update CRAN R packages (#28786)

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

@@ -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"
+    cran = "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"
 
     version('1.4-5', sha256='3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c')
     version('1.4-3', sha256='b6c255878c1ab81701ae701f34546e88be115629b984ac4272e311fa3c0ea6ce')

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

@@ -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"
+    Two nonparametric methods for multiple regression transform selection are
-    url      = "https://cloud.r-project.org/src/contrib/acepack_1.4.1.tar.gz"
+    provided. The first, Alternative Conditional Expectations (ACE), is an
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/acepack"
+    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')

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

@@ -7,12 +7,14 @@
 
 
 class RAda(RPackage):
-    """Performs discrete, real, and gentle boost under both exponential
+    """The R Package Ada for Stochastic Boosting.
-    and logistic loss on a given data set."""
 
-    homepage = "https://cloud.r-project.org/package=ada"
+    Performs discrete, real, and gentle boost under both exponential and
-    url      = "https://cloud.r-project.org/src/contrib/ada_2.0-5.tar.gz"
+    logistic loss on a given data set. The package ada provides a
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/ada"
+    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')
 

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

@@ -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"
+    It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's
-    url      = "https://cloud.r-project.org/src/contrib/adabag_4.1.tar.gz"
+    Bagging algorithm using classification trees as individual classifiers.
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/adabag"
+    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')

var/spack/repos/builtin/packages/r-ade4/package.py

@@ -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"
+    cran = "ade4"
-    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"
 
+    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-pixmap', type=('build', 'run'), when='@1.7-16:')
-    depends_on('r-sp', when='@1.7-16:', type=('build', 'run'))
+    depends_on('r-sp', type=('build', 'run'), when='@1.7-16:')
-    depends_on('r-progress', when='@1.7-16:', type=('build', 'run'))
+
+    depends_on('r-progress', type=('build', 'run'), when='@1.7-16')

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

@@ -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
+    Toolset for the exploration of genetic and genomic data. Adegenet provides
-    provides formal (S4) classes for storing and handling various genetic
+    formal (S4) classes for storing and handling various genetic data,
-    data, including genetic markers with varying ploidy and hierarchical
+    including genetic markers with varying ploidy and hierarchical population
-    population structure ('genind' class), alleles counts by populations
+    structure ('genind' class), alleles counts by populations ('genpop'), and
-    ('genpop'), and genome-wide SNP data ('genlight'). It also implements
+    genome-wide SNP data ('genlight'). It also implements original multivariate
-    original multivariate methods (DAPC, sPCA), graphics, statistical tests,
+    methods (DAPC, sPCA), graphics, statistical tests, simulation tools,
-    simulation tools, distance and similarity measures, and several spatial
+    distance and similarity measures, and several spatial methods. A range of
-    methods. A range of both empirical and simulated datasets is also provided
+    both empirical and simulated datasets is also provided to illustrate
-    to illustrate various methods."""
+    various methods."""
 
-    homepage = "https://github.com/thibautjombart/adegenet/wiki"
+    cran = "adegenet"
-    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"
 
+    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')

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

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

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

@@ -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
+    Multivariate tools to analyze comparative data, i.e. a phylogeny and some
-    some traits measured for each taxa."""
+    traits measured for each taxa."""
 
-    homepage = "https://cloud.r-project.org/package=adephylo"
+    cran = "adephylo"
-    url      = "https://cloud.r-project.org/src/contrib/adephylo_1.1-11.tar.gz"
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/adephylo"
 
     version('1.1-11', sha256='154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a')
 

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

@@ -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"
+    cran = "adespatial"
-    url      = "https://cloud.r-project.org/src/contrib/adespatial_0.3-8.tar.gz"
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/adespatial"
 
+    version('0.3-14', sha256='a2ef7549c1ed7a23651716c633b25eaff468af8ccbf2e9fcd164e485984cbfbf')
     version('0.3-8', sha256='e3fd3209ce3f0a862a0794187e8c884f1697c87c96e569a2f51f252e00022906')
 
     depends_on('r-ade4@1.7-13:', type=('build', 'run'))

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

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

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

@@ -7,16 +7,13 @@
 
 
 class RAer(RPackage):
-    """Applied Econometrics with R
+    """Applied Econometrics with R.
 
-    Functions, data sets, examples, demos, and vignettes
+    Functions, data sets, examples, demos, and vignettes for the book Christian
-    for the book Christian Kleiber and Achim Zeileis (2008),
+    Kleiber and Achim Zeileis (2008), Applied Econometrics with R,
-    Applied Econometrics with R, Springer-Verlag, New York.
+    Springer-Verlag, New York.  ISBN 978-0-387-77316-2."""
-    ISBN 978-0-387-77316-2."""
 
