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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2022-02-21 11:22:33 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-02-21 11:22:33 -0600 |
| commit | 275608e2f2abb8b5423d89fd8c951876cde8e6cd (patch) | |
| tree | 047bfb78a26acf315f9b6bf6f27139ed790a7714 /var | |
| parent | f744640289f8decae475909c242dc2f5d9aca404 (diff) | |
| download | spack-275608e2f2abb8b5423d89fd8c951876cde8e6cd.tar.gz spack-275608e2f2abb8b5423d89fd8c951876cde8e6cd.tar.bz2 spack-275608e2f2abb8b5423d89fd8c951876cde8e6cd.tar.xz spack-275608e2f2abb8b5423d89fd8c951876cde8e6cd.zip | |
update CRAN R packages (#28786)
Diffstat (limited to 'var')
839 files changed, 5894 insertions, 5054 deletions
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index 87170ef0c9..791a125495 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -7,14 +7,15 @@ from spack import * class RAbind(RPackage): - """Combine multidimensional arrays into a single array. This is a + """ + Combine Multidimensional Arrays. + + Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays. Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.""" - homepage = "https://cloud.r-project.org/package=abind" - url = "https://cloud.r-project.org/src/contrib/abind_1.4-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/abind" + cran = "abind" version('1.4-5', sha256='3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c') version('1.4-3', sha256='b6c255878c1ab81701ae701f34546e88be115629b984ac4272e311fa3c0ea6ce') diff --git a/var/spack/repos/builtin/packages/r-acepack/package.py b/var/spack/repos/builtin/packages/r-acepack/package.py index 1deee0c1b0..7283792512 100644 --- a/var/spack/repos/builtin/packages/r-acepack/package.py +++ b/var/spack/repos/builtin/packages/r-acepack/package.py @@ -7,10 +7,24 @@ from spack import * class RAcepack(RPackage): - """ACE and AVAS for Selecting Multiple Regression Transformations.""" + """ACE and AVAS for Selecting Multiple Regression Transformations. - homepage = "https://cloud.r-project.org/package=acepack" - url = "https://cloud.r-project.org/src/contrib/acepack_1.4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/acepack" + Two nonparametric methods for multiple regression transform selection are + provided. The first, Alternative Conditional Expectations (ACE), is an + algorithm to find the fixed point of maximal correlation, i.e. it finds a + set of transformed response variables that maximizes R^2 using smoothing + functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal + Transformations for Multiple Regression and Correlation". Journal of the + American Statistical Association. 80:580-598. + <doi:10.1080/01621459.1985.10478157>]. Also included is the Additivity + Variance Stabilization (AVAS) method which works better than ACE when + correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations + for Regression via Additivity and Variance Stabilization". Journal of the + American Statistical Association. 83:394-405. + <doi:10.1080/01621459.1988.10478610>]. A good introduction to these two + methods is in chapter 16 of Frank Harrel's "Regression Modeling Strategies" + in the Springer Series in Statistics.""" + + cran = "acepack" version('1.4.1', sha256='82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9') diff --git a/var/spack/repos/builtin/packages/r-ada/package.py b/var/spack/repos/builtin/packages/r-ada/package.py index 6edbfa04a5..2b2d40f778 100644 --- a/var/spack/repos/builtin/packages/r-ada/package.py +++ b/var/spack/repos/builtin/packages/r-ada/package.py @@ -7,12 +7,14 @@ from spack import * class RAda(RPackage): - """Performs discrete, real, and gentle boost under both exponential - and logistic loss on a given data set.""" + """The R Package Ada for Stochastic Boosting. - homepage = "https://cloud.r-project.org/package=ada" - url = "https://cloud.r-project.org/src/contrib/ada_2.0-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ada" + Performs discrete, real, and gentle boost under both exponential and + logistic loss on a given data set. The package ada provides a + straightforward, well-documented, and broad boosting routine for + classification, ideally suited for small to moderate-sized data sets.""" + + cran = "ada" version('2.0-5', sha256='d900172059eebeef30c27944fc29737a231fc4f92e3c2661868383fbd9016ac0') diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py index 7722990de1..adb0c7b1dd 100644 --- a/var/spack/repos/builtin/packages/r-adabag/package.py +++ b/var/spack/repos/builtin/packages/r-adabag/package.py @@ -7,17 +7,37 @@ from spack import * class RAdabag(RPackage): - """Applies Multiclass AdaBoost.M1, SAMME and Bagging.""" + """Applies Multiclass AdaBoost.M1, SAMME and Bagging. - homepage = "https://cloud.r-project.org/package=adabag" - url = "https://cloud.r-project.org/src/contrib/adabag_4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/adabag" + It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's + Bagging algorithm using classification trees as individual classifiers. + Once these classifiers have been trained, they can be used to predict on + new data. Also, cross validation estimation of the error can be done. Since + version 2.0 the function margins() is available to calculate the margins + for these classifiers. Also a higher flexibility is achieved giving access + to the rpart.control() argument of 'rpart'. Four important new features + were introduced on version 3.0, AdaBoost-SAMME (Zhu et al., 2009) is + implemented and a new function errorevol() shows the error of the ensembles + as a function of the number of iterations. In addition, the ensembles can + be pruned using the option 'newmfinal' in the predict.bagging() and + predict.boosting() functions and the posterior probability of each class + for observations can be obtained. Version 3.1 modifies the relative + importance measure to take into account the gain of the Gini index given by + a variable in each tree and the weights of these trees. Version 4.0 + includes the margin-based ordered aggregation for Bagging pruning (Guo and + Boukir, 2013) and a function to auto prune the 'rpart' tree. Moreover, + three new plots are also available importanceplot(), plot.errorevol() and + plot.margins(). Version 4.1 allows to predict on unlabeled data. Version + 4.2 includes the parallel computation option for some of the functions.""" + + cran = "adabag" version('4.2', sha256='47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81') version('4.1', sha256='ff938c36122cdf58a71a59a6bf79a3c7816966ee7cc4907c4a0a3c0732e3d028') depends_on('r-rpart', type=('build', 'run')) - depends_on('r-mlbench', when='@:4.1', type=('build', 'run')) depends_on('r-caret', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) depends_on('r-doparallel', type=('build', 'run')) + + depends_on('r-mlbench', type=('build', 'run'), when='@:4.1') diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py index 4db3ebfb33..16caa08e36 100644 --- a/var/spack/repos/builtin/packages/r-ade4/package.py +++ b/var/spack/repos/builtin/packages/r-ade4/package.py @@ -8,7 +8,7 @@ from spack import * class RAde4(RPackage): """Analysis of Ecological Data : Exploratory and Euclidean Methods in - Environmental Sciences + Environmental Sciences. Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component @@ -17,10 +17,9 @@ class RAde4(RPackage): STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.""" - homepage = "https://pbil.univ-lyon1.fr/ADE-4" - url = "https://cloud.r-project.org/src/contrib/ade4_1.7-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ade4" + cran = "ade4" + version('1.7-18', sha256='ecb6f4c42c60f39702aa96f454bb536a333049c9608ee2b6bdf8795e059cc525') version('1.7-16', sha256='9bd7a25ff4fe30a32fd8f6b71909f4c638a0e2f002fc8303c0a4795423385590') version('1.7-13', sha256='f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b') version('1.7-11', sha256='4ccd799ae99bd625840b866a697c4a48adb751660470bf0d6cf9207b1927a572') @@ -28,6 +27,7 @@ class RAde4(RPackage): depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r-pixmap', when='@1.7-16:', type=('build', 'run')) - depends_on('r-sp', when='@1.7-16:', type=('build', 'run')) - depends_on('r-progress', when='@1.7-16:', type=('build', 'run')) + depends_on('r-pixmap', type=('build', 'run'), when='@1.7-16:') + depends_on('r-sp', type=('build', 'run'), when='@1.7-16:') + + depends_on('r-progress', type=('build', 'run'), when='@1.7-16') diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py index b226c6ef54..9c17c86f09 100644 --- a/var/spack/repos/builtin/packages/r-adegenet/package.py +++ b/var/spack/repos/builtin/packages/r-adegenet/package.py @@ -7,22 +7,21 @@ from spack import * class RAdegenet(RPackage): - """Exploratory Analysis of Genetic and Genomic Data - - Toolset for the exploration of genetic and genomic data. Adegenet - provides formal (S4) classes for storing and handling various genetic - data, including genetic markers with varying ploidy and hierarchical - population structure ('genind' class), alleles counts by populations - ('genpop'), and genome-wide SNP data ('genlight'). It also implements - original multivariate methods (DAPC, sPCA), graphics, statistical tests, - simulation tools, distance and similarity measures, and several spatial - methods. A range of both empirical and simulated datasets is also provided - to illustrate various methods.""" - - homepage = "https://github.com/thibautjombart/adegenet/wiki" - url = "https://cloud.r-project.org/src/contrib/adegenet_2.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/adegenet" + """Exploratory Analysis of Genetic and Genomic Data. + Toolset for the exploration of genetic and genomic data. Adegenet provides + formal (S4) classes for storing and handling various genetic data, + including genetic markers with varying ploidy and hierarchical population + structure ('genind' class), alleles counts by populations ('genpop'), and + genome-wide SNP data ('genlight'). It also implements original multivariate + methods (DAPC, sPCA), graphics, statistical tests, simulation tools, + distance and similarity measures, and several spatial methods. A range of + both empirical and simulated datasets is also provided to illustrate + various methods.""" + + cran = "adegenet" + + version('2.1.5', sha256='e4eee8c41dae6cb0841db74ec6f9adb2580873f3e313471f37df58324c1857f2') version('2.1.3', sha256='0790114ecb22642683b5be1f4b3a6a49856e06dc2f9e21b9cba4390c2257f6c6') version('2.1.1', sha256='3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a') version('2.1.0', sha256='7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a') @@ -36,8 +35,9 @@ class RAdegenet(RPackage): depends_on('r-shiny', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-seqinr', type=('build', 'run')) - depends_on('r-spdep', type=('build', 'run')) depends_on('r-boot', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-dplyr@0.4.1:', type=('build', 'run')) depends_on('r-vegan', type=('build', 'run')) + + depends_on('r-spdep', type=('build', 'run'), when='@:2.1.3') diff --git a/var/spack/repos/builtin/packages/r-adegraphics/package.py b/var/spack/repos/builtin/packages/r-adegraphics/package.py index 8b98e15609..9ace764525 100644 --- a/var/spack/repos/builtin/packages/r-adegraphics/package.py +++ b/var/spack/repos/builtin/packages/r-adegraphics/package.py @@ -7,17 +7,15 @@ from spack import * class RAdegraphics(RPackage): - """adegraphics: An S4 Lattice-Based Package for the Representation of - Multivariate Data. + """An S4 Lattice-Based Package for the Representation of Multivariate Data. - Graphical functionalities for the representation of multivariate data. - It is a complete re-implementation of the functions available in the 'ade4' + Graphical functionalities for the representation of multivariate data. It + is a complete re-implementation of the functions available in the 'ade4' package.""" - homepage = "https://pbil.univ-lyon1.fr/ADE-4" - url = "https://cloud.r-project.org/src/contrib/adegraphics_1.0-15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/adegraphics" + cran = "adegraphics" + version('1.0-16', sha256='7ba59ce9aeefe1c25b4b118d08ef458ffd34115412c147cc428629e72a82ec3a') version('1.0-15', sha256='87bbcd072e9a898955f5ede4315e82365086a50a2887bf5bd2e94bbb4d3f678a') depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adephylo/package.py b/var/spack/repos/builtin/packages/r-adephylo/package.py index 9415006db3..8bcf366fd9 100644 --- a/var/spack/repos/builtin/packages/r-adephylo/package.py +++ b/var/spack/repos/builtin/packages/r-adephylo/package.py @@ -7,14 +7,12 @@ from spack import * class RAdephylo(RPackage): - """adephylo: Exploratory Analyses for the Phylogenetic Comparative Method. + """Exploratory Analyses for the Phylogenetic Comparative Method. - Multivariate tools to analyze comparative data, i.e. a phylogeny and - some traits measured for each taxa.""" + Multivariate tools to analyze comparative data, i.e. a phylogeny and some + traits measured for each taxa.""" - homepage = "https://cloud.r-project.org/package=adephylo" - url = "https://cloud.r-project.org/src/contrib/adephylo_1.1-11.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/adephylo" + cran = "adephylo" version('1.1-11', sha256='154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a') diff --git a/var/spack/repos/builtin/packages/r-adespatial/package.py b/var/spack/repos/builtin/packages/r-adespatial/package.py index 6b1397db79..52201d7f5a 100644 --- a/var/spack/repos/builtin/packages/r-adespatial/package.py +++ b/var/spack/repos/builtin/packages/r-adespatial/package.py @@ -7,7 +7,7 @@ from spack import * class RAdespatial(RPackage): - """adespatial: Multivariate Multiscale Spatial Analysis. + """Multivariate Multiscale Spatial Analysis. Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its @@ -15,10 +15,9 @@ class RAdespatial(RPackage): approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.""" - homepage = "https://cloud.r-project.org/package=adespatial" - url = "https://cloud.r-project.org/src/contrib/adespatial_0.3-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/adespatial" + cran = "adespatial" + version('0.3-14', sha256='a2ef7549c1ed7a23651716c633b25eaff468af8ccbf2e9fcd164e485984cbfbf') version('0.3-8', sha256='e3fd3209ce3f0a862a0794187e8c884f1697c87c96e569a2f51f252e00022906') depends_on('r-ade4@1.7-13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adgoftest/package.py b/var/spack/repos/builtin/packages/r-adgoftest/package.py index dd93e0ed26..0a97c1fb63 100644 --- a/var/spack/repos/builtin/packages/r-adgoftest/package.py +++ b/var/spack/repos/builtin/packages/r-adgoftest/package.py @@ -7,11 +7,11 @@ from spack import * class RAdgoftest(RPackage): - """Anderson-Darling GoF test with p-value calculation based on Marsaglia's - 2004 paper 'Evaluating the Anderson-Darling Distribution'""" + """Anderson-Darling GoF test. - homepage = "https://cloud.r-project.org/package=ADGofTest" - url = "https://cloud.r-project.org/src/contrib/ADGofTest_0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ADGofTest" + Anderson-Darling GoF test with p-value calculation based on Marsaglia's + 2004 paper 'Evaluating the Anderson-Darling Distribution'.""" + + cran = "ADGofTest" version('0.3', sha256='9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846') diff --git a/var/spack/repos/builtin/packages/r-aer/package.py b/var/spack/repos/builtin/packages/r-aer/package.py index 7677a61d89..30cf5ca89f 100644 --- a/var/spack/repos/builtin/packages/r-aer/package.py +++ b/var/spack/repos/builtin/packages/r-aer/package.py @@ -7,16 +7,13 @@ from spack import * class RAer(RPackage): - """Applied Econometrics with R + """Applied Econometrics with R. - Functions, data sets, examples, demos, and vignettes - for the book Christian Kleiber and Achim Zeileis (2008), - Applied Econometrics with R, Springer-Verlag, New York. - ISBN 978-0-387-77316-2.""" + Functions, data sets, examples, demos, and vignettes for the book Christian + Kleiber and Achim Zeileis (2008), Applied Econometrics with R, + Springer-Verlag, New York. ISBN 978-0-387-77316-2.""" - homepage = "https://cloud.r-project.org/package=AER" - url = "https://cloud.r-project.org/src/contrib/AER_1.2-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/AER" + cran = "AER" version('1.2-9', sha256='3b79390b14766419fc1e8912689bc462d4beb01aff9dad26d628aed69d04540d') version('1.2-7', sha256='3aee5c606313710c2dca6c1e9b2c20a145aa33f2a3ecc5cfcec66c8e91838a93') diff --git a/var/spack/repos/builtin/packages/r-afex/package.py b/var/spack/repos/builtin/packages/r-afex/package.py index 7afd1114fa..55983afb35 100644 --- a/var/spack/repos/builtin/packages/r-afex/package.py +++ b/var/spack/repos/builtin/packages/r-afex/package.py @@ -7,25 +7,22 @@ from spack import * class RAfex(RPackage): - """Analysis of Factorial Experiments + """Analysis of Factorial Experiments. Convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), - automatically aggregating multiple observations per individual and cell - of the design. mixed() fits mixed models using lme4::lmer() and computes + automatically aggregating multiple observations per individual and cell of + the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger or Satterthwaite - approximation for degrees of freedom (LMM only), parametric bootstrap - (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). - afex_plot() provides a high-level interface for interaction or one-way - plots using ggplot2, combining raw data and model estimates. afex uses - type 3 sums of squares as default (imitating commercial statistical - software). - """ + approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs + and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex_plot() + provides a high-level interface for interaction or one-way plots using + ggplot2, combining raw data and model estimates. afex uses type 3 sums of + squares as default (imitating commercial statistical software).""" - homepage = "https://github.com/singmann/afex" - cran = "afex" + cran = "afex" version('1.0-1', sha256='6febc34b87a1109f5cbcd213c08d2b7b3e9cf99065fa41c19bc88ac99fb104cc') version('0.28-1', sha256='cfb0b79bfa01b590afc3354a5b2ad3640d2f4974b036d6c256fa8e684bc69c2e') diff --git a/var/spack/repos/builtin/packages/r-als/package.py b/var/spack/repos/builtin/packages/r-als/package.py index 16b19c97b3..a75631dfa9 100644 --- a/var/spack/repos/builtin/packages/r-als/package.py +++ b/var/spack/repos/builtin/packages/r-als/package.py @@ -7,17 +7,17 @@ from spack import * class RAls(RPackage): - """Alternating least squares is often used to resolve components - contributing to data with a bilinear structure; the basic - technique may be extended to alternating constrained least squares. - Commonly applied constraints include unimodality, non-negativity, - and normalization of components. Several data matrices may be - decomposed simultaneously by assuming that one of the two matrices - in the bilinear decomposition is shared between datasets.""" + """Multivariate Curve Resolution Alternating Least Squares (MCR-ALS). - homepage = "https://cloud.r-project.org/package=ALS" - url = "https://cloud.r-project.org/src/contrib/ALS_0.0.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ALS" + Alternating least squares is often used to resolve components contributing + to data with a bilinear structure; the basic technique may be extended to + alternating constrained least squares. Commonly applied constraints + include unimodality, non-negativity, and normalization of components. + Several data matrices may be decomposed simultaneously by assuming that one + of the two matrices in the bilinear decomposition is shared between + datasets.""" + + cran = "ALS" version('0.0.6', sha256='ca90d27115ae9e476967f521bf6935723e410a3bf92477e7570e14bfd3b099eb') diff --git a/var/spack/repos/builtin/packages/r-amap/package.py b/var/spack/repos/builtin/packages/r-amap/package.py index a614cf314d..0570b9995d 100644 --- a/var/spack/repos/builtin/packages/r-amap/package.py +++ b/var/spack/repos/builtin/packages/r-amap/package.py @@ -7,18 +7,16 @@ from spack import * class RAmap(RPackage): - """Another Multidimensional Analysis Package + """Another Multidimensional Analysis Package. Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).""" - homepage = "https://cran.r-project.org/web/packages/amap/index.html" - url = "https://cloud.r-project.org/src/contrib/amap_0.8-16.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/amap/" + cran = "amap" version('0.8-18', sha256='7afbbdd681a201121374821b733c9000ca1046a2353ee386507604c2c759ec7e') version('0.8-17', sha256='6b8473d1d35a9cbc611661882c8f681162e8f913f911ccd51629200ae72289c6') version('0.8-16', sha256='d3775ad7f660581f7d2f070e426be95ae0d6743622943e6f5491988e5217d4e2') - depends_on('r@2.10.0:', when='@:0.8-16', type=('build', 'run')) - depends_on('r@3.6.0:', when='@0.8-17:', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r@3.6.0:', type=('build', 'run'), when='@0.8-17:') diff --git a/var/spack/repos/builtin/packages/r-amelia/package.py b/var/spack/repos/builtin/packages/r-amelia/package.py index c5b0e32bfd..9cce1e443b 100644 --- a/var/spack/repos/builtin/packages/r-amelia/package.py +++ b/var/spack/repos/builtin/packages/r-amelia/package.py @@ -7,21 +7,30 @@ from spack import * class RAmelia(RPackage): - """Amelia: A Program for Missing Data + """A Program for Missing Data. - Amelia II "multiply imputes" missing data in a single - cross-section (such as a survey), from a time series (like - variables collected for each year in a country), or from a - time-series-cross-sectional data set (such as collected by - years for each of several countries).""" + A tool that "multiply imputes" missing data in a single cross-section (such + as a survey), from a time series (like variables collected for each year in + a country), or from a time-series-cross-sectional data set (such as + collected by years for each of several countries). Amelia II implements our + bootstrapping-based algorithm that gives essentially the same answers as + the standard IP or EMis approaches, is usually considerably faster than + existing approaches and can handle many more variables. Unlike Amelia I + and other statistically rigorous imputation software, it virtually never + crashes (but please let us know if you find to the contrary!). The program + also generalizes existing approaches by allowing for trends in time series + across observations within a cross-sectional unit, as well as priors that + allow experts to incorporate beliefs they have about the values of missing + cells in their data. Amelia II also includes useful diagnostics of the fit + of multiple imputation models. The program works from the R command line + or via a graphical user interface that does not require users to know R.""" - homepage = "https://gking.harvard.edu/amelia" - url = "https://cloud.r-project.org/src/contrib/Amelia_1.7.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Amelia" + cran = "Amelia" + version('1.8.0', sha256='3ec1d5a68dac601b354227916aa8ec72fa1216b603dd887aae2b24cb69b5995e') version('1.7.6', sha256='63c08d374aaf78af46c34dc78da719b3085e58d9fabdc76c6460d5193a621bea') - depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r-rcpp@0.11:', type=('build', 'run')) - depends_on('r-foreign', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-rcpp@0.11:', type=('build', 'run')) + depends_on('r-foreign', type=('build', 'run')) depends_on('r-rcpparmadillo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py index 420d14297a..301dea0458 100644 --- a/var/spack/repos/builtin/packages/r-animation/package.py +++ b/var/spack/repos/builtin/packages/r-animation/package.py @@ -7,23 +7,25 @@ from spack import * class RAnimation(RPackage): - """Provides functions for animations in statistics, covering topics - in probability theory, mathematical statistics, multivariate statistics, + """A Gallery of Animations in Statistics and Utilities to Create + Animations. + + Provides functions for animations in statistics, covering topics in + probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, - computational statistics, data mining and machine learning. - These functions maybe helpful in teaching statistics and data analysis.""" + computational statistics, data mining and machine learning. These + functions maybe helpful in teaching statistics and data analysis.""" - homepage = "https://cloud.r-project.org/package=animation" - url = "https://cloud.r-project.org/src/contrib/animation_2.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/animation" + cran = "animation" + version('2.7', sha256='88418f1b04ec785963bad492f30eb48b05914e9e5d88c7eef705d949cbd7e469') version('2.6', sha256='90293638920ac436e7e4de76ebfd92e1643ccdb0259b62128f16dd0b13245b0a') version('2.5', sha256='b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f') depends_on('r+X', type=('build', 'run')) depends_on('r@2.14:', type=('build', 'run')) - depends_on('r-magick', when='@2.6:', type=('build', 'run')) + depends_on('r-magick', type=('build', 'run'), when='@2.6:') depends_on('imagemagick') - depends_on('ffmpeg') - depends_on('swftools') depends_on('texlive') + depends_on('swftools') + depends_on('ffmpeg') diff --git a/var/spack/repos/builtin/packages/r-anytime/package.py b/var/spack/repos/builtin/packages/r-anytime/package.py index daa44ce090..5558631c67 100644 --- a/var/spack/repos/builtin/packages/r-anytime/package.py +++ b/var/spack/repos/builtin/packages/r-anytime/package.py @@ -7,16 +7,14 @@ from spack import * class RAnytime(RPackage): - """Anything to 'POSIXct' or 'Date' Converter + """Anything to 'POSIXct' or 'Date' Converter. - Convert input in any one of character, integer, numeric, - factor, or ordered type into 'POSIXct' (or 'Date') objects, - using one of a number of predefined formats, and relying on - Boost facilities for date and time parsing.""" + Convert input in any one of character, integer, numeric, factor, or ordered + type into 'POSIXct' (or 'Date') objects, using one of a number of + predefined formats, and relying on Boost facilities for date and time + parsing.""" - homepage = "https://dirk.eddelbuettel.com/code/anytime.html" - url = "https://cloud.r-project.org/src/contrib/anytime_0.3.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/anytime" + cran = "anytime" version('0.3.9', sha256='1096c15249ac70997a8a41c37eeb2a6d38530621abeae05d3dcd96a8acc7574a') diff --git a/var/spack/repos/builtin/packages/r-aod/package.py b/var/spack/repos/builtin/packages/r-aod/package.py index 3c57049414..8ce19bf352 100644 --- a/var/spack/repos/builtin/packages/r-aod/package.py +++ b/var/spack/repos/builtin/packages/r-aod/package.py @@ -7,16 +7,15 @@ from spack import * class RAod(RPackage): - """Provides a set of functions to analyse overdispersed counts or - proportions. Most of the methods are already available elsewhere but are - scattered in different packages. The proposed functions should be - considered as complements to more sophisticated methods such as generalized - estimating equations (GEE) or generalized linear mixed effect models - (GLMM).""" + """Analysis of Overdispersed Data. - homepage = "https://cloud.r-project.org/package=aod" - url = "https://cloud.r-project.org/src/contrib/aod_1.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/aod" + Provides a set of functions to analyse overdispersed counts or proportions. + Most of the methods are already available elsewhere but are scattered in + different packages. The proposed functions should be considered as + complements to more sophisticated methods such as generalized estimating + equations (GEE) or generalized linear mixed effect models (GLMM).""" + + cran = "aod" version('1.3.1', sha256='052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc') diff --git a/var/spack/repos/builtin/packages/r-ape/package.py b/var/spack/repos/builtin/packages/r-ape/package.py index c1ea7bc8dd..4a489a309a 100644 --- a/var/spack/repos/builtin/packages/r-ape/package.py +++ b/var/spack/repos/builtin/packages/r-ape/package.py @@ -7,28 +7,27 @@ from spack import * class RApe(RPackage): - """Analyses of Phylogenetics and Evolution + """Analyses of Phylogenetics and Evolution. Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide - sequences as well as importing from BioConductor, and several tools such - as Mantel's test, generalized skyline plots, graphical exploration of + sequences as well as importing from BioConductor, and several tools such as + Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and - triangle methods, and several methods handling incomplete distance - matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some - functions call external applications (PhyML, Clustal, T-Coffee, Muscle) - whose results are returned into R.""" + triangle methods, and several methods handling incomplete distance matrices + (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions + call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results + are returned into R.""" - homepage = "http://ape-package.ird.fr/" - url = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ape" + cran = "ape" + version('5.6-1', sha256='25401e036576eed1200e15bf68879ccd85611303a3508b989e15164cd4c0f7f7') version('5.4-1', sha256='f0316c8e74ce900053e8b3e8c9322b9d10e7730f3be2150365f74630bee7eee4') version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23') version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415') diff --git a/var/spack/repos/builtin/packages/r-argparse/package.py b/var/spack/repos/builtin/packages/r-argparse/package.py index 1a9af48c2c..71e75a13ec 100644 --- a/var/spack/repos/builtin/packages/r-argparse/package.py +++ b/var/spack/repos/builtin/packages/r-argparse/package.py @@ -7,23 +7,23 @@ from spack import * class RArgparse(RPackage): - """Command Line Optional and Positional Argument Parser + """Command Line Optional and Positional Argument Parser. A command line parser to be used with Rscript to write "#!" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage.""" - homepage = "https://github.com/trevorld/argparse" - url = "https://cloud.r-project.org/src/contrib/argparse_1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/argparse" + cran = "argparse" + version('2.1.3', sha256='aeda31a54a8d7a0a511cfbf7c5868637e129922671d43938165867437fb6a66e') version('2.0.3', sha256='d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0') version('2.0.1', sha256='949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab') version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b') - depends_on('r-proto@1:', when='@1.0.0:1.9.9', type=('build', 'run')) - depends_on('r-getopt', when='@1.0.0:1.9.9', type=('build', 'run')) - depends_on('r-r6', when='@2.0.0:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run'), when='@2.0.0:') depends_on('r-findpython', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('python@3.2:', type=('build', 'run')) + + depends_on('r-proto@1:', type=('build', 'run'), when='@1.0.0:1.9.9') + depends_on('r-getopt', type=('build', 'run'), when='@1.0.0:1.9.9') diff --git a/var/spack/repos/builtin/packages/r-ash/package.py b/var/spack/repos/builtin/packages/r-ash/package.py index 9d9658276f..9b2bc4f602 100644 --- a/var/spack/repos/builtin/packages/r-ash/package.py +++ b/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' diff --git a/var/spack/repos/builtin/packages/r-askpass/package.py b/var/spack/repos/builtin/packages/r-askpass/package.py index e88404d690..abe0cc3edc 100644 --- a/var/spack/repos/builtin/packages/r-askpass/package.py +++ b/var/spack/repos/builtin/packages/r-askpass/package.py @@ -7,7 +7,9 @@ from spack import * class RAskpass(RPackage): - """Cross-platform utilities for prompting the user for credentials or a + """Safe Password Entry for R, Git, and SSH. + + Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly @@ -16,9 +18,7 @@ class RAskpass(RPackage): environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.""" - homepage = "https://github.com/jeroen/askpass#readme" - url = "https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/askpass" + cran = "askpass" version('1.1', sha256='db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f') diff --git a/var/spack/repos/builtin/packages/r-assertive-base/package.py b/var/spack/repos/builtin/packages/r-assertive-base/package.py index b650706c57..f43506932f 100644 --- a/var/spack/repos/builtin/packages/r-assertive-base/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-base/package.py @@ -7,18 +7,18 @@ from spack import * class RAssertiveBase(RPackage): - """assertive.base: A Lightweight Core of the 'assertive' Package + """A Lightweight Core of the 'assertive' Package. A minimal set of predicates and assertions used by the assertive package. - This is mainly for use by other package developers who want to include run-time - testing features in their own packages. End-users will usually want to use - assertive directly.""" + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.base" - url = "https://cloud.r-project.org/src/contrib/assertive.base_0.0-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.base" + cran = "assertive.base" + version('0.0-9', sha256='4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e') version('0.0-7', sha256='f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7') version('0.0-1', sha256='6a5fb06ad912f01cd8aaf2aa7c8ca03b8ebbb1c5eb2be47fa145930f15f4d258') depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.0-9:') diff --git a/var/spack/repos/builtin/packages/r-assertive-code/package.py b/var/spack/repos/builtin/packages/r-assertive-code/package.py index 4c6bf2ecf5..bcfdea42b9 100644 --- a/var/spack/repos/builtin/packages/r-assertive-code/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-code/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveCode(RPackage): - """assertive.code: Assertions to Check Properties of Code + """Assertions to Check Properties of Code. - A set of predicates and assertions for checking the - properties of code. This is mainly for use by other package - developers who want to include run-time testing features in - their own packages. End-users will usually want to use - assertive directly.""" + A set of predicates and assertions for checking the properties of code. + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.code" - url = "https://cloud.r-project.org/src/contrib/assertive.code_0.0-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.code" + cran = "assertive.code" version('0.0-3', sha256='ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2') diff --git a/var/spack/repos/builtin/packages/r-assertive-data-uk/package.py b/var/spack/repos/builtin/packages/r-assertive-data-uk/package.py index 6498ee089f..6bdd67fc46 100644 --- a/var/spack/repos/builtin/packages/r-assertive-data-uk/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-data-uk/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveDataUk(RPackage): - """assertive.data.uk: Assertions to Check Properties of Strings + """Assertions to Check Properties of Strings. - A set of predicates and assertions for checking the - properties of UK-specific complex data types. This is - mainly for use by other package developers who want to - include run-time testing features in their own packages. - End-users will usually want to use assertive directly.""" + A set of predicates and assertions for checking the properties of + UK-specific complex data types. This is mainly for use by other package + developers who want to include run-time testing features in their own + packages. End-users will usually want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.data.uk" - url = "https://cloud.r-project.org/src/contrib/assertive.data.uk_0.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.data.uk" + cran = "assertive.data.uk" version('0.0-2', sha256='ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb') diff --git a/var/spack/repos/builtin/packages/r-assertive-data-us/package.py b/var/spack/repos/builtin/packages/r-assertive-data-us/package.py index 04874cce97..5fa46f6d50 100644 --- a/var/spack/repos/builtin/packages/r-assertive-data-us/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-data-us/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveDataUs(RPackage): - """assertive.data.us: Assertions to Check Properties of Strings + """Assertions to Check Properties of Strings. - A set of predicates and assertions for checking the - properties of US-specific complex data types. This is - mainly for use by other package developers who want to - include run-time testing features in their own packages. - End-users will usually want to use assertive directly.""" + A set of predicates and assertions for checking the properties of + US-specific complex data types. This is mainly for use by other package + developers who want to include run-time testing features in their own + packages. End-users will usually want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.data.us" - url = "https://cloud.r-project.org/src/contrib/assertive.data.us_0.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.data.us" + cran = "assertive.data.us" version('0.0-2', sha256='180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad') diff --git a/var/spack/repos/builtin/packages/r-assertive-data/package.py b/var/spack/repos/builtin/packages/r-assertive-data/package.py index a1031c67c7..c37636f7f1 100644 --- a/var/spack/repos/builtin/packages/r-assertive-data/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-data/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveData(RPackage): - """assertive.data: Assertions to Check Properties of Data + """Assertions to Check Properties of Data. - A set of predicates and assertions for checking the - properties of (country independent) complex data types. - This is mainly for use by other package developers who want - to include run-time testing features in their own packages. - End-users will usually want to use assertive directly.""" + A set of predicates and assertions for checking the properties of (country + independent) complex data types. This is mainly for use by other package + developers who want to include run-time testing features in their own + packages. End-users will usually want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.data" - url = "https://cloud.r-project.org/src/contrib/assertive.data_0.0-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.data" + cran = "assertive.data" version('0.0-3', sha256='5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01') diff --git a/var/spack/repos/builtin/packages/r-assertive-datetimes/package.py b/var/spack/repos/builtin/packages/r-assertive-datetimes/package.py index ee335e0f4c..7d1667b519 100644 --- a/var/spack/repos/builtin/packages/r-assertive-datetimes/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-datetimes/package.py @@ -7,16 +7,14 @@ from spack import * class RAssertiveDatetimes(RPackage): - """assertive.datetimes: Assertions to Check Properties of Dates and Times + """Assertions to Check Properties of Dates and Times. - A set of predicates and assertions for checking the properties of - dates and times. This is mainly for use by other package developers - who want to include run-time testing features in their own packages. - End-users will usually want to use assertive directly.""" + A set of predicates and assertions for checking the properties of dates and + times. This is mainly for use by other package developers who want to + include run-time testing features in their own packages. End-users will + usually want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.datetimes" - url = "https://cloud.r-project.org/src/contrib/assertive.datetimes_0.0-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.datetimes" + cran = "assertive.datetimes" version('0.0-3', sha256='014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94') diff --git a/var/spack/repos/builtin/packages/r-assertive-files/package.py b/var/spack/repos/builtin/packages/r-assertive-files/package.py index 61fc5e590d..01f1c03b7a 100644 --- a/var/spack/repos/builtin/packages/r-assertive-files/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-files/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveFiles(RPackage): - """assertive.files: Assertions to Check Properties of Files + """Assertions to Check Properties of Files. - A set of predicates and assertions for checking the - properties of files and connections. This is mainly for use - by other package developers who want to include run-time - testing features in their own packages. End-users will + A set of predicates and assertions for checking the properties of files and + connections. This is mainly for use by other package developers who want to + include run-time testing features in their own packages. End-users will usually want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.files" - url = "https://cloud.r-project.org/src/contrib/assertive.files_0.