1.0.0', sha256='2c56808c723aba2ea8a8b6bbdc9b8332c96f59b119079861dd52f5988c27f715')
depends_on('r-processx@3.4.0:', when='@3.0.0:', type=('build', 'run'))
depends_on('r-processx@3.5.0:', when='@3.6.0:', type=('build', 'run'))
depends_on('r-r6', when='@3.0.0:', type=('build', 'run'))
depends_on('r-processx@3.4.0:', type=('build', 'run'), when='@3.0.0:')
depends_on('r-processx@3.5.0:', type=('build', 'run'), when='@3.6.0:')
depends_on('r-r6', type=('build', 'run'), when='@3.0.0:')

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var/spack/repos/builtin/packages/r-car/package.py
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@ -7,12 +7,11 @@
class RCar(RPackage):
"""Companion to Applied Regression
"""Companion to Applied Regression.
Functions and Datasets to Accompany J. Fox and S. Weisberg, An R
Companion to Applied Regression, Second Edition, Sage, 2011."""
Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion
to Applied Regression, Second Edition, Sage, 2011."""
homepage = "https://r-forge.r-project.org/projects/car/"
cran = "car"
version('3.0-12', sha256='b899a6efae3842a90a2349d381dbcf4b4ed36bd03108ebe7380e81120e457302')
@ -23,17 +22,17 @@ class RCar(RPackage):
version('2.1-4', sha256='fd39cf1750cb560a66623fea3fa9e6a94fc24e3dc36367aff24df7d0743edb28')
version('2.1-2', sha256='8cc3e57f172c8782a08960b508906d3201596a21f4b6c1dab8d4e59353093652')
depends_on('r@3.2.0:', when='@:3.0-2', type=('build', 'run'))
depends_on('r@3.5.0:', when='@3.0-3:', type=('build', 'run'))
depends_on('r-cardata@3.0-0:', when='@3.0:', type=('build', 'run'))
depends_on('r-abind', when='@3.0:', type=('build', 'run'))
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@3.0-3:')
depends_on('r-cardata@3.0-0:', type=('build', 'run'), when='@3.0:')
depends_on('r-abind', type=('build', 'run'), when='@3.0:')
depends_on('r-mass', type=('build', 'run'))
depends_on('r-mgcv', type=('build', 'run'))
depends_on('r-nnet', type=('build', 'run'))
depends_on('r-pbkrtest@0.4-4:', type=('build', 'run'))
depends_on('r-quantreg', type=('build', 'run'))
depends_on('r-maptools', when='@3.0:', type=('build', 'run'))
depends_on('r-rio', when='@3.0:3.0-11', type=('build', 'run'))
depends_on('r-lme4@1.1-27.1:', when='@3.0-11:', type=('build', 'run'))
depends_on('r-lme4', when='@3.0:', type=('build', 'run'))
depends_on('r-nlme', when='@3.0:', type=('build', 'run'))
depends_on('r-maptools', type=('build', 'run'), when='@3.0:')
depends_on('r-rio', type=('build', 'run'), when='@3.0:3.0-11')
depends_on('r-lme4@1.1-27.1:', type=('build', 'run'), when='@3.0-11:')
depends_on('r-lme4', type=('build', 'run'), when='@3.0:')
depends_on('r-nlme', type=('build', 'run'), when='@3.0:')

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@ -7,19 +7,19 @@
class RCaracas(RPackage):
"""Computer Algebra
"""Computer Algebra.
Computer algebra via the 'SymPy' library (<https://www.sympy.org/>). This
makes it possible to solve equations symbolically, find symbolic integrals,
symbolic sums and other important quantities."""
homepage = "https://cloud.r-project.org/package=caracas"
url = "https://cloud.r-project.org/src/contrib/caracas_1.0.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caracas"
cran = "caracas"
version('1.1.1', sha256='e14487c9492417cf5c7d7373c37dbb4fea4d91180a1a03154e51eaa7878b2769')
version('1.0.1', sha256='2482dd7b77791243b8174cb41b80b735c3ebd7db837bbf991127514f492af594')
version('1.0.0', sha256='0da6f1d94d1dacb1c11a3635bdff8f7cd8f84373deffa7126636d0876d48e42b')
depends_on('r@3.0:', type=('build', 'run'))
depends_on('r-reticulate@1.14:', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'), when='@1.1.1:')
depends_on('python@3.6:', type=('build', 'run'))