-    homepage = "https://cloud.r-project.org/package=AER"
+    cran = "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"
 
     version('1.2-9', sha256='3b79390b14766419fc1e8912689bc462d4beb01aff9dad26d628aed69d04540d')
     version('1.2-7', sha256='3aee5c606313710c2dca6c1e9b2c20a145aa33f2a3ecc5cfcec66c8e91838a93')

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

@@ -7,25 +7,22 @@
 
 
 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
+    automatically aggregating multiple observations per individual and cell of
-    of the design. mixed() fits mixed models using lme4::lmer() and computes
+    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
+    approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs
-    (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
+    and GLMMs), or likelihood ratio tests (LMMs and GLMMs).  afex_plot()
-    afex_plot() provides a high-level interface for interaction or one-way
+    provides a high-level interface for interaction or one-way plots using
-    plots using ggplot2, combining raw data and model estimates. afex uses
+    ggplot2, combining raw data and model estimates. afex uses type 3 sums of
-    type 3 sums of squares as default (imitating commercial statistical
+    squares as default (imitating commercial statistical software)."""
-    software).
-    """
 
-    homepage = "https://github.com/singmann/afex"
+    cran = "afex"
-    cran     = "afex"
 
     version('1.0-1', sha256='6febc34b87a1109f5cbcd213c08d2b7b3e9cf99065fa41c19bc88ac99fb104cc')
     version('0.28-1', sha256='cfb0b79bfa01b590afc3354a5b2ad3640d2f4974b036d6c256fa8e684bc69c2e')

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

@@ -7,17 +7,17 @@
 
 
 class RAls(RPackage):
-    """Alternating least squares is often used to resolve components
+    """Multivariate Curve Resolution Alternating Least Squares (MCR-ALS).
-    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."""
 
-    homepage = "https://cloud.r-project.org/package=ALS"
+    Alternating least squares is often used to resolve components contributing
-    url      = "https://cloud.r-project.org/src/contrib/ALS_0.0.6.tar.gz"
+    to data with a bilinear structure; the basic technique may be extended to
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/ALS"
+    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')
 

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

@@ -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"
+    cran = "amap"
-    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/"
 
     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@2.10.0:', type=('build', 'run'))
-    depends_on('r@3.6.0:', when='@0.8-17:', type=('build', 'run'))
+    depends_on('r@3.6.0:', type=('build', 'run'), when='@0.8-17:')

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

@@ -7,21 +7,30 @@
 
 
 class RAmelia(RPackage):
-    """Amelia: A Program for Missing Data
+    """A Program for Missing Data.
 
-    Amelia II "multiply imputes" missing data in a single
+    A tool that "multiply imputes" missing data in a single cross-section (such
-    cross-section (such as a survey), from a time series (like
+    as a survey), from a time series (like variables collected for each year in
-    variables collected for each year in a country), or from a
+    a country), or from a time-series-cross-sectional data set (such as
-    time-series-cross-sectional data set (such as collected by
+    collected by years for each of several countries). Amelia II implements our
-    years for each of several countries)."""
+    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"
+    cran = "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"
 
+    version('1.8.0', sha256='3ec1d5a68dac601b354227916aa8ec72fa1216b603dd887aae2b24cb69b5995e')
     version('1.7.6',  sha256='63c08d374aaf78af46c34dc78da719b3085e58d9fabdc76c6460d5193a621bea')
 
-    depends_on('r@3.0.2:',        type=('build', 'run'))
+    depends_on('r@3.0.2:', type=('build', 'run'))
-    depends_on('r-rcpp@0.11:',    type=('build', 'run'))
+    depends_on('r-rcpp@0.11:', type=('build', 'run'))
-    depends_on('r-foreign',       type=('build', 'run'))
+    depends_on('r-foreign', type=('build', 'run'))
     depends_on('r-rcpparmadillo', type=('build', 'run'))

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

@@ -7,23 +7,25 @@
 
 
 class RAnimation(RPackage):
-    """Provides functions for animations in statistics, covering topics
+    """A Gallery of Animations in Statistics and Utilities to Create
-    in probability theory, mathematical statistics, multivariate statistics,
+    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.
+    computational statistics, data mining and machine learning.  These
-    These functions maybe helpful in teaching statistics and data analysis."""
+    functions maybe helpful in teaching statistics and data analysis."""
 
-    homepage = "https://cloud.r-project.org/package=animation"
+    cran = "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"
 
+    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')

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

@@ -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,
+    Convert input in any one of character, integer, numeric, factor, or ordered
-    factor, or ordered type into 'POSIXct' (or 'Date') objects,
+    type into 'POSIXct' (or 'Date') objects, using one of a number of
-    using one of a number of predefined formats, and relying on
+    predefined formats, and relying on Boost facilities for date and time
-    Boost facilities for date and time parsing."""
+    parsing."""
 
-    homepage = "https://dirk.eddelbuettel.com/code/anytime.html"
+    cran = "anytime"
-    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"
 
     version('0.3.9', sha256='1096c15249ac70997a8a41c37eeb2a6d38530621abeae05d3dcd96a8acc7574a')
 

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

@@ -7,16 +7,15 @@
 
 
 class RAod(RPackage):
-    """Provides a set of functions to analyse overdispersed counts or
+    """Analysis of Overdispersed Data.
-    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)."""
 
-    homepage = "https://cloud.r-project.org/package=aod"
+    Provides a set of functions to analyse overdispersed counts or proportions.
-    url      = "https://cloud.r-project.org/src/contrib/aod_1.3.1.tar.gz"
+    Most of the methods are already available elsewhere but are scattered in
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/aod"
+    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')
 

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

@@ -7,28 +7,27 @@
 
 
 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
+    sequences as well as importing from BioConductor, and several tools such as
-    as Mantel's test, generalized skyline plots, graphical exploration of
+    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
+    triangle methods, and several methods handling incomplete distance matrices
-    matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
+    (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions
-    functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
+    call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results
-    whose results are returned into R."""
+    are returned into R."""
 