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.files" + cran = "assertive.files" version('0.0-2', sha256='be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a') diff --git a/var/spack/repos/builtin/packages/r-assertive-matrices/package.py b/var/spack/repos/builtin/packages/r-assertive-matrices/package.py index d1b17cc27c..5a172263d8 100644 --- a/var/spack/repos/builtin/packages/r-assertive-matrices/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-matrices/package.py @@ -7,18 +7,14 @@ from spack import * class RAssertiveMatrices(RPackage): - """assertive.matrices: Assertions to Check Properties of - Matrices + """Assertions to Check Properties of Matrices. - A set of predicates and assertions for checking the - properties of matrices. This is mainly for use by other - package developers who want to include run-time testing - features in their own packages. End-users will usually want - to use assertive directly.""" + A set of predicates and assertions for checking the properties of matrices. + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.matrices" - url = "https://cloud.r-project.org/src/contrib/assertive.matrices_0.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.matrices" + cran = "assertive.matrices" version('0.0-2', sha256='3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b') diff --git a/var/spack/repos/builtin/packages/r-assertive-models/package.py b/var/spack/repos/builtin/packages/r-assertive-models/package.py index 4fa585a63f..6c34b4f8a3 100644 --- a/var/spack/repos/builtin/packages/r-assertive-models/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-models/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveModels(RPackage): - """assertive.models: Assertions to Check Properties of Models + """Assertions to Check Properties of Models. - A set of predicates and assertions for checking the - properties of models. This is mainly for use by other - package developers who want to include run-time testing - features in their own packages. End-users will usually want - to use assertive directly.""" + A set of predicates and assertions for checking the properties of models. + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.models" - url = "https://cloud.r-project.org/src/contrib/assertive.models_0.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.models" + cran = "assertive.models" version('0.0-2', sha256='b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e') diff --git a/var/spack/repos/builtin/packages/r-assertive-numbers/package.py b/var/spack/repos/builtin/packages/r-assertive-numbers/package.py index e16d64c2dc..7d5fb31447 100644 --- a/var/spack/repos/builtin/packages/r-assertive-numbers/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-numbers/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveNumbers(RPackage): - """assertive.numbers: Assertions to Check Properties of Numbers + """Assertions to Check Properties of Numbers. - A set of predicates and assertions for checking the - properties of numbers. This is mainly for use by other - package developers who want to include run-time testing - features in their own packages. End-users will usually want - to use assertive directly.""" + A set of predicates and assertions for checking the properties of numbers. + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.numbers" - url = "https://cloud.r-project.org/src/contrib/assertive.numbers_0.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.numbers" + cran = "assertive.numbers" version('0.0-2', sha256='bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349') diff --git a/var/spack/repos/builtin/packages/r-assertive-properties/package.py b/var/spack/repos/builtin/packages/r-assertive-properties/package.py index 105956cedd..32f294cb86 100644 --- a/var/spack/repos/builtin/packages/r-assertive-properties/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-properties/package.py @@ -7,19 +7,15 @@ from spack import * class RAssertiveProperties(RPackage): - """assertive.properties: Assertions to Check Properties of - Variables + """Assertions to Check Properties of Variables. - A set of predicates and assertions for checking the - properties of variables, such as length, names and - attributes. This is mainly for use by other package - developers who want to include run-time testing features in - their own packages. End-users will usually want to use - assertive directly.""" + A set of predicates and assertions for checking the properties of + variables, such as length, names and attributes. This is mainly for use by + other package developers who want to include run-time testing features in + their own packages. End-users will usually want to use assertive + directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.properties" - url = "https://cloud.r-project.org/src/contrib/assertive.properties_0.0-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.properties" + cran = "assertive.properties" version('0.0-4', sha256='5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b') diff --git a/var/spack/repos/builtin/packages/r-assertive-reflection/package.py b/var/spack/repos/builtin/packages/r-assertive-reflection/package.py index 0b0a9dc713..71d6a0cafc 100644 --- a/var/spack/repos/builtin/packages/r-assertive-reflection/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-reflection/package.py @@ -7,18 +7,15 @@ from spack import * class RAssertiveReflection(RPackage): - """assertive.reflection: Assertions for Checking the State of R + """Assertions for Checking the State of R. - A set of predicates and assertions for checking the state - and capabilities of R, the operating system it is running - on, and the IDE being used. This is mainly for use by other - package developers who want to include run-time testing - features in their own packages. End-users will usually want - to use assertive directly.""" + A set of predicates and assertions for checking the state and capabilities + of R, the operating system it is running on, and the IDE being used. This + is mainly for use by other package developers who want to include run-time + testing features in their own packages. End-users will usually want to use + assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.reflection" - url = "https://cloud.r-project.org/src/contrib/assertive.reflection_0.0-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.reflection" + cran = "assertive.reflection" version('0.0-5', sha256='c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd') diff --git a/var/spack/repos/builtin/packages/r-assertive-sets/package.py b/var/spack/repos/builtin/packages/r-assertive-sets/package.py index a35ac01de1..cb2214c8a9 100644 --- a/var/spack/repos/builtin/packages/r-assertive-sets/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-sets/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveSets(RPackage): - """assertive.sets: Assertions to Check Properties of Sets + """Assertions to Check Properties of Sets. - A set of predicates and assertions for checking the - properties of sets. This is mainly for use by other package - developers who want to include run-time testing features in - their own packages. End-users will usually want to use - assertive directly.""" + A set of predicates and assertions for checking the properties of sets. + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.sets" - url = "https://cloud.r-project.org/src/contrib/assertive.sets_0.0-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.sets" + cran = "assertive.sets" version('0.0-3', sha256='876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3') diff --git a/var/spack/repos/builtin/packages/r-assertive-strings/package.py b/var/spack/repos/builtin/packages/r-assertive-strings/package.py index ea37fb6364..2b6d49f2ae 100644 --- a/var/spack/repos/builtin/packages/r-assertive-strings/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-strings/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveStrings(RPackage): - """assertive.strings: Assertions to Check Properties of Strings + """Assertions to Check Properties of Strings. - A set of predicates and assertions for checking the - properties of strings. This is mainly for use by other - package developers who want to include run-time testing - features in their own packages. End-users will usually want - to use assertive directly.""" + A set of predicates and assertions for checking the properties of strings. + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.strings" - url = "https://cloud.r-project.org/src/contrib/assertive.strings_0.0-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.strings" + cran = "assertive.strings" version('0.0-3', sha256='d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258') diff --git a/var/spack/repos/builtin/packages/r-assertive-types/package.py b/var/spack/repos/builtin/packages/r-assertive-types/package.py index c84b89cabd..a2834f6221 100644 --- a/var/spack/repos/builtin/packages/r-assertive-types/package.py +++ b/var/spack/repos/builtin/packages/r-assertive-types/package.py @@ -7,17 +7,14 @@ from spack import * class RAssertiveTypes(RPackage): - """assertive.types: Assertions to Check Types of Variables + """Assertions to Check Types of Variables. - A set of predicates and assertions for checking the types - of variables. This is mainly for use by other package - developers who want to include run-time testing features in - their own packages. End-users will usually want to use - assertive directly.""" + A set of predicates and assertions for checking the types of variables. + This is mainly for use by other package developers who want to include + run-time testing features in their own packages. End-users will usually + want to use assertive directly.""" - homepage = "https://bitbucket.org/richierocks/assertive.types" - url = "https://cloud.r-project.org/src/contrib/assertive.types_0.0-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive.types" + cran = "assertive.types" version('0.0-3', sha256='ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f') diff --git a/var/spack/repos/builtin/packages/r-assertive/package.py b/var/spack/repos/builtin/packages/r-assertive/package.py index 5ba292bbee..1f979124d9 100644 --- a/var/spack/repos/builtin/packages/r-assertive/package.py +++ b/var/spack/repos/builtin/packages/r-assertive/package.py @@ -7,15 +7,13 @@ from spack import * class RAssertive(RPackage): - """assertive: Readable Check Functions to Ensure Code Integrity + """Readable Check Functions to Ensure Code Integrity. - Lots of predicates (is_* functions) to check the state of your - variables, and assertions (assert_* functions) to throw errors if - they aren't in the right form.""" + Lots of predicates (is_* functions) to check the state of your variables, + and assertions (assert_* functions) to throw errors if they aren't in the + right form.""" - homepage = "https://bitbucket.org/richierocks/assertive" - url = "https://cloud.r-project.org/src/contrib/assertive_0.3-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertive" + cran = "assertive" version('0.3-6', sha256='c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a') diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py index e41e1af092..fd302e29b4 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -7,14 +7,13 @@ from spack import * class RAssertthat(RPackage): - """assertthat is an extension to stopifnot() that makes it easy to declare - the pre and post conditions that you code should satisfy, while also - producing friendly error messages so that your users know what they've done - wrong.""" + """Easy Pre and Post Assertions. - homepage = "https://cloud.r-project.org/package=assertthat" - url = "https://cloud.r-project.org/src/contrib/assertthat_0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/assertthat" + An extension to stopifnot() that makes it easy to declare the pre and post + conditions that you code should satisfy, while also producing friendly + error messages so that your users know what's gone wrong.""" + + cran = "assertthat" version('0.2.1', sha256='85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f') version('0.2.0', sha256='d73ef79b1e75293ed889a99571b237a95829c099f7da094d4763f83ea6fde5f2') diff --git a/var/spack/repos/builtin/packages/r-backports/package.py b/var/spack/repos/builtin/packages/r-backports/package.py index 79f14a7977..5df7aeda47 100644 --- a/var/spack/repos/builtin/packages/r-backports/package.py +++ b/var/spack/repos/builtin/packages/r-backports/package.py @@ -7,7 +7,7 @@ from spack import * 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') diff --git a/var/spack/repos/builtin/packages/r-base64/package.py b/var/spack/repos/builtin/packages/r-base64/package.py index f48ffdc16d..2dc375af85 100644 --- a/var/spack/repos/builtin/packages/r-base64/package.py +++ b/var/spack/repos/builtin/packages/r-base64/package.py @@ -7,13 +7,13 @@ from spack import * class RBase64(RPackage): - """Compatibility wrapper to replace the orphaned package by Romain - Francois. New applications should use the 'openssl' or 'base64enc' - package instead.""" + """Base64 Encoder and Decoder. - homepage = "https://cloud.r-project.org/package=base64" - url = "https://cloud.r-project.org/src/contrib/base64_2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/base64" + Compatibility wrapper to replace the orphaned package by Romain Francois. + New applications should use the 'openssl' or 'base64enc' package + instead.""" + + cran = "base64" version('2.0', sha256='8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1') diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py index 188d72a042..9f7a2abc56 100644 --- a/var/spack/repos/builtin/packages/r-base64enc/package.py +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -7,12 +7,12 @@ from spack import * class RBase64enc(RPackage): - """This package provides tools for handling base64 encoding. It is more + """Tools for base64 encoding. + + This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.""" - homepage = "https://www.rforge.net/base64enc" - url = "https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/base64enc" + cran = "base64enc" version('0.1-3', sha256='6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d') diff --git a/var/spack/repos/builtin/packages/r-bayesm/package.py b/var/spack/repos/builtin/packages/r-bayesm/package.py index 146e7eb353..7ae38491f4 100644 --- a/var/spack/repos/builtin/packages/r-bayesm/package.py +++ b/var/spack/repos/builtin/packages/r-bayesm/package.py @@ -7,7 +7,7 @@ from spack import * class RBayesm(RPackage): - """Bayesian Inference for Marketing/Micro-Econometrics + """Bayesian Inference for Marketing/Micro-Econometrics. Covers many important models used in marketing and micro-econometrics applications. The package includes: Bayes Regression (univariate or @@ -29,9 +29,7 @@ class RBayesm(RPackage): 2005) and Bayesian Non- and Semi-Parametric Methods and Applications (Princeton U Press 2014).""" - homepage = "https://cloud.r-project.org/package=bayesm" - url = "https://cloud.r-project.org/src/contrib/bayesm_3.1-0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bayesm" + cran = "bayesm" version('3.1-4', sha256='061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94') version('3.1-3', sha256='51e4827eca8cd4cf3626f3c2282543df7c392b3ffb843f4bfb386fe104642a10') diff --git a/var/spack/repos/builtin/packages/r-bayesplot/package.py b/var/spack/repos/builtin/packages/r-bayesplot/package.py index 743f695f0b..ba073c77d3 100644 --- a/var/spack/repos/builtin/packages/r-bayesplot/package.py +++ b/var/spack/repos/builtin/packages/r-bayesplot/package.py @@ -7,7 +7,7 @@ from spack import * 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') diff --git a/var/spack/repos/builtin/packages/r-bbmisc/package.py b/var/spack/repos/builtin/packages/r-bbmisc/package.py index 932e15bb6b..4e194b6165 100644 --- a/var/spack/repos/builtin/packages/r-bbmisc/package.py +++ b/var/spack/repos/builtin/packages/r-bbmisc/package.py @@ -7,12 +7,12 @@ from spack import * class RBbmisc(RPackage): - """Miscellaneous helper functions for and from B. Bischl and some other - guys, mainly for package development.""" + """Miscellaneous Helper Functions for B. Bischl. - homepage = "https://github.com/berndbischl/BBmisc" - url = "https://cloud.r-project.org/src/contrib/BBmisc_1.11.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/BBmisc" + Miscellaneous helper functions for and from B. Bischl and some other guys, + mainly for package development.""" + + cran = "BBmisc" version('1.11', sha256='1ea48c281825349d8642a661bb447e23bfd651db3599bf72593bfebe17b101d2') diff --git a/var/spack/repos/builtin/packages/r-beanplot/package.py b/var/spack/repos/builtin/packages/r-beanplot/package.py index 4b944216a9..d13ad54c8a 100644 --- a/var/spack/repos/builtin/packages/r-beanplot/package.py +++ b/var/spack/repos/builtin/packages/r-beanplot/package.py @@ -7,11 +7,11 @@ from spack import * class RBeanplot(RPackage): - """Plots univariate comparison graphs, an alternative to - boxplot/stripchart/violin plot.""" + """Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot). - homepage = "https://cloud.r-project.org/package=beanplot" - url = "https://cloud.r-project.org/src/contrib/beanplot_1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/beanplot" + Plots univariate comparison graphs, an alternative to + boxplot/stripchart/violin plot.""" + + cran = "beanplot" version('1.2', sha256='49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372') diff --git a/var/spack/repos/builtin/packages/r-beeswarm/package.py b/var/spack/repos/builtin/packages/r-beeswarm/package.py index 702f710d94..cbcb00777c 100644 --- a/var/spack/repos/builtin/packages/r-beeswarm/package.py +++ b/var/spack/repos/builtin/packages/r-beeswarm/package.py @@ -7,10 +7,12 @@ from spack import * class RBeeswarm(RPackage): - """beeswarm: The Bee Swarm Plot, an Alternative to Stripchart""" + """The Bee Swarm Plot, an Alternative to Stripchart. - homepage = "https://www.cbs.dtu.dk/~eklund/beeswarm/" - url = "https://cloud.r-project.org/src/contrib/beeswarm_0.2.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/beeswarm" + The bee swarm plot is a one-dimensional scatter plot like "stripchart", but + with closely-packed, non-overlapping points.""" + cran = "beeswarm" + + version('0.4.0', sha256='51f4339bf4080a2be84bb49a844c636625657fbed994abeaa42aead916c3d504') version('0.2.3', sha256='0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843') diff --git a/var/spack/repos/builtin/packages/r-bfast/package.py b/var/spack/repos/builtin/packages/r-bfast/package.py index 835ca1c569..4dd70c5f16 100644 --- a/var/spack/repos/builtin/packages/r-bfast/package.py +++ b/var/spack/repos/builtin/packages/r-bfast/package.py @@ -7,17 +7,37 @@ from spack import * class RBfast(RPackage): - """bfast: Breaks For Additive Season and Trend (BFAST)""" + """Breaks for Additive Season and Trend. - homepage = "https://cloud.r-project.org/package=bfast" - url = "https://cloud.r-project.org/src/contrib/bfast_1.5.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bfast" + Decomposition of time series into trend, seasonal, and remainder components + with methods for detecting and characterizing abrupt changes within the + trend and seasonal components. 'BFAST' can be used to analyze different + types of satellite image time series and can be applied to other + disciplines dealing with seasonal or non-seasonal time series, such as + hydrology, climatology, and econometrics. The algorithm can be extended to + label detected changes with information on the parameters of the fitted + piecewise linear models. 'BFAST' monitoring functionality is described in + Verbesselt et al. (2010) <doi:10.1016/j.rse.2009.08.014>. 'BFAST monitor' + provides functionality to detect disturbance in near real-time based on + 'BFAST'- type models, and is described in Verbesselt et al. (2012) + <doi:10.1016/j.rse.2012.02.022>. 'BFAST Lite' approach is a flexible + approach that handles missing data without interpolation, and will be + described in an upcoming paper. Furthermore, different models can now be + used to fit the time series data and detect structural changes (breaks).""" + cran = "bfast" + + version('1.6.1', sha256='aaf479af1924691cbec8c67c68005c00d97cead51b2b44863c18acd4cea453ee') version('1.5.7', sha256='01585fe8944d05ebdb13795214077bc1365f0c0372e2a1f7edb914356dace558') depends_on('r@2.15.0:', type=('build', 'run')) - depends_on('r-strucchange', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run'), when='@1.6.1:') + depends_on('r-strucchangercpp', type=('build', 'run'), when='@1.6.1:') depends_on('r-zoo', type=('build', 'run')) depends_on('r-forecast', type=('build', 'run')) - depends_on('r-sp', type=('build', 'run')) - depends_on('r-raster', type=('build', 'run')) + depends_on('r-rcpp@0.12.7:', type=('build', 'run'), when='@1.6.1:') + depends_on('r-rdpack@0.7:', type=('build', 'run'), when='@1.6.1:') + + depends_on('r-strucchange', type=('build', 'run'), when='@:1.5.7') + depends_on('r-sp', type=('build', 'run'), when='@:1.5.7') + depends_on('r-raster', type=('build', 'run'), when='@:1.5.7') diff --git a/var/spack/repos/builtin/packages/r-bglr/package.py b/var/spack/repos/builtin/packages/r-bglr/package.py index 81935cbc76..9013942a46 100644 --- a/var/spack/repos/builtin/packages/r-bglr/package.py +++ b/var/spack/repos/builtin/packages/r-bglr/package.py @@ -7,13 +7,13 @@ from spack import * class RBglr(RPackage): - """BGLR: Bayesian Generalized Linear Regression""" + """Bayesian Generalized Linear Regression.""" - homepage = "https://cloud.r-project.org/package=BGLR" - url = "https://cloud.r-project.org/src/contrib/BGLR_1.0.8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/BGLR" + cran = "BGLR" + version('1.0.9', sha256='440a96f9f502e0d6ecc8c00720d1ccdbab5ee8223e1def6c930edaa9a9de9099') version('1.0.8', sha256='5e969590d80b2f272c02a43b487ab1ffa13af386e0342993e6ac484fc82c9b95') depends_on('r@3.5.0:', type=('build', 'run')) depends_on('r-truncnorm', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run'), when='@1.0.9:') diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py index 25d8efbacc..15ef7efdd2 100644 --- a/var/spack/repos/builtin/packages/r-bh/package.py +++ b/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') diff --git a/var/spack/repos/builtin/packages/r-biasedurn/package.py b/var/spack/repos/builtin/packages/r-biasedurn/package.py index 83f24d9b64..91fe62d327 100644 --- a/var/spack/repos/builtin/packages/r-biasedurn/package.py +++ b/var/spack/repos/builtin/packages/r-biasedurn/package.py @@ -7,15 +7,15 @@ from spack import * class RBiasedurn(RPackage): - """Statistical models of biased sampling in the form of univariate and - multivariate noncentral hypergeometric distributions, including - Wallenius' noncentral hypergeometric distribution and Fisher's - noncentral hypergeometric distribution (also called extended - hypergeometric distribution). See vignette("UrnTheory") for - explanation of these distributions.""" + """Biased Urn Model Distributions. - homepage = "https://www.agner.org/random/" - url = "https://cloud.r-project.org/src/contrib/BiasedUrn_1.07.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/BiasedUrn/" + Statistical models of biased sampling in the form of univariate and + multivariate noncentral hypergeometric distributions, including Wallenius' + noncentral hypergeometric distribution and Fisher's noncentral + hypergeometric distribution (also called extended hypergeometric + distribution). See vignette("UrnTheory") for explanation of these + distributions.""" + + cran = "BiasedUrn" version('1.07', sha256='2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e') diff --git a/var/spack/repos/builtin/packages/r-bibtex/package.py b/var/spack/repos/builtin/packages/r-bibtex/package.py index ac71295527..64728425b2 100644 --- a/var/spack/repos/builtin/packages/r-bibtex/package.py +++ b/var/spack/repos/builtin/packages/r-bibtex/package.py @@ -7,13 +7,11 @@ from spack import * 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" - url = "https://cloud.r-project.org/src/contrib/bibtex_0.4.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bibtex/" + cran = "bibtex" version('0.4.2.3', sha256='7bad194920b412781ac9754ad41058d52d3cd7186e1851c2bce3640490e9bc6d') version('0.4.2', sha256='1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372') diff --git a/var/spack/repos/builtin/packages/r-bigalgebra/package.py b/var/spack/repos/builtin/packages/r-bigalgebra/package.py index 92bfadb487..2893325002 100644 --- a/var/spack/repos/builtin/packages/r-bigalgebra/package.py +++ b/var/spack/repos/builtin/packages/r-bigalgebra/package.py @@ -7,14 +7,23 @@ from spack import * class RBigalgebra(RPackage): - """This package provides arithmetic functions for R matrix - and big.matrix objects.""" + """'BLAS' and 'LAPACK' Routines for Native R Matrices and 'big.matrix' + Objects. - homepage = "https://r-forge.r-project.org/R/?group_id=556" - url = "https://cloud.r-project.org/src/contrib/Archive/bigalgebra/bigalgebra_0.8.4.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bigalgebra" + Provides arithmetic functions for R matrix and 'big.matrix' objects as well + as functions for QR factorization, Cholesky factorization, General + eigenvalue, and Singular value decomposition (SVD). A method matrix + multiplication and an arithmetic method -for matrix addition, matrix + difference- allows for mixed type operation -a matrix class object and a + big.matrix class object- and pure type operation for two big.matrix class + objects.""" + cran = "bigalgebra" + + version('1.0.1', sha256='ff7e261d0aa0e0f498e926d923ac62fc5cb783fa1f74bb2ff76a09167388a9d2') + version('1.0.0', sha256='f186b603bd660be0cc5b7a52c943e23e92fef264f0bc96a8858e38df6cfc4085') version('0.8.4.2', sha256='29962468cbfa6416f8628563d5ed8c9f76089190311ff1c618f099ee8d9eea75') depends_on('r-bigmemory@4.0.0:', type=('build', 'run')) depends_on('r-bh', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run'), when='@1.0.0:') diff --git a/var/spack/repos/builtin/packages/r-bigmemory-sri/package.py b/var/spack/repos/builtin/packages/r-bigmemory-sri/package.py index 390a0d0e31..d2ab649def 100644 --- a/var/spack/repos/builtin/packages/r-bigmemory-sri/package.py +++ b/var/spack/repos/builtin/packages/r-bigmemory-sri/package.py @@ -7,11 +7,11 @@ from spack import * class RBigmemorySri(RPackage): - """This package provides a shared resource interface - for the bigmemory and synchronicity packages.""" + """A shared resource interface for Bigmemory Project packages. - homepage = "https://cloud.r-project.org/web/packages/bigmemory.sri/index.html" - url = "https://cloud.r-project.org/src/contrib/bigmemory.sri_0.1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bigmemory.sri" + This package provides a shared resource interface for the bigmemory and + synchronicity packages.""" + + cran = "bigmemory.sri" version('0.1.3', sha256='55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155') diff --git a/var/spack/repos/builtin/packages/r-bigmemory/package.py b/var/spack/repos/builtin/packages/r-bigmemory/package.py index 4a9f2e4d6b..6631228eef 100644 --- a/var/spack/repos/builtin/packages/r-bigmemory/package.py +++ b/var/spack/repos/builtin/packages/r-bigmemory/package.py @@ -7,14 +7,14 @@ from spack import * class RBigmemory(RPackage): - """Create, store, access, and manipulate massive matrices. - Matrices are allocated to shared memory and may use - memory-mapped files. Packages 'biganalytics', 'bigtabulate', - 'synchronicity', and 'bigalgebra' provide advanced functionality.""" + """Manage Massive Matrices with Shared Memory and Memory-Mapped. - homepage = "https://cloud.r-project.org/web/packages/bigmemory/index.html" - url = "https://cloud.r-project.org/src/contrib/bigmemory_4.5.36.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bigmemory" + Files Create, store, access, and manipulate massive matrices. Matrices are + allocated to shared memory and may use memory-mapped files. Packages + 'biganalytics', 'bigtabulate', 'synchronicity', and 'bigalgebra' provide + advanced functionality.""" + + cran = "bigmemory" version('4.5.36', sha256='18c67fbe6344b2f8223456c4f19ceebcf6c1166255eab81311001fd67a45ef0e') diff --git a/var/spack/repos/builtin/packages/r-bindr/package.py b/var/spack/repos/builtin/packages/r-bindr/package.py index 590c3dab8c..4739fa27bc 100644 --- a/var/spack/repos/builtin/packages/r-bindr/package.py +++ b/var/spack/repos/builtin/packages/r-bindr/package.py @@ -7,12 +7,12 @@ from spack import * class RBindr(RPackage): - """Provides a simple interface for creating active bindings where the - bound function accepts additional arguments.""" + """Parametrized Active Bindings. - homepage = "https://github.com/krlmlr/bindr" - url = "https://cloud.r-project.org/src/contrib/bindr_0.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bindr" + Provides a simple interface for creating active bindings where the bound + function accepts additional arguments.""" + + cran = "bindr" version('0.1.1', sha256='7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0') version('0.1', sha256='cca166612eeafd6e1c961b34aaf177f9b47f8b4bc37520e277b9920eaa8b2535') diff --git a/var/spack/repos/builtin/packages/r-bindrcpp/package.py b/var/spack/repos/builtin/packages/r-bindrcpp/package.py index 1cdc12a5d5..63b298a5fc 100644 --- a/var/spack/repos/builtin/packages/r-bindrcpp/package.py +++ b/var/spack/repos/builtin/packages/r-bindrcpp/package.py @@ -7,12 +7,12 @@ from spack import * class RBindrcpp(RPackage): - """Provides an easy way to fill an environment with active bindings that - call a C++ function.""" + """An 'Rcpp' Interface to Active Bindings. - homepage = "https://github.com/krlmlr/bindrcpp" - url = "https://cloud.r-project.org/src/contrib/bindrcpp_0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bindrcpp" + Provides an easy way to fill an environment with active bindings that call + a C++ function.""" + + cran = "bindrcpp" version('0.2.2', sha256='48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467') version('0.2', sha256='d0efa1313cb8148880f7902a4267de1dcedae916f28d9a0ef5911f44bf103450') diff --git a/var/spack/repos/builtin/packages/r-bio3d/package.py b/var/spack/repos/builtin/packages/r-bio3d/package.py index a4a09482b5..847963b16a 100644 --- a/var/spack/repos/builtin/packages/r-bio3d/package.py +++ b/var/spack/repos/builtin/packages/r-bio3d/package.py @@ -7,7 +7,7 @@ from spack import * class RBio3d(RPackage): - """Biological Structure Analysis + """Biological Structure Analysis. Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, @@ -22,10 +22,9 @@ class RBio3d(RPackage): to work with biological sequence and structural data. Please refer to the URLs below for more information.""" - homepage = "http://thegrantlab.org/bio3d/" - url = "https://cloud.r-project.org/src/contrib/bio3d_2.3-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bio3d" + cran = "bio3d" + version('2.4-2', sha256='91415766cda0f96557e6bc568dbce8d44254a9460f2e2d0beed0ce14ffad6ccb') version('2.4-1', sha256='679fbd87fe9fb82a65427d281d3b68906509e411270cd87d2deb95d404333c1f') version('2.3-4', sha256='f9b39ab242cbedafcd98c1732cb1f5c0dd9ef66e28be39695e3420dd93e2bafe') diff --git a/var/spack/repos/builtin/packages/r-biocmanager/package.py b/var/spack/repos/builtin/packages/r-biocmanager/package.py index f98d06af47..73e8e245a7 100644 --- a/var/spack/repos/builtin/packages/r-biocmanager/package.py +++ b/var/spack/repos/builtin/packages/r-biocmanager/package.py @@ -7,10 +7,11 @@ from spack import * class RBiocmanager(RPackage): - """BiocManager: Access the Bioconductor Project Package Repository""" + """Access the Bioconductor Project Package Repository. - homepage = "https://cloud.r-project.org/package=BiocManager" - url = "https://cloud.r-project.org/src/contrib/BiocManager_1.30.10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/BiocManager" + A convenient tool to install and update Bioconductor packages.""" + cran = "BiocManager" + + version('1.30.16', sha256='75a754a55192ef6aa6ac9b054fd5381ff03fe6bb8b2e033eb8143da930ef3855') version('1.30.10', sha256='f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e') diff --git a/var/spack/repos/builtin/packages/r-biom-utils/package.py b/var/spack/repos/builtin/packages/r-biom-utils/package.py index dd6b8436ab..9592481803 100644 --- a/var/spack/repos/builtin/packages/r-biom-utils/package.py +++ b/var/spack/repos/builtin/packages/r-biom-utils/package.py @@ -7,13 +7,12 @@ from spack import * class RBiomUtils(RPackage): - """Provides utilities to facilitate import, export and computation with - the BIOM (Biological Observation Matrix) format (https://biom-format.org/). - """ + """Utilities for the BIOM (Biological Observation Matrix) Format. - homepage = "https://github.com/braithwaite/BIOM.utils/" - url = "https://cloud.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/biom/" + Provides utilities to facilitate import, export and computation with the + BIOM (Biological Observation Matrix) format (https://biom-format.org/).""" + + cran = "BIOM.utils" version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375') diff --git a/var/spack/repos/builtin/packages/r-biomartr/package.py b/var/spack/repos/builtin/packages/r-biomartr/package.py index 5c88b04434..e2c93b9182 100644 --- a/var/spack/repos/builtin/packages/r-biomartr/package.py +++ b/var/spack/repos/builtin/packages/r-biomartr/package.py @@ -7,7 +7,9 @@ from spack import * class RBiomartr(RPackage): - """Perform large scale genomic data retrieval and functional annotation + """Genomic Data Retrieval. + + Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', @@ -19,9 +21,7 @@ class RBiomartr(RPackage): Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.""" - homepage = "https://docs.ropensci.org/biomartr" - url = "https://cloud.r-project.org/src/contrib/biomartr_0.9.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/biomartr" + cran = "biomartr" version('0.9.2', sha256='d88085696e9c5614828602254c33f2cdd3bbfeebc2f21a705eee3cb961097c89') diff --git a/var/spack/repos/builtin/packages/r-bit/package.py b/var/spack/repos/builtin/packages/r-bit/package.py index f1c232463b..c365648b64 100644 --- a/var/spack/repos/builtin/packages/r-bit/package.py +++ b/var/spack/repos/builtin/packages/r-bit/package.py @@ -7,16 +7,14 @@ from spack import * class RBit(RPackage): - """Classes and Methods for Fast Memory-Efficient Boolean Selections + """Classes and Methods for Fast Memory-Efficient Boolean Selections. Provided are classes for boolean and skewed boolean vectors, fast boolean methods, fast unique and non-unique integer sorting, fast set operations on sorted and unsorted sets of integers, and foundations for ff (range index, compression, chunked processing).""" - homepage = "https://cloud.r-project.org/package=bit" - url = "https://cloud.r-project.org/src/contrib/bit_1.1-12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bit" + cran = "bit" version('4.0.4', sha256='e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168') version('1.1-14', sha256='5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254') diff --git a/var/spack/repos/builtin/packages/r-bit64/package.py b/var/spack/repos/builtin/packages/r-bit64/package.py index 4925b663ba..ca6598eae6 100644 --- a/var/spack/repos/builtin/packages/r-bit64/package.py +++ b/var/spack/repos/builtin/packages/r-bit64/package.py @@ -7,7 +7,7 @@ from spack import * class RBit64(RPackage): - """A S3 Class for Vectors of 64bit Integers + """A S3 Class for Vectors of 64bit Integers. Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. @@ -21,13 +21,11 @@ class RBit64(RPackage): active data exploration and manipulation and optionally leverage caching.""" - homepage = "https://cloud.r-project.org/package=bit64" - url = "https://cloud.r-project.org/src/contrib/bit64_0.9-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bit64" + cran = "bit64" version('4.0.5', sha256='25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578') version('0.9-7', sha256='7b9aaa7f971198728c3629f9ba1a1b24d53db5c7e459498b0fdf86bbd3dff61f') depends_on('r@3.0.1:', type=('build', 'run')) - depends_on('r-bit@1.1-12:', when='@:9.9-7', type=('build', 'run')) - depends_on('r-bit@4.0.0:', when='@4.0.5:', type=('build', 'run')) + depends_on('r-bit@1.1-12:', type=('build', 'run')) + depends_on('r-bit@4.0.0:', type=('build', 'run'), when='@4.0.5:') diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py index b6723a1aa7..ce687cc335 100644 --- a/var/spack/repos/builtin/packages/r-bitops/package.py +++ b/var/spack/repos/builtin/packages/r-bitops/package.py @@ -8,10 +8,11 @@ from spack import * class RBitops(RPackage): - """Functions for bitwise operations on integer vectors.""" + """Bitwise Operations. - homepage = "https://cloud.r-project.org/package=bitops" - url = "https://cloud.r-project.org/src/contrib/bitops_1.0-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bitops" + Functions for bitwise operations on integer vectors.""" + cran = "bitops" + + version('1.0-7', sha256='e9b5fc92c39f94a10cd0e13f3d6e2a9c17b75ea01467077a51d47a5f708517c4') version('1.0-6', sha256='9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c') diff --git a/var/spack/repos/builtin/packages/r-blavaan/package.py b/var/spack/repos/builtin/packages/r-blavaan/package.py index 990478d012..eb06e7f84f 100644 --- a/var/spack/repos/builtin/packages/r-blavaan/package.py +++ b/var/spack/repos/builtin/packages/r-blavaan/package.py @@ -7,30 +7,37 @@ from spack import * class RBlavaan(RPackage): - """Bayesian Latent Variable Analysis: + """Bayesian Latent Variable Analysis. - Fit a variety of Bayesian latent variable models, including confirmatory - factor analysis, structural equation models, and latent growth curve - models.""" +Fit a variety of Bayesian latent variable models, including confirmatory factor +analysis, structural equation models, and latent growth curve models. +References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al. +(2021) <doi:10.18637/jss.v100.i06>.""" - cran = "blavaan" + 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')) diff --git a/var/spack/repos/builtin/packages/r-blob/package.py b/var/spack/repos/builtin/packages/r-blob/package.py index 47673efb7c..40b494b84e 100644 --- a/var/spack/repos/builtin/packages/r-blob/package.py +++ b/var/spack/repos/builtin/packages/r-blob/package.py @@ -7,14 +7,13 @@ from spack import * class RBlob(RPackage): - """A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS') + """A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS'). - R's raw vector is useful for storing a single binary object. - What if you want to put a vector of them in a data frame? The blob - package provides the blob object, a list of raw vectors, suitable - for use as a column in data frame.""" + R's raw vector is useful for storing a single binary object. What if you + want to put a vector of them in a data frame? The blob package provides the + blob object, a list of raw vectors, suitable for use as a column in data + frame.""" - homepage = "https://blob.tidyverse.org" cran = "blob" version('1.2.2', sha256='4976053c65994c769a4c22b4553bea0bd9c623b3b991dbaf023d2a164770c7fa') @@ -22,8 +21,9 @@ class RBlob(RPackage): version('1.2.0', sha256='1af1cfa28607bc0e2f1f01598a00a7d5d1385ef160a9e79e568f30f56538e023') version('1.1.0', sha256='16d6603df3ddba177f0ac4d9469c938f89131c4bf8834345db838defd9ffea16') - depends_on('r-tibble', when='@:1.1.0', type=('build', 'run')) - depends_on('r-prettyunits', when='@1.2.0', type=('build', 'run')) - depends_on('r-rlang', when='@1.2.0:', type=('build', 'run')) - depends_on('r-vctrs@0.2.0:', when='@1.2.0:', type=('build', 'run')) - depends_on('r-vctrs@0.2.1:', when='@1.2.1:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@1.2.0:') + depends_on('r-vctrs@0.2.0:', type=('build', 'run'), when='@1.2.0:') + depends_on('r-vctrs@0.2.1:', type=('build', 'run'), when='@1.2.1:') + + depends_on('r-prettyunits', type=('build', 'run'), when='@1.2.0') + depends_on('r-tibble', type=('build', 'run'), when='@:1.1.0') diff --git a/var/spack/repos/builtin/packages/r-blockmodeling/package.py b/var/spack/repos/builtin/packages/r-blockmodeling/package.py index 096865c33f..dbc963dbfa 100644 --- a/var/spack/repos/builtin/packages/r-blockmodeling/package.py +++ b/var/spack/repos/builtin/packages/r-blockmodeling/package.py @@ -7,21 +7,21 @@ from spack import * class RBlockmodeling(RPackage): - """Generalized and Classical Blockmodeling of Valued Networks + """Generalized and Classical Blockmodeling of Valued Networks. This is primarily meant as an implementation of generalized blockmodeling for valued networks.""" - homepage = "https://cloud.r-project.org/package=blockmodeling" - url = "https://cloud.r-project.org/src/contrib/blockmodeling_0.