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@ -7,17 +7,16 @@
class RCardata(RPackage):
"""Companion to Applied Regression Data Sets
"""Companion to Applied Regression Data Sets.
Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied
Regression, Third Edition, Sage (2019)."""
homepage = "https://r-forge.r-project.org/projects/car/"
url = "https://cloud.r-project.org/src/contrib/carData_3.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/carData"
cran = "carData"
version('3.0-5', sha256='02e77159b33e3afb8cd9cfab11cf5a996a93175f924b07d991ce44bc6e16451a')
version('3.0-4', sha256='cda6f5e3efc1d955a4a0625e9c33f90d49f5455840e88b3bd757129b86044724')
version('3.0-2', sha256='3b5c4eff1cc1e456a5331084774503eaa06cf61fb7acf6b9e8a6bfabd5735494')
depends_on('r@3.0:', type=('build', 'run'))
depends_on('r@3.5:', when='@3.0-4:', type=('build', 'run'))
depends_on('r@3.5:', type=('build', 'run'), when='@3.0-4:')

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@ -7,15 +7,14 @@
class RCaret(RPackage):
"""Classification and Regression Training
"""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"
cran = "caret"
version('6.0-90', sha256='e851a4ed7d939c665e57e3551a5464b09fe4285e7c951236efdd890b0da866bc')
version('6.0-86', sha256='da4a1c7c3fbf645c5b02871e563a77404622b83623f0d1c5dc1425de7aa4ce37')
version('6.0-84', sha256='a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d')
version('6.0-83', sha256='9bde5e4da1f0b690bfe06c2439c0136504e851a8d360bf56b644f171fe20dcef')
@ -23,17 +22,19 @@ class RCaret(RPackage):
version('6.0-70', sha256='21c5bdf7cf07bece38729465366564d8ca104c2466ee9fd800ca1fd88eb82f38')
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@3.2.0:', type=('build', 'run'), when='@6.0-82:')
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-lattice@0.20:', type=('build', 'run'))
depends_on('r-e1071', type=('build', 'run'), when='@6.0-90:')
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-modelmetrics@1.2.2.2:', type=('build', 'run'), when='@6.0-86:')
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-proc', type=('build', 'run'), when='@6.0-86:')
depends_on('r-recipes@0.1.4:', type=('build', 'run'), when='@6.0-83:6.0-84')
depends_on('r-recipes@0.1.10:', type=('build', 'run'), when='@6.0-86:')
depends_on('r-reshape2', 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'))
depends_on('r-withr@2.0.0:', type=('build', 'run'), when='@6.0-83:')
depends_on('r-car', type=('build', 'run'), when='@:6.0-73')

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@ -7,7 +7,7 @@
class RCaretensemble(RPackage):
"""caretEnsemble: Ensembles of Caret Models
"""Ensembles of Caret Models.
Functions for creating ensembles of caret models: caretList() and
caretStack(). caretList() is a convenience function for fitting multiple
@ -16,9 +16,7 @@ class RCaretensemble(RPackage):
meta-model, and caretEnsemble() will make a robust linear combination of
models using a GLM."""
homepage = "https://github.com/zachmayer/caretEnsemble"
url = "https://cloud.r-project.org/src/contrib/caretEnsemble_2.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caretEnsemble"
cran = "caretEnsemble"
version('2.0.1', sha256='7e595e604ce2d9d32afbc5404e6fcbcd7f80e687316e9ca3303aca3e44c3ef88')