-    homepage = "http://ape-package.ird.fr/"
+    cran = "ape"
-    url      = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz"
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/ape"
 
+    version('5.6-1', sha256='25401e036576eed1200e15bf68879ccd85611303a3508b989e15164cd4c0f7f7')
     version('5.4-1', sha256='f0316c8e74ce900053e8b3e8c9322b9d10e7730f3be2150365f74630bee7eee4')
     version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23')
     version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415')

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

@@ -7,23 +7,23 @@
 
 
 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"
+    cran = "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"
 
+    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-r6', type=('build', 'run'), when='@2.0.0:')
-    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-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')

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

@@ -5,7 +5,9 @@
 
 
 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'
 

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

@@ -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"
+    cran = "askpass"
-    url      = "https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz"
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/askpass"
 
     version('1.1', sha256='db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f')
 

var/spack/repos/builtin/packages/r-assertive-base/package.py

@@ -7,18 +7,18 @@
 
 
 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
+    This is mainly for use by other package developers who want to include
-    testing features in their own packages. End-users will usually want to use
+    run-time testing features in their own packages. End-users will usually
-    assertive directly."""
+    want to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.base"
+    cran = "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"
 
+    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:')

var/spack/repos/builtin/packages/r-assertive-code/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of code.
-    properties of code. This is mainly for use by other package
+    This is mainly for use by other package developers who want to include
-    developers who want to include run-time testing features in
+    run-time testing features in their own packages. End-users will usually
-    their own packages. End-users will usually want to use
+    want to use assertive directly."""
-    assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.code"
+    cran = "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"
 
     version('0.0-3', sha256='ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2')
 

var/spack/repos/builtin/packages/r-assertive-data-uk/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of
-    properties of UK-specific complex data types. This is
+    UK-specific complex data types. This is mainly for use by other package
-    mainly for use by other package developers who want to
+    developers who want to include run-time testing features in their own
-    include run-time testing features in their own packages.
+    packages.  End-users will usually want to use assertive directly."""
-    End-users will usually want to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.data.uk"
+    cran = "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"
 
     version('0.0-2', sha256='ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb')
 

var/spack/repos/builtin/packages/r-assertive-data-us/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of
-    properties of US-specific complex data types. This is
+    US-specific complex data types. This is mainly for use by other package
-    mainly for use by other package developers who want to
+    developers who want to include run-time testing features in their own
-    include run-time testing features in their own packages.
+    packages.  End-users will usually want to use assertive directly."""
-    End-users will usually want to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.data.us"
+    cran = "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"
 
     version('0.0-2', sha256='180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad')
 

var/spack/repos/builtin/packages/r-assertive-data/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of (country
-    properties of (country independent) complex data types.
+    independent) complex data types.  This is mainly for use by other package
-    This is mainly for use by other package developers who want
+    developers who want to include run-time testing features in their own
-    to include run-time testing features in their own packages.
+    packages.  End-users will usually want to use assertive directly."""
-    End-users will usually want to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.data"
+    cran = "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"
 
     version('0.0-3', sha256='5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01')
 

var/spack/repos/builtin/packages/r-assertive-datetimes/package.py

@@ -7,16 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of dates and
-    dates and times. This is mainly for use by other package developers
+    times. This is mainly for use by other package developers who want to
-    who want to include run-time testing features in their own packages.
+    include run-time testing features in their own packages.  End-users will
-    End-users will usually want to use assertive directly."""
+    usually want to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.datetimes"
+    cran = "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"
 
     version('0.0-3', sha256='014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94')
 

var/spack/repos/builtin/packages/r-assertive-files/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of files and
-    properties of files and connections. This is mainly for use
+    connections. This is mainly for use by other package developers who want to
-    by other package developers who want to include run-time
+    include run-time testing features in their own packages. End-users will
-    testing features in their own packages. End-users will
     usually want to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.files"
+    cran = "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"
 
     version('0.0-2', sha256='be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a')
 

var/spack/repos/builtin/packages/r-assertive-matrices/package.py

@@ -7,18 +7,14 @@
 
 
 class RAssertiveMatrices(RPackage):
-    """assertive.matrices: Assertions to Check Properties of
+    """Assertions to Check Properties of Matrices.
-    Matrices
 
-    A set of predicates and assertions for checking the
+    A set of predicates and assertions for checking the properties of matrices.
-    properties of matrices. This is mainly for use by other
+    This is mainly for use by other package developers who want to include
-    package developers who want to include run-time testing
+    run-time testing features in their own packages. End-users will usually
-    features in their own packages. End-users will usually want
+    want to use assertive directly."""
-    to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.matrices"
+    cran = "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"
 
     version('0.0-2', sha256='3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b')
 

var/spack/repos/builtin/packages/r-assertive-models/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of models.
-    properties of models. This is mainly for use by other
+    This is mainly for use by other package developers who want to include
-    package developers who want to include run-time testing
+    run-time testing features in their own packages. End-users will usually
-    features in their own packages. End-users will usually want
+    want to use assertive directly."""
-    to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.models"
+    cran = "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"
 
     version('0.0-2', sha256='b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e')
 

var/spack/repos/builtin/packages/r-assertive-numbers/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of numbers.
-    properties of numbers. This is mainly for use by other
+    This is mainly for use by other package developers who want to include
-    package developers who want to include run-time testing
+    run-time testing features in their own packages. End-users will usually
-    features in their own packages. End-users will usually want
+    want to use assertive directly."""
-    to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.numbers"
+    cran = "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"
 
     version('0.0-2', sha256='bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349')
 

var/spack/repos/builtin/packages/r-assertive-properties/package.py

@@ -7,19 +7,15 @@
 
 
 class RAssertiveProperties(RPackage):
-    """assertive.properties: Assertions to Check Properties of
+    """Assertions to Check Properties of Variables.
-    Variables
 