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/blockmodeling/" + cran = "blockmodeling" + version('1.0.5', sha256='18c227bb52f28aff4dae8929563474e3e006e238438c823b67dc6baa897f88ed') version('1.0.0', sha256='f10c41fff56dc7dc46dffbceacb8ff905eca06578d610a5a590fb408f0149cfc') version('0.3.4', sha256='a269c83669dd5294cff0adddab36bc023db6a276a06b74b1fa94b7e407486987') version('0.3.1', sha256='39e8360400cec6baa920d5589d4e779568bdf2954f7331be0e3cadf22a217d31') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) - depends_on('r-doparallel', when='@:0.3.4', type=('build', 'run')) - depends_on('r-dorng', when='@:0.3.4', type=('build', 'run')) - depends_on('r-foreach', when='@:0.3.4', type=('build', 'run')) + + depends_on('r-doparallel', type=('build', 'run'), when='@:0.3.4') + depends_on('r-dorng', type=('build', 'run'), when='@:0.3.4') + depends_on('r-foreach', type=('build', 'run'), when='@:0.3.4') diff --git a/var/spack/repos/builtin/packages/r-bmp/package.py b/var/spack/repos/builtin/packages/r-bmp/package.py index e45f69cf84..a65ab87c57 100644 --- a/var/spack/repos/builtin/packages/r-bmp/package.py +++ b/var/spack/repos/builtin/packages/r-bmp/package.py @@ -7,12 +7,12 @@ from spack import * class RBmp(RPackage): - """Reads Windows BMP format images. Currently limited to 8 bit greyscale + """Read Windows Bitmap (BMP) Images. + + Reads Windows BMP format images. Currently limited to 8 bit greyscale images and 24,32 bit (A)RGB images. Pure R implementation without external dependencies.""" - homepage = "https://cloud.r-project.org/package=bmp" - url = "https://cloud.r-project.org/src/contrib/bmp_0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bmp" + cran = "bmp" version('0.3', sha256='bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649') diff --git a/var/spack/repos/builtin/packages/r-bookdown/package.py b/var/spack/repos/builtin/packages/r-bookdown/package.py index 17645f80dc..67f8c4015e 100644 --- a/var/spack/repos/builtin/packages/r-bookdown/package.py +++ b/var/spack/repos/builtin/packages/r-bookdown/package.py @@ -7,15 +7,14 @@ from spack import * class RBookdown(RPackage): - """Authoring Books and Technical Documents with R Markdown + """Authoring Books and Technical Documents with R Markdown. - Output formats and utilities for authoring books and technical - documents with R Markdown.""" + Output formats and utilities for authoring books and technical documents + with R Markdown.""" - homepage = "https://cloud.r-project.org/package=bookdown" - url = "https://cloud.r-project.org/src/contrib/bookdown_0.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/bookdown" + cran = "bookdown" + version('0.24', sha256='8bead2a20542d05f643fe77a949689a17b0ae9ff23efbb918ddab47597db1be3') version('0.21', sha256='47c0fa7a65da83753c2f445e0e972913f9203460f1daae3ab255d0d4b30eba76') version('0.12', sha256='38eb4c5b877ccd85b16cfe74a48c3bc53de2f276da98e5515f37e7a06e065bb0') version('0.5', sha256='b7331fd56f64bd2bddc34e2a188fc491f9ff5308f44f7e3151721247f21ca67e') @@ -23,11 +22,15 @@ class RBookdown(RPackage): depends_on('r+X', type=('build', 'run')) depends_on('r-htmltools@0.3.6:', type=('build', 'run')) depends_on('r-knitr@1.22:', type=('build', 'run')) - depends_on('r-rmarkdown@1.12:', when='@:0.12', type=('build', 'run')) - depends_on('r-rmarkdown@2.4:', when='@0.21:', type=('build', 'run')) - depends_on('r-xfun@0.6:', when='@:0.12', type=('build', 'run')) - depends_on('r-xfun@0.13:', when='@0.21:', type=('build', 'run')) - depends_on('r-tinytex@0.12:', when='@0.12:', type=('build', 'run')) - depends_on('r-yaml@2.1.14:', when='@:0.12', type=('build', 'run')) - depends_on('r-yaml@2.1.19:', when='@0.21:', type=('build', 'run')) + depends_on('r-knitr@1.31:', type=('build', 'run'), when='@0.24:') + depends_on('r-rmarkdown@1.12:', type=('build', 'run')) + depends_on('r-rmarkdown@2.4:', type=('build', 'run'), when='@0.21:') + depends_on('r-rmarkdown@2.9:', type=('build', 'run'), when='@0.24:') + depends_on('r-jquerylib', type=('build', 'run'), when='@0.24:') + depends_on('r-xfun@0.6:', type=('build', 'run')) + depends_on('r-xfun@0.13:', type=('build', 'run'), when='@0.21:') + depends_on('r-xfun@0.22:', type=('build', 'run'), when='@0.24:') + depends_on('r-tinytex@0.12:', type=('build', 'run'), when='@0.12:') + depends_on('r-yaml@2.1.14:', type=('build', 'run')) + depends_on('r-yaml@2.1.19:', type=('build', 'run'), when='@0.21:') depends_on('pandoc@1.17.2:') diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py index 52652d8781..3e617c1a43 100644 --- a/var/spack/repos/builtin/packages/r-boot/package.py +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -7,15 +7,13 @@ from spack import * class RBoot(RPackage): - """Bootstrap Functions (Originally by Angelo Canty for S) + """Bootstrap Functions (Originally by Angelo Canty for S). - Functions and datasets for bootstrapping from the book "Bootstrap - Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, - CUP), originally written by Angelo Canty for S.""" + Functions and datasets for bootstrapping from the book "Bootstrap Methods + and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), + originally written by Angelo Canty for S.""" - homepage = "https://cloud.r-project.org/package=boot" - url = "https://cloud.r-project.org/src/contrib/boot_1.3-18.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/boot" + cran = "boot" version('1.3-28', sha256='9f7158fd2714659f590c3955651893dc24bd8f39196bc5a4cc35b0b031744a32') version('1.3-25', sha256='464835fcb453072346ce49e4ae318e04c9dba682349be49db616623b6088fbbe') diff --git a/var/spack/repos/builtin/packages/r-boruta/package.py b/var/spack/repos/builtin/packages/r-boruta/package.py index 385c6e1407..e3ea8ff34e 100644 --- a/var/spack/repos/builtin/packages/r-boruta/package.py +++ b/var/spack/repos/builtin/packages/r-boruta/package.py @@ -7,15 +7,13 @@ from spack import * class RBoruta(RPackage): - """An all relevant feature selection wrapper algorithm. It finds - relevant features by comparing original attributes' importance - with importance achievable at random, estimated using their - permuted copies (shadows). - """ + """Wrapper Algorithm for All Relevant Feature Selection. - homepage = "https://cloud.r-project.org/package=Boruta" - url = "https://cloud.r-project.org/src/contrib/Boruta_7.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Boruta" + An all relevant feature selection wrapper algorithm. It finds relevant + features by comparing original attributes' importance with importance + achievable at random, estimated using their permuted copies (shadows).""" + + cran = "Boruta" version('7.0.0', sha256='6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78') version('6.0.0', sha256='1c9a7aabe09f040e147f6c614f5fe1d0b951d3b0f0024161fbb4c31da8fae8de') diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py index 9be9612bb1..ad5b5debbc 100644 --- a/var/spack/repos/builtin/packages/r-brew/package.py +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -7,12 +7,12 @@ from spack import * class RBrew(RPackage): - """brew implements a templating framework for mixing text and R code for + """Templating Framework for Report Generation. + + Brew implements a templating framework for mixing text and R code for report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.""" - homepage = "https://cloud.r-project.org/package=brew" - url = "https://cloud.r-project.org/src/contrib/brew_1.0-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/brew" + cran = "brew" version('1.0-6', sha256='d70d1a9a01cf4a923b4f11e4374ffd887ad3ff964f35c6f9dc0f29c8d657f0ed') diff --git a/var/spack/repos/builtin/packages/r-bridgesampling/package.py b/var/spack/repos/builtin/packages/r-bridgesampling/package.py index 070a9994aa..47c3319d64 100644 --- a/var/spack/repos/builtin/packages/r-bridgesampling/package.py +++ b/var/spack/repos/builtin/packages/r-bridgesampling/package.py @@ -7,7 +7,7 @@ from spack import * 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') diff --git a/var/spack/repos/builtin/packages/r-brio/package.py b/var/spack/repos/builtin/packages/r-brio/package.py index d01679b97d..a7e183fb23 100644 --- a/var/spack/repos/builtin/packages/r-brio/package.py +++ b/var/spack/repos/builtin/packages/r-brio/package.py @@ -7,13 +7,12 @@ from spack import * 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') diff --git a/var/spack/repos/builtin/packages/r-brms/package.py b/var/spack/repos/builtin/packages/r-brms/package.py index 669c584764..e3ac3ed4fb 100644 --- a/var/spack/repos/builtin/packages/r-brms/package.py +++ b/var/spack/repos/builtin/packages/r-brms/package.py @@ -7,7 +7,7 @@ from spack import * 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') diff --git a/var/spack/repos/builtin/packages/r-brobdingnag/package.py b/var/spack/repos/builtin/packages/r-brobdingnag/package.py index 548efde05b..1f39d5dc3e 100644 --- a/var/spack/repos/builtin/packages/r-brobdingnag/package.py +++ b/var/spack/repos/builtin/packages/r-brobdingnag/package.py @@ -7,14 +7,13 @@ from spack import * 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') diff --git a/var/spack/repos/builtin/packages/r-broom/package.py b/var/spack/repos/builtin/packages/r-broom/package.py index bda2de502e..8632aa022e 100644 --- a/var/spack/repos/builtin/packages/r-broom/package.py +++ b/var/spack/repos/builtin/packages/r-broom/package.py @@ -7,7 +7,7 @@ from spack import * class RBroom(RPackage): - """Convert Statistical Objects into Tidy Tibbles + """Convert Statistical Objects into Tidy Tibbles. Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with @@ -18,9 +18,10 @@ class RBroom(RPackage): measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.""" - homepage = "https://github.com/tidyverse/broom" cran = "broom" + version('0.7.12', sha256='04fac12b2546689603a474fb92a0572f4241ae87b51b21b0808814a489227bd9') + version('0.7.11', sha256='9e3999d2635ac72e8f4c3a81decd50ee5d464c001c155375b5a970a629ba2e19') version('0.7.10', sha256='129fd5a53abef7f42b7efac6c64ebd71269b136aa648846d640562357927464f') version('0.7.9', sha256='1d5695f97b378b2b77fb8f64a4a54b72b278913d4adf9d61a7ca4f38a1c7c5fc') version('0.7.3', sha256='de5650e46ca6884876b63bc401d22bef9eace671147774466406d43324aebc2f') @@ -29,22 +30,22 @@ class RBroom(RPackage): version('0.4.2', sha256='9f409413623cf25e7110452e6215353af5114f7044d73af182bd6c10971c5a44') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r-backports', when='@0.5.0:', type=('build', 'run')) + depends_on('r-backports', type=('build', 'run'), when='@0.5.0:') depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-dplyr@1.0.0:', when='@0.7.3:', type=('build', 'run')) - depends_on('r-ellipsis', when='@0.7.3:', type=('build', 'run')) - depends_on('r-generics@0.0.2:', when='@0.5.1:', type=('build', 'run')) - depends_on('r-glue', when='@0.7.3:', type=('build', 'run')) - depends_on('r-purrr', when='@0.5.0:', type=('build', 'run')) - depends_on('r-rlang', when='@0.7.3:', type=('build', 'run')) + depends_on('r-dplyr@1.0.0:', type=('build', 'run'), when='@0.7.3:') + depends_on('r-ellipsis', type=('build', 'run'), when='@0.7.3:') + depends_on('r-generics@0.0.2:', type=('build', 'run'), when='@0.5.1:') + depends_on('r-glue', type=('build', 'run'), when='@0.7.3:') + depends_on('r-purrr', type=('build', 'run'), when='@0.5.0:') + depends_on('r-rlang', type=('build', 'run'), when='@0.7.3:') depends_on('r-stringr', type=('build', 'run')) - depends_on('r-tibble', when='@0.5.0:', type=('build', 'run')) - depends_on('r-tibble@3.0.0:', when='@0.7.3:', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run'), when='@0.5.0:') + depends_on('r-tibble@3.0.0:', type=('build', 'run'), when='@0.7.3:') depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-tidyr@1.0.0:', when='@0.7.3:', type=('build', 'run')) - depends_on('r-ggplot2', when='@0.7.10:', type=('build', 'run')) + depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@0.7.3:') + depends_on('r-ggplot2', type=('build', 'run'), when='@0.7.10:') - depends_on('r-plyr', when='@:0.4.2', type=('build', 'run')) - depends_on('r-psych', when='@:0.4.2', type=('build', 'run')) - depends_on('r-reshape2', when='@:0.5.2', type=('build', 'run')) - depends_on('r-nlme', when='@:0.5.2', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run'), when='@:0.4.2') + depends_on('r-psych', type=('build', 'run'), when='@:0.4.2') + depends_on('r-reshape2', type=('build', 'run'), when='@:0.5.2') + depends_on('r-nlme', type=('build', 'run'), when='@:0.5.2') diff --git a/var/spack/repos/builtin/packages/r-bslib/package.py b/var/spack/repos/builtin/packages/r-bslib/package.py new file mode 100644 index 0000000000..97437fffc6 --- /dev/null +++ b/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')) diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py index 7a02f2c36e..87f2d16853 100644 --- a/var/spack/repos/builtin/packages/r-c50/package.py +++ b/var/spack/repos/builtin/packages/r-c50/package.py @@ -8,15 +8,14 @@ from spack import * class RC50(RPackage): - """C5.0 Decision Trees and Rule-Based Models + """C5.0 Decision Trees and Rule-Based Models. C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).""" - homepage = "https://cloud.r-project.org/package=C50" - url = "https://cloud.r-project.org/src/contrib/C50_0.1.0-24.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/C50" + cran = "C50" + version('0.1.5', sha256='f0c17b4830371832ca64f5fcc702351a394ee90b384e0865307de9447f3f16d7') version('0.1.3.1', sha256='0b151ba8deef50ab2e2ad8469d87f54f0c6ab862f5c790ed8bb16cb3b8027546') version('0.1.2', sha256='8f459856e0309274bee24462b7145db4eba1d71031c236db39000a5375bdfaba') version('0.1.1', sha256='03bc1fc2f64bcd5c680568a24902deafab1965074a66f8802bc4cd0335bd01df') @@ -24,5 +23,6 @@ class RC50(RPackage): depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-partykit', type=('build', 'run')) - depends_on('r-cubist@0.2.1:', when='@:0.1.2', type=('build', 'run')) - depends_on('r-cubist@0.2.3:', when='@0.1.3.1:', type=('build', 'run')) + depends_on('r-cubist@0.2.1:', type=('build', 'run')) + depends_on('r-cubist@0.2.3:', type=('build', 'run'), when='@0.1.3.1:') + depends_on('r-cubist@0.3.0:', type=('build', 'run'), when='@0.1.5:') diff --git a/var/spack/repos/builtin/packages/r-ca/package.py b/var/spack/repos/builtin/packages/r-ca/package.py index 6e7a07c565..3fa69c422d 100644 --- a/var/spack/repos/builtin/packages/r-ca/package.py +++ b/var/spack/repos/builtin/packages/r-ca/package.py @@ -8,14 +8,12 @@ from spack import * class RCa(RPackage): - """Simple, Multiple and Joint Correspondence Analysis + """Simple, Multiple and Joint Correspondence Analysis. - Computation and visualization of simple, multiple and joint - correspondence analysis.""" + Computation and visualization of simple, multiple and joint correspondence + analysis.""" - homepage = "http://www.carme-n.org/?sec=ca" - url = "https://cloud.r-project.org/src/contrib/ca_0.71.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ca" + cran = "ca" version('0.71.1', sha256='040c2fc94c356075f116cc7cd880530b3c9e02206c0035182c03a525ee99b424') diff --git a/var/spack/repos/builtin/packages/r-cachem/package.py b/var/spack/repos/builtin/packages/r-cachem/package.py new file mode 100644 index 0000000000..461fd9e90d --- /dev/null +++ b/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')) diff --git a/var/spack/repos/builtin/packages/r-cairo/package.py b/var/spack/repos/builtin/packages/r-cairo/package.py index 6f411beaa3..599c7e3f06 100644 --- a/var/spack/repos/builtin/packages/r-cairo/package.py +++ b/var/spack/repos/builtin/packages/r-cairo/package.py @@ -9,7 +9,7 @@ from spack import * class RCairo(RPackage): """R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 - and Win32) output + and Win32) output. R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output @@ -23,10 +23,9 @@ class RCairo(RPackage): support or anti-aliasing. Backends are modular such that any subset of backends is supported.""" - homepage = "https://cloud.r-project.org/package=Cairo" - url = "https://cloud.r-project.org/src/contrib/Cairo_1.5-9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Cairo" + cran = "Cairo" + version('1.5-14', sha256='067751face3b5771e72f9fb49bfeefb3a7bbecc060b672ab4393cb5935204c7b') version('1.5-12.2', sha256='dd524105c83b82b5c3b3ee2583ef90d4cafa54b0c29817dac48b425b79f90f92') version('1.5-10', sha256='7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5') version('1.5-9', sha256='2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4') diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py index fe0b148e17..de4e7e9361 100644 --- a/var/spack/repos/builtin/packages/r-callr/package.py +++ b/var/spack/repos/builtin/packages/r-callr/package.py @@ -7,13 +7,12 @@ from spack import * class RCallr(RPackage): - """Call R from R + """Call R from R. It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.""" - homepage = "https://github.com/MangoTheCat/callr" cran = "callr" version('3.7.0', sha256='d67255148595c6d0ba4c4d241bc9f6b5e00cafe25fdc13e38c10acc38653360a') @@ -24,6 +23,6 @@ class RCallr(RPackage): version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7') version('1.0.0', sha256='2c56808c723aba2ea8a8b6bbdc9b8332c96f59b119079861dd52f5988c27f715') - depends_on('r-processx@3.4.0:', when='@3.0.0:', type=('build', 'run')) - depends_on('r-processx@3.5.0:', when='@3.6.0:', type=('build', 'run')) - depends_on('r-r6', when='@3.0.0:', type=('build', 'run')) + depends_on('r-processx@3.4.0:', type=('build', 'run'), when='@3.0.0:') + depends_on('r-processx@3.5.0:', type=('build', 'run'), when='@3.6.0:') + depends_on('r-r6', type=('build', 'run'), when='@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index 1d51e1cf8b..484309ab83 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -7,12 +7,11 @@ from spack import * class RCar(RPackage): - """Companion to Applied Regression + """Companion to Applied Regression. - Functions and Datasets to Accompany J. Fox and S. Weisberg, An R - Companion to Applied Regression, Second Edition, Sage, 2011.""" + Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion + to Applied Regression, Second Edition, Sage, 2011.""" - homepage = "https://r-forge.r-project.org/projects/car/" cran = "car" version('3.0-12', sha256='b899a6efae3842a90a2349d381dbcf4b4ed36bd03108ebe7380e81120e457302') @@ -23,17 +22,17 @@ class RCar(RPackage): version('2.1-4', sha256='fd39cf1750cb560a66623fea3fa9e6a94fc24e3dc36367aff24df7d0743edb28') version('2.1-2', sha256='8cc3e57f172c8782a08960b508906d3201596a21f4b6c1dab8d4e59353093652') - depends_on('r@3.2.0:', when='@:3.0-2', type=('build', 'run')) - depends_on('r@3.5.0:', when='@3.0-3:', type=('build', 'run')) - depends_on('r-cardata@3.0-0:', when='@3.0:', type=('build', 'run')) - depends_on('r-abind', when='@3.0:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.0-3:') + depends_on('r-cardata@3.0-0:', type=('build', 'run'), when='@3.0:') + depends_on('r-abind', type=('build', 'run'), when='@3.0:') depends_on('r-mass', type=('build', 'run')) depends_on('r-mgcv', type=('build', 'run')) depends_on('r-nnet', type=('build', 'run')) depends_on('r-pbkrtest@0.4-4:', type=('build', 'run')) depends_on('r-quantreg', type=('build', 'run')) - depends_on('r-maptools', when='@3.0:', type=('build', 'run')) - depends_on('r-rio', when='@3.0:3.0-11', type=('build', 'run')) - depends_on('r-lme4@1.1-27.1:', when='@3.0-11:', type=('build', 'run')) - depends_on('r-lme4', when='@3.0:', type=('build', 'run')) - depends_on('r-nlme', when='@3.0:', type=('build', 'run')) + depends_on('r-maptools', type=('build', 'run'), when='@3.0:') + depends_on('r-rio', type=('build', 'run'), when='@3.0:3.0-11') + depends_on('r-lme4@1.1-27.1:', type=('build', 'run'), when='@3.0-11:') + depends_on('r-lme4', type=('build', 'run'), when='@3.0:') + depends_on('r-nlme', type=('build', 'run'), when='@3.0:') diff --git a/var/spack/repos/builtin/packages/r-caracas/package.py b/var/spack/repos/builtin/packages/r-caracas/package.py index d2134463a2..72bacbc250 100644 --- a/var/spack/repos/builtin/packages/r-caracas/package.py +++ b/var/spack/repos/builtin/packages/r-caracas/package.py @@ -7,19 +7,19 @@ from spack import * class RCaracas(RPackage): - """Computer Algebra + """Computer Algebra. Computer algebra via the 'SymPy' library (<https://www.sympy.org/>). This makes it possible to solve equations symbolically, find symbolic integrals, symbolic sums and other important quantities.""" - homepage = "https://cloud.r-project.org/package=caracas" - url = "https://cloud.r-project.org/src/contrib/caracas_1.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/caracas" + cran = "caracas" + version('1.1.1', sha256='e14487c9492417cf5c7d7373c37dbb4fea4d91180a1a03154e51eaa7878b2769') version('1.0.1', sha256='2482dd7b77791243b8174cb41b80b735c3ebd7db837bbf991127514f492af594') version('1.0.0', sha256='0da6f1d94d1dacb1c11a3635bdff8f7cd8f84373deffa7126636d0876d48e42b') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-reticulate@1.14:', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run'), when='@1.1.1:') depends_on('python@3.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cardata/package.py b/var/spack/repos/builtin/packages/r-cardata/package.py index c6d010dbaf..ae19934b51 100644 --- a/var/spack/repos/builtin/packages/r-cardata/package.py +++ b/var/spack/repos/builtin/packages/r-cardata/package.py @@ -7,17 +7,16 @@ from spack import * class RCardata(RPackage): - """Companion to Applied Regression Data Sets + """Companion to Applied Regression Data Sets. Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (2019).""" - homepage = "https://r-forge.r-project.org/projects/car/" - url = "https://cloud.r-project.org/src/contrib/carData_3.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/carData" + cran = "carData" + version('3.0-5', sha256='02e77159b33e3afb8cd9cfab11cf5a996a93175f924b07d991ce44bc6e16451a') version('3.0-4', sha256='cda6f5e3efc1d955a4a0625e9c33f90d49f5455840e88b3bd757129b86044724') version('3.0-2', sha256='3b5c4eff1cc1e456a5331084774503eaa06cf61fb7acf6b9e8a6bfabd5735494') depends_on('r@3.0:', type=('build', 'run')) - depends_on('r@3.5:', when='@3.0-4:', type=('build', 'run')) + depends_on('r@3.5:', type=('build', 'run'), when='@3.0-4:') diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py index f33c575bc7..51e8b12fd4 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -7,15 +7,14 @@ from spack import * class RCaret(RPackage): - """Classification and Regression Training + """Classification and Regression Training. Misc functions for training and plotting classification and regression models.""" - homepage = "https://github.com/topepo/caret/" - url = "https://cloud.r-project.org/src/contrib/caret_6.0-73.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/caret" + cran = "caret" + version('6.0-90', sha256='e851a4ed7d939c665e57e3551a5464b09fe4285e7c951236efdd890b0da866bc') version('6.0-86', sha256='da4a1c7c3fbf645c5b02871e563a77404622b83623f0d1c5dc1425de7aa4ce37') version('6.0-84', sha256='a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d') version('6.0-83', sha256='9bde5e4da1f0b690bfe06c2439c0136504e851a8d360bf56b644f171fe20dcef') @@ -23,17 +22,19 @@ class RCaret(RPackage): version('6.0-70', sha256='21c5bdf7cf07bece38729465366564d8ca104c2466ee9fd800ca1fd88eb82f38') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r@3.2.0:', when='@6.0-82:', type=('build', 'run')) - depends_on('r-lattice@0.20:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@6.0-82:') depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-lattice@0.20:', type=('build', 'run')) + depends_on('r-e1071', type=('build', 'run'), when='@6.0-90:') depends_on('r-foreach', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) depends_on('r-modelmetrics@1.1.0:', type=('build', 'run')) - depends_on('r-modelmetrics@1.2.2.2:', when='@6.0-86:', type=('build', 'run')) + depends_on('r-modelmetrics@1.2.2.2:', type=('build', 'run'), when='@6.0-86:') depends_on('r-nlme', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-proc', type=('build', 'run'), when='@6.0-86:') + depends_on('r-recipes@0.1.4:', type=('build', 'run'), when='@6.0-83:6.0-84') + depends_on('r-recipes@0.1.10:', type=('build', 'run'), when='@6.0-86:') depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-recipes@0.1.4:', when='@6.0-83:6.0-84', type=('build', 'run')) - depends_on('r-recipes@0.1.10:', when='@6.0-86:', type=('build', 'run')) - depends_on('r-withr@2.0.0:', when='@6.0-83:', type=('build', 'run')) - depends_on('r-proc', when='@6.0-86:', type=('build', 'run')) - depends_on('r-car', when='@:6.0-73', type=('build', 'run')) + depends_on('r-withr@2.0.0:', type=('build', 'run'), when='@6.0-83:') + + depends_on('r-car', type=('build', 'run'), when='@:6.0-73') diff --git a/var/spack/repos/builtin/packages/r-caretensemble/package.py b/var/spack/repos/builtin/packages/r-caretensemble/package.py index 8380dc81d5..51b3025b9a 100644 --- a/var/spack/repos/builtin/packages/r-caretensemble/package.py +++ b/var/spack/repos/builtin/packages/r-caretensemble/package.py @@ -7,7 +7,7 @@ from spack import * class RCaretensemble(RPackage): - """caretEnsemble: Ensembles of Caret Models + """Ensembles of Caret Models. Functions for creating ensembles of caret models: caretList() and caretStack(). caretList() is a convenience function for fitting multiple @@ -16,9 +16,7 @@ class RCaretensemble(RPackage): meta-model, and caretEnsemble() will make a robust linear combination of models using a GLM.""" - homepage = "https://github.com/zachmayer/caretEnsemble" - url = "https://cloud.r-project.org/src/contrib/caretEnsemble_2.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/caretEnsemble" + cran = "caretEnsemble" version('2.0.1', sha256='7e595e604ce2d9d32afbc5404e6fcbcd7f80e687316e9ca3303aca3e44c3ef88') diff --git a/var/spack/repos/builtin/packages/r-caroline/package.py b/var/spack/repos/builtin/packages/r-caroline/package.py index 6a2faa4f39..40e95fbd7c 100644 --- a/var/spack/repos/builtin/packages/r-caroline/package.py +++ b/var/spack/repos/builtin/packages/r-caroline/package.py @@ -7,12 +7,20 @@ from spack import * class RCaroline(RPackage): - """caroline: A Collection of Database, Data Structure, Visualization, - andUtility Functions for R""" + """A Collection of Database, Data Structure, Visualization, andUtility + Functions for R. - homepage = "https://cloud.r-project.org/package=caroline" - url = "https://cloud.r-project.org/src/contrib/caroline_0.7.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/caroline" + The caroline R library contains dozens of functions useful for: database + migration (dbWriteTable2), database style joins & aggregation (nerge, + groupBy & bestBy), data structure conversion (nv, tab2df), legend table + making (sstable & leghead), plot annotation (labsegs & mvlabs), data + visualization (violins, pies & raPlot), character string manipulation (m & + pad), file I/O (write.delim), batch scripting and more. The package's + greatest contributions lie in the database style merge, aggregation and + interface functions as well as in it's extensive use and propagation of + row, column and vector names in most functions.""" + + cran = "caroline" version('0.7.6', sha256='e7ba948f7d87f091b498dd0eec2ca4fdad7af4e2bbb67e0945c2f0d3f2eadda9') diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py index d0fa2c3ab9..0ec682adeb 100644 --- a/var/spack/repos/builtin/packages/r-catools/package.py +++ b/var/spack/repos/builtin/packages/r-catools/package.py @@ -8,22 +8,21 @@ from spack import * class RCatools(RPackage): - """Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc + """Moving Window Statistics, GIF, Base64, ROC AUC, etc. Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.""" - homepage = "https://cloud.r-project.org/package=caTools" - url = "https://cloud.r-project.org/src/contrib/caTools_1.17.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/caTools" + cran = "caTools" + version('1.18.2', sha256='75d61115afec754b053ed1732cc034f2aeb27b13e6e1932aa0f26bf590cf0293') version('1.18.1', sha256='ffeba4ffbeed5d491bf79b1fde3477f413341e412f77316af20439f54447c9f9') version('1.17.1.2', sha256='69cc542fab5677462b1a768709d0c4a0a0790f5db53e1fe9ae7123787c18726b') version('1.17.1.1', sha256='d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06') version('1.17.1', sha256='d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4') depends_on('r@2.2.0:', type=('build', 'run')) - depends_on('r@3.6.0:', when='@1.18.1:', type=('build', 'run')) + depends_on('r@3.6.0:', type=('build', 'run'), when='@1.18.1:') depends_on('r-bitops', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cca/package.py b/var/spack/repos/builtin/packages/r-cca/package.py index dcc819bfb0..7e583170e3 100644 --- a/var/spack/repos/builtin/packages/r-cca/package.py +++ b/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 - with new numerical and graphical outputs. It also include a - regularized extension of the canonical correlation analysis to - deal with datasets with more variables than observations.""" + """Canonical Correlation Analysis. + + Provides a set of functions that extend the 'cancor' function with new + numerical and graphical outputs. It also include a regularized extension of + the canonical correlation analysis to deal with datasets with more + variables than observations.""" cran = 'CCA' diff --git a/var/spack/repos/builtin/packages/r-ccp/package.py b/var/spack/repos/builtin/packages/r-ccp/package.py index a1eaf25e15..c206f84964 100644 --- a/var/spack/repos/builtin/packages/r-ccp/package.py +++ b/var/spack/repos/builtin/packages/r-ccp/package.py @@ -5,8 +5,10 @@ class RCcp(RPackage): - """Significance tests for canonical correlation analysis, - including asymptotic tests and a Monte Carlo method""" + """Significance Tests for Canonical Correlation Analysis (CCA). + + Significance tests for canonical correlation analysis, including asymptotic + tests and a Monte Carlo method""" cran = 'CCP' diff --git a/var/spack/repos/builtin/packages/r-cdcfluview/package.py b/var/spack/repos/builtin/packages/r-cdcfluview/package.py index 297950748f..df99bd5391 100644 --- a/var/spack/repos/builtin/packages/r-cdcfluview/package.py +++ b/var/spack/repos/builtin/packages/r-cdcfluview/package.py @@ -8,7 +8,7 @@ from spack import * class RCdcfluview(RPackage): """Retrieve Flu Season Data from the United States Centers for Disease - Control and Prevention ('CDC') 'FluView' Portal + Control and Prevention ('CDC') 'FluView' Portal. The 'U.S.' Centers for Disease Control ('CDC') maintains a portal <https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing @@ -17,21 +17,20 @@ class RCdcfluview(RPackage): to select and retrieve influenza data. Tools are provided to access the data provided by the portal's underlying 'API'.""" - homepage = "https://cloud.r-project.org/package=cdcfluview" - url = "https://cloud.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/cdcfluview" + cran = "cdcfluview" + version('0.9.4', sha256='776a155c4f0cc678fde94a6d47cc2783ff5c199f26cce642461092e1b6311dad') version('0.9.2', sha256='f2080fc80c5e0241f8b657f5ac3a251ea89dfc26c1ab13bdfaed4d4e97495015') version('0.9.0', sha256='1b2064886858cbb1790ef808d88fbab75d3a9cf55e720638221a3377ff8dd244') version('0.7.0', sha256='8c8978d081f8472a6ed5ec54c4e6dd906f97ee28d0f88eef1514088f041ecc03') - depends_on('r@3.2.0:', when='@:0.9.0', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.9.2:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.9.2:') depends_on('r-httr', type=('build', 'run')) - depends_on('r-progress', when='@0.9.2:', type=('build', 'run')) + depends_on('r-progress', type=('build', 'run'), when='@0.9.2:') depends_on('r-dplyr', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-tibble', when='@0.9.2:', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run'), when='@0.9.2:') depends_on('r-sf', type=('build', 'run')) depends_on('r-xml2', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cellranger/package.py b/var/spack/repos/builtin/packages/r-cellranger/package.py index 836fc76310..d31a6a65ce 100644 --- a/var/spack/repos/builtin/packages/r-cellranger/package.py +++ b/var/spack/repos/builtin/packages/r-cellranger/package.py @@ -7,12 +7,12 @@ from spack import * class RCellranger(RPackage): - """Helper functions to work with spreadsheets and the "A1:D10" - style of cell range specification.""" + """Translate Spreadsheet Cell Ranges to Rows and Columns. - homepage = "https://cloud.r-project.org/package=cellranger" - url = "https://cloud.r-project.org/src/contrib/cellranger_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/cellranger" + Helper functions to work with spreadsheets and the "A1:D10" style of cell + range specification.""" + + cran = "cellranger" version('1.1.0', sha256='5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99') diff --git a/var/spack/repos/builtin/packages/r-checkmate/package.py b/var/spack/repos/builtin/packages/r-checkmate/package.py index b7ae065d18..4ec0a37f38 100644 --- a/var/spack/repos/builtin/packages/r-checkmate/package.py +++ b/var/spack/repos/builtin/packages/r-checkmate/package.py @@ -7,15 +7,13 @@ from spack import * class RCheckmate(RPackage): - """Fast and Versatile Argument Checks + """Fast and Versatile Argument Checks. - Tests and assertions to perform frequent argument checks. - A substantial part of the package was written in C to - minimize any worries about execution time overhead.""" + Tests and assertions to perform frequent argument checks. A substantial + part of the package was written in C to minimize any worries about + execution time overhead.""" - homepage = "https://cloud.r-project.org/package=checkmate" - url = "https://cloud.r-project.org/src/contrib/checkmate_1.8.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/checkmate" + cran = "checkmate" version('2.0.0', sha256='0dc25b0e20c04836359df1885d099c6e4ad8ae0e585a9e4107f7ea945d9c6fa4') version('1.9.4', sha256='faa25754b757fe483b876f5d07b73f76f69a1baa971420892fadec4af4bbad21') diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index 4767d60d4b..b12dce32e0 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -7,7 +7,8 @@ from spack import * class RCheckpoint(RPackage): - """Install Packages from Snapshots on the Checkpoint Server for Reproducibility + """Install Packages from Snapshots on the Checkpoint Server for + Reproducibility. The goal of checkpoint is to solve the problem of package reproducibility in R. Specifically, checkpoint allows you to install packages as they @@ -25,13 +26,19 @@ class RCheckpoint(RPackage): thus creating the archive. Snapshot archives exist starting from 2014-09-17.""" - homepage = "https://cloud.r-project.org/package=checkpoint" - url = "https://cloud.r-project.org/src/contrib/checkpoint_0.4.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint" + cran = "checkpoint" + version('1.0.2', sha256='a80390d834534e908058a597a2a5ee60a111023e76f13f370949963582dd07a5') + version('1.0.1', sha256='8542029395b7d557c1b39423326611f408788fcd02f5cbeb5ed252f368f8dcd2') + version('1.0.0', sha256='d36146093763ca29e0296729399b96e0f2e7764745283d6cea1066a96fa085a7') version('0.4.10', sha256='7362ae9703763fe4652d0b592cd913ce506f072a18e5cf5970d08d7cdf4d126a') version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') version('0.4.3', sha256='c3e862f89f8838183d6028f7ed13683aec562e6dab77ad4b6a5e24ec653cfb64') version('0.3.15', sha256='09f1feeb2b5b8b409a2e16a9185827b8da5e555f1aa84442a287f15e452beed7') depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-jsonlite', type=('build', 'run'), when='@1.0.0:') + depends_on('r-yaml', type=('build', 'run'), when='@1.0.0:') + depends_on('r-withr', type=('build', 'run'), when='@1.0.0:') + depends_on('r-pkgdepends', type=('build', 'run'), when='@1.0.0:') diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py index e2d3b30b6c..a757e9b7a5 100644 --- a/var/spack/repos/builtin/packages/r-chemometrics/package.py +++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py @@ -7,13 +7,12 @@ from spack import * class RChemometrics(RPackage): - """R companion to the book "Introduction to Multivariate Statistical - Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser - (2009).""" + """Multivariate Statistical Analysis in Chemometrics. - homepage = "https://cloud.r-project.org/package=chemometrics" - url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/chemometrics" + R companion to the book "Introduction to Multivariate Statistical Analysis + in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).""" + + cran = "chemometrics" version('1.4.2', sha256='b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a') version('1.4.1', sha256='7646da0077657d672356204aa2094be68e10ec13617f92ae97ff53a389053905') diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py index a5e42ecca2..96a3b2c67f 100644 --- a/var/spack/repos/builtin/packages/r-chron/package.py +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -9,12 +9,9 @@ from spack import * class RChron(RPackage): """Chronological objects which can handle dates and times. - Provides chronological objects which can handle dates and times. - """ + Provides chronological objects which can handle dates and times.""" - homepage = "https://cloud.r-project.org/package=chron" - url = "https://cloud.r-project.org/src/contrib/chron_2.3-47.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/chron" + cran = "chron" version('2.3-56', sha256='863ecbb951a3da994761ea9062fa96d34e94e19fbc4122521ac179274dfa3f5d') version('2.3-53', sha256='521814b46ba958eae28e29d8766aebd285da5e6fa16c5806603df3ae39f77309') diff --git a/var/spack/repos/builtin/packages/r-circlize/package.py b/var/spack/repos/builtin/packages/r-circlize/package.py index f0b9292c25..3690f5610f 100644 --- a/var/spack/repos/builtin/packages/r-circlize/package.py +++ b/var/spack/repos/builtin/packages/r-circlize/package.py @@ -7,7 +7,7 @@ from spack import * class RCirclize(RPackage): - """Circular Visualization + """Circular Visualization. Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular @@ -21,17 +21,16 @@ class RCirclize(RPackage): package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.""" - homepage = "https://cloud.r-project.org/package=circlize" - url = "https://cloud.r-project.org/src/contrib/circlize_0.4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/circlize" + cran = "circlize" + version('0.4.13', sha256='6cbadbf8e8b1abbd71a79080677d2b95f2bdd18f2e4d707c32d5c2ff26c5369b') version('0.4.12', sha256='b3b60caa5292cf980cf474c85f59582f6862925631a4da86a78eac05903252f4') version('0.4.6', sha256='cec88cfc5e512a111cc37177552c25698ccc0e9bbecb0d6e60657e7b115a56fa') version('0.4.1', sha256='204a170ae3b982f09b652c4583189907cfa42a29bc7efaba02a1e0d79f1cf1f0') version('0.4.0', sha256='abdc1bbe264be42c1d7b65869979da7cd131032fd6fd3f11f9744dae54e83f5c') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r-globaloptions@0.1.0:', when='@:0.4.6', type=('build', 'run')) - depends_on('r-globaloptions@0.1.2:', when='@0.4.12:', type=('build', 'run')) + depends_on('r-globaloptions@0.1.0:', type=('build', 'run')) + depends_on('r-globaloptions@0.1.2:', type=('build', 'run'), when='@0.4.12:') depends_on('r-shape', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-circstats/package.py b/var/spack/repos/builtin/packages/r-circstats/package.py index 821ccffed6..721165372a 100644 --- a/var/spack/repos/builtin/packages/r-circstats/package.py +++ b/var/spack/repos/builtin/packages/r-circstats/package.py @@ -7,14 +7,12 @@ from spack import * class RCircstats(RPackage): - """Circular Statistics, from "Topics in Circular Statistics" (2001) + """Circular Statistics, from "Topics in Circular Statistics" (2001). - Circular Statistics, from "Topics in Circular Statistics" (2001) S. - Rao Jammalamadaka and A. SenGupta, World Scientific.""" + Circular Statistics, from "Topics in Circular Statistics" (2001) S. Rao + Jammalamadaka and A. SenGupta, World Scientific.""" - homepage = "https://cloud.r-project.org/package=CircStats" - url = "https://cloud.r-project.org/src/contrib/CircStats_0.2-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/CircStats" + cran = "CircStats" maintainers = ['dorton21'] diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index 4f7da7e9bb..771d4b5fac 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -7,15 +7,15 @@ from spack import * class RClass(RPackage): - """Functions for Classification + """Functions for Classification. Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.""" - homepage = "https://www.stats.ox.ac.uk/pub/MASS4/" - url = "https://cloud.r-project.org/src/contrib/class_7.3-14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/class" + cran = "class" + version('7.3-20', sha256='e65b046bc72b312ff0c5dc7feba4fa3e9bc63387274d44911493782b85f65483') + version('7.3-19', sha256='7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37') version('7.3-17', sha256='be1f85b6df7556db93f50cb08106aac6620d4b5bb3fee846422863a022461313') version('7.3-15', sha256='f6bf33d610c726d58622b6cea78a808c7d6a317d02409d27c17741dfd1c730f4') version('7.3-14', sha256='18b876dbc18bebe6a00890eab7d04ef72b903ba0049d5ce50731406a82426b9c') diff --git a/var/spack/repos/builtin/packages/r-classint/package.py b/var/spack/repos/builtin/packages/r-classint/package.py index 390aaf036b..75bf07e5ca 100644 --- a/var/spack/repos/builtin/packages/r-classint/package.py +++ b/var/spack/repos/builtin/packages/r-classint/package.py @@ -7,14 +7,12 @@ from spack import * class RClassint(RPackage): - """Choose Univariate Class Intervals + """Choose Univariate Class Intervals. Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.""" - homepage = "https://cloud.r-project.org/package=classInt" - url = "https://cloud.r-project.org/src/contrib/classInt_0.1-24.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/classInt" + cran = "classInt" version('0.4-3', sha256='9ede7a2a7a6b6c114919a3315a884fb592e33b037a50a4fe45cbd4fe2fc434ac') version('0.4-1', sha256='39c63f8e37b379033d73d57929b5b8ea41b0023626cc1cec648d66bade5d0103') diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py index 3ef62f346c..a37d470ae6 100644 --- a/var/spack/repos/builtin/packages/r-cli/package.py +++ b/var/spack/repos/builtin/packages/r-cli/package.py @@ -7,7 +7,7 @@ from spack import * class RCli(RPackage): - """Helpers for Developing Command Line Interfaces + """Helpers for Developing Command Line Interfaces. A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports @@ -16,9 +16,9 @@ class RCli(RPackage): 'ASCII' alternatives. It integrates with the 'crayon' package to support 'ANSI' terminal colors.""" - homepage = "https://github.com/r-lib/cli" cran = "cli" + version('3.1.1', sha256='c8b3e6014ad60593ba21897255acfe90c0e3f98bd4f7e22c1f3acb2644cf54cf') version('3.1.0', sha256='c70a61830bf706a84c59eb74a809978846cee93742198ab4192742a5df1ace11') version('3.0.1', sha256='d89a25b6cd760e157605676e104ce65473a7d8d64c289efdd9640e949968b4fd') version('2.2.0', sha256='39a77af61724f8cc1f5117011e17bb2a488cbac61a7c112db078a675d3ac40b8') @@ -28,7 +28,8 @@ class RCli(RPackage): version('1.0.0', sha256='8fa3dbfc954ca61b8510f767ede9e8a365dac2ef95fe87c715a0f37d721b5a1d') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r-glue', when='@2:', type=('build', 'run')) - depends_on('r-assertthat', when='@:2.3', type=('build', 'run')) - depends_on('r-crayon@1.3.4:', when='@:2.2', type=('build', 'run')) - depends_on('r-fansi', when='@2:2.2', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run'), when='@2:') + + depends_on('r-assertthat', type=('build', 'run'), when='@:2.3') + depends_on('r-crayon@1.3.4:', type=('build', 'run'), when='@:2.2') + depends_on('r-fansi', type=('build', 'run'), when='@2:2.2') diff --git a/var/spack/repos/builtin/packages/r-clipr/package.py b/var/spack/repos/builtin/packages/r-clipr/package.py index 1ec8919a23..7ab04944d7 100644 --- a/var/spack/repos/builtin/packages/r-clipr/package.py +++ b/var/spack/repos/builtin/packages/r-clipr/package.py @@ -7,18 +7,17 @@ from spack import * class RClipr(RPackage): - """Read and Write from the System Clipboard + """Read and Write from the System Clipboard. Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.""" - homepage = "https://github.com/mdlincoln/clipr" - url = "https://cloud.r-project.org/src/contrib/clipr_0.4.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/clipr" + cran = "clipr" version('0.7.1', sha256='ffad477b07847e3b68f7e4406bbd323025a8dae7e3c768943d4d307ee3248afb') version('0.7.0', sha256='03a4e4b72ec63bd08b53fe62673ffc19a004cc846957a335be2b30d046b8c2e2') version('0.5.0', sha256='fd303f8b7f29badcdf490bb2d579acdfc4f4e1aa9c90ac77ab9d05ce3d053dbf') version('0.4.0', sha256='44a2f1ab4fde53e4fe81cf5800aa6ad45b72b5da93d6fe4d3661d7397220e8af') + depends_on('r+X') depends_on('xclip') diff --git a/var/spack/repos/builtin/packages/r-clisymbols/package.py b/var/spack/repos/builtin/packages/r-clisymbols/package.py index ac7534efd4..d51c0d8560 100644 --- a/var/spack/repos/builtin/packages/r-clisymbols/package.py +++ b/var/spack/repos/builtin/packages/r-clisymbols/package.py @@ -7,13 +7,13 @@ from spack import * class RClisymbols(RPackage): - """A small subset of Unicode symbols, that are useful when building command + """Unicode Symbols at the R Prompt. + + A small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. Many symbols were taken from the 'figures' 'npm' package (see <https://github.com/sindresorhus/figures>).""" - homepage = "https://github.com/gaborcsardi/clisymbols" - url = "https://cloud.r-project.org/src/contrib/clisymbols_1.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/clisymbols" + cran = "clisymbols" version('1.2.0', sha256='0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0') diff --git a/var/spack/repos/builtin/packages/r-clue/package.py b/var/spack/repos/builtin/packages/r-clue/package.py index 0640318407..41392115ff 100644 --- a/var/spack/repos/builtin/packages/r-clue/package.py +++ b/var/spack/repos/builtin/packages/r-clue/package.py @@ -7,12 +7,11 @@ from spack import * class RClue(RPackage): - """Cluster Ensembles""" + """Cluster Ensembles.""" - homepage = "https://cloud.r-project.org/package=clue" - url = "https://cloud.r-project.org/src/contrib/clue_0.3-57.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/clue" + cran = "clue" + version('0.3-60', sha256='6d21ddfd0d621ed3bac861890c600884b6ed5ff7d2a36c9778b892636dbbef2a') version('0.3-58', sha256='2ab6662eaa1103a7b633477e8ebd266b262ed54fac6f9326b160067a2ded9ce7') version('0.3-57', sha256='6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17') diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index 5fdd4229a6..839fc5315d 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -7,19 +7,21 @@ from spack import * class RCluster(RPackage): - """Methods for Cluster analysis. Much extended the original from Peter + """"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. + + Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".""" - homepage = "https://cloud.r-project.org/package=cluster" - url = "https://cloud.r-project.org/src/contrib/cluster_2.0.7-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/cluster" + cran = "cluster" + version('2.1.2', sha256='5c8aa760fb6dda4fcfe6196e561ffcd2dc12b1a6c7659cb90be2cde747311499') version('2.1.0', sha256='eaf955bef8f616ea563351ec7f597c445aec43e65991ca975e382ef1fd70aa14') version('2.0.7-1', sha256='b10141090cf3c2b62260611a0ea822eb2f7bab9f4fd656c48bdc12b65c5c3dbf') version('2.0.5', sha256='4b309133bc2ad7b8fe4fa538dd69635bc8a4cd724a3c95f01084098876c57bae') version('2.0.4', sha256='d4d925c4fc1fc4f2e2e3c9208e518507aad6c28bb143b4358a05a8a8944ac6e4') - depends_on('r@3.0.1:', when='@:2.0.6', type=('build', 'run')) - depends_on('r@3.2.0:', when='@2.0.7:2.0.7-1', type=('build', 'run')) - depends_on('r@3.3.0:', when='@2.0.8:', type=('build', 'run')) + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@2.0.7:') + depends_on('r@3.3.0:', type=('build', 'run'), when='@2.0.8:') + depends_on('r@3.4.0:', type=('build', 'run'), when='@2.1.2:') diff --git a/var/spack/repos/builtin/packages/r-clustergeneration/package.py b/var/spack/repos/builtin/packages/r-clustergeneration/package.py index 02ac6620b3..6f862881a2 100644 --- a/var/spack/repos/builtin/packages/r-clustergeneration/package.py +++ b/var/spack/repos/builtin/packages/r-clustergeneration/package.py @@ -7,7 +7,7 @@ from spack import * class RClustergeneration(RPackage): - """Random Cluster Generation (with Specified Degree of Separation) + """Random Cluster Generation (with Specified Degree of Separation). We developed the clusterGeneration package to provide functions for generating random clusters, generating random covariance/correlation @@ -18,13 +18,11 @@ class RClustergeneration(RPackage): degree of separation, number of clusters, number of variables, number of noisy variables.""" - homepage = "https://cloud.r-project.org/package=clusterGeneration" - url = "https://cloud.r-project.org/src/contrib/clusterGeneration_1.3.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/clusterGeneration/" + cran = "clusterGeneration" version('1.3.7', sha256='534f29d8f7ed11e6e9a496f15845b588ec7133f3da5e6def8140b88500e52d5c') version('1.3.4', sha256='7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa') depends_on('r@2.9.1:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.3.7:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.3.7:') depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py index 105e9c0f0c..dcb4439506 100644 --- a/var/spack/repos/builtin/packages/r-coda/package.py +++ b/var/spack/repos/builtin/packages/r-coda/package.py @@ -7,15 +7,13 @@ from spack import * class RCoda(RPackage): - """Output Analysis and Diagnostics for MCMC + """Output Analysis and Diagnostics for MCMC. Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.""" - homepage = "https://cloud.r-project.org/package=coda" - url = "https://cloud.r-project.org/src/contrib/coda_0.19-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/coda" + cran = "coda" version('0.19-4', sha256='422d3cfd34797a3631e9c4812431940599c0ca4bb9937797bed07b7b1d6fe58f') version('0.19-3', sha256='d3df1fc848bcf1af8fae13d61eeab60e99a3d4b4db384bec4326f909f502c5d6') diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index 396f28e524..46b52d3429 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -9,9 +9,7 @@ from spack import * class RCodetools(RPackage): """Code analysis tools for R.""" - homepage = "https://cloud.r-project.org/package=codetools" - url = "https://cloud.r-project.org/src/contrib/codetools_0.2-15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/codetools" + cran = "codetools" version('0.2-18', sha256='1a9ea6b9792dbd1688078455929385acc3a5e4bef945c77bec1261fa4a084c28') version('0.2-16', sha256='c276757c3adabaf700f2ea25835892b09bc1bd438ebd17c805ea9073ed8a74b6') diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py index 8d6a7bf0cd..5892ed16be 100644 --- a/var/spack/repos/builtin/packages/r-coin/package.py +++ b/var/spack/repos/builtin/packages/r-coin/package.py @@ -7,26 +7,27 @@ from spack import * class RCoin(RPackage): - """Conditional Inference Procedures in a Permutation Test Framework + """Conditional Inference Procedures in a Permutation Test Framework. Conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.""" - homepage = "https://cloud.r-project.org/package=coin" - url = "https://cloud.r-project.org/src/contrib/coin_1.1-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/coin" + cran = "coin" + version('1.4-2', sha256='7546d1f27a82d98b4b3e43e4659eba0f74a67d5919ce85d2fb360282ba3cfbb2') version('1.3-1', sha256='5de2519a6e2b059bba9d74c58085cccaff1aaaa0454586ed164a108ebd1b2062') version('1.3-0', sha256='adcebb37e0a7dfddbf8ec1e09c12a809bd76d90b5b8ff2b1048a75252ba11ef8') version('1.2-2', sha256='d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb') version('1.1-3', sha256='8b88ecc25903c83539dfc73cdc31a160e2aa4a7bea1773b22c79133d2f006035') - depends_on('r@2.14.0:', when='@:1.2-2', type=('build', 'run')) - depends_on('r@3.4.0:', when='@1.3-0:', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@1.3-0:') + depends_on('r@3.6.0:', type=('build', 'run'), when='@1.4-2:') depends_on('r-survival', type=('build', 'run')) - depends_on('r-libcoin@1.0-0:', when='@1.3-0:', type=('build', 'run')) - depends_on('r-matrixstats@0.54.0:', when='@1.3-0:', type=('build', 'run')) + depends_on('r-libcoin@1.0-0:', type=('build', 'run'), when='@1.3-0:') + depends_on('r-libcoin@1.0-9:', type=('build', 'run'), when='@1.4-2:') + depends_on('r-matrixstats@0.54.0:', type=('build', 'run'), when='@1.3-0:') depends_on('r-modeltools@0.2-9:', type=('build', 'run')) depends_on('r-mvtnorm@1.0-5:', type=('build', 'run')) depends_on('r-multcomp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index c3f09c14fc..85e19c6851 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -7,7 +7,7 @@ from spack import * class RColorspace(RPackage): - """A Toolbox for Manipulating and Assessing Colors and Palettes + """A Toolbox for Manipulating and Assessing Colors and Palettes. Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, @@ -25,7 +25,6 @@ class RColorspace(RPackage): scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).""" - homepage = "https://colorspace.R-Forge.R-project.org" cran = "colorspace" version('2.0-2', sha256='b891cd2ec129ed5f116429345947bcaadc33969758a108521eb0cf36bd12183a') diff --git a/var/spack/repos/builtin/packages/r-colourpicker/package.py b/var/spack/repos/builtin/packages/r-colourpicker/package.py index 84da831fd0..0e8d2d507f 100644 --- a/var/spack/repos/builtin/packages/r-colourpicker/package.py +++ b/var/spack/repos/builtin/packages/r-colourpicker/package.py @@ -7,7 +7,7 @@ from spack import * class RColourpicker(RPackage): - """A Colour Picker Tool for Shiny and for Selecting Colours in Plots: + """A Colour Picker Tool for Shiny and for Selecting Colours in Plots. A colour picker that can be used as an input in 'Shiny' apps or Rmarkdown documents. The colour picker supports alpha opacity, custom colour @@ -16,8 +16,7 @@ class RColourpicker(RPackage): more generic Colour Picker 'RStudio' Addin is also provided to let you select colours to use in your R code.""" - homepage = "https://github.com/daattali/colourpicker" - cran = "colourpicker" + cran = "colourpicker" version('1.1.1', sha256='a0d09982b048b143e2c3438ccec039dd20d6f892fa0dedc9fdcb0d40de883ce0') version('1.1.0', sha256='2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2') diff --git a/var/spack/repos/builtin/packages/r-combinat/package.py b/var/spack/repos/builtin/packages/r-combinat/package.py index 2dada701e9..2baae0b0cf 100644 --- a/var/spack/repos/builtin/packages/r-combinat/package.py +++ b/var/spack/repos/builtin/packages/r-combinat/package.py @@ -7,10 +7,10 @@ from spack import * class RCombinat(RPackage): - """routines for combinatorics""" + """combinatorics utilities. - homepage = "https://cloud.r-project.org/package=combinat" - url = "https://cloud.r-project.org/src/contrib/combinat_0.0-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/combinat/" + routines for combinatorics.""" + + cran = "combinat" version('0.0-8', sha256='1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1') diff --git a/var/spack/repos/builtin/packages/r-commonmark/package.py b/var/spack/repos/builtin/packages/r-commonmark/package.py index 8ebf5e0be4..0c7fa616bd 100644 --- a/var/spack/repos/builtin/packages/r-commonmark/package.py +++ b/var/spack/repos/builtin/packages/r-commonmark/package.py @@ -7,10 +7,15 @@ from spack import * class RCommonmark(RPackage): - """commonmark: CommonMark and Github Markdown Rendering in R""" + """High Performance CommonMark and Github Markdown Rendering in R. - homepage = "https://cloud.r-project.org/package=commonmark" - url = "https://cloud.r-project.org/src/contrib/commonmark_1.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/commonmark/" + The CommonMark specification defines a rationalized version of markdown + syntax. This package uses the 'cmark' reference implementation for + converting markdown text into various formats including html, latex and + groff man. In addition it exposes the markdown parse tree in xml format. + Also includes opt-in support for GFM extensions including tables, + autolinks, and strikethrough text.""" + + cran = "commonmark" version('1.7', sha256='d14a767a3ea9778d6165f44f980dd257423ca6043926e3cd8f664f7171f89108') diff --git a/var/spack/repos/builtin/packages/r-compositions/package.py b/var/spack/repos/builtin/packages/r-compositions/package.py index 1ac3a5fe6d..5e2aaf562b 100644 --- a/var/spack/repos/builtin/packages/r-compositions/package.py +++ b/var/spack/repos/builtin/packages/r-compositions/package.py @@ -7,22 +7,23 @@ from spack import * class RCompositions(RPackage): - """Compositional Data Analysis + """Compositional Data Analysis. Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.""" - homepage = "https://cloud.r-project.org/package=compositions" - url = "https://cloud.r-project.org/src/contrib/compositions_1.40-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/compositions" + cran = "compositions" + version('2.0-4', sha256='7b9c7a3bf654fb02d9eb1b4a7566469b2f5232f3b2c1b324c02239fd31060faf') version('2.0-1', sha256='84a291308faf858e5a9d9570135c2da5e57b0887f407903485fa85d09da61a0f') version('1.40-2', sha256='110d71ae000561987cb73fc76cd953bd69d37562cb401ed3c36dca137d01b78a') depends_on('r@2.2.0:', type=('build', 'run')) + depends_on('r@3.6:', type=('build', 'run'), when='@2.0-4:') depends_on('r-tensora', type=('build', 'run')) depends_on('r-robustbase', type=('build', 'run')) depends_on('r-bayesm', type=('build', 'run')) - depends_on('r-mass', when='@2.0-1:', type=('build', 'run')) - depends_on('r-energy', when='@:1.40-2', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run'), when='@2.0-1:') + + depends_on('r-energy', type=('build', 'run'), when='@:1.40-2') diff --git a/var/spack/repos/builtin/packages/r-compquadform/package.py b/var/spack/repos/builtin/packages/r-compquadform/package.py index 613d5ce4ea..137359af80 100644 --- a/var/spack/repos/builtin/packages/r-compquadform/package.py +++ b/var/spack/repos/builtin/packages/r-compquadform/package.py @@ -7,12 +7,12 @@ from spack import * class RCompquadform(RPackage): - """Distribution Function of Quadratic Forms in Normal Variables: + """Distribution Function of Quadratic Forms in Normal Variables. Computes the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm.""" - cran = "CompQuadForm" + cran = "CompQuadForm" version('1.4.3', sha256='042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4') diff --git a/var/spack/repos/builtin/packages/r-condop/package.py b/var/spack/repos/builtin/packages/r-condop/package.py index 950e4e162e..a7935b2c95 100644 --- a/var/spack/repos/builtin/packages/r-condop/package.py +++ b/var/spack/repos/builtin/packages/r-condop/package.py @@ -7,16 +7,14 @@ from spack import * class RCondop(RPackage): - """CONDOP: Condition-Dependent Operon Predictions. + """Condition-Dependent Operon Predictions. An implementation of the computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes proposed by Fortino et al. (2014) <doi:10.1186/1471-2105-15-145>. It uses RNA-seq transcriptome profiles to improve prokaryotic operon map inference.""" - homepage = "https://cloud.r-project.org/package=CONDOP" - url = "https://cloud.r-project.org/src/contrib/CONDOP_1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/CONDOP" + cran = "CONDOP" version('1.0', sha256='3a855880f5c6b33f949c7e6de53c8e014b4d72b7024a93878b344d3e52b5296a') diff --git a/var/spack/repos/builtin/packages/r-conquer/package.py b/var/spack/repos/builtin/packages/r-conquer/package.py index ae0b337e99..0820d1e795 100644 --- a/var/spack/repos/builtin/packages/r-conquer/package.py +++ b/var/spack/repos/builtin/packages/r-conquer/package.py @@ -7,14 +7,13 @@ from spack import * class RConquer(RPackage): - """Convolution-Type Smoothed Quantile Regression + """Convolution-Type Smoothed Quantile Regression. Fast and accurate convolution-type smoothed quantile regression. Implemented using Barzilai-Borwein gradient descent with a Huber regression warm start. Construct confidence intervals for regression coefficients using multiplier bootstrap.""" - homepage = "https://github.com/XiaoouPan/conquer" cran = "conquer" version('1.2.1', sha256='1354f90f962a2124e155227cdc0ed2c6e54682f1e08934c49a827e51dc112f45') @@ -24,5 +23,5 @@ class RConquer(RPackage): depends_on('r-rcpp@1.0.3:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r-caret', when='@1.2:', type=('build', 'run')) + depends_on('r-caret', type=('build', 'run'), when='@1.2:') depends_on('r-rcpparmadillo@0.9.850.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-construct/package.py b/var/spack/repos/builtin/packages/r-construct/package.py index 2b4aa2a74c..fa1a631f0e 100644 --- a/var/spack/repos/builtin/packages/r-construct/package.py +++ b/var/spack/repos/builtin/packages/r-construct/package.py @@ -7,7 +7,7 @@ from spack import * class RConstruct(RPackage): - """Models Spatially Continuous and Discrete Population GeneticStructure + """Models Spatially Continuous and Discrete Population GeneticStructure. A method for modeling genetic data as a combination of discrete layers, within each of which relatedness may decay continuously with geographic @@ -16,9 +16,7 @@ class RConstruct(RPackage): interpreting output. See the paper for more details on the model and its utility.""" - homepage = "https://cloud.r-project.org/package=conStruct" - url = "https://cloud.r-project.org/src/contrib/conStruct_1.0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/conStruct" + cran = "conStruct" version('1.0.4', sha256='4e585b718a361061bc1432cea46fc65f802fb0ef58e4516d33e1af99bbfe90ce') version('1.0.3', sha256='b449c133a944ad05a28f84f312ed4ccbc1574c4659aa09c678618d2ae9008310') diff --git a/var/spack/repos/builtin/packages/r-convevol/package.py b/var/spack/repos/builtin/packages/r-convevol/package.py index 1944b5c25e..081c478ed7 100644 --- a/var/spack/repos/builtin/packages/r-convevol/package.py +++ b/var/spack/repos/builtin/packages/r-convevol/package.py @@ -7,11 +7,14 @@ from spack import * class RConvevol(RPackage): - """Quantifies and assesses the significance of convergent evolution""" + """Analysis of Convergent Evolution. - homepage = "https://cloud.r-project.org/package=convevol" - url = "https://cloud.r-project.org/src/contrib/convevol_1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/convevol/" + Quantifies and assesses the significance of convergent evolution using two + different methods (and 5 different measures) as described in Stayton (2015) + <doi:10.1111/evo.12729>. Also displays results in a phylomorphospace + framework.""" + + cran = "convevol" version('1.3', sha256='d6b24b9796a559f5280e277746189d141151ade4b14cc6b4c2d9d496d7f314ac') diff --git a/var/spack/repos/builtin/packages/r-copula/package.py b/var/spack/repos/builtin/packages/r-copula/package.py index 8280c24559..1cfb22e1aa 100644 --- a/var/spack/repos/builtin/packages/r-copula/package.py +++ b/var/spack/repos/builtin/packages/r-copula/package.py @@ -7,7 +7,7 @@ from spack import * class RCopula(RPackage): - """Multivariate Dependence with Copulas + """Multivariate Dependence with Copulas. Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and @@ -22,15 +22,13 @@ class RCopula(RPackage): copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.""" - homepage = "https://copula.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/copula_0.999-20.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/copula" + cran = "copula" version('1.0-1', sha256='d09b2ccffc7379e48b00952aa6b282baf502feebaf55cc44e93f881d7b909742') version('0.999-20', sha256='7d3d47bce2dacb05b94a772f84dbf3d83c99ac2ac11e5f1b4b03d50d9d5c0fb0') depends_on('r@3.2.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.0-1:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.0-1:') depends_on('r-matrix', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-corhmm/package.py b/var/spack/repos/builtin/packages/r-corhmm/package.py index e78be07148..ed7200541e 100644 --- a/var/spack/repos/builtin/packages/r-corhmm/package.py +++ b/var/spack/repos/builtin/packages/r-corhmm/package.py @@ -7,16 +7,15 @@ from spack import * class RCorhmm(RPackage): - """Hidden Markov Models of Character Evolution + """Hidden Markov Models of Character Evolution. Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.""" - homepage = "https://cloud.r-project.org/package=corHMM" - url = "https://cloud.r-project.org/src/contrib/corHMM_1.22.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/corHMM/" + cran = "corHMM" + version('2.7', sha256='0d54ba0f6b3f884343bcc26919d8febc05efb0b739cb962d3072ca0bc0ce270a') version('2.6', sha256='726de9707ede8ef447915171a3abe1003a0e42fe8e17eb440442cac9adf8cdcf') version('1.22', sha256='d262fa1183eab32087afb70f1789fabae6fb49bec01d627974c54a088a48b10d') @@ -26,10 +25,10 @@ class RCorhmm(RPackage): depends_on('r-expm', type=('build', 'run')) depends_on('r-numderiv', type=('build', 'run')) depends_on('r-corpcor', type=('build', 'run')) - depends_on('r-mass', when='@2.6:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run'), when='@2.6:') depends_on('r-nnet', type=('build', 'run')) depends_on('r-phangorn', type=('build', 'run')) - depends_on('r-viridis', when='@2.6:', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run'), when='@2.6:') depends_on('r-rmpfr', type=('build', 'run')) - depends_on('r-igraph', when='@2.6:', type=('build', 'run')) - depends_on('r-phytools', when='@2.6:', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run'), when='@2.6:') + depends_on('r-phytools', type=('build', 'run'), when='@2.6:') diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py index f7cc51da05..631917e976 100644 --- a/var/spack/repos/builtin/packages/r-corpcor/package.py +++ b/var/spack/repos/builtin/packages/r-corpcor/package.py @@ -7,12 +7,26 @@ from spack import * class RCorpcor(RPackage): - """Efficient Estimation of Covariance and (Partial) Correlation""" + """Efficient Estimation of Covariance and (Partial) Correlation. - homepage = "https://cloud.r-project.org/package=corpcor" - url = "https://cloud.r-project.org/src/contrib/corpcor_1.6.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/corpcor" + Implements a James-Stein-type shrinkage estimator for the covariance + matrix, with separate shrinkage for variances and correlations. The + details of the method are explained in Schafer and Strimmer (2005) + <DOI:10.2202/1544-6115.1175> and Opgen-Rhein and Strimmer (2007) + <DOI:10.2202/1544-6115.1252>. The approach is both computationally as well + as statistically very efficient, it is applicable to "small n, large p" + data, and always returns a positive definite and well-conditioned + covariance matrix. In addition to inferring the covariance matrix the + package also provides shrinkage estimators for partial correlations and + partial variances. The inverse of the covariance and correlation matrix + can be efficiently computed, as well as any arbitrary power of the + shrinkage correlation matrix. Furthermore, functions are available for + fast singular value decomposition, for computing the pseudoinverse, and + for checking the rank and positive definiteness of a matrix.""" + cran = "corpcor" + + version('1.6.10', sha256='71a04c503c93ec95ddde09abe8c7ddeb36175b7da76365a14b27066383e10e09') version('1.6.9', sha256='2e4fabd1d3936fecea67fa365233590147ca50bb45cf80efb53a10345a8a23c2') depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-corrplot/package.py b/var/spack/repos/builtin/packages/r-corrplot/package.py index e5c79c6f53..25649c9cb5 100644 --- a/var/spack/repos/builtin/packages/r-corrplot/package.py +++ b/var/spack/repos/builtin/packages/r-corrplot/package.py @@ -7,12 +7,14 @@ from spack import * class RCorrplot(RPackage): - """A graphical display of a correlation matrix or general matrix. - It also contains some algorithms to do matrix reordering.""" + """Visualization of a Correlation Matrix. - homepage = "https://cloud.r-project.org/package=corrplot" - url = "https://cloud.r-project.org/src/contrib/corrplot_0.77.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/corrplot" + Provides a visual exploratory tool on correlation matrix that supports + automatic variable reordering to help detect hidden patterns among + variables.""" + cran = "corrplot" + + version('0.92', sha256='e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd') version('0.84', sha256='0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc') version('0.77', sha256='54b66ff995eaf2eee3f3002509c6f27bb5bd970b0abde41893ed9387e93828d3') diff --git a/var/spack/repos/builtin/packages/r-countrycode/package.py b/var/spack/repos/builtin/packages/r-countrycode/package.py index af2897eb35..0d7b8421c0 100644 --- a/var/spack/repos/builtin/packages/r-countrycode/package.py +++ b/var/spack/repos/builtin/packages/r-countrycode/package.py @@ -7,13 +7,14 @@ from spack import * class RCountrycode(RPackage): - """Countrycode standardizes country names, converts them into - ~40 different coding schemes, and assigns region descriptors.""" + """Convert Country Names and Country Codes. - homepage = "https://vincentarelbundock.github.io/countrycode/" - url = "https://cloud.r-project.org/src/contrib/countrycode_1.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/countrycode" + Countrycode standardizes country names, converts them into ~40 different + coding schemes, and assigns region descriptors.""" + cran = "countrycode" + + version('1.3.0', sha256='34361416e771ece1d56dc56f79416c8b7f9591885773becae270684d095bc70f') version('1.2.0', sha256='32c65702dcc33d512ff99f14c12f4e0c48fe7ed7c8aa2f0a64194576d129dd40') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py index 24b5e3e4f1..511d5c9f2c 100644 --- a/var/spack/repos/builtin/packages/r-covr/package.py +++ b/var/spack/repos/builtin/packages/r-covr/package.py @@ -7,20 +7,17 @@ from spack import * class RCovr(RPackage): - """Test Coverage for Packages + """Test Coverage for Packages. - Track and report code coverage for your package and (optionally) - upload the results to a coverage service like 'Codecov' - <http://codecov.io> or 'Coveralls' <https://coveralls.io/>. Code - coverage is a measure of the amount of code being exercised by a - set of tests. It is an indirect measure of test quality and - completeness. This package is compatible with any testing methodology - or framework and tracks coverage of both R code and compiled - C/C++/FORTRAN code.""" + Track and report code coverage for your package and (optionally) upload the + results to a coverage service like 'Codecov' <http://codecov.io> or + 'Coveralls' <https://coveralls.io/>. Code coverage is a measure of the + amount of code being exercised by a set of tests. It is an indirect measure + of test quality and completeness. This package is compatible with any + testing methodology or framework and tracks coverage of both R code and + compiled C/C++/FORTRAN code.""" - homepage = "https://cloud.r-project.org/package=covr" - url = "https://cloud.r-project.org/src/contrib/covr_3.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/covr" + cran = "covr" version('3.5.1', sha256='a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c') version('3.5.0', sha256='cb919912018130164a40803ac573a37dde2186678c058c03c6303d79604979df') @@ -30,10 +27,10 @@ class RCovr(RPackage): version('3.0.1', sha256='66b799fd03cb83a9ab382d9cf4ff40603d1e3f3a89905a3174546b0c63e8d184') depends_on('r@3.1.0:', type=('build', 'run')) - depends_on('r-digest', when='@3.2.0:', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run'), when='@3.2.0:') depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-rex', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) depends_on('r-withr@1.0.2:', type=('build', 'run')) - depends_on('r-yaml', when='@3.3.0:', type=('build', 'run')) + depends_on('r-yaml', type=('build', 'run'), when='@3.3.0:') diff --git a/var/spack/repos/builtin/packages/r-cowplot/package.py b/var/spack/repos/builtin/packages/r-cowplot/package.py index c4af607d09..5de2356912 100644 --- a/var/spack/repos/builtin/packages/r-cowplot/package.py +++ b/var/spack/repos/builtin/packages/r-cowplot/package.py @@ -7,7 +7,7 @@ from spack import * class RCowplot(RPackage): - """Streamlined Plot Theme and Plot Annotations for 'ggplot2' + """Streamlined Plot Theme and Plot Annotations for 'ggplot2'. Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots @@ -17,9 +17,7 @@ class RCowplot(RPackage): O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.""" - homepage = "https://cloud.r-project.org/package=cowplot" - url = "https://cloud.r-project.org/src/contrib/cowplot_0.8.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/cowplot" + cran = "cowplot" version('1.1.1', sha256='c7dce625b456dffc59ba100c816e16226048d12fdd29a7335dc1f6f6e12eed48') version('1.0.0', sha256='70f9a7c46d10f409d1599f1afc9fd3c947051cf2b430f01d903c64ef1e6c98a5') @@ -29,11 +27,12 @@ class RCowplot(RPackage): version('0.9.0', sha256='d5632f78294c3678c08d3eb090abe1eec5cc9cd15cb5d96f9c43794ead098cb5') version('0.8.0', sha256='a617fde25030fe764f20967fb753a953d73b47745a2146c97c2565eb4d06700d') - depends_on('r@3.3.0:', when='@:0.9.4', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-ggplot2@2.1.1:', when='@:1.0.0', type=('build', 'run')) - depends_on('r-ggplot2@2.2.1:', when='@1.1.1:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-ggplot2@2.1.1:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.1:', type=('build', 'run'), when='@1.1.1:') depends_on('r-gtable', type=('build', 'run')) - depends_on('r-rlang', when='@1.0.0:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@1.0.0:') depends_on('r-scales', type=('build', 'run')) - depends_on('r-plyr@1.8.2:', when='@:0.9.9', type=('build', 'run')) + + depends_on('r-plyr@1.8.2:', type=('build', 'run'), when='@:0.9.9') diff --git a/var/spack/repos/builtin/packages/r-cpp11/package.py b/var/spack/repos/builtin/packages/r-cpp11/package.py index 30daa693b3..b66d6d0a01 100644 --- a/var/spack/repos/builtin/packages/r-cpp11/package.py +++ b/var/spack/repos/builtin/packages/r-cpp11/package.py @@ -7,14 +7,13 @@ from spack import * class RCpp11(RPackage): - """cpp11: A C++11 Interface for R's C Interface + """A C++11 Interface for R's C Interface. Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.""" - homepage = "https://github.com/r-lib/cpp11" cran = "cpp11" version('0.4.2', sha256='403ce0bf82358d237176053b0fb1e958cb6bfa4d0fb3555bf5801db6a6939b99') diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py index affa02b10c..060e073de7 100644 --- a/var/spack/repos/builtin/packages/r-crayon/package.py +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -7,13 +7,14 @@ from spack import * class RCrayon(RPackage): - """Colored terminal output on terminals that support 'ANSI' color and + """Colored Terminal Output. + + Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.""" - homepage = "https://github.com/r-lib/crayon#readme" cran = "crayon" version('1.4.2', sha256='ee34397f643e76e30588068d4c93bd3c9afd2193deacccacb3bffcadf141b857') diff --git a/var/spack/repos/builtin/packages/r-credentials/package.py b/var/spack/repos/builtin/packages/r-credentials/package.py index 11f16396d6..4f4b67f4e5 100644 --- a/var/spack/repos/builtin/packages/r-credentials/package.py +++ b/var/spack/repos/builtin/packages/r-credentials/package.py @@ -7,7 +7,7 @@ from spack import * class RCredentials(RPackage): - """Tools for Managing SSH and Git Credentials + """Tools for Managing SSH and Git Credentials. Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' @@ -17,10 +17,9 @@ class RCredentials(RPackage): and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.""" - homepage = "https://docs.ropensci.org/credentials" - url = "https://cloud.r-project.org/src/contrib/credentials_1.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/credentials" + cran = "credentials" + version('1.3.2', sha256='2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8') version('1.3.0', sha256='c119ec26fd97b977c3b0cd1eb8fad3c59b84df6262c3adbf5ee9f3d6c9903ff1') depends_on('r-openssl@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-crosstalk/package.py b/var/spack/repos/builtin/packages/r-crosstalk/package.py index d4a636f747..719d018f1f 100644 --- a/var/spack/repos/builtin/packages/r-crosstalk/package.py +++ b/var/spack/repos/builtin/packages/r-crosstalk/package.py @@ -7,13 +7,12 @@ from spack import * class RCrosstalk(RPackage): - """Inter-Widget Interactivity for HTML Widgets + """Inter-Widget Interactivity for HTML Widgets. Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.""" - homepage = "https://rstudio.github.io/crosstalk" cran = "crosstalk" version('1.2.0', sha256='4237baab35cd246a8a98fb9cf4ce53b6ddbc31d00742ded4edea0479613d1ea0') @@ -21,9 +20,10 @@ class RCrosstalk(RPackage): version('1.0.0', sha256='b31eada24cac26f24c9763d9a8cbe0adfd87b264cf57f8725027fe0c7742ca51') depends_on('r-htmltools@0.3.5:', type=('build', 'run')) - depends_on('r-htmltools@0.3.6:', when='@1.1.0.1:', type=('build', 'run')) + depends_on('r-htmltools@0.3.6:', type=('build', 'run'), when='@1.1.0.1:') depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) - depends_on('r-ggplot2', when='@:1.0.0', type=('build', 'run')) - depends_on('r-shiny@0.11:', when='@:1.0.0', type=('build', 'run')) + + depends_on('r-ggplot2', type=('build', 'run'), when='@:1.0.0') + depends_on('r-shiny@0.11:', type=('build', 'run'), when='@:1.0.0') diff --git a/var/spack/repos/builtin/packages/r-crul/package.py b/var/spack/repos/builtin/packages/r-crul/package.py index 0a916d4a12..fa8b4dc2a7 100644 --- a/var/spack/repos/builtin/packages/r-crul/package.py +++ b/var/spack/repos/builtin/packages/r-crul/package.py @@ -7,7 +7,7 @@ from spack import * class RCrul(RPackage): - """HTTP Client + """HTTP Client. A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's @@ -16,10 +16,9 @@ class RCrul(RPackage): is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.haxx.se/libcurl>).""" - homepage = "https://cloud.r-project.org/package=crul" - url = "https://cloud.r-project.org/src/contrib/crul_0.7.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/crul" + cran = "crul" + version('1.2.0', sha256='be1a149b21cf219ef55adfb56a6a5eb9892a9acf0d5f5421a22e52f2a7066f8c') version('1.0.0', sha256='2ade500f6cf89b2d0ca8496b8d4df9937d6f802a35c9ad10d9fab8632cdb1027') version('0.8.4', sha256='dbd950ad3b68402e5a5955615b1abcb5c9bdc846c93aa25f96a7a58913d04c8b') version('0.7.4', sha256='c963dd666ae3fc89b661ce19fce2fa19a16fc3825e1502105cae98ceb92c6014') @@ -28,5 +27,5 @@ class RCrul(RPackage): depends_on('r-r6@2.2.0:', type=('build', 'run')) depends_on('r-urltools@1.6.0:', type=('build', 'run')) depends_on('r-httpcode@0.2.0:', type=('build', 'run')) - depends_on('r-jsonlite', when='@0.8.4:', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run'), when='@0.8.4:') depends_on('r-mime', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py index 2bf5a13fab..19747e7113 100644 --- a/var/spack/repos/builtin/packages/r-cubature/package.py +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -7,21 +7,24 @@ from spack import * class RCubature(RPackage): - """Adaptive multivariate integration over hypercubes + """Adaptive multivariate integration over hypercubes. R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector - interfaces for cubature and Cuba routines are provided""" + interfaces for cubature and Cuba routines are provided; the vector + interfaces are highly recommended as demonstrated in the package + vignette.""" - homepage = "https://cloud.r-project.org/package=cubature" - url = "https://cloud.r-project.org/src/contrib/cubature_1.1-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/cubature" + cran = "cubature" + version('2.0.4.2', sha256='605bdd9d90fb6645359cccd1b289c5afae235b46360ef5bdd2001aa307a7694e') version('2.0.4.1', sha256='383fbdf49d1cdf760ad5d88d353e69118c7c663cde126c5bdd33b6fecc50d400') version('2.0.3', sha256='79bf03ebdb64b0de1ef19d24051b9d922df9310254bee459bb47764522407a73') version('2.0.2', sha256='641165c665ff490c523bccc05c42bb6851e42676b6b366b55fc442a51a8fbe8c') version('1.1-2', sha256='0a05469bdc85d6bd8165a42a3fc5c35a06700d279e4e8b3cf4669df19edffeed') - depends_on('r-rcpp', when='@2.0.3:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run'), when='@2.0.3:') depends_on('gmake', type='build') + + parallel = False diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py index 7f73798ee1..4b6927cfbe 100644 --- a/var/spack/repos/builtin/packages/r-cubist/package.py +++ b/var/spack/repos/builtin/packages/r-cubist/package.py @@ -7,14 +7,13 @@ from spack import * class RCubist(RPackage): - """Rule- And Instance-Based Regression Modeling + """Rule- And Instance-Based Regression Modeling. - Regression modeling using rules with added instance-based corrections""" + Regression modeling using rules with added instance-based corrections.""" - homepage = "https://cloud.r-project.org/package=Cubist" - url = "https://cloud.r-project.org/src/contrib/Cubist_0.0.19.