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var/spack/repos/builtin/packages/r-caroline/package.py
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@ -7,12 +7,20 @@
class RCaroline(RPackage):
"""caroline: A Collection of Database, Data Structure, Visualization,
andUtility Functions for R"""
"""A Collection of Database, Data Structure, Visualization, andUtility
Functions for R.
homepage = "https://cloud.r-project.org/package=caroline"
url = "https://cloud.r-project.org/src/contrib/caroline_0.7.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caroline"
The caroline R library contains dozens of functions useful for: database
migration (dbWriteTable2), database style joins & aggregation (nerge,
groupBy & bestBy), data structure conversion (nv, tab2df), legend table
making (sstable & leghead), plot annotation (labsegs & mvlabs), data
visualization (violins, pies & raPlot), character string manipulation (m &
pad), file I/O (write.delim), batch scripting and more. The package's
greatest contributions lie in the database style merge, aggregation and
interface functions as well as in it's extensive use and propagation of
row, column and vector names in most functions."""
cran = "caroline"
version('0.7.6', sha256='e7ba948f7d87f091b498dd0eec2ca4fdad7af4e2bbb67e0945c2f0d3f2eadda9')

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@ -8,22 +8,21 @@
class RCatools(RPackage):
"""Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
"""Moving Window Statistics, GIF, Base64, ROC AUC, etc.
Contains several basic utility functions including: moving (rolling,
running) window statistic functions, read/write for GIF and ENVI binary
files, fast calculation of AUC, LogitBoost classifier, base64
encoder/decoder, round-off-error-free sum and cumsum, etc."""
homepage = "https://cloud.r-project.org/package=caTools"
url = "https://cloud.r-project.org/src/contrib/caTools_1.17.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caTools"
cran = "caTools"
version('1.18.2', sha256='75d61115afec754b053ed1732cc034f2aeb27b13e6e1932aa0f26bf590cf0293')
version('1.18.1', sha256='ffeba4ffbeed5d491bf79b1fde3477f413341e412f77316af20439f54447c9f9')
version('1.17.1.2', sha256='69cc542fab5677462b1a768709d0c4a0a0790f5db53e1fe9ae7123787c18726b')
version('1.17.1.1', sha256='d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06')
version('1.17.1', sha256='d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4')
depends_on('r@2.2.0:', type=('build', 'run'))
depends_on('r@3.6.0:', when='@1.18.1:', type=('build', 'run'))
depends_on('r@3.6.0:', type=('build', 'run'), when='@1.18.1:')
depends_on('r-bitops', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-cca/package.py
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@ -5,10 +5,12 @@
class RCca(RPackage):
"""Provides a set of functions that extend the 'cancor' function
with new numerical and graphical outputs. It also include a
regularized extension of the canonical correlation analysis to
deal with datasets with more variables than observations."""
"""Canonical Correlation Analysis.
Provides a set of functions that extend the 'cancor' function with new
numerical and graphical outputs. It also include a regularized extension of
the canonical correlation analysis to deal with datasets with more
variables than observations."""
cran = 'CCA'

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var/spack/repos/builtin/packages/r-ccp/package.py
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@ -5,8 +5,10 @@
class RCcp(RPackage):
"""Significance tests for canonical correlation analysis,
including asymptotic tests and a Monte Carlo method"""
"""Significance Tests for Canonical Correlation Analysis (CCA).
Significance tests for canonical correlation analysis, including asymptotic
tests and a Monte Carlo method"""
cran = 'CCP'