-    A set of predicates and assertions for checking the
+    A set of predicates and assertions for checking the properties of
-    properties of variables, such as length, names and
+    variables, such as length, names and attributes. This is mainly for use by
-    attributes. This is mainly for use by other package
+    other package developers who want to include run-time testing features in
-    developers who want to include run-time testing features in
+    their own packages. End-users will usually want to use assertive
-    their own packages. End-users will usually want to use
+    directly."""
-    assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.properties"
+    cran = "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"
 
     version('0.0-4', sha256='5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b')
 

var/spack/repos/builtin/packages/r-assertive-reflection/package.py

@@ -7,18 +7,15 @@
 
 
 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
+    A set of predicates and assertions for checking the state and capabilities
-    and capabilities of R, the operating system it is running
+    of R, the operating system it is running on, and the IDE being used. This
-    on, and the IDE being used. This is mainly for use by other
+    is mainly for use by other package developers who want to include run-time
-    package developers who want to include run-time testing
+    testing features in their own packages. End-users will usually want to use
-    features in their own packages. End-users will usually want
+    assertive directly."""
-    to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.reflection"
+    cran = "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"
 
     version('0.0-5',   sha256='c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd')
 

var/spack/repos/builtin/packages/r-assertive-sets/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the properties of sets.
-    properties of sets. This is mainly for use by other package
+    This is mainly for use by other package developers who want to include
-    developers who want to include run-time testing features in
+    run-time testing features in their own packages. End-users will usually
-    their own packages. End-users will usually want to use
+    want to use assertive directly."""
-    assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.sets"
+    cran = "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"
 
     version('0.0-3', sha256='876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3')
 

var/spack/repos/builtin/packages/r-assertive-strings/package.py

@@ -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
+    A set of predicates and assertions for checking the properties of strings.
-    properties of strings. This is mainly for use by other
+    This is mainly for use by other package developers who want to include
-    package developers who want to include run-time testing
+    run-time testing features in their own packages. End-users will usually
-    features in their own packages. End-users will usually want
+    want to use assertive directly."""
-    to use assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.strings"
+    cran = "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"
 
     version('0.0-3', sha256='d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258')
 

var/spack/repos/builtin/packages/r-assertive-types/package.py

@@ -7,17 +7,14 @@
 
 
 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
+    A set of predicates and assertions for checking the types of variables.
-    of variables. This is mainly for use by other package
+    This is mainly for use by other package developers who want to include
-    developers who want to include run-time testing features in
+    run-time testing features in their own packages. End-users will usually
-    their own packages. End-users will usually want to use
+    want to use assertive directly."""
-    assertive directly."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive.types"
+    cran = "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"
 
     version('0.0-3', sha256='ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f')
 

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

@@ -7,15 +7,13 @@
 
 
 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
+    Lots of predicates (is_* functions) to check the state of your variables,
-    variables, and assertions (assert_* functions) to throw errors if
+    and assertions (assert_* functions) to throw errors if they aren't in the
-    they aren't in the right form."""
+    right form."""
 
-    homepage = "https://bitbucket.org/richierocks/assertive"
+    cran = "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"
 
     version('0.3-6',   sha256='c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a')
 

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

@@ -7,14 +7,13 @@
 
 
 class RAssertthat(RPackage):
-    """assertthat is an extension to stopifnot() that makes it easy to declare
+    """Easy Pre and Post Assertions.
-    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."""
 
-    homepage = "https://cloud.r-project.org/package=assertthat"
+    An extension to stopifnot() that makes it easy to declare the pre and post
-    url      = "https://cloud.r-project.org/src/contrib/assertthat_0.1.tar.gz"
+    conditions that you code should satisfy, while also producing friendly
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/assertthat"
+    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')

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

@@ -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')

var/spack/repos/builtin/packages/r-base64/package.py

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

var/spack/repos/builtin/packages/r-base64enc/package.py

@@ -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"
+    cran = "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"
 
     version('0.1-3', sha256='6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d')
 

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

@@ -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"
+    cran = "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"
 
     version('3.1-4', sha256='061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94')
     version('3.1-3', sha256='51e4827eca8cd4cf3626f3c2282543df7c392b3ffb843f4bfb386fe104642a10')

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

@@ -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
@@ -18,8 +18,7 @@ class RBayesplot(RPackage):
     R packages for Bayesian modeling, particularly (but not exclusively)
     packages interfacing with 'Stan'."""
 