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Cubist" + cran = "Cubist" + version('0.3.0', sha256='88a76e7f858a8e978a73a97ce6a3504201d889517b39ce862cef734dcf9eb263') version('0.2.3', sha256='19845f585e073f316bb4bdf74b28a624e839561faeedd40ef5548960c5b1e1f4') version('0.2.2', sha256='cd3e152cc72ab33f720a8fb6b8b6787171e1c037cfda48f1735ab692ed6d85d4') version('0.2.1', sha256='b310c3f166f15fa3e16f8d110d39931b0bb1b0aa8d0c9ac2af5a9a45081588a3') diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index 73168ed77b..c94b24d213 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -19,7 +19,6 @@ class RCurl(RPackage): more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.""" - homepage = "https://github.com/jeroen/curl" cran = "curl" version('4.3.2', sha256='90b1facb4be8b6315bb3d272ba2dd90b88973f6ea1ab7f439550230f8500a568') diff --git a/var/spack/repos/builtin/packages/r-data-table/package.py b/var/spack/repos/builtin/packages/r-data-table/package.py index 9ed564c593..1f7ee72aa2 100644 --- a/var/spack/repos/builtin/packages/r-data-table/package.py +++ b/var/spack/repos/builtin/packages/r-data-table/package.py @@ -7,14 +7,13 @@ from spack import * class RDataTable(RPackage): - """Extension of `data.frame` + """Extension of `data.frame`. Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development.""" - homepage = "https://github.com/Rdatatable/data.table/wiki" cran = "data.table" version('1.14.2', sha256='f741b951e5937440139514aedbae78dbd6862d825066848bdb006aa02c2f3d2b') diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py index 0faade10a2..71ecf51cfe 100644 --- a/var/spack/repos/builtin/packages/r-dbi/package.py +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -9,13 +9,13 @@ from spack import * class RDbi(RPackage): """R Database Interface. - A database interface definition for communication between R and - relational database management systems. All classes in this package are - virtual and need to be extended by the various R/DBMS implementations.""" + A database interface definition for communication between R and relational + database management systems. All classes in this package are virtual and + need to be extended by the various R/DBMS implementations.""" - homepage = "https://dbi.r-dbi.org" cran = "DBI" + version('1.1.2', sha256='56ec377d471c76ac234ddfd313bd01a050c99fb6fa5f704f5333b34a5d714f58') version('1.1.1', sha256='572ab3b8a6421d0ac3e7665c4c842826f1723af98fca25d4f43edb419e771344') version('1.1.0', sha256='a96db7fa39a58f1ed34c6e78d8f5f7e4cf0882afb301323b5c6975d6729203e4') version('1.0.0', sha256='ff16f118eb3f759183441835e932b87358dd80ab9800ce576a8f3df1b6f01cf5') diff --git a/var/spack/repos/builtin/packages/r-dbplyr/package.py b/var/spack/repos/builtin/packages/r-dbplyr/package.py index 08e13b2da4..7728f420ae 100644 --- a/var/spack/repos/builtin/packages/r-dbplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dbplyr/package.py @@ -7,14 +7,13 @@ from spack import * class RDbplyr(RPackage): - """A 'dplyr' Back End for Databases + """A 'dplyr' Back End for Databases. A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.""" - homepage = "https://github.com/tidyverse/dbplyr" cran = "dbplyr" version('2.1.1', sha256='aba4cf47b85ab240fd3ec4cd8d512f6e1958201e151577c1a2ebc3d6ebc5bc08') @@ -28,20 +27,20 @@ class RDbplyr(RPackage): depends_on('r@3.1:', type=('build', 'run')) depends_on('r-assertthat@0.2.0:', type=('build', 'run')) - depends_on('r-blob@1.2.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-blob@1.2.0:', type=('build', 'run'), when='@2.0.0:') depends_on('r-dbi@1.0.0:', type=('build', 'run')) depends_on('r-dplyr@0.8.0:', type=('build', 'run')) - depends_on('r-dplyr@1.0.3:', when='@2.1.0', type=('build', 'run')) - depends_on('r-dplyr@1.0.4:', when='@2.1.1:', type=('build', 'run')) - depends_on('r-ellipsis', when='@2.1:', type=('build', 'run')) + depends_on('r-dplyr@1.0.3:', type=('build', 'run'), when='@2.1.0') + depends_on('r-dplyr@1.0.4:', type=('build', 'run'), when='@2.1.1:') + depends_on('r-ellipsis', type=('build', 'run'), when='@2.1:') depends_on('r-glue@1.2.0:', type=('build', 'run')) - depends_on('r-lifecycle', when='@2.0.0:', type=('build', 'run')) - depends_on('r-lifecycle@1.0.0:', when='@2.1.1:', type=('build', 'run')) - depends_on('r-magrittr', when='@2.0.0:', type=('build', 'run')) + depends_on('r-lifecycle', type=('build', 'run'), when='@2.0.0:') + depends_on('r-lifecycle@1.0.0:', type=('build', 'run'), when='@2.1.1:') + depends_on('r-magrittr', type=('build', 'run'), when='@2.0.0:') depends_on('r-purrr@0.2.5:', type=('build', 'run')) depends_on('r-r6@2.2.2:', type=('build', 'run')) depends_on('r-rlang@0.2.0:', type=('build', 'run')) depends_on('r-tibble@1.4.2:', type=('build', 'run')) depends_on('r-tidyselect@0.2.4:', type=('build', 'run')) - depends_on('r-vctrs', when='@2.1:', type=('build', 'run')) - depends_on('r-withr', when='@2.0.0:', type=('build', 'run')) + depends_on('r-vctrs', type=('build', 'run'), when='@2.1:') + depends_on('r-withr', type=('build', 'run'), when='@2.0.0:') diff --git a/var/spack/repos/builtin/packages/r-debugme/package.py b/var/spack/repos/builtin/packages/r-debugme/package.py index 14728bfef7..28dbdb67b4 100644 --- a/var/spack/repos/builtin/packages/r-debugme/package.py +++ b/var/spack/repos/builtin/packages/r-debugme/package.py @@ -7,12 +7,12 @@ from spack import * class RDebugme(RPackage): - """Specify debug messages as special string constants, and control - debugging of packages via environment variables.""" + """Debug R Packages. - homepage = "https://github.com/r-lib/debugme#readme" - url = "https://cloud.r-project.org/src/contrib/debugme_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/debugme" + Specify debug messages as special string constants, and control debugging + of packages via environment variables.""" + + cran = "debugme" version('1.1.0', sha256='4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1') diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py index fd4a044a13..7fe64faaee 100644 --- a/var/spack/repos/builtin/packages/r-deldir/package.py +++ b/var/spack/repos/builtin/packages/r-deldir/package.py @@ -7,22 +7,21 @@ from spack import * class RDeldir(RPackage): - """Delaunay Triangulation and Dirichlet (Voronoi) Tessellation + """Delaunay Triangulation and Dirichlet (Voronoi) Tessellation. Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. - Plots triangulations and tessellations in various ways. Clips - tessellations to sub-windows. Calculates perimeters of tessellations. - Summarises information about the tiles of the tessellation.""" + Plots triangulations and tessellations in various ways. Clips tessellations + to sub-windows. Calculates perimeters of tessellations. Summarises + information about the tiles of the tessellation.""" - homepage = "https://cloud.r-project.org/package=deldir" - url = "https://cloud.r-project.org/src/contrib/deldir_0.1-14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/deldir" + cran = "deldir" + version('1.0-6', sha256='6df6d8325c607e0b7d63cbc53c29e774eff95ad4acf9c7ec8f70693b0505f8c5') version('0.2-3', sha256='2d24800f5ec6ad9dc57b9b265365b29c07717f4562d8f3e6344336d3340c364e') version('0.1-23', sha256='e0112bce9fc94daf73596a0fff9b3958b80872e3bbb487be73e157b13a6f201d') version('0.1-21', sha256='b9dabcc1813c7a0f8edaf720a94bdd611a83baf3d3e52e861d352369e815690c') version('0.1-14', sha256='89d365a980ef8589971e5d311c6bd59fe32c48dbac8000a880b9655032c99289') depends_on('r@0.99:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.2-3:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.2-3:') diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py index 4661d3653e..1210c24e0a 100644 --- a/var/spack/repos/builtin/packages/r-dendextend/package.py +++ b/var/spack/repos/builtin/packages/r-dendextend/package.py @@ -7,7 +7,7 @@ from spack import * class RDendextend(RPackage): - """Extending 'Dendrogram' Functionality in R + """Extending 'Dendrogram' Functionality in R. Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) @@ -15,10 +15,9 @@ class RDendextend(RPackage): branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.""" - homepage = "https://cloud.r-project.org/package=dendextend" - url = "https://cloud.r-project.org/src/contrib/dendextend_1.5.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dendextend" + cran = "dendextend" + version('1.15.2', sha256='4ba3885b66694589d455ffef31c218fe653fa25aff3efb7e8db6c25008d2921b') version('1.14.0', sha256='3789461bc474e146b077ad26566b1fa05be32fc7e57ab1fb5e78bdabcc797858') version('1.12.0', sha256='b487fed8c1878a23b9e28394ee11f16a1831b76c90793eb486e6963c7162fa55') version('1.10.0', sha256='88f0fb3362d69144daf4f35d0ea09f32c2df1adf614e040327a42552a8fd3224') @@ -28,5 +27,6 @@ class RDendextend(RPackage): depends_on('r-magrittr@1.0.1:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-viridis', type=('build', 'run')) - depends_on('r-fpc', when='@:1.10.0', type=('build', 'run')) - depends_on('r-whisker', when='@:1.5.2', type=('build', 'run')) + + depends_on('r-fpc', type=('build', 'run'), when='@:1.10.0') + depends_on('r-whisker', type=('build', 'run'), when='@:1.5.2') diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py index 818d9f3c6b..c5bbabaf2d 100644 --- a/var/spack/repos/builtin/packages/r-deoptim/package.py +++ b/var/spack/repos/builtin/packages/r-deoptim/package.py @@ -8,15 +8,14 @@ from spack import * class RDeoptim(RPackage): - """Global Optimization by Differential Evolution + """Global Optimization by Differential Evolution. - Implements the differential evolution algorithm for global optimization - of a real-valued function of a real-valued parameter vector.""" + Implements the differential evolution algorithm for global optimization of + a real-valued function of a real-valued parameter vector.""" - homepage = "https://cloud.r-project.org/package=DEoptim" - url = "https://cloud.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptim" + cran = "DEoptim" + version('2.2-6', sha256='8c63397d83a067212d003ef3e639fd81f5f00bf61e3c271b4e4999031a69e2e1') version('2.2-5', sha256='ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a') version('2.2-4', sha256='0a547784090d1e9b93efc53768110621f35bed3692864f6ce5c0dda2ebd6d482') version('2.2-3', sha256='af2120feea3a736ee7a5a93c6767d464abc0d45ce75568074b233405e73c9a5d') diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py index 5e8df0c7ae..13e24dc92a 100644 --- a/var/spack/repos/builtin/packages/r-deoptimr/package.py +++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py @@ -7,12 +7,17 @@ from spack import * class RDeoptimr(RPackage): - """An implementation of a bespoke jDE variant of the Differential - Evolution stochastic algorithm for global optimization of - nonlinear programming problems.""" + """Differential Evolution Optimization in Pure R. - homepage = "https://cloud.r-project.org/package=DEoptimR" - url = "https://cloud.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptimR" + Differential Evolution (DE) stochastic algorithms for global optimization + of problems with and without constraints. The aim is to curate a collection + of its state-of-the-art variants that (1) do not sacrifice simplicity of + design, (2) are essentially tuning-free, and (3) can be efficiently + implemented directly in the R language. Currently, it only provides an + implementation of the 'jDE' algorithm by Brest et al. (2006) + <doi:10.1109/TEVC.2006.872133>.""" + cran = "DEoptimR" + + version('1.0-10', sha256='774f7ba0ac9c73aaab4567024b98afdb58098905726e72bceeeb9e380e782ad5') version('1.0-8', sha256='846911c1b2561a9fae73a8c60a21a5680963ebb0050af3c1f1147ae9a121e5ef') diff --git a/var/spack/repos/builtin/packages/r-deriv/package.py b/var/spack/repos/builtin/packages/r-deriv/package.py index 025404dff5..7af74312a1 100644 --- a/var/spack/repos/builtin/packages/r-deriv/package.py +++ b/var/spack/repos/builtin/packages/r-deriv/package.py @@ -7,15 +7,13 @@ from spack import * class RDeriv(RPackage): - """Deriv: Symbolic Differentiation + """Symbolic Differentiation. R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.""" - homepage = "https://cloud.r-project.org/package=Deriv" - url = "https://cloud.r-project.org/src/contrib/Deriv_4.1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Deriv" + cran = "Deriv" version('4.1.3', sha256='dbdbf5ed8babf706373ae33a937d013c46110a490aa821bcd158a70f761d0f8c') version('4.1.2', sha256='c4b0c3f351f6df53778d48033460cf8674e7a7878fbc542085d66a9a78803ac9') diff --git a/var/spack/repos/builtin/packages/r-desc/package.py b/var/spack/repos/builtin/packages/r-desc/package.py index 70a5ec2e87..23291f795c 100644 --- a/var/spack/repos/builtin/packages/r-desc/package.py +++ b/var/spack/repos/builtin/packages/r-desc/package.py @@ -12,7 +12,6 @@ class RDesc(RPackage): Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.""" - homepage = "https://github.com/r-lib/desc" cran = "desc" version('1.4.0', sha256='8220e4c706449b8121b822e70b1414f391ef419aed574836a234c63b83e5d649') @@ -22,4 +21,5 @@ class RDesc(RPackage): depends_on('r-r6', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) depends_on('r-rprojroot', type=('build', 'run')) - depends_on('r-assertthat', when='@:1.2', type=('build', 'run')) + + depends_on('r-assertthat', type=('build', 'run'), when='@:1.2') diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py index 663c280fb1..841bf43709 100644 --- a/var/spack/repos/builtin/packages/r-desolve/package.py +++ b/var/spack/repos/builtin/packages/r-desolve/package.py @@ -8,7 +8,7 @@ from spack import * class RDesolve(RPackage): """Solvers for Initial Value Problems of Differential Equations ('ODE', - 'DAE', 'DDE') + 'DAE', 'DDE'). Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations @@ -21,14 +21,13 @@ class RDesolve(RPackage): 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.""" - homepage = "https://cloud.r-project.org/package=deSolve" - url = "https://cloud.r-project.org/src/contrib/deSolve_1.20.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/deSolve" + cran = "deSolve" + version('1.30', sha256='39f65d7af6b4d85eb023cce2a200c2de470644b22d45e210c5b7d558c3abf548') version('1.28', sha256='4c55ef4cae841df91034382d277b483985af120240f87af587ff82177fdb5a49') version('1.24', sha256='3aa52c822abb0348a904d5bbe738fcea2b2ba858caab9f2831125d07f0d57b42') version('1.21', sha256='45c372d458fe4c7c11943d4c409517849b1be6782dc05bd9a74b066e67250c63') version('1.20', sha256='56e945835b0c66d36ebc4ec8b55197b616e387d990788a2e52e924ce551ddda2') depends_on('r@2.15.0:', type=('build', 'run')) - depends_on('r@3.3.0:', when='@1.28:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@1.28:') diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 62b43a2114..70843d32d0 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -7,14 +7,13 @@ from spack import * class RDevtools(RPackage): - """Tools to Make Developing R Packages Easier + """Tools to Make Developing R Packages Easier. Collection of package development tools.""" - homepage = "https://github.com/hadley/devtools" - url = "https://cloud.r-project.org/src/contrib/devtools_1.12.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/devtools" + cran = "devtools" + version('2.4.3', sha256='e42159a9bca0b219170e76c282862e27ca283649d6cbf6a868175d8982e06b4f') version('2.3.2', sha256='e5086106baef6bb925445dfdddb3cd5ff4f8fff96353365b135aba5618d1986d') version('2.3.0', sha256='4fc375c171335c67bd71df4e0b1b3dff2ae3aa17b3e0566b790ba0808b39dcd0') version('2.1.0', sha256='c1f75346a90adf0669b5508fe68cc78bd3b114c1303fa7d22bf90991edd9230d') @@ -23,57 +22,73 @@ class RDevtools(RPackage): version('1.11.1', sha256='51c876f9ddbfdf611f6ea0b06c0b46da8cefcb8cc98d60e06d576b61f0a06346') depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r-usethis@1.5.0:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-usethis@1.6.0:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-usethis@1.6.3:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-callr', when='@2.0.0:', type=('build', 'run')) - depends_on('r-callr@3.4.3:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-callr@3.4.4:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-cli', when='@2.0.0:', type=('build', 'run')) - depends_on('r-cli@2.0.2:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-covr@3.5.0:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-covr@3.5.1:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-desc@1.2.0:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-dt@0.13:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-dt@0.15:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-ellipsis@0.3.0:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-ellipsis@0.3.1:', when='@2.3.2:', type=('build', 'run')) + depends_on('r-usethis@1.5.0:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-usethis@1.6.0:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-usethis@1.6.3:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-usethis@2.0.1:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-callr', type=('build', 'run'), when='@2.0.0:') + depends_on('r-callr@3.4.3:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-callr@3.4.4:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-callr@3.4.4:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-callr@3.6.0:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-cli', type=('build', 'run'), when='@2.0.0:') + depends_on('r-cli@2.0.2:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-cli@3.0.0:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-covr@3.5.0:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-covr@3.5.1:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-desc@1.2.0:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-desc@1.3.0:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-ellipsis@0.3.0:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-ellipsis@0.3.1:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-fs@1.5.0:', type=('build', 'run'), when='@2.4.3:') depends_on('r-httr@0.4:', type=('build', 'run')) - depends_on('r-httr@1.4.1:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-httr@1.4.2:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-jsonlite@1.6.1:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-jsonlite@1.7.1:', when='@2.3.2:', type=('build', 'run')) + depends_on('r-httr@1.4.1:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-httr@1.4.2:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-lifecycle@1.0.0:', type=('build', 'run'), when='@2.4.3:') depends_on('r-memoise@1.0.0:', type=('build', 'run')) - depends_on('r-memoise@1.1.0:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-pkgbuild@1.0.3:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-pkgbuild@1.0.6:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-pkgbuild@1.1.0:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-pkgload@1.0.2:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-pkgload@1.1.0:', when='@2.0.2:', type=('build', 'run')) - depends_on('r-rcmdcheck@1.3.3:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-remotes@2.1.0:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-remotes@2.1.1:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-remotes@2.2.0:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-rlang@0.4.5:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.7:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-roxygen2@6.1.1:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-roxygen2@7.1.0:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-roxygen2@7.1.1:', when='@2.3.2:', type=('build', 'run')) + depends_on('r-memoise@1.1.0:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-memoise@2.0.0:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-pkgbuild@1.0.3:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-pkgbuild@1.0.6:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-pkgbuild@1.1.0:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-pkgbuild@1.2.0:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-pkgload@1.0.2:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-pkgload@1.1.0:', type=('build', 'run'), when='@2.0.2:') + depends_on('r-pkgload@1.2.1:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-rcmdcheck@1.3.3:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-remotes@2.1.0:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-remotes@2.1.1:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-remotes@2.2.0:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-remotes@2.3.0:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-rlang@0.4.5:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-rlang@0.4.7:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-roxygen2@6.1.1:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-roxygen2@7.1.0:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-roxygen2@7.1.1:', type=('build', 'run'), when='@2.3.2:') depends_on('r-rstudioapi@0.7.0:', type=('build', 'run')) - depends_on('r-rstudioapi@0.11:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-rversions@2.0.1:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-rversions@2.0.2:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-sessioninfo@1.1.1:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-testthat@2.1.1:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-testthat@2.3.2:', when='@2.3.0:', type=('build', 'run')) + depends_on('r-rstudioapi@0.11:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-rstudioapi@0.13:', type=('build', 'run'), when='@2.4.3:') + depends_on('r-rversions@2.0.1:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-rversions@2.0.2:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-sessioninfo@1.1.1:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-testthat@2.1.1:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-testthat@2.3.2:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-testthat@3.0.2:', type=('build', 'run'), when='@2.4.3:') depends_on('r-withr', type=('build', 'run')) - depends_on('r-withr@2.1.2:', when='@2.3.0:', type=('build', 'run')) - depends_on('r-withr@2.2.0:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-crayon@1.3.4:', when='@2.3.0', type=('build', 'run')) - depends_on('r-digest', when='@:2.3.0', type=('build', 'run')) - depends_on('r-digest@0.6.25:', when='@2.3.0', type=('build', 'run')) - depends_on('r-glue@1.4.0:', when='@2.3.0', type=('build', 'run')) - depends_on('r-git2r@0.23.0:', when='@:2.3.0', type=('build', 'run')) - depends_on('r-git2r@0.26.1:', when='@2.3.0', type=('build', 'run')) - depends_on('r-whisker', when='@:1.9.9', type=('build', 'run')) + depends_on('r-withr@2.1.2:', type=('build', 'run'), when='@2.3.0:') + depends_on('r-withr@2.2.0:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-withr@2.4.1:', type=('build', 'run'), when='@2.4.3:') + + depends_on('r-crayon@1.3.4:', type=('build', 'run'), when='@2.3.0') + depends_on('r-digest', type=('build', 'run'), when='@:2.3.0') + depends_on('r-digest@0.6.25:', type=('build', 'run'), when='@2.3.0') + depends_on('r-glue@1.4.0:', type=('build', 'run'), when='@2.3.0') + depends_on('r-git2r@0.23.0:', type=('build', 'run'), when='@:2.3.0') + depends_on('r-git2r@0.26.1:', type=('build', 'run'), when='@2.3.0') + depends_on('r-whisker', type=('build', 'run'), when='@:1.12.0') + depends_on('r-dt@0.13:', type=('build', 'run'), when='@:2.3.0') + depends_on('r-dt@0.15:', type=('build', 'run'), when='@2.3.2') + depends_on('r-jsonlite', type=('build', 'run'), when='@:2.3.2') + depends_on('r-jsonlite@1.6.1:', type=('build', 'run'), when='@2.3.0') + depends_on('r-jsonlite@1.7.1:', type=('build', 'run'), when='@2.3.2') diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py index 0bd68e8eae..564921f466 100644 --- a/var/spack/repos/builtin/packages/r-diagrammer/package.py +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -7,7 +7,7 @@ from spack import * class RDiagrammer(RPackage): - """Graph/Network Visualization + """Graph/Network Visualization. Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk @@ -16,44 +16,61 @@ class RDiagrammer(RPackage): graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.""" - homepage = "https://github.com/rich-iannone/DiagrammeR" - url = "https://cloud.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/DiagrammeR" + cran = "DiagrammeR" + version('1.0.8', sha256='b9157b26215edda4fe0a1b9330a597d5b01a5d7e660a9832f593b87c584dd233') + version('1.0.7', sha256='6af291a7136657b9f7c67b96cd7f3afe99662cf5a477ebbb213a6c53df623050') version('1.0.6.1', sha256='be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d') version('1.0.1', sha256='ccee8acf608fc909e73c6de4374cef5a570cb62e5f454ac55dda736f22f3f013') version('1.0.0', sha256='2b186dae1b19018681b979e9444bf16559c42740d8382676fbaf3b0f8a44337e') version('0.8.4', sha256='0503935fa120c7c7cdcfd4dce85558b23fd0bcb7e6b32fa6989087d3c88ec404') - depends_on('r@3.2.0:', when='@0.9.2:', type=('build', 'run')) - depends_on('r-dplyr@0.7.4:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-dplyr@0.7.6:', when='@1.0.6.1:', type=('build', 'run')) - depends_on('r-downloader@0.4:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-glue@1.2.0:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-glue@1.3.0:', when='@1.0.6.1:', type=('build', 'run')) - depends_on('r-htmltools@0.3.6:', when='@1.0.0:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@0.9.2:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.0.7') + depends_on('r-dplyr@0.7.4:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-dplyr@0.7.6:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-dplyr@1.0.7:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-downloader@0.4:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-glue@1.2.0:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-glue@1.3.0:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-glue@1.5.0:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-htmltools@0.3.6:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-htmltools@0.5.2:', type=('build', 'run'), when='@1.0.7:') depends_on('r-htmlwidgets@1.0:', type=('build', 'run')) - depends_on('r-htmlwidgets@1.2:', when='@1.0.6.1:', type=('build', 'run')) + depends_on('r-htmlwidgets@1.2:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-htmlwidgets@1.5:', type=('build', 'run'), when='@1.0.7:') depends_on('r-igraph@1.1.2:', type=('build', 'run')) - depends_on('r-igraph@1.2.2:', when='@1.0.6.1:', type=('build', 'run')) + depends_on('r-igraph@1.2.2:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-igraph@1.2.11:', type=('build', 'run'), when='@1.0.7:') depends_on('r-influencer@0.1.0:', type=('build', 'run')) - depends_on('r-magrittr@1.5:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-purrr@0.2.4:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-purrr@0.2.5:', when='@1.0.6.1:', type=('build', 'run')) - depends_on('r-rcolorbrewer@1.1-2:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-readr@1.1.1:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-rlang@0.2.0:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-rlang@0.2.2:', when='@1.0.6.1:', type=('build', 'run')) + depends_on('r-influencer@0.1.0.1:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-magrittr@1.5:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-purrr@0.2.4:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-purrr@0.2.5:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-purrr@0.3.4:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-rcolorbrewer@1.1-2:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-readr@1.1.1:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-readr@2.1.1:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-rlang@0.2.0:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-rlang@0.2.2:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-rlang@0.4:', type=('build', 'run'), when='@1.0.7:') depends_on('r-rstudioapi@0.7:', type=('build', 'run')) depends_on('r-scales@0.5.0:', type=('build', 'run')) - depends_on('r-scales@1.0.0:', when='@1.0.6.1:', type=('build', 'run')) + depends_on('r-scales@1.0.0:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-scales@1.1:', type=('build', 'run'), when='@1.0.7:') depends_on('r-stringr@1.3.0:', type=('build', 'run')) - depends_on('r-stringr@1.3.1:', when='@1.0.6.1:', type=('build', 'run')) - depends_on('r-tibble@1.4.2:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-tidyr@0.8.0:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-tidyr@0.8.1:', when='@1.0.6.1:', type=('build', 'run')) - depends_on('r-viridis@0.5.0:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-viridis@0.5.1:', when='@1.0.6.1:', type=('build', 'run')) + depends_on('r-stringr@1.3.1:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-stringr@1.4:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-tibble@1.4.2:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-tibble@3.1:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-tidyr@0.8.0:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-tidyr@0.8.1:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-tidyr@1.1:', type=('build', 'run'), when='@1.0.7:') + depends_on('r-viridis@0.5.0:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-viridis@0.5.1:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-viridis@0.6.2:', type=('build', 'run'), when='@1.0.7:') depends_on('r-visnetwork@2.0.3:', type=('build', 'run')) - depends_on('r-visnetwork@2.0.4:', when='@1.0.6.1:', type=('build', 'run')) - depends_on('r-rgexf@0.15.3:', when='@1.0.0:1.0.1', type=('build', 'run')) + depends_on('r-visnetwork@2.0.4:', type=('build', 'run'), when='@1.0.6.1:') + depends_on('r-visnetwork@2.1.0:', type=('build', 'run'), when='@1.0.7:') + + depends_on('r-rgexf@0.15.3:', type=('build', 'run'), when='@1.0.0:1.0.1') diff --git a/var/spack/repos/builtin/packages/r-dicekriging/package.py b/var/spack/repos/builtin/packages/r-dicekriging/package.py index 1f2b2599ed..7ebf99fe7a 100644 --- a/var/spack/repos/builtin/packages/r-dicekriging/package.py +++ b/var/spack/repos/builtin/packages/r-dicekriging/package.py @@ -7,15 +7,14 @@ from spack import * class RDicekriging(RPackage): - """Kriging Methods for Computer Experiments + """Kriging Methods for Computer Experiments. Estimation, validation and prediction of kriging models. Important - functions : km, print.km, plot.km, predict.km.""" + functions: km, print.km, plot.km, predict.km.""" - homepage = "http://dice.emse.fr/" - url = "https://cloud.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/DiceKriging" + cran = "DiceKriging" + version('1.6.0', sha256='ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49') version('1.5.8', sha256='11d02b894cb509dbb8887ae27b6d08ba25aa52ac3ece134c3759c2b3b1bf4d77') version('1.5.6', sha256='25466d2db9f17083d1c7b9545e5ec88f630be934f9373c2f7b36c38de4e64e92') version('1.5.5', sha256='55fe161f867a0c3772023c3047041b877aa54d29cb474ec87293ec31cc5cb30c') diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py index d9258dc011..2163758ae5 100644 --- a/var/spack/repos/builtin/packages/r-dichromat/package.py +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -7,12 +7,12 @@ from spack import * class RDichromat(RPackage): - """Collapse red-green or green-blue distinctions to simulate the effects of + """Color Schemes for Dichromats. + + Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.""" - homepage = "https://cloud.r-project.org/package=dichromat" - url = "https://cloud.r-project.org/src/contrib/dichromat_2.0-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dichromat" + cran = "dichromat" version('2.0-0', sha256='31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1') diff --git a/var/spack/repos/builtin/packages/r-diffobj/package.py b/var/spack/repos/builtin/packages/r-diffobj/package.py index 5167b76fe8..81e5f746dd 100644 --- a/var/spack/repos/builtin/packages/r-diffobj/package.py +++ b/var/spack/repos/builtin/packages/r-diffobj/package.py @@ -7,12 +7,11 @@ from spack import * class RDiffobj(RPackage): - """Diffs for R Objects + """Diffs for R Objects. Generate a colorized diff of two R objects for an intuitive visualization of their differences.""" - homepage = "https://github.com/brodieG/diffobj" cran = "diffobj" version('0.3.5', sha256='d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60') diff --git a/var/spack/repos/builtin/packages/r-diffusionmap/package.py b/var/spack/repos/builtin/packages/r-diffusionmap/package.py index 6f3395b7a6..20cf3ccd5b 100644 --- a/var/spack/repos/builtin/packages/r-diffusionmap/package.py +++ b/var/spack/repos/builtin/packages/r-diffusionmap/package.py @@ -7,16 +7,14 @@ from spack import * class RDiffusionmap(RPackage): - """Diffusion Map + """Diffusion Map. Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model. Richards (2009) <doi:10.1088/0004-637X/691/1/32>.""" - homepage = "https://cloud.r-project.org/package=diffusionMap" - url = "https://cloud.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/diffusionMap" + cran = "diffusionMap" version('1.2.0', sha256='523847592fbc3a29252bc92b5821e17564ce6b188c483c930e95e6950c3873e7') version('1.1-0.1', sha256='b24cf841af2566ac36f4ede2885f2ff355a7905398444d6d89747315d99a8486') @@ -26,7 +24,7 @@ class RDiffusionmap(RPackage): version('0.0-1', sha256='38c4af2d2a4fa4116c2e01a5e67ba313e7a8e76f724a3312a3c12b26e299f844') depends_on('r@2.4.0:', type=('build', 'run')) - depends_on('r@2.10:', when='@1.2.0:', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run'), when='@1.2.0:') depends_on('r-scatterplot3d', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py index 9a6e189e6a..d9bbadf287 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -7,10 +7,10 @@ from spack import * class RDigest(RPackage): - """Create Compact Hash Digests of R Objects + """Create Compact Hash Digests of R Objects. - Implementation of a function 'digest()' for the creation of hash digests - of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and + Implementation of a function 'digest()' for the creation of hash digests of + arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 @@ -26,9 +26,9 @@ class RDigest(RPackage): comprehensive (and widely tested) libraries such as OpenSSL should be used.""" - homepage = "https://dirk.eddelbuettel.com/code/digest.html" cran = "digest" + version('0.6.29', sha256='792c1f14a4c8047745152f5e45ce7351978af8d770c29d2ea39c7acd5d619cd9') version('0.6.28', sha256='4a328c75e95f8522fc07390d1dd00c19fb643f558e761a8aed04f99c1dc7db00') version('0.6.27', sha256='f485f75122907da24c41d4a62c91a232f0c371befd2f77e973342a1bef00253f') version('0.6.25', sha256='15ccadb7b8bccaa221b6700bb549011719d0f4b38dbd3a1f29face3e019e2de5') @@ -39,5 +39,5 @@ class RDigest(RPackage): version('0.6.9', sha256='95fdc36011869fcfe21b40c3b822b931bc01f8a531e2c9260582ba79560dbe47') depends_on('r@2.4.1:', type=('build', 'run')) - depends_on('r@3.1.0:', when='@0.6.16:', type=('build', 'run')) - depends_on('r@3.3.0:', when='@0.6.27:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@0.6.16:') + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.6.27:') diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py index 5e98047876..7c467d8d73 100644 --- a/var/spack/repos/builtin/packages/r-diptest/package.py +++ b/var/spack/repos/builtin/packages/r-diptest/package.py @@ -7,10 +7,13 @@ from spack import * class RDiptest(RPackage): - """diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected""" + """Hartigan's Dip Test Statistic for Unimodality - Corrected. - homepage = "https://cloud.r-project.org/package=diptest" - url = "https://cloud.r-project.org/src/contrib/diptest_0.75-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/diptest" + Compute Hartigan's dip test statistic for unimodality /; multimodality and + provide a test with simulation based p-values, where; the original public + code has been corrected.""" + cran = "diptest" + + version('0.76-0', sha256='508a5ebb161519cd0fcd156dc047b51becb216d545d62c6522496463f94ec280') version('0.75-7', sha256='462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b') diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py index 482336a087..d1c3ef1c01 100644 --- a/var/spack/repos/builtin/packages/r-dismo/package.py +++ b/var/spack/repos/builtin/packages/r-dismo/package.py @@ -7,20 +7,22 @@ from spack import * class RDismo(RPackage): - """Species Distribution Modeling + """Species Distribution Modeling. Methods for species distribution modeling, that is, predicting the environmental similarity of any site to that of the locations of known occurrences of a species.""" - homepage = "https://cloud.r-project.org/package=dismo" - url = "https://cloud.r-project.org/src/contrib/dismo_1.1-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dismo" + cran = "dismo" + version('1.3-5', sha256='812e1932d42c0f40acf2ab5c5b2d068f93128caf648626e1d11baf1a09340ee7') version('1.3-3', sha256='fd65331ac18a4287ba0856b90508ddd0e2738c653eecc5f3eb2b14e1d06949ca') version('1.1-4', sha256='f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8') depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@1.3-5:') depends_on('r-raster@2.5-2:', type=('build', 'run')) + depends_on('r-raster@3.5-2:', type=('build', 'run'), when='@1.3-5:') depends_on('r-sp@1.2-0:', type=('build', 'run')) + depends_on('r-sp@1.4-5:', type=('build', 'run'), when='@1.3-5:') depends_on('java@8:', when='@1.3-3:') diff --git a/var/spack/repos/builtin/packages/r-distributional/package.py b/var/spack/repos/builtin/packages/r-distributional/package.py index 0211baea05..5ea286b4c5 100644 --- a/var/spack/repos/builtin/packages/r-distributional/package.py +++ b/var/spack/repos/builtin/packages/r-distributional/package.py @@ -12,13 +12,12 @@ class RDistributional(RPackage): Vectorised distribution objects with tools for manipulating, visualising, and using probability distributions. Designed to allow model prediction outputs to return distributions rather than their parameters, allowing - users to directly interact with predictive distributions in a - data-oriented workflow. In addition to providing generic replacements for - p/d/q/r functions, other useful statistics can be computed including - means, variances, intervals, and highest density regions.""" + users to directly interact with predictive distributions in a data-oriented + workflow. In addition to providing generic replacements for p/d/q/r + functions, other useful statistics can be computed including means, + variances, intervals, and highest density regions.""" - homepage = "https://github.com/mitchelloharawild/distributional" - cran = "distributional" + cran = "distributional" version('0.3.0', sha256='fab36c7346617d8f2ca4b3cd0e3c9da93cb2f95fb7f102a3ae88670e694751d6') version('0.2.2', sha256='028e5a91aabe3a676eb7b7f3dc907f7f34735a123fe0d9adcabc03476504435f') diff --git a/var/spack/repos/builtin/packages/r-diversitree/package.py b/var/spack/repos/builtin/packages/r-diversitree/package.py index 00f384565d..d652343aa9 100644 --- a/var/spack/repos/builtin/packages/r-diversitree/package.py +++ b/var/spack/repos/builtin/packages/r-diversitree/package.py @@ -8,20 +8,18 @@ from spack import * class RDiversitree(RPackage): - """Comparative 'Phylogenetic' Analyses of Diversification + """Comparative 'Phylogenetic' Analyses of Diversification. - Mostly focusing on analysing diversification and character - evolution. Contains implementations of 'BiSSE' (Binary State - 'Speciation' and Extinction) and its unresolved tree extensions, - 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', - 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov - models of discrete and continuous trait evolution and constant - rate 'speciation' and extinction.""" + Mostly focusing on analysing diversification and character evolution. + Contains implementations of 'BiSSE' (Binary State 'Speciation' and + Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State + 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other + included methods include Markov models of discrete and continuous trait + evolution and constant rate 'speciation' and extinction.""" - homepage = "https://www.zoology.ubc.ca/prog/diversitree" - url = "https://cloud.r-project.org/src/contrib/diversitree_0.9-10.tar.gz" - list_url = "https://cron.r-project.org/src/contrib/Archive/diversitree" + cran = "diversitree" + version('0.9-16', sha256='4c236970b58e56b922352f3f5d97010c74d8ec5783b375c311fe11abfb99f967') version('0.9-15', sha256='c739ef3d4fcc24fd6855b1d297d31e0f89fbaff1efe8a2d149044458ecd363ea') version('0.9-11', sha256='4caa6a468f93de9f1c8c30e4457f34bb8346e1acdaf74f684005bfa86a950ecb') version('0.9-10', sha256='e7df5910c8508a5c2c2d6d3deea53dd3f947bb762196901094c32a7033cb043e') diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py index e392560896..c769940bcd 100644 --- a/var/spack/repos/builtin/packages/r-domc/package.py +++ b/var/spack/repos/builtin/packages/r-domc/package.py @@ -7,14 +7,12 @@ from spack import * class RDomc(RPackage): - """Foreach Parallel Adaptor for 'parallel' + """Foreach Parallel Adaptor for 'parallel'. - Provides a parallel backend for the %dopar% function using - the multicore functionality of the parallel package.""" + Provides a parallel backend for the %dopar% function using the multicore + functionality of the parallel package.""" - homepage = "https://cloud.r-project.org/package=doMC" - url = "https://cloud.r-project.org/src/contrib/doMC_1.3.