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@ -8,7 +8,7 @@
class RCdcfluview(RPackage):
"""Retrieve Flu Season Data from the United States Centers for Disease
Control and Prevention ('CDC') 'FluView' Portal
Control and Prevention ('CDC') 'FluView' Portal.
The 'U.S.' Centers for Disease Control ('CDC') maintains a portal
<https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing
@ -17,21 +17,20 @@ class RCdcfluview(RPackage):
to select and retrieve influenza data. Tools are provided to access the
data provided by the portal's underlying 'API'."""
homepage = "https://cloud.r-project.org/package=cdcfluview"
url = "https://cloud.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cdcfluview"
cran = "cdcfluview"
version('0.9.4', sha256='776a155c4f0cc678fde94a6d47cc2783ff5c199f26cce642461092e1b6311dad')
version('0.9.2', sha256='f2080fc80c5e0241f8b657f5ac3a251ea89dfc26c1ab13bdfaed4d4e97495015')
version('0.9.0', sha256='1b2064886858cbb1790ef808d88fbab75d3a9cf55e720638221a3377ff8dd244')
version('0.7.0', sha256='8c8978d081f8472a6ed5ec54c4e6dd906f97ee28d0f88eef1514088f041ecc03')
depends_on('r@3.2.0:', when='@:0.9.0', type=('build', 'run'))
depends_on('r@3.5.0:', when='@0.9.2:', type=('build', 'run'))
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@0.9.2:')
depends_on('r-httr', type=('build', 'run'))
depends_on('r-progress', when='@0.9.2:', type=('build', 'run'))
depends_on('r-progress', type=('build', 'run'), when='@0.9.2:')
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-tibble', when='@0.9.2:', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'), when='@0.9.2:')
depends_on('r-sf', type=('build', 'run'))
depends_on('r-xml2', type=('build', 'run'))
depends_on('r-purrr', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-cellranger/package.py
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@ -7,12 +7,12 @@
class RCellranger(RPackage):
"""Helper functions to work with spreadsheets and the "A1:D10"
style of cell range specification."""
"""Translate Spreadsheet Cell Ranges to Rows and Columns.
homepage = "https://cloud.r-project.org/package=cellranger"
url = "https://cloud.r-project.org/src/contrib/cellranger_1.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cellranger"
Helper functions to work with spreadsheets and the "A1:D10" style of cell
range specification."""
cran = "cellranger"
version('1.1.0', sha256='5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99')

12
var/spack/repos/builtin/packages/r-checkmate/package.py
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@ -7,15 +7,13 @@
class RCheckmate(RPackage):
"""Fast and Versatile Argument Checks
"""Fast and Versatile Argument Checks.
Tests and assertions to perform frequent argument checks.
A substantial part of the package was written in C to
minimize any worries about execution time overhead."""
Tests and assertions to perform frequent argument checks. A substantial
part of the package was written in C to minimize any worries about
execution time overhead."""
homepage = "https://cloud.r-project.org/package=checkmate"
url = "https://cloud.r-project.org/src/contrib/checkmate_1.8.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/checkmate"
cran = "checkmate"
version('2.0.0', sha256='0dc25b0e20c04836359df1885d099c6e4ad8ae0e585a9e4107f7ea945d9c6fa4')
version('1.9.4', sha256='faa25754b757fe483b876f5d07b73f76f69a1baa971420892fadec4af4bbad21')

15
var/spack/repos/builtin/packages/r-checkpoint/package.py
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@ -7,7 +7,8 @@
class RCheckpoint(RPackage):
"""Install Packages from Snapshots on the Checkpoint Server for Reproducibility
"""Install Packages from Snapshots on the Checkpoint Server for
Reproducibility.
The goal of checkpoint is to solve the problem of package reproducibility
in R. Specifically, checkpoint allows you to install packages as they
@ -25,13 +26,19 @@ class RCheckpoint(RPackage):
thus creating the archive. Snapshot archives exist starting from
2014-09-17."""
homepage = "https://cloud.r-project.org/package=checkpoint"
url = "https://cloud.r-project.org/src/contrib/checkpoint_0.4.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint"
cran = "checkpoint"
version('1.0.2', sha256='a80390d834534e908058a597a2a5ee60a111023e76f13f370949963582dd07a5')
version('1.0.1', sha256='8542029395b7d557c1b39423326611f408788fcd02f5cbeb5ed252f368f8dcd2')
version('1.0.0', sha256='d36146093763ca29e0296729399b96e0f2e7764745283d6cea1066a96fa085a7')
version('0.4.10', sha256='7362ae9703763fe4652d0b592cd913ce506f072a18e5cf5970d08d7cdf4d126a')
version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2')
version('0.4.3', sha256='c3e862f89f8838183d6028f7ed13683aec562e6dab77ad4b6a5e24ec653cfb64')
version('0.3.15', sha256='09f1feeb2b5b8b409a2e16a9185827b8da5e555f1aa84442a287f15e452beed7')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r@3.3.0:', type=('build', 'run'), when='@1.0.0:')
depends_on('r-jsonlite', type=('build', 'run'), when='@1.0.0:')
depends_on('r-yaml', type=('build', 'run'), when='@1.0.0:')
depends_on('r-withr', type=('build', 'run'), when='@1.0.0:')
depends_on('r-pkgdepends', type=('build', 'run'), when='@1.0.0:')