-    homepage = "https://mc-stan.org/bayesplot/"
+    cran = "bayesplot"
-    cran     = "bayesplot"
 
     version('1.8.1', sha256='d8d74201ea91fa5438714686ca22a947ec9375b6c12b0cfef010c57104b1aa2a')
     version('1.8.0', sha256='a605f9929e681593a3ef3ca9c836e713314994aaea00f359f71cfc42d151c948')

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

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

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

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

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

@@ -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/"
+    The bee swarm plot is a one-dimensional scatter plot like "stripchart", but
-    url      = "https://cloud.r-project.org/src/contrib/beeswarm_0.2.3.tar.gz"
+    with closely-packed, non-overlapping points."""
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/beeswarm"
 
+    cran = "beeswarm"
+
+    version('0.4.0', sha256='51f4339bf4080a2be84bb49a844c636625657fbed994abeaa42aead916c3d504')
     version('0.2.3', sha256='0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843')

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

@@ -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"
+    Decomposition of time series into trend, seasonal, and remainder components
-    url      = "https://cloud.r-project.org/src/contrib/bfast_1.5.7.tar.gz"
+    with methods for detecting and characterizing abrupt changes within the
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/bfast"
+    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-rcpp@0.12.7:', type=('build', 'run'), when='@1.6.1:')
-    depends_on('r-raster', type=('build', 'run'))
+    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')

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

@@ -7,13 +7,13 @@
 
 
 class RBglr(RPackage):
-    """BGLR: Bayesian Generalized Linear Regression"""
+    """Bayesian Generalized Linear Regression."""
 
-    homepage = "https://cloud.r-project.org/package=BGLR"
+    cran = "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"
 
+    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:')

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

@@ -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')

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

@@ -7,15 +7,15 @@
 
 
 class RBiasedurn(RPackage):
-    """Statistical models of biased sampling in the form of univariate and
+    """Biased Urn Model Distributions.
-       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."""
 
-    homepage = "https://www.agner.org/random/"
+    Statistical models of biased sampling in the form of univariate and
-    url      = "https://cloud.r-project.org/src/contrib/BiasedUrn_1.07.tar.gz"
+    multivariate noncentral hypergeometric distributions, including Wallenius'
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/BiasedUrn/"
+    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')

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

@@ -7,13 +7,11 @@
 
 
 class RBibtex(RPackage):
-    """Bibtex Parser
+    """Bibtex Parser.
 
-       Utility to parse a bibtex file."""
+    Utility to parse a bibtex file."""
 
-    homepage = "https://cloud.r-project.org/package=bibtex"
+    cran = "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/"
 
     version('0.4.2.3', sha256='7bad194920b412781ac9754ad41058d52d3cd7186e1851c2bce3640490e9bc6d')
     version('0.4.2', sha256='1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372')

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

@@ -7,14 +7,23 @@
 
 
 class RBigalgebra(RPackage):
-    """This package provides arithmetic functions for R matrix
+    """'BLAS' and 'LAPACK' Routines for Native R Matrices and 'big.matrix'
-       and big.matrix objects."""
+    Objects.
 
-    homepage = "https://r-forge.r-project.org/R/?group_id=556"
+    Provides arithmetic functions for R matrix and 'big.matrix' objects as well
-    url      = "https://cloud.r-project.org/src/contrib/Archive/bigalgebra/bigalgebra_0.8.4.2.tar.gz"
+    as functions for QR factorization, Cholesky factorization, General
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/bigalgebra"
+    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:')

var/spack/repos/builtin/packages/r-bigmemory-sri/package.py

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

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

@@ -7,14 +7,14 @@
 
 
 class RBigmemory(RPackage):
-    """Create, store, access, and manipulate massive matrices.
+    """Manage Massive Matrices with Shared Memory and Memory-Mapped.
-       Matrices are allocated to shared memory and may use
-       memory-mapped files. Packages 'biganalytics', 'bigtabulate',
-       'synchronicity', and 'bigalgebra' provide advanced functionality."""
 
-    homepage = "https://cloud.r-project.org/web/packages/bigmemory/index.html"
+    Files Create, store, access, and manipulate massive matrices.  Matrices are
-    url      = "https://cloud.r-project.org/src/contrib/bigmemory_4.5.36.tar.gz"
+    allocated to shared memory and may use memory-mapped files. Packages
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/bigmemory"
+    'biganalytics', 'bigtabulate', 'synchronicity', and 'bigalgebra' provide
+    advanced functionality."""
+
+    cran = "bigmemory"
 
     version('4.5.36', sha256='18c67fbe6344b2f8223456c4f19ceebcf6c1166255eab81311001fd67a45ef0e')
 

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

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

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

@@ -7,12 +7,12 @@
 
 
 class RBindrcpp(RPackage):
-    """Provides an easy way to fill an environment with active bindings that
+    """An 'Rcpp' Interface to Active Bindings.
-       call a C++ function."""
 