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/doMC" + cran = "doMC" version('1.3.7', sha256='defab27adc298a6746896d83251f8355d62c01012d51ef96d491875a2e74b54d') version('1.3.6', sha256='2977fc9e2dc54d85d45b4a36cd286dff72834fbc73f38b6ee45a6eb8557fc9b2') diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py index f1b735a261..0a203c5da5 100644 --- a/var/spack/repos/builtin/packages/r-doparallel/package.py +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -7,14 +7,12 @@ from spack import * class RDoparallel(RPackage): - """Foreach Parallel Adaptor for the 'parallel' Package + """Foreach Parallel Adaptor for the 'parallel' Package. Provides a parallel backend for the %dopar% function using the parallel package.""" - homepage = "https://cloud.r-project.org/package=doParallel" - url = "https://cloud.r-project.org/src/contrib/doParallel_1.0.10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/doParallel" + cran = "doParallel" version('1.0.16', sha256='f1bb26f964f30d47ae4d6cf2b0a2ca0c2122d376424875e82d9abe9e7b054eb2') version('1.0.15', sha256='71ad7ea69616468996aefdd8d02a4a234759a21ddde9ed1657e3c537145cd86e') diff --git a/var/spack/repos/builtin/packages/r-dorng/package.py b/var/spack/repos/builtin/packages/r-dorng/package.py index 1e337c9f14..0ebace01c8 100644 --- a/var/spack/repos/builtin/packages/r-dorng/package.py +++ b/var/spack/repos/builtin/packages/r-dorng/package.py @@ -7,7 +7,7 @@ from spack import * class RDorng(RPackage): - """Generic Reproducible Parallel Backend for 'foreach' Loops + """Generic Reproducible Parallel Backend for 'foreach' Loops. Provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined @@ -17,9 +17,7 @@ class RDorng(RPackage): workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.""" - homepage = "https://cloud.r-project.org/package=doRNG" - url = "https://cloud.r-project.org/src/contrib/doRNG_1.6.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/doRNG" + cran = "doRNG" version('1.8.2', sha256='33e9d45b91b0fde2e35e911b9758d0c376049121a98a1e4c73a1edfcff11cec9') version('1.7.1', sha256='27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9') @@ -28,6 +26,7 @@ class RDorng(RPackage): depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) depends_on('r-rngtools@1.3:', type=('build', 'run')) - depends_on('r-rngtools@1.5:', when='@1.8.2:', type=('build', 'run')) + depends_on('r-rngtools@1.5:', type=('build', 'run'), when='@1.8.2:') depends_on('r-iterators', type=('build', 'run')) - depends_on('r-pkgmaker@0.20:', when='@:1.7.1', type=('build', 'run')) + + depends_on('r-pkgmaker@0.20:', type=('build', 'run'), when='@:1.7.1') diff --git a/var/spack/repos/builtin/packages/r-dosnow/package.py b/var/spack/repos/builtin/packages/r-dosnow/package.py index 11d3f84db3..c903dccdf6 100644 --- a/var/spack/repos/builtin/packages/r-dosnow/package.py +++ b/var/spack/repos/builtin/packages/r-dosnow/package.py @@ -7,14 +7,12 @@ from spack import * class RDosnow(RPackage): - """Foreach Parallel Adaptor for the 'snow' Package + """Foreach Parallel Adaptor for the 'snow' Package. - Provides a parallel backend for the %dopar% function using the snow - package of Tierney, Rossini, Li, and Sevcikova.""" + Provides a parallel backend for the %dopar% function using the snow package + of Tierney, Rossini, Li, and Sevcikova.""" - homepage = "https://cloud.r-project.org/package=doSNOW" - url = "https://cloud.r-project.org/src/contrib/doSNOW_1.0.18.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/doSNOW" + cran = "doSNOW" version('1.0.19', sha256='4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738') version('1.0.18', sha256='70e7bd82186e477e3d1610676d4c6a75258ac08f104ecf0dcc971550ca174766') diff --git a/var/spack/repos/builtin/packages/r-dotcall64/package.py b/var/spack/repos/builtin/packages/r-dotcall64/package.py index a0cd901d2d..72a1dc799d 100644 --- a/var/spack/repos/builtin/packages/r-dotcall64/package.py +++ b/var/spack/repos/builtin/packages/r-dotcall64/package.py @@ -7,13 +7,18 @@ from spack import * class RDotcall64(RPackage): - """dotCall64: Enhanced Foreign Function Interface Supporting Long - Vectors.""" + """Enhanced Foreign Function Interface Supporting Long + Vectors. - homepage = "https://git.math.uzh.ch/reinhard.furrer/dotCall64" - url = "https://cloud.r-project.org/src/contrib/dotCall64_1.0-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dotCall64" + Provides .C64(), which is an enhanced version of .C() and .Fortran() from + the foreign function interface. .C64() supports long vectors, arguments of + type 64-bit integer, and provides a mechanism to avoid unnecessary copies + of read-only and write-only arguments. This makes it a convenient and fast + interface to C/C++ and Fortran code.""" + cran = "dotCall64" + + version('1.0-1', sha256='f10b28fcffb9453b1d8888a72c8fd2112038b5ac33e02a481492c7bd249aa5c6') version('1.0-0', sha256='69318dc6b8aecc54d4f789c8105e672198363b395f1a764ebaeb54c0473d17ad') depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-downloader/package.py b/var/spack/repos/builtin/packages/r-downloader/package.py index 5549b00bc4..8fc18c6715 100644 --- a/var/spack/repos/builtin/packages/r-downloader/package.py +++ b/var/spack/repos/builtin/packages/r-downloader/package.py @@ -7,16 +7,16 @@ from spack import * class RDownloader(RPackage): - """Provides a wrapper for the download.file function, making it possible to - download files over HTTPS on Windows, Mac OS X, and other Unix-like - platforms. The 'RCurl' package provides this functionality - (and much more) but can be difficult to install because it must be - compiled with external dependencies. This package has no external - dependencies, so it is much easier to install.""" + """Download Files over HTTP and HTTPS. - homepage = "https://cloud.r-project.org/package=downloader" - url = "https://cloud.r-project.org/src/contrib/downloader_0.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/downloader" + Provides a wrapper for the download.file function, making it possible to + download files over HTTPS on Windows, Mac OS X, and other Unix-like + platforms. The 'RCurl' package provides this functionality (and much more) + but can be difficult to install because it must be compiled with external + dependencies. This package has no external dependencies, so it is much + easier to install.""" + + cran = "downloader" version('0.4', sha256='1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab') diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index 7143444c7a..3ea6b5d5ac 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -7,12 +7,11 @@ from spack import * class RDplyr(RPackage): - """A Grammar of Data Manipulation + """A Grammar of Data Manipulation. - A fast, consistent tool for working with data frame like objects, both - in memory and out of memory.""" + A fast, consistent tool for working with data frame like objects, both in + memory and out of memory.""" - homepage = "https://cloud.r-project.org/package=dplyr" cran = "dplyr" version('1.0.7', sha256='d2fe3aedbce02fdddce09a8a80f85f5918a9d1f15f792ad4a98f254959d7123d') @@ -30,29 +29,29 @@ class RDplyr(RPackage): version('0.5.0', sha256='93d3b829f1c2d38e14a4f2fa7d6398fc6c1a9e4189b3e78bc38a0eb0e864454f') depends_on('r@3.1.2:', type=('build', 'run')) - depends_on('r@3.2.0:', when='@0.8.1:', type=('build', 'run')) - depends_on('r@3.3.0:', when='@1.0.3:', type=('build', 'run')) - depends_on('r-ellipsis', when='@1.0.3:', type=('build', 'run')) - depends_on('r-generics', when='@1.0.3:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@0.8.1:') + depends_on('r@3.3.0:', type=('build', 'run'), when='@1.0.3:') + depends_on('r-ellipsis', type=('build', 'run'), when='@1.0.3:') + depends_on('r-generics', type=('build', 'run'), when='@1.0.3:') depends_on('r-glue@1.3.0:', type=('build', 'run')) - depends_on('r-glue@1.3.2:', when='@1.0.3:', type=('build', 'run')) - depends_on('r-lifecycle@0.2.0:', when='@1.0.3:', type=('build', 'run')) - depends_on('r-lifecycle@1.0.0:', when='@1.0.5:', type=('build', 'run')) + depends_on('r-glue@1.3.2:', type=('build', 'run'), when='@1.0.3:') + depends_on('r-lifecycle@0.2.0:', type=('build', 'run'), when='@1.0.3:') + depends_on('r-lifecycle@1.0.0:', type=('build', 'run'), when='@1.0.5:') depends_on('r-magrittr@1.5:', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) depends_on('r-rlang@0.4.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.9:', when='@1.0.3:', type=('build', 'run')) - depends_on('r-rlang@0.4.10:', when='@1.0.5:', type=('build', 'run')) + depends_on('r-rlang@0.4.9:', type=('build', 'run'), when='@1.0.3:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@1.0.5:') depends_on('r-tibble@2.0.0:', type=('build', 'run')) - depends_on('r-tibble@2.1.3:', when='@1.0.3:', type=('build', 'run')) + depends_on('r-tibble@2.1.3:', type=('build', 'run'), when='@1.0.3:') depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) - depends_on('r-tidyselect@1.1.0:', when='@1.0.3:', type=('build', 'run')) - depends_on('r-vctrs@0.3.5:', when='@1.0.3:', type=('build', 'run')) - depends_on('r-pillar@1.5.1:', when='@1.0.6:', type=('build', 'run')) - - depends_on('r-assertthat@0.2.0:', when='@:0.8.3', type=('build', 'run')) - depends_on('r-bindrcpp@0.2.0:', when='@:0.7.9', type=('build', 'run')) - depends_on('r-pkgconfig', when='@:0.8.3', type=('build', 'run')) - depends_on('r-rcpp@1.0.1:', when='@:0.8.3', type=('build', 'run')) - depends_on('r-bh', when='@:0.8.3', type=('build', 'run')) - depends_on('r-plogr@0.2.0:', when='@0.7.0:0.8.3', type=('build', 'run')) + depends_on('r-tidyselect@1.1.0:', type=('build', 'run'), when='@1.0.3:') + depends_on('r-vctrs@0.3.5:', type=('build', 'run'), when='@1.0.3:') + depends_on('r-pillar@1.5.1:', type=('build', 'run'), when='@1.0.6:') + + depends_on('r-assertthat@0.2.0:', type=('build', 'run'), when='@:0.8.3') + depends_on('r-bindrcpp@0.2.0:', type=('build', 'run'), when='@:0.7.9') + depends_on('r-pkgconfig', type=('build', 'run'), when='@:0.8.3') + depends_on('r-rcpp@1.0.1:', type=('build', 'run'), when='@:0.8.3') + depends_on('r-bh', type=('build', 'run'), when='@:0.8.3') + depends_on('r-plogr@0.2.0:', type=('build', 'run'), when='@0.7.0:0.8.3') diff --git a/var/spack/repos/builtin/packages/r-dqrng/package.py b/var/spack/repos/builtin/packages/r-dqrng/package.py index bbdb7e4db9..9fbbfc7b17 100644 --- a/var/spack/repos/builtin/packages/r-dqrng/package.py +++ b/var/spack/repos/builtin/packages/r-dqrng/package.py @@ -7,7 +7,9 @@ from spack import * class RDqrng(RPackage): - """Several fast random number generators are provided as C++ header only + """Fast Pseudo Random Number Generators. + + Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018 <arXiv:1805.01407>). In @@ -20,10 +22,9 @@ class RDqrng(RPackage): 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011 <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.""" - homepage = "https://www.daqana.org/dqrng" - url = "https://cloud.r-project.org/src/contrib/dqrng_0.2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dqrng" + cran = "dqrng" + version('0.3.0', sha256='4beeabfe245ce7196b07369f2a7d277cb08869ad8b45a22c6354c4cc70a39abb') version('0.2.1', sha256='e149c105b1db31e7f46b1aebf31d911a109e380923f3696fc56a53197fc1e866') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py index dedf588972..f0e0e0d9d5 100644 --- a/var/spack/repos/builtin/packages/r-dt/package.py +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -7,14 +7,13 @@ from spack import * class RDt(RPackage): - """A Wrapper of the JavaScript Library 'DataTables' + """A Wrapper of the JavaScript Library 'DataTables'. Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.""" - homepage = "https://rstudio.github.io/DT" cran = "DT" version('0.20', sha256='c66d7f49ec101fdbb91c6d26c06fb1373f9ebdefe29fe99f2ae1a641220aba9f') @@ -30,8 +29,8 @@ class RDt(RPackage): depends_on('r-htmltools@0.3.6:', type=('build', 'run')) depends_on('r-htmlwidgets@1.3:', type=('build', 'run')) - depends_on('r-jsonlite@0.9.16:', when='@0.8:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', type=('build', 'run'), when='@0.8:') depends_on('r-magrittr', type=('build', 'run')) depends_on('r-crosstalk', type=('build', 'run')) - depends_on('r-jquerylib', when='@0.19:', type=('build', 'run')) - depends_on('r-promises', when='@0.5:', type=('build', 'run')) + depends_on('r-jquerylib', type=('build', 'run'), when='@0.19:') + depends_on('r-promises', type=('build', 'run'), when='@0.5:') diff --git a/var/spack/repos/builtin/packages/r-dtplyr/package.py b/var/spack/repos/builtin/packages/r-dtplyr/package.py index d6334e0f00..73190bacc9 100644 --- a/var/spack/repos/builtin/packages/r-dtplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dtplyr/package.py @@ -9,18 +9,20 @@ from spack import * class RDtplyr(RPackage): """Data Table Back-End for 'dplyr'. - Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to - allow you to write 'dplyr' code that is automatically translated to the + Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow + you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.""" - homepage = "https://github.com/tidyverse/dtplyr" - cran = "dtplyr" + cran = "dtplyr" + version('1.2.1', sha256='2640e9cde4eaa06f02cff29e3f2b99fdd08488df07ea2e6629b2ed6a8285d0f3') + version('1.2.0', sha256='a6dedfb6dd80dfc1d29d005ab634c060b7bfda8cb49835ece84d3b7d12077414') version('1.1.0', sha256='99681b7285d7d5086e5595ca6bbeebf7f4e2ee358a32b694cd9d35916cdfc732') depends_on('r@3.3:', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) depends_on('r-data-table@1.12.4:', type=('build', 'run')) + depends_on('r-data-table@1.13.0:', type=('build', 'run'), when='@1.2.0:') depends_on('r-dplyr@1.0.3:', type=('build', 'run')) depends_on('r-ellipsis', type=('build', 'run')) depends_on('r-glue', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dtw/package.py b/var/spack/repos/builtin/packages/r-dtw/package.py index 44debf31bf..289406741c 100644 --- a/var/spack/repos/builtin/packages/r-dtw/package.py +++ b/var/spack/repos/builtin/packages/r-dtw/package.py @@ -7,7 +7,7 @@ from spack import * class RDtw(RPackage): - """Dynamic Time Warping Algorithms + """Dynamic Time Warping Algorithms. A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between @@ -17,9 +17,7 @@ class RDtw(RPackage): Provides cumulative distances, alignments, specialized plot styles, etc., as described in Giorgino (2009) <doi:10.18637/jss.v031.i07>.""" - homepage = "https://cloud.r-project.org/package=dtw" - url = "https://cloud.r-project.org/src/contrib/dtw_1.18-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dtw" + cran = "dtw" version('1.22-3', sha256='df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00') version('1.20-1', sha256='43ca1a47a7c81a2b5d5054da1be8b8af79a85d6f9ce7b4512e9ed91f790f60f0') diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py index f8b90d7b6e..c1354060a6 100644 --- a/var/spack/repos/builtin/packages/r-dygraphs/package.py +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -7,15 +7,15 @@ from spack import * class RDygraphs(RPackage): - """An R interface to the 'dygraphs' JavaScript charting library (a copy of + """Interface to 'Dygraphs' Interactive Time Series Charting Library. + + An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.""" - homepage = "https://cloud.r-project.org/package=dygraphs" - url = "https://cloud.r-project.org/src/contrib/dygraphs_0.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dygraphs" + cran = "dygraphs" version('1.1.1.6', sha256='c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208') version('1.1.1.5', sha256='274035988fdd6833121fd5831692355d383acc828d540788dbcecaf88eb2d72d') @@ -26,4 +26,4 @@ class RDygraphs(RPackage): depends_on('r-htmlwidgets@0.6:', type=('build', 'run')) depends_on('r-zoo@1.7-10:', type=('build', 'run')) depends_on('r-xts@0.9-7:', type=('build', 'run')) - depends_on('r-htmltools@0.3.5:', when='@1.1.1.0:', type=('build', 'run')) + depends_on('r-htmltools@0.3.5:', type=('build', 'run'), when='@1.1.1.0:') diff --git a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py index c2fd4bcd62..8e9af85a2e 100644 --- a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py +++ b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py @@ -7,12 +7,12 @@ from spack import * class RDynamictreecut(RPackage): - """dynamicTreeCut: Methods for Detection of Clusters in Hierarchical - Clustering Dendrograms""" + """Methods for Detection of Clusters in Hierarchical Clustering Dendrograms - homepage = "https://cloud.r-project.org/package=dynamicTreeCut" - url = "https://cloud.r-project.org/src/contrib/dynamicTreeCut_1.63-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/dynamicTreeCut/" + Contains methods for detection of clusters in hierarchical clustering + dendrograms.""" + + cran = "dynamicTreeCut" version('1.63-1', sha256='831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9') diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py index 74668bb967..f215e14d4a 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -8,19 +8,19 @@ from spack import * class RE1071(RPackage): """Misc Functions of the Department of Statistics, Probability Theory Group - (Formerly: E1071), TU Wien + (Formerly: E1071), TU Wien. Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged - clustering, naive Bayes classifier, ...""" + clustering, naive Bayes classifier, generalized k-nearest neighbour ...""" - homepage = "https://cloud.r-project.org/package=e1071" - url = "https://cloud.r-project.org/src/contrib/e1071_1.6-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/e1071" + cran = "e1071" + version('1.7-9', sha256='9bf9a15e7ce0b9b1a57ce3048d29cbea7f2a5bb2e91271b1b6aaafe07c852226') version('1.7-4', sha256='e6ab871b06f500dc65f8f781cc7253f43179698784c06dab040b4aa6592f2309') version('1.7-2', sha256='721c299ce83047312acfa3e0c4b3d4c223d84a4c53400c73465cca2c92913752') version('1.7-1', sha256='5c5f04a51c1cd2c7dbdf69987adef9bc07116804c63992cd36d804a1daf89dfe') version('1.6-7', sha256='7048fbc0ac17d7e3420fe68081d0e0a2176b1154ee3191d53558ea9724c7c980') depends_on('r-class', type=('build', 'run')) + depends_on('r-proxy', type=('build', 'run'), when='@1.7-9:') diff --git a/var/spack/repos/builtin/packages/r-earth/package.py b/var/spack/repos/builtin/packages/r-earth/package.py index e0f396ce64..33f4f6ad06 100644 --- a/var/spack/repos/builtin/packages/r-earth/package.py +++ b/var/spack/repos/builtin/packages/r-earth/package.py @@ -13,15 +13,14 @@ class REarth(RPackage): "Fast MARS" and "Multivariate Adaptive Regression Splines" <doi:10.1214/aos/1176347963>.""" - homepage = "http://www.milbo.users.sonic.net/earth" - url = "https://cloud.r-project.org/src/contrib/earth_5.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/earth" + cran = "earth" + version('5.3.1', sha256='0bbe06ba974ceb8ec5de1d59cb53f9487d1828d7130fe2503c48b6cb449c4b03') version('5.3.0', sha256='05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437') version('5.1.2', sha256='326f98e8c29365ca3cd5584cf2bd6529358f5ef81664cbd494162f92b6c3488d') depends_on('r@3.4.0:', type=('build', 'run')) depends_on('r-formula@1.2-3:', type=('build', 'run')) depends_on('r-plotmo@3.5.4:', type=('build', 'run')) - depends_on('r-plotmo@3.6.0:', when='@5.3.0', type=('build', 'run')) + depends_on('r-plotmo@3.6.0:', type=('build', 'run'), when='@5.3.0') depends_on('r-teachingdemos@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ecp/package.py b/var/spack/repos/builtin/packages/r-ecp/package.py index 33ccc4d515..55b7a72bc0 100644 --- a/var/spack/repos/builtin/packages/r-ecp/package.py +++ b/var/spack/repos/builtin/packages/r-ecp/package.py @@ -7,7 +7,7 @@ from spack import * class REcp(RPackage): - """Non-Parametric Multiple Change-Point Analysis of MultivariateData + """Non-Parametric Multiple Change-Point Analysis of MultivariateData. Implements various procedures for finding multiple change-points from Matteson D. et al (2013) <doi:10.1080/01621459.2013.849605>, Zhang W. et al @@ -17,9 +17,7 @@ class REcp(RPackage): Hierarchical and exact search methods are included. All methods return the set of estimated change-points as well as other summary information.""" - homepage = "https://cloud.r-project.org/package=ecp" - url = "https://cloud.r-project.org/src/contrib/ecp_3.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ecp" + cran = "ecp" version('3.1.3', sha256='a80ab10bafe30cc96287b9220e44c4b4eda40f5dd0546e4d2a2e1baab514c058') version('3.1.1', sha256='d2ab194e22e6ab0168222fbccfcf2e25c6cd51a73edc959086b0c6e0a7410268') diff --git a/var/spack/repos/builtin/packages/r-effects/package.py b/var/spack/repos/builtin/packages/r-effects/package.py index 7922aeb56e..5a4e709f93 100644 --- a/var/spack/repos/builtin/packages/r-effects/package.py +++ b/var/spack/repos/builtin/packages/r-effects/package.py @@ -7,13 +7,14 @@ from spack import * class REffects(RPackage): - """Effect Displays for Linear, Generalized Linear, and Other Models + """Effect Displays for Linear, Generalized Linear, and Other Models. Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.""" - cran = "effects" + cran = "effects" + version('4.2-1', sha256='5397254214d55eb0e0441786f9329f9e3e3ef864366c0a93f0adb941da147640') version('4.2-0', sha256='6833dfbc65f3f33191a24e9b0d2aa0c964caeebb6c4fd2036ad94ed2723a7a46') depends_on('r@3.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-elemstatlearn/package.py b/var/spack/repos/builtin/packages/r-elemstatlearn/package.py index e478559413..b540b01f0d 100644 --- a/var/spack/repos/builtin/packages/r-elemstatlearn/package.py +++ b/var/spack/repos/builtin/packages/r-elemstatlearn/package.py @@ -7,13 +7,11 @@ from spack import * class RElemstatlearn(RPackage): - """ElemStatLearn: Data Sets, Functions and Examples from the Book: "The - Elements of Statistical Learning, Data Mining, Inference, and Prediction" by - Trevor Hastie, Robert Tibshirani and Jerome Friedman""" + """Data Sets, Functions and Examples from the Book: "The Elements of + Statistical Learning, Data Mining, Inference, and Prediction" by Trevor + Hastie, Robert Tibshirani and Jerome Friedman""" - homepage = "https://cloud.r-project.org/package=ElemStatLearn" - url = "https://cloud.r-project.org/src/contrib/Archive/ElemStatLearn/ElemStatLearn_2015.6.26.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ElemStatLearn" + cran = "ElemStatLearn" version('2015.6.26.2', sha256='a0f94a72f6188a0a5c855e3362b6b849bf7fd14efc2d824a8d2581f8bb1bd7fa') diff --git a/var/spack/repos/builtin/packages/r-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py index dc586dec31..1330270ffb 100644 --- a/var/spack/repos/builtin/packages/r-ellipse/package.py +++ b/var/spack/repos/builtin/packages/r-ellipse/package.py @@ -7,7 +7,7 @@ from spack import * class REllipse(RPackage): - """Functions for Drawing Ellipses and Ellipse-Like Confidence Regions + """Functions for Drawing Ellipses and Ellipse-Like Confidence Regions. Contains various routines for drawing ellipses and ellipse-like confidence regions, implementing the plots described in Murdoch and Chow (1996), A @@ -16,9 +16,7 @@ class REllipse(RPackage): described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.""" - homepage = "https://cloud.r-project.org/package=ellipse" - url = "https://cloud.r-project.org/src/contrib/ellipse_0.3-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ellipse" + cran = "ellipse" version('0.4.2', sha256='1719ce9a00b9ac4d56dbf961803085b892d3359726fda3567bb989ddfed9a5f2') version('0.4.1', sha256='1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d') diff --git a/var/spack/repos/builtin/packages/r-ellipsis/package.py b/var/spack/repos/builtin/packages/r-ellipsis/package.py index 0f110c4f64..d2d72d427b 100644 --- a/var/spack/repos/builtin/packages/r-ellipsis/package.py +++ b/var/spack/repos/builtin/packages/r-ellipsis/package.py @@ -14,7 +14,6 @@ class REllipsis(RPackage): The ellipsis package provides a collection of functions to catch problems and alert the user.""" - homepage = "https://github.com/r-lib/ellipsis" cran = "ellipsis" version('0.3.2', sha256='a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558') @@ -23,5 +22,5 @@ class REllipsis(RPackage): version('0.2.0.1', sha256='0e6528c5e8016c3617cc1cfcdb5a4bfeb073e0bd5ea76b43e56b0c3208a0a943') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r@3.2:', when='@0.3:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@0.3:') depends_on('r-rlang@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-emmeans/package.py b/var/spack/repos/builtin/packages/r-emmeans/package.py index 9629865b90..579eca19c4 100644 --- a/var/spack/repos/builtin/packages/r-emmeans/package.py +++ b/var/spack/repos/builtin/packages/r-emmeans/package.py @@ -7,20 +7,19 @@ from spack import * class REmmeans(RPackage): - """Estimated Marginal Means, aka Least-Squares Means + """Estimated Marginal Means, aka Least-Squares Means. - Obtain estimated marginal means (EMMs) for many linear, generalized - linear, and mixed models. Compute contrasts or linear functions of EMMs, - trends, and comparisons of slopes. Plots and other displays. - Least-squares means are discussed, and the term "estimated marginal means" - is suggested, in Searle, Speed, and Milliken (1980) Population marginal - means in the linear model: An alternative to least squares means, The - American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>. - """ + Obtain estimated marginal means (EMMs) for many linear, generalized linear, + and mixed models. Compute contrasts or linear functions of EMMs, trends, + and comparisons of slopes. Plots and other displays. Least-squares means + are discussed, and the term "estimated marginal means" is suggested, in + Searle, Speed, and Milliken (1980) Population marginal means in the linear + model: An alternative to least squares means, The American Statistician + 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.""" - homepage = "https://github.com/rvlenth/emmeans" - cran = "emmeans" + cran = "emmeans" + version('1.7.2', sha256='d3e51c2a4b6c74dd9840efebe241a53072172f269f4324421f28f68db71721bc') version('1.7.1-1', sha256='6b01eaad1ea0f96245db8563cc77929a3c3b96cd61c24ce1d452308d6e0250de') version('1.7.0', sha256='d4b654896197dfda8354b33257380a66ee06117d6177b1ed7f1e42176525e9c5') version('1.6.0', sha256='201bb7b008dde94231ed60bcc6a32749442faaab4baeea99ad28b97c951b3c1e') @@ -31,4 +30,4 @@ class REmmeans(RPackage): depends_on('r-mvtnorm', type=('build', 'run')) depends_on('r-xtable@1.8-2:', type=('build', 'run')) - depends_on('r-plyr', when='@:1.6', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run'), when='@:1.6') diff --git a/var/spack/repos/builtin/packages/r-emmli/package.py b/var/spack/repos/builtin/packages/r-emmli/package.py index 44edab9cb1..50c983c5fe 100644 --- a/var/spack/repos/builtin/packages/r-emmli/package.py +++ b/var/spack/repos/builtin/packages/r-emmli/package.py @@ -7,12 +7,12 @@ from spack import * class REmmli(RPackage): - """Fit models of modularity to morphological landmarks. Perform model selection - on results. Fit models with a single within-module correlation or with - separate within-module correlations fitted to each module.""" + """A Maximum Likelihood Approach to the Analysis of Modularity. - homepage = "https://cloud.r-project.org/package=EMMLi" - url = "https://cloud.r-project.org/src/contrib/EMMLi_0.0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/EMMLi" + Fit models of modularity to morphological landmarks. Perform model + selection on results. Fit models with a single within-module correlation or + with separate within-module correlations fitted to each module.""" + + cran = "EMMLi" version('0.0.3', sha256='57c04953200d2253bc90b0035dc590179d1b959768bfa7fdac92b6bcbf9f66ac') diff --git a/var/spack/repos/builtin/packages/r-energy/package.py b/var/spack/repos/builtin/packages/r-energy/package.py index abee56dbbd..9147f72d20 100644 --- a/var/spack/repos/builtin/packages/r-energy/package.py +++ b/var/spack/repos/builtin/packages/r-energy/package.py @@ -7,7 +7,7 @@ from spack import * class REnergy(RPackage): - """Statistics: Multivariate Inference via the Energy of Data + """E-Statistics: Multivariate Inference via the Energy of Data. E-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and @@ -19,10 +19,10 @@ class REnergy(RPackage): for non-parametric analysis of structured data, and other energy statistics/methods are implemented.""" - homepage = "https://cloud.r-project.org/package=energy" - url = "https://cloud.r-project.org/src/contrib/energy_1.7-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/energy" + cran = "energy" + version('1.7-9', sha256='68d0e0ed99f5a8a03858603ed36010a2f67b87a947dbcc65a9da2e08a2d3bad9') + version('1.7-8', sha256='de08e8de037bb30068bbf0c1880b153a586d342304681f4ba103ab808c7f4789') version('1.7-7', sha256='67b88fb33ee6e7bec2e4fe356a4efd36f70c3cf9b0ebe2f6d9da9ec96de9968f') version('1.7-6', sha256='900edbb28e1f1bccd78580828470628cf75eb6333b63e1a58e4da7fc5c5fa89a') version('1.7-5', sha256='24c2cf080939f8f56cd9cda06d2dfc30d0389cd3ec7250af4f9a09a4c06b6996') @@ -30,3 +30,4 @@ class REnergy(RPackage): depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rcpp@0.12.6:', type=('build', 'run')) depends_on('r-boot', type=('build', 'run')) + depends_on('r-gsl', type=('build', 'run'), when='@1.7-8:') diff --git a/var/spack/repos/builtin/packages/r-envstats/package.py b/var/spack/repos/builtin/packages/r-envstats/package.py index 06ae529b7b..3ed79ae904 100644 --- a/var/spack/repos/builtin/packages/r-envstats/package.py +++ b/var/spack/repos/builtin/packages/r-envstats/package.py @@ -7,7 +7,7 @@ from spack import * class REnvstats(RPackage): - """Package for Environmental Statistics, Including US EPA Guidance + """Package for Environmental Statistics, Including US EPA Guidance. Graphical and statistical analyses of environmental data, with focus on analyzing chemical concentrations and physical parameters, usually in the @@ -21,10 +21,9 @@ class REnvstats(RPackage): Springer, ISBN 978-1-4614-8455-4, <https://www.springer.com/book/9781461484554>).""" - homepage = "https://cloud.r-project.org/package=EnvStats" - url = "https://cloud.r-project.org/src/contrib/EnvStats_2.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/EnvStats" + cran = "EnvStats" + version('2.5.0', sha256='4f77aa66c9dbbe411370a6dd5b9e514823d5506bbcdad9dc09a9e4268d65a7f7') version('2.4.0', sha256='49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514') version('2.3.1', sha256='d753d42b42ff28c1cd25c63916fb2aa9e325941672fb16f7dfd97e218416cf2a') version('2.3.0', sha256='51b7c982b4ffc6506579ec6933c817b780b8dade9f5e7754122e4132cb677a75') diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py index 719bf5381b..ca1fcdb275 100644 --- a/var/spack/repos/builtin/packages/r-ergm/package.py +++ b/var/spack/repos/builtin/packages/r-ergm/package.py @@ -7,35 +7,52 @@ from spack import * class RErgm(RPackage): - """Fit, Simulate and Diagnose Exponential-Family Models for Networks + """Fit, Simulate and Diagnose Exponential-Family Models for Networks. An integrated set of tools to analyze and simulate networks based on - exponential-family random graph models (ERGM). "ergm" is a part of the - "statnet" suite of packages for network analysis.""" + exponential-family random graph models (ERGMs). 'ergm' is a part of the + Statnet suite of packages for network analysis. See Hunter, Handcock, + Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and + Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.""" - homepage = "https://statnet.org" - url = "https://cloud.r-project.org/src/contrib/ergm_3.7.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ergm" + cran = "ergm" + version('4.1.2', sha256='1abc6ef53376a4132530c376ce477ae7a2590e95fe8feb011c0da9cfb4d49ba0') version('3.11.0', sha256='4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2') version('3.10.4', sha256='885f0b1a23c5a2c1947962350cfab66683dfdfd1db173c115e90396d00831f22') version('3.10.1', sha256='a2ac249ff07ba55b3359242f20389a892543b4fff5956d74143d2d41fa6d4beb') version('3.7.1', sha256='91dd011953b93ecb2b84bb3ababe7bddae25d9d86e69337156effd1da84b54c3') + depends_on('r@3.5:', type=('build', 'run'), when='@4.1.2:') depends_on('r-network@1.15:', type=('build', 'run')) + depends_on('r-network@1.17:', type=('build', 'run'), when='@4.1.2:') depends_on('r-robustbase@0.93-5:', type=('build', 'run')) + depends_on('r-robustbase@0.93-7:', type=('build', 'run'), when='@4.1.2:') depends_on('r-coda@0.19-2:', type=('build', 'run')) + depends_on('r-coda@0.19-4:', type=('build', 'run'), when='@4.1.2:') depends_on('r-trust@0.1.7:', type=('build', 'run')) + depends_on('r-trust@0.1.8:', type=('build', 'run'), when='@4.1.2:') depends_on('r-matrix@1.2-17:', type=('build', 'run')) - depends_on('r-lpsolve@5.6.13:', type=('build', 'run')) + depends_on('r-matrix@1.3.2:', type=('build', 'run'), when='@4.1.2:') + depends_on('r-lpsolveapi@5.5.2.0.17.7:', type=('build', 'run'), when='@4.1.2:') depends_on('r-mass@7.3-51.4:', type=('build', 'run')) + depends_on('r-mass@7.3.53.1:', type=('build', 'run'), when='@4.1.2:') depends_on('r-statnet-common@4.3.0:', type=('build', 'run')) - depends_on('r-statnet-common@4.4.0:', when='@3.11.0:', type=('build', 'run')) - depends_on('r-rle', when='@3.11.0:', type=('build', 'run')) - depends_on('r-purrr@0.3.2:', when='@3.10.0:', type=('build', 'run')) - depends_on('r-rlang@0.3.4:', when='@3.10.0:', type=('build', 'run')) - depends_on('r-tibble@2.1.1:', when='@3.10.0:', type=('build', 'run')) - depends_on('r-dplyr@0.8.0.1:', when='@3.10.0:3.10.4', type=('build', 'run')) + depends_on('r-statnet-common@4.4.0:', type=('build', 'run'), when='@3.11.0:') + depends_on('r-statnet-common@4.5.0:', type=('build', 'run'), when='@4.1.2:') + depends_on('r-rle', type=('build', 'run'), when='@3.11.0:') + depends_on('r-rle@0.9.2:', type=('build', 'run'), when='@4.1.2:') + depends_on('r-purrr@0.3.2:', type=('build', 'run'), when='@3.10.0:') + depends_on('r-purrr@0.3.4:', type=('build', 'run'), when='@4.1.2:') + depends_on('r-rlang@0.3.4:', type=('build', 'run'), when='@3.10.0:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@4.1.2:') + depends_on('r-memoise@2.0.0:', type=('build', 'run'), when='@4.1.2:') + depends_on('r-tibble@2.1.1:', type=('build', 'run'), when='@3.10.0:') + depends_on('r-tibble@3.1.0:', type=('build', 'run'), when='@4.1.2:') + + depends_on('r-dplyr@0.8.0.1:', type=('build', 'run'), when='@3.10.0:3.10.4') + depends_on('r-lpsolve@5.6.13:', type=('build', 'run'), when='@:3.11.0') + # The CRAN page list OpenMPI as a dependency but this is not a dependency # for using the package. If one wishes to use MPI, simply load an MPI # package, along with r-dosnow and r-rmpi when using r-ergm, and set the diff --git a/var/spack/repos/builtin/packages/r-estimability/package.py b/var/spack/repos/builtin/packages/r-estimability/package.py index 02af356d6e..197c30a3de 100644 --- a/var/spack/repos/builtin/packages/r-estimability/package.py +++ b/var/spack/repos/builtin/packages/r-estimability/package.py @@ -7,16 +7,14 @@ from spack import * class REstimability(RPackage): - """Tools for Assessing Estimability of Linear Predictions + """Tools for Assessing Estimability of Linear Predictions. - Provides tools for determining estimability of linear functions - of regression coefficients, and 'epredict' methods that handle - non-estimable cases correctly. Estimability theory is discussed in - many linear-models textbooks including Chapter 3 of Monahan, JF (2008), - "A Primer on Linear Models", Chapman and Hall (ISBN 978-1-4200-6201-4). - """ + Provides tools for determining estimability of linear functions of + regression coefficients, and 'epredict' methods that handle non-estimable + cases correctly. Estimability theory is discussed in many linear-models + textbooks including Chapter 3 of Monahan, JF (2008), "A Primer on Linear + Models", Chapman and Hall (ISBN 978-1-4200-6201-4).""" - homepage = "https://github.com/rvlenth/estimability" cran = "estimability" version('1.3', sha256='a33179c5fbd6a1a623d90cb6f1743148f92c09429fac466867f3ea70946a2e32') diff --git a/var/spack/repos/builtin/packages/r-europepmc/package.py b/var/spack/repos/builtin/packages/r-europepmc/package.py index 946ea1d6a2..1df85568be 100644 --- a/var/spack/repos/builtin/packages/r-europepmc/package.py +++ b/var/spack/repos/builtin/packages/r-europepmc/package.py @@ -7,7 +7,7 @@ from spack import * class REuropepmc(RPackage): - """R Interface to the Europe PubMed Central RESTful Web Service + """R Interface to the Europe PubMed Central RESTful Web Service. An R Client for the Europe PubMed Central RESTful Web Service (see <https://europepmc.org/RestfulWebService> for more information). It gives @@ -21,10 +21,9 @@ class REuropepmc(RPackage): registration or API key is required. See the vignettes for usage examples.""" - homepage = "https://github.com/ropensci/europepmc/" - url = "https://cloud.r-project.org/src/contrib/europepmc_0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/europepmc" + cran = "europepmc" + version('0.4.1', sha256='c1ba91a2a99432cabe18e86fea33ac9d20dbb3ac0b58f430d464b4d8ecba4a9a') version('0.4', sha256='d55f62963d0ee84830654bbc78f4ad8285e376b04be137cbeaf8ad2a98b7969c') version('0.3', sha256='5044a253d223e2bb8502063cd03c0fe4db856467e497d650da7ccd8f75d0f8d9') @@ -37,6 +36,6 @@ class REuropepmc(RPackage): depends_on('r-urltools', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) depends_on('r-xml2', type=('build', 'run')) - depends_on('r-tibble', when='@0.4:', type=('build', 'run')) - depends_on('r-tidyr', when='@0.4:', type=('build', 'run')) - depends_on('r-rlang', when='@0.4:', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run'), when='@0.4:') + depends_on('r-tidyr', type=('build', 'run'), when='@0.4:') + depends_on('r-rlang', type=('build', 'run'), when='@0.4:') diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index d84217a558..46a3a02229 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -7,12 +7,12 @@ from spack import * class REvaluate(RPackage): - """Parsing and evaluation tools that make it easy to recreate the command + """Parsing and Evaluation Tools that Provide More Details than the Default. + + Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.""" - homepage = "https://cloud.r-project.org/package=evaluate" - url = "https://cloud.r-project.org/src/contrib/evaluate_0.10.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/evaluate" + cran = "evaluate" version('0.14', sha256='a8c88bdbe4e60046d95ddf7e181ee15a6f41cdf92127c9678f6f3d328a3c5e28') version('0.10.1', sha256='c9a763895d3f460dbf87c43a6469e4b41a251a74477df8c5d7e7d2b66cdd1b1c') @@ -20,4 +20,5 @@ class REvaluate(RPackage): version('0.9', sha256='e8118c9d6ec479c0e712913848404431b6b6c0282f3c131acaf9a677ab5fc6ae') depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r-stringr@0.6.2:', when='@:0.11', type=('build', 'run')) + + depends_on('r-stringr@0.6.2:', type=('build', 'run'), when='@:0.11') diff --git a/var/spack/repos/builtin/packages/r-evd/package.py b/var/spack/repos/builtin/packages/r-evd/package.py index 45f74212e9..ff0f241efb 100644 --- a/var/spack/repos/builtin/packages/r-evd/package.py +++ b/var/spack/repos/builtin/packages/r-evd/package.py @@ -7,10 +7,14 @@ from spack import * class REvd(RPackage): - """evd: Functions for Extreme Value Distributions""" + """Functions for Extreme Value Distributions. - homepage = "https://cloud.r-project.org/package=evd" - url = "https://cloud.r-project.org/src/contrib/evd_2.3-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/evd" + Extends simulation, distribution, quantile and density functions to + univariate and multivariate parametric extreme value distributions, and + provides fitting functions which calculate maximum likelihood estimates for + univariate and bivariate maxima models, and for univariate and bivariate + threshold models.""" + + cran = "evd" version('2.3-3', sha256='2fc5ef2e0c3a2a9392425ddd45914445497433d90fb80b8c363877baee4559b4') diff --git a/var/spack/repos/builtin/packages/r-exactextractr/package.py b/var/spack/repos/builtin/packages/r-exactextractr/package.py index 675143110b..425c6dc666 100644 --- a/var/spack/repos/builtin/packages/r-exactextractr/package.py +++ b/var/spack/repos/builtin/packages/r-exactextractr/package.py @@ -7,15 +7,14 @@ from spack import * class RExactextractr(RPackage): - """Fast Extraction from Raster Datasets using Polygons + """Fast Extraction from Raster Datasets using Polygons. Provides a replacement for the 'extract' function from the 'raster' package that is suitable for extracting raster values using 'sf' polygons.""" - homepage = "https://cloud.r-project.org/package=exactextractr" - url = "https://cloud.r-project.org/src/contrib/exactextractr_0.