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var/spack/repos/builtin/packages/r-chemometrics/package.py
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@ -7,13 +7,12 @@
class RChemometrics(RPackage):
"""R companion to the book "Introduction to Multivariate Statistical
Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser
(2009)."""
"""Multivariate Statistical Analysis in Chemometrics.
homepage = "https://cloud.r-project.org/package=chemometrics"
url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/chemometrics"
R companion to the book "Introduction to Multivariate Statistical Analysis
in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)."""
cran = "chemometrics"
version('1.4.2', sha256='b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a')
version('1.4.1', sha256='7646da0077657d672356204aa2094be68e10ec13617f92ae97ff53a389053905')

7
var/spack/repos/builtin/packages/r-chron/package.py
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@ -9,12 +9,9 @@
class RChron(RPackage):
"""Chronological objects which can handle dates and times.
Provides chronological objects which can handle dates and times.
"""
Provides chronological objects which can handle dates and times."""
homepage = "https://cloud.r-project.org/package=chron"
url = "https://cloud.r-project.org/src/contrib/chron_2.3-47.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/chron"
cran = "chron"
version('2.3-56', sha256='863ecbb951a3da994761ea9062fa96d34e94e19fbc4122521ac179274dfa3f5d')
version('2.3-53', sha256='521814b46ba958eae28e29d8766aebd285da5e6fa16c5806603df3ae39f77309')

11
var/spack/repos/builtin/packages/r-circlize/package.py
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@ -7,7 +7,7 @@
class RCirclize(RPackage):
"""Circular Visualization
"""Circular Visualization.
Circular layout is an efficient way for the visualization of huge amounts
of information. Here this package provides an implementation of circular
@ -21,17 +21,16 @@ class RCirclize(RPackage):
package is described in Gu et al. 2014
<doi:10.1093/bioinformatics/btu393>."""
homepage = "https://cloud.r-project.org/package=circlize"
url = "https://cloud.r-project.org/src/contrib/circlize_0.4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/circlize"
cran = "circlize"
version('0.4.13', sha256='6cbadbf8e8b1abbd71a79080677d2b95f2bdd18f2e4d707c32d5c2ff26c5369b')
version('0.4.12', sha256='b3b60caa5292cf980cf474c85f59582f6862925631a4da86a78eac05903252f4')
version('0.4.6', sha256='cec88cfc5e512a111cc37177552c25698ccc0e9bbecb0d6e60657e7b115a56fa')
version('0.4.1', sha256='204a170ae3b982f09b652c4583189907cfa42a29bc7efaba02a1e0d79f1cf1f0')
version('0.4.0', sha256='abdc1bbe264be42c1d7b65869979da7cd131032fd6fd3f11f9744dae54e83f5c')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.0:', when='@:0.4.6', type=('build', 'run'))
depends_on('r-globaloptions@0.1.2:', when='@0.4.12:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.0:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.2:', type=('build', 'run'), when='@0.4.12:')
depends_on('r-shape', type=('build', 'run'))
depends_on('r-colorspace', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-circstats/package.py
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@ -7,14 +7,12 @@
class RCircstats(RPackage):
"""Circular Statistics, from "Topics in Circular Statistics" (2001)
"""Circular Statistics, from "Topics in Circular Statistics" (2001).
Circular Statistics, from "Topics in Circular Statistics" (2001) S.
Rao Jammalamadaka and A. SenGupta, World Scientific."""
Circular Statistics, from "Topics in Circular Statistics" (2001) S. Rao
Jammalamadaka and A. SenGupta, World Scientific."""
homepage = "https://cloud.r-project.org/package=CircStats"
url = "https://cloud.r-project.org/src/contrib/CircStats_0.2-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/CircStats"
cran = "CircStats"
maintainers = ['dorton21']

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