-    homepage = "https://github.com/krlmlr/bindrcpp"
+    Provides an easy way to fill an environment with active bindings that call
-    url      = "https://cloud.r-project.org/src/contrib/bindrcpp_0.2.tar.gz"
+    a C++ function."""
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/bindrcpp"
+
+    cran = "bindrcpp"
 
     version('0.2.2', sha256='48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467')
     version('0.2', sha256='d0efa1313cb8148880f7902a4267de1dcedae916f28d9a0ef5911f44bf103450')

var/spack/repos/builtin/packages/r-bio3d/package.py

@@ -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/"
+    cran = "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"
 
+    version('2.4-2', sha256='91415766cda0f96557e6bc568dbce8d44254a9460f2e2d0beed0ce14ffad6ccb')
     version('2.4-1', sha256='679fbd87fe9fb82a65427d281d3b68906509e411270cd87d2deb95d404333c1f')
     version('2.3-4', sha256='f9b39ab242cbedafcd98c1732cb1f5c0dd9ef66e28be39695e3420dd93e2bafe')
 

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

@@ -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"
+    A convenient tool to install and update Bioconductor packages."""
-    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"
 
+    cran = "BiocManager"
+
+    version('1.30.16', sha256='75a754a55192ef6aa6ac9b054fd5381ff03fe6bb8b2e033eb8143da930ef3855')
     version('1.30.10', sha256='f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e')

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

@@ -7,13 +7,12 @@
 
 
 class RBiomUtils(RPackage):
-    """Provides utilities to facilitate import, export and computation with
+    """Utilities for the BIOM (Biological Observation Matrix) Format.
-    the BIOM (Biological Observation Matrix) format (https://biom-format.org/).
-    """
 
-    homepage = "https://github.com/braithwaite/BIOM.utils/"
+    Provides utilities to facilitate import, export and computation with the
-    url      = "https://cloud.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
+    BIOM (Biological Observation Matrix) format (https://biom-format.org/)."""
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/biom/"
+
+    cran = "BIOM.utils"
 
     version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375')
 

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

@@ -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"
+    cran = "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"
 
     version('0.9.2', sha256='d88085696e9c5614828602254c33f2cdd3bbfeebc2f21a705eee3cb961097c89')
 

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

@@ -7,16 +7,14 @@
 
 
 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"
+    cran = "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"
 
     version('4.0.4', sha256='e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168')
     version('1.1-14', sha256='5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254')

var/spack/repos/builtin/packages/r-bit64/package.py

@@ -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"
+    cran = "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"
 
     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@1.1-12:', type=('build', 'run'))
-    depends_on('r-bit@4.0.0:', when='@4.0.5:', type=('build', 'run'))
+    depends_on('r-bit@4.0.0:', type=('build', 'run'), when='@4.0.5:')

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

@@ -8,10 +8,11 @@
 
 
 class RBitops(RPackage):
-    """Functions for bitwise operations on integer vectors."""
+    """Bitwise Operations.
 
-    homepage = "https://cloud.r-project.org/package=bitops"
+    Functions for bitwise operations on integer vectors."""
-    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"
 
+    cran = "bitops"
+
+    version('1.0-7', sha256='e9b5fc92c39f94a10cd0e13f3d6e2a9c17b75ea01467077a51d47a5f708517c4')
     version('1.0-6', sha256='9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c')

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

@@ -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
+Fit a variety of Bayesian latent variable models, including confirmatory factor
-    factor analysis, structural equation models, and latent growth curve
+analysis, structural equation models, and latent growth curve models.
-    models."""
+References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al.
+(2021) <doi:10.18637/jss.v100.i06>."""
 
-    cran     = "blavaan"
+    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'))

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

@@ -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.
+    R's raw vector is useful for storing a single binary object.  What if you
-    What if you want to put a vector of them in a data frame? The blob
+    want to put a vector of them in a data frame? The blob package provides the
-    package provides the blob object, a list of raw vectors, suitable
+    blob object, a list of raw vectors, suitable for use as a column in data
-    for use as a column in data frame."""
+    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-rlang', type=('build', 'run'), when='@1.2.0:')
-    depends_on('r-prettyunits', when='@1.2.0', type=('build', 'run'))
+    depends_on('r-vctrs@0.2.0:', type=('build', 'run'), when='@1.2.0:')
-    depends_on('r-rlang', when='@1.2.0:', type=('build', 'run'))
+    depends_on('r-vctrs@0.2.1:', type=('build', 'run'), when='@1.2.1:')
-    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-prettyunits', type=('build', 'run'), when='@1.2.0')
+    depends_on('r-tibble', type=('build', 'run'), when='@:1.1.0')

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

@@ -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"
+    cran = "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/"
 
+    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-doparallel', type=('build', 'run'), when='@:0.3.4')
-    depends_on('r-foreach', when='@:0.3.4', type=('build', 'run'))
+    depends_on('r-dorng', type=('build', 'run'), when='@:0.3.4')
+    depends_on('r-foreach', type=('build', 'run'), when='@:0.3.4')

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

@@ -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"
+    cran = "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"
 
     version('0.3', sha256='bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649')

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

@@ -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
+    Output formats and utilities for authoring books and technical documents
-    documents with R Markdown."""
+    with R Markdown."""
 
-    homepage = "https://cloud.r-project.org/package=bookdown"
+    cran = "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"
 
+    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-knitr@1.31:', type=('build', 'run'), when='@0.24:')
-    depends_on('r-rmarkdown@2.4:', when='@0.21:', type=('build', 'run'))
+    depends_on('r-rmarkdown@1.12:', type=('build', 'run'))
-    depends_on('r-xfun@0.6:', when='@:0.12', type=('build', 'run'))
+    depends_on('r-rmarkdown@2.4:', type=('build', 'run'), when='@0.21:')
-    depends_on('r-xfun@0.13:', when='@0.21:', type=('build', 'run'))
+    depends_on('r-rmarkdown@2.9:', type=('build', 'run'), when='@0.24:')
-    depends_on('r-tinytex@0.12:', when='@0.12:', type=('build', 'run'))
+    depends_on('r-jquerylib', type=('build', 'run'), when='@0.24:')
-    depends_on('r-yaml@2.1.14:', when='@:0.12', type=('build', 'run'))
+    depends_on('r-xfun@0.6:', type=('build', 'run'))
-    depends_on('r-yaml@2.1.19:', when='@0.21:', 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:')

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

@@ -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
+    Functions and datasets for bootstrapping from the book "Bootstrap Methods
-    Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997,
+    and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP),
-    CUP), originally written by Angelo Canty for S."""
+    originally written by Angelo Canty for S."""
 
-    homepage = "https://cloud.r-project.org/package=boot"
+    cran = "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"
 
     version('1.3-28', sha256='9f7158fd2714659f590c3955651893dc24bd8f39196bc5a4cc35b0b031744a32')
     version('1.3-25', sha256='464835fcb453072346ce49e4ae318e04c9dba682349be49db616623b6088fbbe')

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

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

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

@@ -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"
+    cran = "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"
 
     version('1.0-6', sha256='d70d1a9a01cf4a923b4f11e4374ffd887ad3ff964f35c6f9dc0f29c8d657f0ed')

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

@@ -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
@@ -15,8 +15,7 @@ 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"
-    cran     = "bridgesampling"
 
     version('1.1-2', sha256='54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b')
 

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

@@ -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')

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

@@ -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
@@ -25,8 +25,7 @@ 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"
-    cran     = "brms"
 
     version('2.16.3', sha256='68302b10b5264f72d163d01c17792c002306cf37f0ee778dcec4c7e118f923e1')
     version('2.16.1', sha256='749efbd9fb061fe207cf2e729c1387d9a8538b922f12ceec4e82a9f8dd9c1bc4')
@@ -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')

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

@@ -7,14 +7,13 @@
 
 
 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"
-    cran     = "Brobdingnag"
 
     version('1.2-6', sha256='19eccaed830ce9d93b70642f6f126ac66722a98bbd48586899cc613dd9966ad4')
 

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

@@ -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-dplyr@1.0.0:', type=('build', 'run'), when='@0.7.3:')
-    depends_on('r-ellipsis', when='@0.7.3:', type=('build', 'run'))
+    depends_on('r-ellipsis', type=('build', 'run'), when='@0.7.3:')
-    depends_on('r-generics@0.0.2:', when='@0.5.1:', type=('build', 'run'))
+    depends_on('r-generics@0.0.2:', type=('build', 'run'), when='@0.5.1:')
-    depends_on('r-glue', when='@0.7.3:', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'), when='@0.7.3:')
-    depends_on('r-purrr', when='@0.5.0:', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'), when='@0.5.0:')
-    depends_on('r-rlang', when='@0.7.3:', type=('build', 'run'))
+    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', type=('build', 'run'), when='@0.5.0:')
-    depends_on('r-tibble@3.0.0:', when='@0.7.3:', type=('build', 'run'))
+    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-tidyr@1.0.0:', type=('build', 'run'), when='@0.7.3:')
-    depends_on('r-ggplot2', when='@0.7.10:', type=('build', 'run'))
+    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-plyr', type=('build', 'run'), when='@:0.4.2')
-    depends_on('r-psych', when='@:0.4.2', type=('build', 'run'))
+    depends_on('r-psych', type=('build', 'run'), when='@:0.4.2')
-    depends_on('r-reshape2', when='@:0.5.2', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'), when='@:0.5.2')
-    depends_on('r-nlme', when='@:0.5.2', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'), when='@:0.5.2')

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

@@ -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'))

var/spack/repos/builtin/packages/r-c50/package.py

@@ -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"
+    cran = "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"
 
+    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@0.2.1:', type=('build', 'run'))
-    depends_on('r-cubist@0.2.3:', when='@0.1.3.1:', 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:')

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

@@ -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
+    Computation and visualization of simple, multiple and joint correspondence
-    correspondence analysis."""
+    analysis."""
 
-    homepage = "http://www.carme-n.org/?sec=ca"
+    cran = "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"
 
     version('0.71.1', sha256='040c2fc94c356075f116cc7cd880530b3c9e02206c0035182c03a525ee99b424')
 

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

@@ -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'))

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

@@ -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"
+    cran = "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"
 
+    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')

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

@@ -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@3.4.0:', type=('build', 'run'), when='@3.0.0:')
-    depends_on('r-processx@3.5.0:', when='@3.6.0:', type=('build', 'run'))
+    depends_on('r-processx@3.5.0:', type=('build', 'run'), when='@3.6.0:')
-    depends_on('r-r6', when='@3.0.0:', type=('build', 'run'))
+    depends_on('r-r6', type=('build', 'run'), when='@3.0.0:')

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

@@ -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
+    Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion
-    Companion to Applied Regression, Second Edition, Sage, 2011."""
+    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@3.2.0:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@3.0-3:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@3.0-3:')
-    depends_on('r-cardata@3.0-0:', when='@3.0:', type=('build', 'run'))
+    depends_on('r-cardata@3.0-0:', type=('build', 'run'), when='@3.0:')
-    depends_on('r-abind', when='@3.0:', type=('build', 'run'))
+    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-maptools', type=('build', 'run'), when='@3.0:')
-    depends_on('r-rio', when='@3.0:3.0-11', type=('build', 'run'))
+    depends_on('r-rio', type=('build', 'run'), when='@3.0:3.0-11')
-    depends_on('r-lme4@1.1-27.1:', when='@3.0-11:', type=('build', 'run'))
+    depends_on('r-lme4@1.1-27.1:', type=('build', 'run'), when='@3.0-11:')
-    depends_on('r-lme4', when='@3.0:', type=('build', 'run'))
+    depends_on('r-lme4', type=('build', 'run'), when='@3.0:')
-    depends_on('r-nlme', when='@3.0:', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'), when='@3.0:')

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

@@ -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"
+    cran = "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"
 
+    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'))

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

@@ -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/"
+    cran = "carData"
-    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"
 
+    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:')

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

@@ -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/"
+    cran = "caret"
-    url      = "https://cloud.r-project.org/src/contrib/caret_6.0-73.tar.gz"
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/caret"
 
+    version('6.0-90', 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@3.2.0:', type=('build', 'run'), when='@6.0-82:')
-    depends_on('r-lattice@0.20:', type=('build', 'run'))
     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-withr@2.0.0:', type=('build', 'run'), when='@6.0-83:')
-    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-car', type=('build', 'run'), when='@:6.0-73')
-    depends_on('r-proc', when='@6.0-86:', type=('build', 'run'))
-    depends_on('r-car', when='@:6.0-73', type=('build', 'run'))

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

@@ -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"
+    cran = "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"
 
     version('2.0.1', sha256='7e595e604ce2d9d32afbc5404e6fcbcd7f80e687316e9ca3303aca3e44c3ef88')
 

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

@@ -7,12 +7,20 @@
 
 
 class RCaroline(RPackage):
-    """caroline: A Collection of Database, Data Structure, Visualization,
+    """A Collection of Database, Data Structure, Visualization, andUtility
-       andUtility Functions for R"""
+    Functions for R.
 
-    homepage = "https://cloud.r-project.org/package=caroline"
+    The caroline R library contains dozens of functions useful for: database
-    url      = "https://cloud.r-project.org/src/contrib/caroline_0.7.6.tar.gz"
+    migration (dbWriteTable2), database style joins & aggregation (nerge,
-    list_url = "https://cloud.r-project.org/src/contrib/Archive/caroline"
+    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')
 

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

@@ -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"
+    cran = "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"
 
+    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'))

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

@@ -5,10 +5,12 @@
 
 
 class RCca(RPackage):
-    """Provides a set of functions that extend the 'cancor' function
+    """Canonical Correlation Analysis.
-    with new numerical and graphical outputs. It also include a
+
-    regularized extension of the canonical correlation analysis to
+    Provides a set of functions that extend the 'cancor' function with new
-    deal with datasets with more variables than observations."""
+    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'
 

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

@@ -5,8 +5,10 @@
 
 
 class RCcp(RPackage):
-    """Significance tests for canonical correlation analysis,
+    """Significance Tests for Canonical Correlation Analysis (CCA).
-    including asymptotic tests and a Monte Carlo method"""
+
+    Significance tests for canonical correlation analysis, including asymptotic
+    tests and a Monte Carlo method"""
 
     cran = 'CCP'
 

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

@@ -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"
+    cran = "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"
 
+    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@3.2.0:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@0.9.2:', 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'))

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

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

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

@@ -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.
+    Tests and assertions to perform frequent argument checks.  A substantial
-    A substantial part of the package was written in C to
+    part of the package was written in C to minimize any worries about
-    minimize any worries about execution time overhead."""
+    execution time overhead."""
 
-    homepage = "https://cloud.r-project.org/package=checkmate"
+    cran = "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"
 
     version('2.0.0', sha256='0dc25b0e20c04836359df1885d099c6e4ad8ae0e585a9e4107f7ea945d9c6fa4')
     version('1.9.4', sha256='faa25754b757fe483b876f5d07b73f76f69a1baa971420892fadec4af4bbad21')

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

@@ -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"
+    cran = "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"
 
+    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:')

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

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

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

@@ -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"
+    cran = "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"
 
     version('2.3-56', sha256='863ecbb951a3da994761ea9062fa96d34e94e19fbc4122521ac179274dfa3f5d')
     version('2.3-53', sha256='521814b46ba958eae28e29d8766aebd285da5e6fa16c5806603df3ae39f77309')

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

@@ -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"
+    cran = "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"
 
+    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@0.1.0:', type=('build', 'run'))
-    depends_on('r-globaloptions@0.1.2:', when='@0.4.12:', 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'))

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

@@ -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.
+    Circular Statistics, from "Topics in Circular Statistics" (2001) S.  Rao
-    Rao Jammalamadaka and A. SenGupta, World Scientific."""
+    Jammalamadaka and A. SenGupta, World Scientific."""
 
-    homepage = "https://cloud.r-project.org/package=CircStats"
+    cran = "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"
 
     maintainers = ['dorton21']