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/exactextractr" + cran = "exactextractr" + version('0.7.2', sha256='2eb2b5eb2156cca875e7004b80687589217abd6fce5ebb7d8acb7fa71f6e6958') version('0.5.1', sha256='47ddfb4b9e42e86957e03b1c745d657978d7c4bed12ed3aa053e1bc89f20616d') version('0.3.0', sha256='c7fb38b38b9dc8b3ca5b8f1f84f4ba3256efd331f2b4636b496d42689ffc3fb0') version('0.2.1', sha256='d0b998c77c3fd9265a600a0e08e9bf32a2490a06c19df0d0c0dea4b5c9ab5773') @@ -24,4 +23,5 @@ class RExactextractr(RPackage): depends_on('r-rcpp@0.12.12:', type=('build', 'run')) depends_on('r-raster', type=('build', 'run')) depends_on('r-sf', type=('build', 'run')) - depends_on('geos@3.5.0:', type=('build', 'run', 'link')) + depends_on('r-sf@0.9.0:', type=('build', 'run'), when='@0.7.2:') + depends_on('geos@3.5.0:') diff --git a/var/spack/repos/builtin/packages/r-exomedepth/package.py b/var/spack/repos/builtin/packages/r-exomedepth/package.py index ad924cff54..a9064f2716 100644 --- a/var/spack/repos/builtin/packages/r-exomedepth/package.py +++ b/var/spack/repos/builtin/packages/r-exomedepth/package.py @@ -7,13 +7,13 @@ from spack import * class RExomedepth(RPackage): - """Calls copy number variants (CNVs) from targeted sequence data, typically + """Calls Copy Number Variants from Targeted Sequence Data. + + Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.""" - homepage = "https://cloud.r-project.org/package=ExomeDepth" - url = "https://cloud.r-project.org/src/contrib/ExomeDepth_1.1.15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ExomeDepth" + cran = "ExomeDepth" version('1.1.15', sha256='112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2') diff --git a/var/spack/repos/builtin/packages/r-expint/package.py b/var/spack/repos/builtin/packages/r-expint/package.py index e2def43b9c..7bbd6fc966 100644 --- a/var/spack/repos/builtin/packages/r-expint/package.py +++ b/var/spack/repos/builtin/packages/r-expint/package.py @@ -8,7 +8,7 @@ from spack import * class RExpint(RPackage): - """Exponential Integral and Incomplete Gamma Function + """Exponential Integral and Incomplete Gamma Function. The exponential integrals E_1(x), E_2(x), E_n(x) and Ei(x), and the incomplete gamma function G(a, x) defined for negative values of its first @@ -18,9 +18,7 @@ class RExpint(RPackage): routines derived from the GNU Scientific Library <https://www.gnu.org/software/gsl/>.""" - homepage = "https://cloud.r-project.org/package=expint" - url = "https://cloud.r-project.org/src/contrib/expint_0.1-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/expint" + cran = "expint" version('0.1-6', sha256='c7d13a8e299a91e94622047fe22b0006137e7bf82e34d10871b631fa58115145') version('0.1-5', sha256='b03d60938cd6cf615aa3a02b1bf73436785eca89eaff56059ee0807b8244718a') diff --git a/var/spack/repos/builtin/packages/r-expm/package.py b/var/spack/repos/builtin/packages/r-expm/package.py index 2c89b7f4b9..082f4b28e8 100644 --- a/var/spack/repos/builtin/packages/r-expm/package.py +++ b/var/spack/repos/builtin/packages/r-expm/package.py @@ -7,14 +7,12 @@ from spack import * class RExpm(RPackage): - """Matrix Exponential, Log, 'etc' + """Matrix Exponential, Log, 'etc'. Computation of the matrix exponential, logarithm, sqrt, and related quantities.""" - homepage = "https://r-forge.r-project.org/projects/expm" - url = "https://cloud.r-project.org/src/contrib/expm_0.999-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/expm" + cran = "expm" version('0.999-6', sha256='2c79912fd2e03fcf89c29f09555880934402fcb2359af8b4579d79b4f955addc') version('0.999-4', sha256='58d06427a08c9442462b00a5531e2575800be13ed450c5a1546261251e536096') diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py index 80a364efc9..73225eb8a1 100644 --- a/var/spack/repos/builtin/packages/r-factoextra/package.py +++ b/var/spack/repos/builtin/packages/r-factoextra/package.py @@ -7,7 +7,7 @@ from spack import * class RFactoextra(RPackage): - """Extract and Visualize the Results of Multivariate Data Analyses + """Extract and Visualize the Results of Multivariate Data Analyses. Provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), @@ -18,9 +18,7 @@ class RFactoextra(RPackage): analysis steps and provides 'ggplot2' - based elegant data visualization.""" - homepage = "http://www.sthda.com/english/rpkgs/factoextra" - url = "https://cloud.r-project.org/src/contrib/factoextra_1.0.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/factoextra" + cran = "factoextra" version('1.0.7', sha256='624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa') version('1.0.5', sha256='8177a3f5107883ae248b2cd0afa388a1794741f5155a9455b3883788cf44d5d0') diff --git a/var/spack/repos/builtin/packages/r-factominer/package.py b/var/spack/repos/builtin/packages/r-factominer/package.py index 7008c833fa..3a86f101ee 100644 --- a/var/spack/repos/builtin/packages/r-factominer/package.py +++ b/var/spack/repos/builtin/packages/r-factominer/package.py @@ -7,7 +7,7 @@ from spack import * class RFactominer(RPackage): - """Multivariate Exploratory Data Analysis and Data Mining + """Multivariate Exploratory Data Analysis and Data Mining. Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with @@ -18,9 +18,7 @@ class RFactominer(RPackage): groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).""" - homepage = "http://factominer.free.fr" - url = "https://cloud.r-project.org/src/contrib/FactoMineR_1.35.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/FactoMineR" + cran = "FactoMineR" version('2.4', sha256='b9e3adce9a66b4daccc85fa67cb0769d6be230beeb126921b386ccde5db2e851') version('1.42', sha256='4cd9efb3681767c3bd48ddc3504ebead1493fcbbc0a9f759a00955b16c3481fa') @@ -32,15 +30,15 @@ class RFactominer(RPackage): version('1.35', sha256='afe176fe561d1d16c5965ecb2b80ec90a56d0fbcd75c43ec8025a401a5b715a9') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@2.4:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@2.4:') depends_on('r-car', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) - depends_on('r-dt', when='@2.4:', type=('build', 'run')) + depends_on('r-dt', type=('build', 'run'), when='@2.4:') depends_on('r-ellipse', type=('build', 'run')) depends_on('r-flashclust', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-leaps', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-scatterplot3d', type=('build', 'run')) - depends_on('r-ggplot2', when='@2.4:', type=('build', 'run')) - depends_on('r-ggrepel', when='@2.4:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run'), when='@2.4:') + depends_on('r-ggrepel', type=('build', 'run'), when='@2.4:') diff --git a/var/spack/repos/builtin/packages/r-fansi/package.py b/var/spack/repos/builtin/packages/r-fansi/package.py index 65a8f8dbe9..c92497a07f 100644 --- a/var/spack/repos/builtin/packages/r-fansi/package.py +++ b/var/spack/repos/builtin/packages/r-fansi/package.py @@ -7,12 +7,14 @@ from spack import * class RFansi(RPackage): - """Counterparts to R string manipulation functions that account - for the effects of ANSI text formatting control sequences.""" + """ANSI Control Sequence Aware String Functions. + + Counterparts to R string manipulation functions that account for the + effects of ANSI text formatting control sequences.""" - homepage = "https://cloud.r-project.org/package=fansi" cran = "fansi" + version('1.0.2', sha256='d1e2cf2e10613abe19071e3dab7c564ebcf85ad13cbee25fa1999267af01b557') version('0.5.0', sha256='9d1bf8c316969c163abd3dd41cc1425b2671df9471fe806bf8783794a19ca54f') version('0.4.1', sha256='3c69eec803a3827e5227f9cf084976eeb738b22c7eb7665bb5faa251bce41e09') version('0.4.0', sha256='e104e9d01c7ff8a847f6b332ef544c0ef912859f9c6a514fe2e6f3b34fcfc209') diff --git a/var/spack/repos/builtin/packages/r-farver/package.py b/var/spack/repos/builtin/packages/r-farver/package.py index f14837bddb..9ed8a3e02d 100644 --- a/var/spack/repos/builtin/packages/r-farver/package.py +++ b/var/spack/repos/builtin/packages/r-farver/package.py @@ -7,7 +7,7 @@ from spack import * class RFarver(RPackage): - """High Performance Colour Space Manipulation + """High Performance Colour Space Manipulation. The encoding of colour can be handled in many different ways, using different colour spaces. As different colour spaces have different uses, @@ -17,7 +17,6 @@ class RFarver(RPackage): speed improvements over the 'convertColor' function in the 'grDevices' package.""" - homepage = "https://github.com/thomasp85/farver" cran = "farver" version('2.1.0', sha256='e5c8630607049f682fb3002b99ca4f5e7c6b94f8b2a4342df594e7853b77cef4') diff --git a/var/spack/repos/builtin/packages/r-fastcluster/package.py b/var/spack/repos/builtin/packages/r-fastcluster/package.py index 9ca71b9f82..40384bf80a 100644 --- a/var/spack/repos/builtin/packages/r-fastcluster/package.py +++ b/var/spack/repos/builtin/packages/r-fastcluster/package.py @@ -7,21 +7,22 @@ from spack import * class RFastcluster(RPackage): - """This is a two-in-one package which provides interfaces to both R - and 'Python'. It implements fast hierarchical, agglomerative - clustering routines. Part of the functionality is designed as drop-in - replacement for existing routines: linkage() in the 'SciPy' package - 'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the - 'flashClust' package. It provides the same functionality with the - benefit of a much faster implementation. Moreover, there are - memory-saving routines for clustering of vector data, which go beyond - what the existing packages provide. For information on how to install - the 'Python' files, see the file INSTALL in the source distribution.""" + """Fast Hierarchical Clustering Routines for R and 'Python'. - homepage = "http://danifold.net/fastcluster.html" - url = "https://cloud.r-project.org/src/contrib/fastcluster_1.1.25.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fastcluster/" + This is a two-in-one package which provides interfaces to both R and + 'Python'. It implements fast hierarchical, agglomerative clustering + routines. Part of the functionality is designed as drop-in replacement for + existing routines: linkage() in the 'SciPy' package + 'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the + 'flashClust' package. It provides the same functionality with the benefit + of a much faster implementation. Moreover, there are memory-saving routines + for clustering of vector data, which go beyond what the existing packages + provide. For information on how to install the 'Python' files, see the file + INSTALL in the source distribution.""" + cran = "fastcluster" + + version('1.2.3', sha256='1f229129e1cddc78c7bb5ecc90c4d28ed810ee68cf210004c7cdfa12cfaf2a01') version('1.1.25', sha256='f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fastdigest/package.py b/var/spack/repos/builtin/packages/r-fastdigest/package.py index 0fce5610be..1b2610f949 100644 --- a/var/spack/repos/builtin/packages/r-fastdigest/package.py +++ b/var/spack/repos/builtin/packages/r-fastdigest/package.py @@ -7,19 +7,17 @@ from spack import * class RFastdigest(RPackage): - """Fast, Low Memory-Footprint Digests of R Objects + """Fast, Low Memory-Footprint Digests of R Objects. Provides an R interface to Bob Jenkin's streaming, non-cryptographic 'SpookyHash' hash algorithm for use in digest-based comparisons of R objects. 'fastdigest' plugs directly into R's internal serialization machinery, allowing digests of all R objects the serialize() function - supports, including reference-style objects via custom hooks. Speed is - high and scales linearly by object size; - memory usage is constant and negligible.""" + supports, including reference-style objects via custom hooks. Speed is high + and scales linearly by object size; memory usage is constant and + negligible.""" - homepage = "https://cloud.r-project.org/web/packages/fastdigest/index.html" - url = "https://cloud.r-project.org/src/contrib/fastdigest_0.6-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fastdigest" + cran = "fastdigest" maintainers = ['dorton21'] diff --git a/var/spack/repos/builtin/packages/r-fastica/package.py b/var/spack/repos/builtin/packages/r-fastica/package.py index edeec802ff..c4ac788a25 100644 --- a/var/spack/repos/builtin/packages/r-fastica/package.py +++ b/var/spack/repos/builtin/packages/r-fastica/package.py @@ -7,13 +7,15 @@ from spack import * class RFastica(RPackage): - """FastICA Algorithms to Perform ICA and Projection Pursuit: + """FastICA Algorithms to Perform ICA and Projection Pursuit. Implementation of FastICA algorithm to perform Independent Component Analysis (ICA) and Projection Pursuit.""" - cran = "fastICA" + cran = "fastICA" + version('1.2-3', sha256='e9ef82644cb64bb49ae3b7b6e0885f4fb2dc08ae030f8c76fe8dd8507b658950') version('1.2-2', sha256='32223593374102bf54c8fdca7b57231e4f4d0dd0be02d9f3500ad41b1996f1fe') depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@1.2-3:') diff --git a/var/spack/repos/builtin/packages/r-fastmap/package.py b/var/spack/repos/builtin/packages/r-fastmap/package.py index 97499d53ae..4a68e9d0a4 100644 --- a/var/spack/repos/builtin/packages/r-fastmap/package.py +++ b/var/spack/repos/builtin/packages/r-fastmap/package.py @@ -7,7 +7,7 @@ from spack import * class RFastmap(RPackage): - """Fast Implementation of a Key-Value Store + """Fast Implementation of a Key-Value Store. Fast implementation of a key-value store. Environments are commonly used as key-value stores, but every time a new key is used, it is added to R's @@ -16,9 +16,7 @@ class RFastmap(RPackage): this memory leak issue by implementing the map using data structures in C++.""" - homepage = "https://r-lib.github.io/fastmap/" - url = "https://cloud.r-project.org/src/contrib/fastmap_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fastmap" + cran = "fastmap" version('1.1.0', sha256='9113e526b4c096302cfeae660a06de2c4c82ae4e2d3d6ef53af6de812d4c822b') version('1.0.1', sha256='4778b05dfebd356f8df980dfeff3b973a72bca14898f870e5c40c1d84db9faec') diff --git a/var/spack/repos/builtin/packages/r-fastmatch/package.py b/var/spack/repos/builtin/packages/r-fastmatch/package.py index f2611383e7..ae2e4cefdf 100644 --- a/var/spack/repos/builtin/packages/r-fastmatch/package.py +++ b/var/spack/repos/builtin/packages/r-fastmatch/package.py @@ -7,13 +7,16 @@ from spack import * class RFastmatch(RPackage): - """Package providing a fast match() replacement for cases that require - repeated look-ups. It is slightly faster that R's built-in match() - function on first match against a table, but extremely fast on any - subsequent lookup as it keeps the hash table in memory.""" + """Fast 'match()' Function. - homepage = "https://www.rforge.net/fastmatch" - url = "https://cloud.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fastmatch" + Package providing a fast match() replacement for cases that require + repeated look-ups. It is slightly faster that R's built-in match() function + on first match against a table, but extremely fast on any subsequent lookup + as it keeps the hash table in memory.""" + cran = "fastmatch" + + version('1.1-3', sha256='1defa0b08bc3f48e4c3e4ba8df4f1b9e8299932fd8c747c67d32de44f90b9861') version('1.1-0', sha256='20b51aa4838dbe829e11e951444a9c77257dcaf85130807508f6d7e76797007d') + + depends_on('r@2.3.0:', type=('build', 'run'), when='@1.1-3:') diff --git a/var/spack/repos/builtin/packages/r-fastmatrix/package.py b/var/spack/repos/builtin/packages/r-fastmatrix/package.py index 720fb900e2..8cbc2401df 100644 --- a/var/spack/repos/builtin/packages/r-fastmatrix/package.py +++ b/var/spack/repos/builtin/packages/r-fastmatrix/package.py @@ -7,15 +7,28 @@ from spack import * class RFastmatrix(RPackage): - """Fast Computation of some Matrices Useful in Statistics + """Fast Computation of some Matrices Useful in Statistics. Small set of functions to fast computation of some matrices and operations - useful in statistics.""" + useful in statistics and econometrics. Currently, there are functions for + efficient computation of duplication, commutation and symmetrizer matrices + with minimal storage requirements. Some commonly used matrix decompositions + (LU and LDL), basic matrix operations (for instance, Hadamard, Kronecker + products and the Sherman-Morrison formula) and iterative solvers for linear + systems are also available. In addition, the package includes a number of + common statistical procedures such as the sweep operator, weighted mean and + covariance matrix using an online algorithm, linear regression (using + Cholesky, QR, SVD, sweep operator and conjugate gradients methods), ridge + regression (with optimal selection of the ridge parameter considering the + GCV procedure), functions to compute the multivariate skewness, kurtosis, + Mahalanobis distance (checking the positive defineteness) and the + Wilson-Hilferty transformation of chi squared variables. Furthermore, the + package provides interfaces to C code callable by another C code from other + R packages.""" - homepage = "https://faosorios.github.io/fastmatrix/" - url = "https://cloud.r-project.org/src/contrib/fastmatrix_0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fastmatrix" + cran = "fastmatrix" + version('0.3-8196', sha256='72fae07c627b995a091ccc3e14b2b2167474e3b1f14d723e87252538cf978fb6') version('0.3', sha256='d92e789454a129db5f6f5b23e0d2245f3d55ff34b167427af265b9a6331e7c21') depends_on('r@3.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fda/package.py b/var/spack/repos/builtin/packages/r-fda/package.py index d8147e9961..6b22e264b0 100644 --- a/var/spack/repos/builtin/packages/r-fda/package.py +++ b/var/spack/repos/builtin/packages/r-fda/package.py @@ -5,7 +5,9 @@ class RFda(RPackage): - """These functions were developed to support functional data + """Functional Data Analysis. + + These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). """ diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py index f01c1cd83f..51e012e40a 100644 --- a/var/spack/repos/builtin/packages/r-ff/package.py +++ b/var/spack/repos/builtin/packages/r-ff/package.py @@ -7,7 +7,8 @@ from spack import * class RFf(RPackage): - """Memory-Efficient Storage of Large Data on Disk and Fast Access Functions + """Memory-Efficient Storage of Large Data on Disk and Fast Access + Functions. The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section @@ -29,8 +30,8 @@ class RFf(RPackage): have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R - objects (using different data en/de-coding schemes) in the same process - or from multiple R processes to exploit parallelism. A wide choice of + objects (using different data en/de-coding schemes) in the same process or + from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without @@ -51,16 +52,15 @@ class RFf(RPackage): datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.x """ - homepage = "https://ff.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/ff_2.2-13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ff" + cran = "ff" + version('4.0.5', sha256='9aba9e271144ec224063ddba0d791e2fcdb9c912d48fdc49e204fce628355037') version('4.0.4', sha256='22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5') version('2.2-14', sha256='1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0') version('2.2-13', sha256='8bfb08afe0651ef3c23aaad49208146d5f929af5af12a25262fe7743fa346ddb') depends_on('r@2.10.1:', type=('build', 'run')) depends_on('r-bit@1.1-13:', type=('build', 'run')) - depends_on('r-bit@4.0.0:', when='@4.0.4:', type=('build', 'run')) + depends_on('r-bit@4.0.0:', type=('build', 'run'), when='@4.0.4:') patch('utk_platform_macros.hpp.patch', when='target=aarch64:') diff --git a/var/spack/repos/builtin/packages/r-fftwtools/package.py b/var/spack/repos/builtin/packages/r-fftwtools/package.py index 7d61f5d1eb..a5595e07f8 100644 --- a/var/spack/repos/builtin/packages/r-fftwtools/package.py +++ b/var/spack/repos/builtin/packages/r-fftwtools/package.py @@ -8,7 +8,7 @@ from spack import * class RFftwtools(RPackage): """Wrapper for 'FFTW3' Includes: One-Dimensional Univariate, - One-Dimensional Multivariate, and Two-Dimensional Transform + One-Dimensional Multivariate, and Two-Dimensional Transform. Provides a wrapper for several 'FFTW' functions. This package provides access to the two-dimensional 'FFT', the multivariate 'FFT', and the @@ -18,12 +18,12 @@ class RFftwtools(RPackage): functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.""" - homepage = "https://github.com/krahim/fftwtools" - url = "https://cloud.r-project.org/src/contrib/fftwtools_0.9-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fftwtools" + cran = "fftwtools" + version('0.9-11', sha256='f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f') version('0.9-9', sha256='a9273b7e495d228d740ab4525467e4bbefe8614bd2d97e7234017f1305f51441') version('0.9-8', sha256='4641c8cd70938c2a8bde0b6da6cf7f83e96175ef52f1ca42ec3920a1dabf1bdb') depends_on('r@2.15.2:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run'), when='@0.9-11:') depends_on('fftw@3.1.2:') diff --git a/var/spack/repos/builtin/packages/r-fields/package.py b/var/spack/repos/builtin/packages/r-fields/package.py index 08251a9120..bbb38ed793 100644 --- a/var/spack/repos/builtin/packages/r-fields/package.py +++ b/var/spack/repos/builtin/packages/r-fields/package.py @@ -7,7 +7,7 @@ from spack import * class RFields(RPackage): - """Tools for Spatial Data + """Tools for Spatial Data. For curve, surface and function fitting with an emphasis; on splines, spatial data, geostatistics, and spatial statistics. The major methods; @@ -34,13 +34,13 @@ class RFields(RPackage): URL; for a vignette on using this package and some background on spatial statistics.""" - homepage = "https://github.com/NCAR/Fields" - url = "https://cloud.r-project.org/src/contrib/fields_9.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fields" + cran = "fields" + version('13.3', sha256='c652838b1ae7eb368831522824bfbc1d1db7b9d1db5e9bb52b194098549944c3') version('11.6', sha256='8600d1d992c40668cc2ab01b3c17d0e1bd44a001ec7ba9f468bc0e9ef87c59db') version('9.9', sha256='262f03c630773b580c7162ab2a031c894ca489fd83989fd8a2f67573306e78e1') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-spam', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run'), when='@13.3:') depends_on('r-maps', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index 49342eaa81..b9ec258173 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -7,7 +7,9 @@ from spack import * class RFilehash(RPackage): - """Implements a simple key-value style database where character string keys + """Simple Key-Value Database. + + Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be @@ -17,9 +19,7 @@ class RFilehash(RPackage): are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.""" - homepage = "https://cloud.r-project.org/package=filehash" - url = "https://cloud.r-project.org/src/contrib/filehash_2.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/filehash" + cran = "filehash" version('2.4-2', sha256='b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93') version('2.4-1', sha256='d0e087d338d89372c251c18fc93b53fb24b1750ea154833216ff16aff3b1eaf4') diff --git a/var/spack/repos/builtin/packages/r-filelock/package.py b/var/spack/repos/builtin/packages/r-filelock/package.py new file mode 100644 index 0000000000..552a3fd654 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-filelock/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 RFilelock(RPackage): + """Portable File Locking. + + Place an exclusive or shared lock on a file. It uses 'LockFile' on Windows + and 'fcntl' locks on Unix-like systems.""" + + cran = "filelock" + + version('1.0.2', sha256='ac2915950789b16c43a625a2b8dab6ba423588db4a7d0daa75b74518b82b1403') + + depends_on('r-callr@2.0.0:', type=('build', 'run')) + depends_on('r-covr', type=('build', 'run')) + depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-findpython/package.py b/var/spack/repos/builtin/packages/r-findpython/package.py index ca1d51a327..516cc65f1b 100644 --- a/var/spack/repos/builtin/packages/r-findpython/package.py +++ b/var/spack/repos/builtin/packages/r-findpython/package.py @@ -9,10 +9,9 @@ from spack import * class RFindpython(RPackage): """Package designed to find an acceptable python binary.""" - homepage = "https://github.com/trevorld/findpython" - url = "https://cloud.r-project.org/src/contrib/findpython_1.0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/findpython" + cran = "findpython" + version('1.0.7', sha256='59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149') version('1.0.5', sha256='3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145') version('1.0.4', sha256='a58fb46d53d3bdea1e00b2f4f9bdb5e98be9329ea9d8e2fe150d91462e6bccfd') version('1.0.3', sha256='5486535ae2f0a123b630d8eabf93a61b730765f55dfcc8ef4f6e56e7c49408f8') diff --git a/var/spack/repos/builtin/packages/r-fit-models/package.py b/var/spack/repos/builtin/packages/r-fit-models/package.py index 52dd6a557d..85933ca59b 100644 --- a/var/spack/repos/builtin/packages/r-fit-models/package.py +++ b/var/spack/repos/builtin/packages/r-fit-models/package.py @@ -7,7 +7,7 @@ from spack import * class RFitModels(RPackage): - """Compare Fitted Models + """Compare Fitted Models. The fit.models function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the robust package to @@ -19,9 +19,7 @@ class RFitModels(RPackage): methods (e.g., classical, robust, Bayesian, regularized, etc.) more generally.""" - homepage = "https://cloud.r-project.org/package=fit.models" - url = "https://cloud.r-project.org/src/contrib/fit.models_0.5-14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fit.models" + cran = "fit.models" version('0.64', sha256='f70806bfa85a05337fa5a665264d640e307584714a07a329fbe96c86b0e864da') version('0.5-14', sha256='93b9d119e97b36c648a19c891fc5e69f5306eb5b9bac16bf377555057afd4b6e') diff --git a/var/spack/repos/builtin/packages/r-fitdistrplus/package.py b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py index 2e2393e1df..5d21466bb4 100644 --- a/var/spack/repos/builtin/packages/r-fitdistrplus/package.py +++ b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py @@ -7,7 +7,8 @@ from spack import * class RFitdistrplus(RPackage): - """Help to Fit of a Parametric Distribution to Non-Censored or Censored Data + """Help to Fit of a Parametric Distribution to Non-Censored or Censored + Data. Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or @@ -19,14 +20,15 @@ class RFitdistrplus(RPackage): versions of MLE, MME and QME are available. See e.g. Casella & Berger (2002). Statistical inference. Pacific Grove.""" - homepage = "https://lbbe.univ-lyon1.fr/fitdistrplus.html" - url = "https://cloud.r-project.org/src/contrib/fitdistrplus_1.0-14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fitdistrplus" + cran = "fitdistrplus" + version('1.1-6', sha256='17c2990041a3bb7479f3c3a6d13d96c989db8eaddab17eff7e1fbe172a5b96be') version('1.1-3', sha256='776d5456e14398e44b78b3d7db526559bb7a3537e546a29c88aa192141c756de') version('1.0-14', sha256='85082590f62aa08d99048ea3414c5cc1e5b780d97b3779d2397c6cb435470083') depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.1-6:') depends_on('r-mass', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) - depends_on('r-npsurv', when='@:1.0-14', type=('build', 'run')) + + depends_on('r-npsurv', type=('build', 'run'), when='@:1.0-14') diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py index dc956a56fc..ceb4be7663 100644 --- a/var/spack/repos/builtin/packages/r-flashclust/package.py +++ b/var/spack/repos/builtin/packages/r-flashclust/package.py @@ -7,11 +7,9 @@ from spack import * class RFlashclust(RPackage): - """flashClust: Implementation of optimal hierarchical clustering""" + """Implementation of optimal hierarchical clustering.""" - homepage = "https://cloud.r-project.org/package=flashClust" - url = "https://cloud.r-project.org/src/contrib/flashClust_1.01-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/flashClust" + cran = "flashClust" version('1.01-2', sha256='48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450') diff --git a/var/spack/repos/builtin/packages/r-flexclust/package.py b/var/spack/repos/builtin/packages/r-flexclust/package.py index 508f11d498..04d86bc306 100644 --- a/var/spack/repos/builtin/packages/r-flexclust/package.py +++ b/var/spack/repos/builtin/packages/r-flexclust/package.py @@ -7,7 +7,9 @@ from spack import * class RFlexclust(RPackage): - """The main function kcca implements a general framework for k-centroids + """Flexible Cluster Algorithms. + + The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for @@ -15,9 +17,7 @@ class RFlexclust(RPackage): centroids, ...), and bootstrap methods for the analysis of cluster stability.""" - homepage = "https://cloud.r-project.org/package=flexclust" - url = "https://cloud.r-project.org/src/contrib/flexclust_1.3-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/flexclust" + cran = "flexclust" version('1.4-0', sha256='82fe445075a795c724644864c7ee803c5dd332a89ea9e6ccf7cd1ae2d1ecfc74') version('1.3-5', sha256='dbf49969c93a7b314d9dc3299a0764ed9a804ba7dcbdc08a1235f244f4b85059') diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py index 8bd7952261..3aebc2812b 100644 --- a/var/spack/repos/builtin/packages/r-flexmix/package.py +++ b/var/spack/repos/builtin/packages/r-flexmix/package.py @@ -7,7 +7,7 @@ from spack import * class RFlexmix(RPackage): - """Flexible Mixture Modeling + """Flexible Mixture Modeling. A general framework for finite mixtures of regression models using the EM algorithm is implemented. The E-step and all data handling are provided, @@ -15,9 +15,7 @@ class RFlexmix(RPackage): Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.""" - homepage = "https://cloud.r-project.org/package=flexmix" - url = "https://cloud.r-project.org/src/contrib/flexmix_2.3-14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/flexmix" + cran = "flexmix" version('2.3-17', sha256='36019b7833032409ac61720dd625fa5a581a1d8bcba9045b04979c90907b5649') version('2.3-15', sha256='ba444c0bfe33ab87d440ab590c06b03605710acd75811c1622253171bb123f43') diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py index ae18d71ade..f54d5f881b 100644 --- a/var/spack/repos/builtin/packages/r-fnn/package.py +++ b/var/spack/repos/builtin/packages/r-fnn/package.py @@ -7,13 +7,13 @@ from spack import * class RFnn(RPackage): - """Cover-tree and kd-tree fast k-nearest neighbor search algorithms and + """Fast Nearest Neighbor Search Algorithms and Applications. + + Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.""" - homepage = "https://cloud.r-project.org/package=FNN" - url = "https://cloud.r-project.org/src/contrib/FNN_1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/FNN" + cran = "FNN" version('1.1.3', sha256='de763a25c9cfbd19d144586b9ed158135ec49cf7b812938954be54eb2dc59432') version('1.1.2.2', sha256='b51a60fbbeff58c48cc90c2023c48972d5082d68efd02284c17ccd9820986326') diff --git a/var/spack/repos/builtin/packages/r-fontawesome/package.py b/var/spack/repos/builtin/packages/r-fontawesome/package.py new file mode 100644 index 0000000000..0e3672d429 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fontawesome/package.py @@ -0,0 +1,24 @@ +# 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 RFontawesome(RPackage): + """Easily Work with 'Font Awesome' Icons. + + Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents + and 'Shiny' apps. These icons can be inserted into HTML content through + inline 'SVG' tags or 'i' tags. There is also a utility function for + exporting 'Font Awesome' icons as 'PNG' images for those situations where + raster graphics are needed.""" + + cran = "fontawesome" + + version('0.2.2', sha256='572db64d1b3c9be301935e0ca7baec69f3a6e0aa802e23f1f224b3724259df64') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rlang@0.4.10:', type=('build', 'run')) + depends_on('r-htmltools@0.5.1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-forcats/package.py b/var/spack/repos/builtin/packages/r-forcats/package.py index 686eb8acfd..2aa1cbd379 100644 --- a/var/spack/repos/builtin/packages/r-forcats/package.py +++ b/var/spack/repos/builtin/packages/r-forcats/package.py @@ -7,14 +7,13 @@ from spack import * class RForcats(RPackage): - """Tools for Working with Categorical Variables (Factors) + """Tools for Working with Categorical Variables (Factors). Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').""" - homepage = "https://forcats.tidyverse.org/" cran = "forcats" version('0.5.1', sha256='c4fb96e874e2bedaa8a1aa32ea22abdee7906d93b5c5c7b42c0894c0c5b6a289') @@ -24,8 +23,8 @@ class RForcats(RPackage): version('0.2.0', sha256='b5bce370422d4c0ec9509249ae645373949bfbe9217cdf50dce2bfbdad9f7cd7') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r@3.2:', when='@0.5.0:', type=('build', 'run')) - depends_on('r-ellipsis', when='@0.4.0:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@0.5.0:') + depends_on('r-ellipsis', type=('build', 'run'), when='@0.4.0:') depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-rlang', when='@0.4.0:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@0.4.0:') depends_on('r-tibble', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py index d0f62d0f6a..36c69a3826 100644 --- a/var/spack/repos/builtin/packages/r-foreach/package.py +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -7,19 +7,17 @@ from spack import * class RForeach(RPackage): - """Provides Foreach Looping Construct + """Provides Foreach Looping Construct. - Support for the foreach looping construct. Foreach is an idiom that - allows for iterating over elements in a collection, without the use of an - explicit loop counter. This package in particular is intended to be used - for its return value, rather than for its side effects. In that sense, it - is similar to the standard lapply function, but doesn't require the - evaluation of a function. Using foreach without side effects also - facilitates executing the loop in parallel.""" + Support for the foreach looping construct. Foreach is an idiom that allows + for iterating over elements in a collection, without the use of an explicit + loop counter. This package in particular is intended to be used for its + return value, rather than for its side effects. In that sense, it is + similar to the standard lapply function, but doesn't require the evaluation + of a function. Using foreach without side effects also facilitates + executing the loop in parallel.""" - homepage = "https://cloud.r-project.org/package=foreach" - url = "https://cloud.r-project.org/src/contrib/foreach_1.4.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/foreach" + cran = "foreach" version('1.5.1', sha256='fb5ad69e295618c52b2ac7dff84a0771462870a97345374d43b3de2dc31a68e1') version('1.4.7', sha256='95632c0b1182fc01490718d82fa3b2bce864f2a011ae53282431c7c2a3f5f160') diff --git a/var/spack/repos/builtin/packages/r-forecast/package.py b/var/spack/repos/builtin/packages/r-forecast/package.py index d409418343..77fdd9cc8d 100644 --- a/var/spack/repos/builtin/packages/r-forecast/package.py +++ b/var/spack/repos/builtin/packages/r-forecast/package.py @@ -7,16 +7,16 @@ from spack import * class RForecast(RPackage): - """Forecasting Functions for Time Series and Linear Models + """Forecasting Functions for Time Series and Linear Models. - Methods and tools for displaying and analysing univariate time - series forecasts including exponential smoothing via state space - models and automatic ARIMA modelling.""" + Methods and tools for displaying and analysing univariate time series + forecasts including exponential smoothing via state space models and + automatic ARIMA modelling.""" - homepage = "https://cloud.r-project.org/package=forecast" - url = "https://cloud.r-project.org/src/contrib/forecast_8.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/forecast" + cran = "forecast" + version('8.16', sha256='9f01eb895a883a7e1e23725b167b46edc1b0b152fd4120278aaa5f7b2621767f') + version('8.15', sha256='c73aabed083095b457ed875c240716686fbd41d1cbafa116b7b890a54b919174') version('8.13', sha256='490e3a2beb71c238dd26e7afa0b33394b9906dd0dc54712d4808894d5aa1386f') version('8.8', sha256='d077074d77d3ea00e9215c828b3689a8c841a16af1e6859bb2dfdede081c2c1d') version('8.6', sha256='4279e4f700e26310bae39419ab4a9b5918a850148667a5e577a4807d53eb4d02') @@ -32,6 +32,6 @@ class RForecast(RPackage): depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-timedate', type=('build', 'run')) depends_on('r-tseries', type=('build', 'run')) - depends_on('r-urca', when='@8.6:', type=('build', 'run')) + depends_on('r-urca', type=('build', 'run'), when='@8.6:') depends_on('r-zoo', type=('build', 'run')) depends_on('r-rcpparmadillo@0.2.35:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py index d5c04e355c..49bc58802a 100644 --- a/var/spack/repos/builtin/packages/r-foreign/package.py +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -14,14 +14,13 @@ class RForeign(RPackage): 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.""" - homepage = "https://cloud.r-project.org/package=foreign" - url = "https://cloud.r-project.org/src/contrib/foreign_0.8-66.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/foreign" + cran = "foreign" + version('0.8-82', sha256='f8ed0684d59bec7f3a39cde1aa5ec7b3e6e36aaecacb28120c9c54f7b13f80fb') version('0.8-81', sha256='1ae8f9f18f2a037697fa1a9060417ff255c71764f0145080b2bd23ba8262992c') version('0.8-72', sha256='439c17c9cd387e180b1bb640efff3ed1696b1016d0f7b3b3b884e89884488c88') version('0.8-70.2', sha256='ae82fad68159860b8ca75b49538406ef3d2522818e649d7ccc209c18085ef179') version('0.8-66', sha256='d7401e5fcab9ce6e697d3520dbb8475e229c30341c0004c4fa489c82aa4447a4') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@4.0.0:', when='@0.8-81:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@0.8-81:') diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 9489d7288e..c503293619 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -8,19 +8,21 @@ from spack import * class RFormatr(RPackage): - """Provides a function tidy_source() to format R source code. Spaces and + """Format R Code Automatically. + + Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.""" - homepage = "https://cloud.r-project.org/package=formatR" - url = "https://cloud.r-project.org/src/contrib/formatR_1.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/formatR" + cran = "formatR" + version('1.11', sha256='bd81662d09cf363652761e63ba5969c71be4dd5ae6fc9098f440d6729254a30c') version('1.7', sha256='a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb') version('1.6', sha256='f5c98f0c3506ca51599671a2cdbc17738d0f326e8e3bb18b7a38e9f172122229') version('1.5', sha256='874c197ae3720ec11b44984a055655b99a698e1912104eb9034c11fdf6104da7') version('1.4', sha256='6ec47a7b1f18efb5fd7559b81427363b66415d81cded9d5e7e2907e900b67ebb') depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r@3.2.3:', type=('build', 'run'), when='@1.11:') diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py index 0bc92df4ce..413cd61380 100644 --- a/var/spack/repos/builtin/packages/r-formula/package.py +++ b/var/spack/repos/builtin/packages/r-formula/package.py @@ -8,15 +8,13 @@ from spack import * class RFormula(RPackage): - """Extended Model Formulas + """Extended Model Formulas. Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see <doi:10.18637/jss.v034.i01>).""" - homepage = "https://cloud.r-project.org/package=Formula" - url = "https://cloud.r-project.org/src/contrib/Formula_1.2-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Formula" + cran = "Formula" version('1.2-4', sha256='cb70e373b5ed2fc8450937fb3321d37dfd22dcc6f07cb872a419d51205125caf') version('1.2-3', sha256='1411349b20bd09611a9fd0ee6d15f780c758ad2b0e490e908facb49433823872') diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py index a052275b82..d5d626c31b 100644 --- a/var/spack/repos/builtin/packages/r-fpc/package.py +++ b/var/spack/repos/builtin/packages/r-fpc/package.py @@ -7,7 +7,7 @@ from spack import * class RFpc(RPackage): - """Flexible Procedures for Clustering + """Flexible Procedures for Clustering. Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian @@ -26,9 +26,7 @@ class RFpc(RPackage): Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.""" - homepage = "https://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cloud.r-project.org/src/contrib/fpc_2.1-10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fpc" + cran = "fpc" version('2.2-9', sha256='29b0006e96c8645645d215d3378551bd6525aaf45abde2d9f12933cf6e75fa38') version('2.2-3', sha256='8100a74e6ff96b1cd65fd22494f2d200e54ea5ea533cfca321fa494914bdc3b7') @@ -45,5 +43,6 @@ class RFpc(RPackage): depends_on('r-diptest', type=('build', 'run')) depends_on('r-robustbase', type=('build', 'run')) depends_on('r-kernlab', type=('build', 'run')) - depends_on('r-trimcluster', when='@:2.1-10', type=('build', 'run')) - depends_on('r-mvtnorm', when='@:2.2-2', type=('build', 'run')) + + depends_on('r-trimcluster', type=('build', 'run'), when='@:2.1-10') + depends_on('r-mvtnorm', type=('build', 'run'), when='@:2.2-2') diff --git a/var/spack/repos/builtin/packages/r-fpcompare/package.py b/var/spack/repos/builtin/packages/r-fpcompare/package.py index d8e5b2cdd6..c1fe27160e 100644 --- a/var/spack/repos/builtin/packages/r-fpcompare/package.py +++ b/var/spack/repos/builtin/packages/r-fpcompare/package.py @@ -7,20 +7,18 @@ from spack import * class RFpcompare(RPackage): - """Reliable Comparison of Floating Point Numbers + """Reliable Comparison of Floating Point Numbers. Comparisons of floating point numbers are problematic due to errors - associated with the binary representation of decimal numbers. Despite - being aware of these problems, people still use numerical methods - that fail to account for these and other rounding errors (this pitfall - is the first to be highlighted in Circle 1 of Burns (2012) 'The R - Inferno' <https://www.burns-stat.com/pages/Tutor/R_inferno.pdf>). This - package provides new relational operators useful for performing - floating point number comparisons with a set tolerance.""" - - homepage = "https://github.com/PredictiveEcology/fpCompare" - url = "https://cloud.r-project.org/src/contrib/fpCompare_0.2.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fpCompare" + associated with the binary representation of decimal numbers. Despite being + aware of these problems, people still use numerical methods that fail to + account for these and other rounding errors (this pitfall is the first to + be highlighted in Circle 1 of Burns (2012) 'The R Inferno' + <https://www.burns-stat.com/pages/Tutor/R_inferno.pdf>). This package + provides new relational operators useful for performing floating point + number comparisons with a set tolerance.""" + + cran = "fpCompare" maintainers = ['dorton21'] diff --git a/var/spack/repos/builtin/packages/r-fracdiff/package.py b/var/spack/repos/builtin/packages/r-fracdiff/package.py index 25ee5759fc..b87bad6255 100644 --- a/var/spack/repos/builtin/packages/r-fracdiff/package.py +++ b/var/spack/repos/builtin/packages/r-fracdiff/package.py @@ -7,16 +7,14 @@ from spack import * class RFracdiff(RPackage): - """Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models + """Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models. Maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); including inference and basic methods. Some alternative algorithms to estimate "H".""" - homepage = "https://cloud.r-project.org/package=fracdiff" - url = "https://cloud.r-project.org/src/contrib/fracdiff_1.4-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fracdiff" + cran = "fracdiff" version('1.5-1', sha256='b8103b32a4ca3a59dda1624c07da08ecd144c7a91a747d1f4663e99421950eb6') version('1.4-2', sha256='983781cedc2b4e3ba9fa020213957d5133ae9cd6710bc61d6225728e2f6e850e') diff --git a/var/spack/repos/builtin/packages/r-fs/package.py b/var/spack/repos/builtin/packages/r-fs/package.py index 8ae9563ba9..1d90807c3c 100644 --- a/var/spack/repos/builtin/packages/r-fs/package.py +++ b/var/spack/repos/builtin/packages/r-fs/package.py @@ -7,18 +7,18 @@ from spack import * class RFs(RPackage): - """Cross-Platform File System Operations Based on 'libuv' + """Cross-Platform File System Operations Based on 'libuv'. - A cross-platform interface to file system operations, built on top of - the 'libuv' C library.""" + A cross-platform interface to file system operations, built on top of the + 'libuv' C library.""" - homepage = "https://ggplot2.tidyverse.org/" - url = "https://cloud.r-project.org/src/contrib/fs_1.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/fs" + cran = "fs" + version('1.5.2', sha256='35cad1781d6d17c1feb56adc4607079c6844b63794d0ce1e74bb18dbc11e1987') version('1.5.0', sha256='36df1653571de3c628a4f769c4627f6ac53d0f9e4106d9d476afb22ae9603897') version('1.3.1', sha256='d6934dca8f835d8173e3fb9fd4d5e2740c8c04348dd2bcc57df1b711facb46bc') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r-rcpp', when='@:1.3.1', type=('build', 'run')) depends_on('gmake', type='build') + + depends_on('r-rcpp', type=('build', 'run'), when='@:1.3.1') diff --git a/var/spack/repos/builtin/packages/r-futile-logger/package.py b/var/spack/repos/builtin/packages/r-futile-logger/package.py index e1a06817b6..ff9f032de1 100644 --- a/var/spack/repos/builtin/packages/r-futile-logger/package.py +++ b/var/spack/repos/builtin/packages/r-futile-logger/package.py @@ -7,13 +7,13 @@ from spack import * class RFutileLogger(RPackage): - """Provides a simple yet powerful logging utility. Based loosely on log4j, - futile.logger takes advantage of R idioms to make logging a convenient - and easy to use replacement for cat and print statements.""" + """A Logging Utility for R. - homepage = "https://cloud.r-project.org/package=futile.logger" - url = "https://cloud.r-project.org/src/contrib/futile.logger_1.4.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/futile.logger" + Provides a simple yet powerful logging utility. Based loosely on log4j, + futile.logger takes advantage of R idioms to make logging a convenient and + easy to use replacement for cat and print statements.""" + + cran = "futile.logger" version('1.4.3', sha256='5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4') diff --git a/var/spack/repos/builtin/packages/r-futile-options/package.py b/var/spack/repos/builtin/packages/r-futile-options/package.py index 7c5c2c188c..4ee3ad1597 100644 --- a/var/spack/repos/builtin/packages/r-futile-options/package.py +++ b/var/spack/repos/builtin/packages/r-futile-options/package.py @@ -7,11 +7,11 @@ from spack import * class RFutileOptions(RPackage): - """A scoped options management framework""" + """Futile Options Management. - homepage = "https://cloud.r-project.org/package=futile.options" - url = "https://cloud.r-project.org/src/contrib/futile.options_1.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/futile.options" + A scoped options management framework.""" + + cran = "futile.options" version('1.0.1', sha256='7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570') version('1.0.0', sha256='ee84ece359397fbb63f145d11af678f5c8618570971e78cc64ac60dc0d14e8c2') diff --git a/var/spack/repos/builtin/packages/r-future-apply/package.py b/var/spack/repos/builtin/packages/r-future-apply/package.py index 6db2f3dca0..4ffc0d3c56 100644 --- a/var/spack/repos/builtin/packages/r-future-apply/package.py +++ b/var/spack/repos/builtin/packages/r-future-apply/package.py @@ -7,7 +7,7 @@ from spack import * class RFutureApply(RPackage): - """Apply Function to Elements in Parallel using Futures + """Apply Function to Elements in Parallel using Futures. Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using @@ -17,15 +17,16 @@ class RFutureApply(RPackage): with the additional feature of being able to be processed via the future framework.""" - homepage = "https://github.com/HenrikBengtsson/future.apply" - url = "https://cloud.r-project.org/src/contrib/future.apply_1.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/future.apply" + cran = "future.apply" + version('1.8.1', sha256='0d5bc3cb0289665bb27ae4ccad51fcc5ebf6dca46872b0a4e57790b9dc0aa6c7') version('1.7.0', sha256='2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db') version('1.3.0', sha256='6374eca49bb81e05c013509c8e324cf9c5d023f9f8217b29ce7b7e12025ca371') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-future@1.13.0:', type=('build', 'run')) - depends_on('r-future@1.17.0:', when='@1.7.0:', type=('build', 'run')) + depends_on('r-future@1.17.0:', type=('build', 'run'), when='@1.7.0:') + depends_on('r-future@1.21.0:', type=('build', 'run'), when='@1.8.1:') depends_on('r-globals@0.12.4:', type=('build', 'run')) - depends_on('r-globals@0.12.5:', when='@1.7.0:', type=('build', 'run')) + depends_on('r-globals@0.12.5:', type=('build', 'run'), when='@1.7.0:') + depends_on('r-globals@0.14.0:', type=('build', 'run'), when='@1.8.1:') diff --git a/var/spack/repos/builtin/packages/r-future/package.py b/var/spack/repos/builtin/packages/r-future/package.py index aa1f03aaa1..a3ca388177 100644 --- a/var/spack/repos/builtin/packages/r-future/package.py +++ b/var/spack/repos/builtin/packages/r-future/package.py @@ -7,12 +7,12 @@ from spack import * class RFuture(RPackage): - """Unified Parallel and Distributed Processing in R for Everyone + """Unified Parallel and Distributed Processing in R for Everyone. - The purpose of this package is to provide a lightweight and unified - Future API for sequential and parallel processing of R expression via - futures. The simplest way to evaluate an expression in parallel is to use - 'x %<-% { expression }' with 'plan(multiprocess)'. This package implements + The purpose of this package is to provide a lightweight and unified Future + API for sequential and parallel processing of R expression via futures. The + simplest way to evaluate an expression in parallel is to use 'x %<-% { + expression }' with 'plan(multiprocess)'. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. @@ -24,18 +24,18 @@ class RFuture(RPackage): automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.""" - homepage = "https://github.com/HenrikBengtsson/future" cran = "future" + version('1.23.0', sha256='d869c80e837c0937a414b8050deff081aefeac586b796f3d634d64f0f4fdb8f8') version('1.22.1', sha256='87b24a85caf08e1d809eab28f9258444105cd7788eee2e3e2f21727ba3bbedcd') version('1.21.0', sha256='909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d') version('1.14.0', sha256='0a535010d97a01b21aaf9d863603e44359335e273019c1e1980bbb5b2917dbcb') depends_on('r-digest', type=('build', 'run')) depends_on('r-globals@0.12.4:', type=('build', 'run')) - depends_on('r-globals@0.13.1:', when='@1.21.0:', type=('build', 'run')) - depends_on('r-globals@0.14.0:', when='@1.22.0:', type=('build', 'run')) + depends_on('r-globals@0.13.1:', type=('build', 'run'), when='@1.21.0:') + depends_on('r-globals@0.14.0:', type=('build', 'run'), when='@1.22.0:') depends_on('r-listenv@0.7.0:', type=('build', 'run')) - depends_on('r-listenv@0.8.0:', when='@1.21.0:', type=('build', 'run')) - depends_on('r-parallelly@1.21.0:', when='@1.21.0:', type=('build', 'run')) - depends_on('r-parallelly@1.26.1:', when='@1.22.0:', type=('build', 'run')) + depends_on('r-listenv@0.8.0:', type=('build', 'run'), when='@1.21.0:') + depends_on('r-parallelly@1.21.0:', type=('build', 'run'), when='@1.21.0:') + depends_on('r-parallelly@1.26.1:', type=('build', 'run'), when='@1.22.0:') diff --git a/var/spack/repos/builtin/packages/r-gamlss-data/package.py b/var/spack/repos/builtin/packages/r-gamlss-data/package.py index 287d434010..7e97a46452 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-data/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-data/package.py @@ -7,14 +7,18 @@ from spack import * class RGamlssData(RPackage): - """gamlss.data: GAMLSS Data""" + """GAMLSS Data. - homepage = "https://cloud.r-project.org/package=gamlss.data" - url = "https://cloud.r-project.org/src/contrib/gamlss.data_5.1-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gamlss.data/" + Data used as examples in the current two books on Generalised Additive + Models for Location Scale and Shape introduced by Rigby and Stasinopoulos + (2005), <doi:10.1111/j.1467-9876.2005.00510.x>.""" + cran = "gamlss.data" + + version('6.0-2', sha256='dbb3b6f855540928ccdbda497f8d552144895e34565799e8b595e704096db71e') version('5.1-4', sha256='0d3777d8c3cd76cef273aa6bde40a91688719be401195ed9bfd1e85bd7d5eeb5') version('5.1-3', sha256='4941180e7eebe97678ba02ca24c2a797bcb69d92cd34600215a94110e2a70470') version('5.1-0', sha256='0aad438ea1aa6395677e52cd2cb496f9f4c9ba2d39edc92c8cb42e7fc91fe6c1') depends_on('r@2.10:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@6.0-2:') diff --git a/var/spack/repos/builtin/packages/r-gamlss-dist/package.py b/var/spack/repos/builtin/packages/r-gamlss-dist/package.py index 1c7e0633ca..0cb7a58c6f 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-dist/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-dist/package.py @@ -7,8 +7,8 @@ from spack import * class RGamlssDist(RPackage): - """dist: Distributions for Generalized Additive Models for Location Scale - and Shape + """Distributions for Generalized Additive Models for Location Scale and + Shape. A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, @@ -19,10 +19,9 @@ class RGamlssDist(RPackage): infinity or 0 to 1, by using a ''log'' or a ''logit' transformation respectively.""" - homepage = "https://cloud.r-project.org/package=gamlss.dist" - url = "https://cloud.r-project.org/src/contrib/gamlss.dist_5.1-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gamlss.dist/" + cran = "gamlss.dist" + version('6.0-1', sha256='b563b4de6bcedcfa4f8d29198a47004e38fd2de6e0509c788015d4e3feb18154') version('5.1-7', sha256='9871c38c893a8df7874c533351858dfe4e7587c71021dbbf88c0c76ff3c0ef5b') version('5.1-4', sha256='343c6ca0fd8a1c1dfdf9ffc65c95d4dae0c6c80b3e60fccba003e5171f3d287e') version('5.1-3', sha256='87fd643c82579519b67c66c1d87383fa1e203e8b09f607649ee7bce142bda404') diff --git a/var/spack/repos/builtin/packages/r-gamlss/package.py b/var/spack/repos/builtin/packages/r-gamlss/package.py index 1c02d995aa..c57b195ce4 100644 --- a/var/spack/repos/builtin/packages/r-gamlss/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss/package.py @@ -7,7 +7,7 @@ from spack import * class RGamlss(RPackage): - """Generalised Additive Models for Location Scale and Shape + """Generalised Additive Models for Location Scale and Shape. Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), @@ -16,10 +16,9 @@ class RGamlss(RPackage): distribution of the response variable are modelled using explanatory variables.""" - homepage = "https://cloud.r-project.org/package=gamlss" - url = "https://cloud.r-project.org/src/contrib/gamlss_5.1-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gamlss/" + cran = "gamlss" + version('5.3-4', sha256='72707187471fd35c5379ae8c9b7b0ca87e302557f09cb3979d1cdb2e2500b01a') version('5.2-0', sha256='d3927547109064cbe7b0f955144f53204b5dc86c6b2dbc8f0551a74140ab02e1') version('5.1-4', sha256='e2fc36fe6ca3a69d69cdafd9533a4ff35090fdfb01df126f6a49156f4aa3376c') version('5.1-3', sha256='d37d121bc2acdbacc20cea04a1ed4489a575079e2a7b17b4a9823ee283857317') diff --git a/var/spack/repos/builtin/packages/r-gamm4/package.py b/var/spack/repos/builtin/packages/r-gamm4/package.py index b3d817b265..b8d76204f8 100644 --- a/var/spack/repos/builtin/packages/r-gamm4/package.py +++ b/var/spack/repos/builtin/packages/r-gamm4/package.py @@ -7,12 +7,12 @@ from spack import * class RGamm4(RPackage): - """Generalized Additive Mixed Models using 'mgcv' and 'lme4': + """Generalized Additive Mixed Models using 'mgcv' and 'lme4'. Estimate generalized additive mixed models via a version of function gamm() from 'mgcv', using 'lme4' for estimation.""" - cran = "gamm4" + cran = "gamm4" version('0.2-6', sha256='57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89') diff --git a/var/spack/repos/builtin/packages/r-gargle/package.py b/var/spack/repos/builtin/packages/r-gargle/package.py index d33095972f..ac2afcc418 100644 --- a/var/spack/repos/builtin/packages/r-gargle/package.py +++ b/var/spack/repos/builtin/packages/r-gargle/package.py @@ -14,8 +14,7 @@ class RGargle(RPackage): classes for handling common credential types and for preparing, executing, and processing HTTP requests.""" - homepage = "https://github.com/r-lib/gargle" - cran = "gargle" + cran = "gargle" version('1.2.0', sha256='4d46ca2933f19429ca5a2cfe47b4130a75c7cd9931c7758ade55bac0c091d73b') diff --git a/var/spack/repos/builtin/packages/r-gbm/package.py b/var/spack/repos/builtin/packages/r-gbm/package.py index bc2904d858..516971bcc5 100644 --- a/var/spack/repos/builtin/packages/r-gbm/package.py +++ b/var/spack/repos/builtin/packages/r-gbm/package.py @@ -7,19 +7,16 @@ from spack import * class RGbm(RPackage): - """Generalized Boosted Regression Models + """Generalized Boosted Regression Models. - An implementation of extensions to Freund and Schapire's AdaBoost - algorithm and Friedman's gradient boosting machine. Includes regression - methods for least squares, absolute loss, t-distribution loss, quantile - regression, logistic, multinomial logistic, Poisson, Cox proportional - hazards partial likelihood, AdaBoost exponential loss, Huberized hinge - loss, and Learning to Rank measures (LambdaMart). Originally developed by - Greg Ridgeway.""" + An implementation of extensions to Freund and Schapire's AdaBoost algorithm + and Friedman's gradient boosting machine. Includes regression methods for + least squares, absolute loss, t-distribution loss, quantile regression, + logistic, multinomial logistic, Poisson, Cox proportional hazards partial + likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning + to Rank measures (LambdaMart). Originally developed by Greg Ridgeway.""" - homepage = "https://cloud.r-project.org/package=gbm" - url = "https://cloud.r-project.org/src/contrib/gbm_2.1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gbm" + cran = "gbm" version('2.1.8', sha256='7d5de3b980b8f23275e86ac9bed48a497c9aa53c58e407dfd676309f38272ec1') version('2.1.5', sha256='06fbde10639dfa886554379b40a7402d1f1236a9152eca517e97738895a4466f') @@ -28,4 +25,5 @@ class RGbm(RPackage): depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) - depends_on('r-gridextra', when='@2.1.5', type=('build', 'run')) + + depends_on('r-gridextra', type=('build', 'run'), when='@2.1.5') diff --git a/var/spack/repos/builtin/packages/r-gbrd/package.py b/var/spack/repos/builtin/packages/r-gbrd/package.py index 842095de9a..e2bd9a42c4 100644 --- a/var/spack/repos/builtin/packages/r-gbrd/package.py +++ b/var/spack/repos/builtin/packages/r-gbrd/package.py @@ -7,11 +7,11 @@ from spack import * class RGbrd(RPackage): - """Provides utilities for processing Rd objects and files. Extract argument + """Utilities for processing Rd objects and files. + + Provides utilities for processing Rd objects and files. Extract argument descriptions and other parts of the help pages of functions.""" - homepage = "https://cloud.r-project.org/package=gbRd" - url = "https://cloud.r-project.org/src/contrib/gbRd_0.4-11.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gbRd" + cran = "gbRd" version('0.4-11', sha256='0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b') diff --git a/var/spack/repos/builtin/packages/r-gdalutilities/package.py b/var/spack/repos/builtin/packages/r-gdalutilities/package.py new file mode 100644 index 0000000000..154299fce1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gdalutilities/package.py @@ -0,0 +1,28 @@ +# 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 RGdalutilities(RPackage): + """Wrappers for 'GDAL' Utilities Executables. + + R's 'sf' package ships with self-contained 'GDAL' executables, including a + bare bones interface to several 'GDAL'-related utility programs + collectively known as the 'GDAL utilities'. For each of those utilities, + this package provides an R wrapper whose formal arguments closely mirror + those of the 'GDAL' command line interface. The utilities operate on data + stored in files and typically write their output to other files. Therefore, + to process data stored in any of R's more common spatial formats (i.e. + those supported by the 'sp', 'sf', and 'raster' packages), first write them + to disk, then process them with the package's wrapper functions before + reading the outputted results back into R. GDAL function arguments + introduced in GDAL version 3.2.1 or earlier are supported.""" + + cran = "gdalUtilities" + + version('1.2.0', sha256='ead446f7f77f952b72b9ed80c5e415cb9d8d30cfb2439c8d1a8156fa55e2b65b') + + depends_on('r-sf', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gdalutils/package.py b/var/spack/repos/builtin/packages/r-gdalutils/package.py index 722700083c..f6d30c4360 100644 --- a/var/spack/repos/builtin/packages/r-gdalutils/package.py +++ b/var/spack/repos/builtin/packages/r-gdalutils/package.py @@ -7,11 +7,10 @@ from spack import * class RGdalutils(RPackage): - """Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities""" + """Wrappers for the Geospatial Data Abstraction Library (GDAL) + Utilities.""" - homepage = "https://cloud.r-project.org/package=gdalUtils" - url = "https://cloud.r-project.org/src/contrib/gdalUtils_2.0.1.14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gdalUtils" + cran = "gdalUtils" version('2.0.3.2', sha256='4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f') version('2.0.1.14', sha256='890a502b2eb5f1b23655fab94caad5d32adca05b93f5db1d96d9dcde3f0e7737') diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py index 945d3de966..b336dbb3cf 100644 --- a/var/spack/repos/builtin/packages/r-gdata/package.py +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -7,27 +7,31 @@ from spack import * class RGdata(RPackage): - """Various R programming tools for data manipulation, including: - medical - unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects - ('bindData', 'cbindX', 'combine', 'interleave'), - character vector - operations ('centerText', 'startsWith', 'trim'), - factor manipulation - ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R - objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', - 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel - formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', - 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - - extricating components of date & time objects ('getYear', 'getMonth', - 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data - frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', - 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', - 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames - ('frameApply', 'wideByFactor'), - value of last evaluated expression - ('ans'), and - wrapper for 'sample' that ensures consistent behavior for - both scalar and vector arguments ('resample').""" + """Various R Programming Tools for Data Manipulation. - homepage = "https://cloud.r-project.org/package=gdata" - url = "https://cloud.r-project.org/src/contrib/gdata_2.18.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gdata" + Various R programming tools for data manipulation, including: + [1] medical unit conversions ('ConvertMedUnits', 'MedUnits'), + [2] combining objects ('bindData', 'cbindX', 'combine', 'interleave'), + [3] character vector operations ('centerText', 'startsWith', 'trim'), + [4] factor manipulation ('levels', 'reorder.factor', 'mapLevels'), + [5] obtaining information about R objects ('object.size', 'elem', 'env', + 'humanReadable', 'is.what', 'll', 'keep', 'ls.funs', 'Args','nPairs', + 'nobs'), + [6] manipulating MS-Excel formatted files ('read.xls', + 'installXLSXsupport', 'sheetCount', 'xlsFormats'), + [7] generating fixed-width format files ('write.fwf'), + [8] extricating components of date & time objects ('getYear', 'getMonth', + 'getDay', 'getHour', 'getMin', 'getSec'), + [9] operations on columns of data frames ('matchcols', 'rename.vars'), + [10] matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'), + [11] operations on vectors ('case', 'unknownToNA', 'duplicated2', + 'trimSum'), + [12] operations on data frames ('frameApply', 'wideByFactor'), + [13] value of last evaluated expression ('ans'), and + [14] wrapper for 'sample' that ensures consistent behavior for both scalar + and vector arguments ('resample').""" + + cran = "gdata" version('2.18.0', sha256='4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f') version('2.17.0', sha256='8097ec0e4868f6bf746f821cff7842f696e874bb3a84f1b2aa977ecd961c3e4e') diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py index 6ef9d56718..4d1e5822b8 100644 --- a/var/spack/repos/builtin/packages/r-geiger/package.py +++ b/var/spack/repos/builtin/packages/r-geiger/package.py @@ -7,14 +7,12 @@ from spack import * class RGeiger(RPackage): - """Analysis of Evolutionary Diversification + """Analysis of Evolutionary Diversification. Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.""" - homepage = "https://cloud.r-project.org/package=geiger" - url = "https://cloud.r-project.org/src/contrib/geiger_2.0.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/geiger" + cran = "geiger" version('2.0.7', sha256='d200736c4ad7ed4bc55a13e7d0126ddc7fed88e245cd5706d4692aaa437e9596') version('2.0.6.2', sha256='9153047b608d652821251206d1450bb3f517c8884379f498a695315574ae001d') @@ -32,4 +30,4 @@ class RGeiger(RPackage): depends_on('r-coda', type=('build', 'run')) depends_on('r-ncbit', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) - depends_on('r-phytools@0.7.31:', when='@2.0.7:', type=('build', 'run')) + depends_on('r-phytools@0.7.31:', type=('build', 'run'), when='@2.0.7:') diff --git a/var/spack/repos/builtin/packages/r-generics/package.py b/var/spack/repos/builtin/packages/r-generics/package.py index 3b1f8b1253..2130bd8af0 100644 --- a/var/spack/repos/builtin/packages/r-generics/package.py +++ b/var/spack/repos/builtin/packages/r-generics/package.py @@ -7,12 +7,12 @@ from spack import * class RGenerics(RPackage): - """Common S3 Generics not Provided by Base R Methods Related to Model Fitting + """Common S3 Generics not Provided by Base R Methods Related to Model + Fitting. - In order to reduce potential package dependencies and conflicts, - generics provides a number of commonly used S3 generics.""" + In order to reduce potential package dependencies and conflicts, generics + provides a number of commonly used S3 generics.""" - homepage = "https://github.com/r-lib/generics" cran = "generics" version('0.1.1', sha256='a2478ebf1a0faa8855a152f4e747ad969a800597434196ed1f71975a9eb11912') @@ -20,4 +20,4 @@ class RGenerics(RPackage): version('0.0.2', sha256='71b3d1b719ce89e71dd396ac8bc6aa5f1cd99bbbf03faff61dfbbee32fec6176') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r@3.2:', when='@0.1.1:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@0.1.1:') diff --git a/var/spack/repos/builtin/packages/r-genetics/package.py b/var/spack/repos/builtin/packages/r-genetics/package.py index 3bce88dbf3..9b91dd90f7 100644 --- a/var/spack/repos/builtin/packages/r-genetics/package.py +++ b/var/spack/repos/builtin/packages/r-genetics/package.py @@ -7,12 +7,18 @@ from spack import * class RGenetics(RPackage): - """genetics: Population Genetics""" + """Population Genetics. - homepage = "https://cloud.r-project.org/package=genetics" - url = "https://cloud.r-project.org/src/contrib/genetics_1.3.8.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/genetics" + Classes and methods for handling genetic data. Includes classes to + represent genotypes and haplotypes at single markers up to multiple markers + on multiple chromosomes. Function include allele frequencies, flagging + homo/heterozygotes, flagging carriers of certain alleles, estimating and + testing for Hardy-Weinberg disequilibrium, estimating and testing for + linkage disequilibrium, ...""" + cran = "genetics" + + version('1.3.8.1.3', sha256='fef2c95f6a57f32b3cf4acf003480439462bb28297c501c617de307bfeee9252') version('1.3.8.1.2', sha256='30cb67de2e901578fd802deb7fbfea6c93024c9fb6ea66cad88430a3a2a51eec') depends_on('r-combinat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gensa/package.py b/var/spack/repos/builtin/packages/r-gensa/package.py index 537202bf48..ab768cb489 100644 --- a/var/spack/repos/builtin/packages/r-gensa/package.py +++ b/var/spack/repos/builtin/packages/r-gensa/package.py @@ -7,14 +7,12 @@ from spack import * class RGensa(RPackage): - """GenSA: Generalized Simulated Annealing + """Generalized Simulated Annealing. - Performs search for global minimum of a very complex non-linear - objective function with a very large number of optima.""" + Performs search for global minimum of a very complex non-linear objective + function with a very large number of optima.""" - homepage = "https://cloud.r-project.org/package=GenSA" - url = "https://cloud.r-project.org/src/contrib/GenSA_1.1.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GenSA/" + cran = "GenSA" version('1.1.7', sha256='9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f') diff --git a/var/spack/repos/builtin/packages/r-geojsonsf/package.py b/var/spack/repos/builtin/packages/r-geojsonsf/package.py new file mode 100644 index 0000000000..5b56a4697a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-geojsonsf/package.py @@ -0,0 +1,23 @@ +# 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 RGeojsonsf(RPackage): + """GeoJSON to Simple Feature Converter. + + Converts Between GeoJSON and simple feature objects.""" + + cran = "geojsonsf" + + version('2.0.1', sha256='42df40433bfbece5a39cd97b5bd4690b4424855241fcc3e7322ee68a3988bfbf') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-geometries', type=('build', 'run')) + depends_on('r-jsonify@1.1.1:', type=('build', 'run')) + depends_on('r-rapidjsonr@1.2.0:', type=('build', 'run')) + depends_on('r-sfheaders@0.2.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geometries/package.py b/var/spack/repos/builtin/packages/r-geometries/package.py new file mode 100644 index 0000000000..cbb4c2a31e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-geometries/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 RGeometries(RPackage): + """Convert Between R Objects and Geometric Structures. + + Geometry shapes in 'R' are typically represented by matrices (points, + lines), with more complex shapes being lists of matrices (polygons). + 'Geometries' will convert various 'R' objects into these shapes. Conversion + functions are available at both the 'R' level, and through 'Rcpp'.""" + + cran = "geometries" + + version('0.2.0', sha256='8cf5094f3c2458fef5d755799c766afd27c66cd1c292574a6ab532d608360314') + + depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geomorph/package.py b/var/spack/repos/builtin/packages/r-geomorph/package.py index 6023f80a97..b2ef1d385d 100644 --- a/var/spack/repos/builtin/packages/r-geomorph/package.py +++ b/var/spack/repos/builtin/packages/r-geomorph/package.py @@ -7,17 +7,16 @@ from spack import * class RGeomorph(RPackage): - """Geometric Morphometric Analyses of 2D/3D Landmark Data + """Geometric Morphometric Analyses of 2D/3D Landmark Data. Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.""" - homepage = "https://cloud.r-project.org/package=geomorph" - url = "https://cloud.r-project.org/src/contrib/geomorph_3.0.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/geomorph" + cran = "geomorph" + version('4.0.1', sha256='9d54fba96dd8b8f2dcc8d0e4c427f6232bed1934da41f25084c16ec0b2c71117') version('3.3.2', sha256='5f1d17cb98c54e40c4bbc650f7ccb5cb26e8d63934f810644facc69e91c1b7b7') version('3.1.2', sha256='29cf1c484f756cb44808cfdbc20137a6fbc4bd0c5c6f98c6c3f397c5aebda8f1') version('3.1.1', sha256='8eb222011433100860b308beef6f02ade7c421785f575ab4461ee25e38dfa1bd') @@ -26,10 +25,13 @@ class RGeomorph(RPackage): depends_on('r+X', type=('build', 'run')) depends_on('r@3.1.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@3.3.2:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.3.2:') depends_on('r-rrpp', type=('build', 'run'), when='@3.0.7:') + depends_on('r-rrpp@1.0.0:', type=('build', 'run'), when='@4.0.1:') depends_on('r-rgl', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run'), when='@:3.1.1,4.0.1:') depends_on('r-jpeg', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) - depends_on('r-geiger', when='@:3.1.1', type=('build', 'run')) - depends_on('r-matrix', when='@:3.1.1', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run'), when='@4.0.1:') + + depends_on('r-geiger', type=('build', 'run'), when='@:3.1.1') diff --git a/var/spack/repos/builtin/packages/r-geonames/package.py b/var/spack/repos/builtin/packages/r-geonames/package.py index a339c91246..3d122c640d 100644 --- a/var/spack/repos/builtin/packages/r-geonames/package.py +++ b/var/spack/repos/builtin/packages/r-geonames/package.py @@ -7,11 +7,14 @@ from spack import * class RGeonames(RPackage): - """geonames: Interface to the "Geonames" Spatial Query Web Service""" + """Interface to the "Geonames" Spatial Query Web Service. - homepage = "https://cloud.r-project.org/package=geonames" - url = "https://cloud.r-project.org/src/contrib/geonames_0.999.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/geonames" + The web service at <https://www.geonames.org/> provides a number of spatial + data queries, including administrative area hierarchies, city locations and + some country postal code queries. A (free) username is required and rate + limits exist.""" + + cran = "geonames" version('0.999', sha256='1dd7bbd82d9425d14eb36f8e5bf431feaccfe3b0c4e70bf38f44f13dfc59e17b') diff --git a/var/spack/repos/builtin/packages/r-geor/package.py b/var/spack/repos/builtin/packages/r-geor/package.py index 63e519505f..57a7d1f44a 100644 --- a/var/spack/repos/builtin/packages/r-geor/package.py +++ b/var/spack/repos/builtin/packages/r-geor/package.py @@ -7,15 +7,13 @@ from spack import * class RGeor(RPackage): - """Analysis of Geostatistical Data + """Analysis of Geostatistical Data. Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.""" - homepage = "https://cloud.r-project.org/package=geoR" - url = "https://cloud.r-project.org/src/contrib/geoR_1.7-5.2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/geoR" + cran = "geoR" version('1.8-1', sha256='990647804590b925a50f72897b24bbabd331cebef0be1696a60528b2f79d6fd3') version('1.7-5.2.1', sha256='3895e49c005a5745738d190ccaad43bb0aa49c74465d4d0b4dd88c5850ed63b9') diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py index c10bfa1114..4f4382dd29 100644 --- a/var/spack/repos/builtin/packages/r-geosphere/package.py +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -7,14 +7,15 @@ from spack import * class RGeosphere(RPackage): - """Spherical trigonometry for geographic applications. That is, compute + """Spherical Trigonometry. + + Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.""" - homepage = "https://cloud.r-project.org/package=geosphere" - url = "https://cloud.r-project.org/src/contrib/geosphere_1.5-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/geosphere" + cran = "geosphere" + version('1.5-14', sha256='f2c3a4ae1c87c86c123d48f134721c809fb33675cb5cd0959080049eabdbe42d') version('1.5-10', sha256='56cd4f787101e2e18f19ddb83794154b58697e63cad81168f0936f60ab7eb497') version('1.5-7', sha256='9d9b555e2d59a5ae174ae654652121f169fbc3e9cf66c2491bfbe0684b6dd8a0') version('1.5-5', sha256='8b6fe012744fc45b88e0ef6f20e60e103ef013e761e99dcff3f9dceeedbdce6d') diff --git a/var/spack/repos/builtin/packages/r-gert/package.py b/var/spack/repos/builtin/packages/r-gert/package.py index 34e919a6a7..13fe131864 100644 --- a/var/spack/repos/builtin/packages/r-gert/package.py +++ b/var/spack/repos/builtin/packages/r-gert/package.py @@ -7,25 +7,23 @@ from spack import * class RGert(RPackage): - """Simple Git Client for R + """Simple Git Client for R. - Simple git client for R based on 'libgit2' with support for SSH and HTTPS + Simple git client for R based on 'libgit2' with support for SSH and HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line 'git' through the git-credential store and ssh - keys stored on disk or ssh-agent. On Linux, a somewhat recent version of - 'libgit2' is required; we provide a 'PPA' for older Ubuntu 'LTS' - versions.""" + keys stored on disk or ssh-agent.""" - homepage = "https://docs.ropensci.org/gert/" - url = "https://cloud.r-project.org/src/contrib/gert_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gert" + cran = "gert" + version('1.5.0', sha256='9fc330893b0cb43360905fd204e674813e1906449a95dc4037fe8802bd74a2ae') version('1.0.2', sha256='36687ab98291d50a35752fcb2e734a926a6b845345c18d36e3f48823f68304d3') depends_on('r-askpass', type=('build', 'run')) depends_on('r-credentials@1.2.1:', type=('build', 'run')) depends_on('r-openssl@1.4.1:', type=('build', 'run')) depends_on('r-rstudioapi@0.11:', type=('build', 'run')) + depends_on('r-sys', type=('build', 'run'), when='@1.5.0:') depends_on('r-zip@2.1.0:', type=('build', 'run')) depends_on('libgit2@0.26:') diff --git a/var/spack/repos/builtin/packages/r-getopt/package.py b/var/spack/repos/builtin/packages/r-getopt/package.py index 179b7464df..8d178c7a7b 100644 --- a/var/spack/repos/builtin/packages/r-getopt/package.py +++ b/var/spack/repos/builtin/packages/r-getopt/package.py @@ -7,15 +7,15 @@ from spack import * class RGetopt(RPackage): - """Package designed to be used with Rscript to write "#!" shebang scripts - that accept short and long flags/options. Many users will prefer using - instead the packages optparse or argparse which add extra features like - automatically generated help option and usage, support for default - values, positional argument support, etc.""" + """C-Like 'getopt' Behavior. - homepage = "https://github.com/trevorld/getopt" - url = "https://cloud.r-project.org/src/contrib/getopt_1.20.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/getopt" + Package designed to be used with Rscript to write "#!" shebang scripts that + accept short and long flags/options. Many users will prefer using instead + the packages optparse or argparse which add extra features like + automatically generated help option and usage, support for default values, + positional argument support, etc.""" + + cran = "getopt" version('1.20.3', sha256='531f5fdfdcd6b96a73df2b39928418de342160ac1b0043861e9ea844f9fbf57f') version('1.20.2', sha256='3d6c12d32d6cd4b2909be626e570e158b3ed960e4739510e3a251e7f172de38e') diff --git a/var/spack/repos/builtin/packages/r-getoptlong/package.py b/var/spack/repos/builtin/packages/r-getoptlong/package.py index 7136c158f0..4d9d3f8310 100644 --- a/var/spack/repos/builtin/packages/r-getoptlong/package.py +++ b/var/spack/repos/builtin/packages/r-getoptlong/package.py @@ -7,25 +7,23 @@ from spack import * class RGetoptlong(RPackage): - """Parsing Command-Line Arguments and Simple Variable Interpolation + """Parsing Command-Line Arguments and Simple Variable Interpolation. This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.""" - homepage = "https://cloud.r-project.org/package=GetoptLong" - url = "https://cloud.r-project.org/src/contrib/GetoptLong_0.1.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GetoptLong" + cran = "GetoptLong" version('1.0.5', sha256='8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701') version('0.1.7', sha256='b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba') version('0.1.6', sha256='f526f006e3ed8507f1f236430ac9e97341c1ee9c207fbb68f936dd4d377b28b5') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.3.0:', when='@1.0.5:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@1.0.5:') depends_on('r-rjson', type=('build', 'run')) depends_on('r-globaloptions@0.1.0:', type=('build', 'run')) - depends_on('r-crayon', when='@1.0.5:', type=('build', 'run')) + depends_on('r-crayon', type=('build', 'run'), when='@1.0.5:') # The CRAN site lists SystemRequirments as: Perl, Getopt::Long. The # Getop::Long package will be installed with Perl so just depend on perl. diff --git a/var/spack/repos/builtin/packages/r-ggally/package.py b/var/spack/repos/builtin/packages/r-ggally/package.py index 8f1b575120..c16b38b3f6 100644 --- a/var/spack/repos/builtin/packages/r-ggally/package.py +++ b/var/spack/repos/builtin/packages/r-ggally/package.py @@ -7,7 +7,7 @@ from spack import * class RGgally(RPackage): - """Extension to 'ggplot2' + """Extension to 'ggplot2'. The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce @@ -16,26 +16,26 @@ class RGgally(RPackage): plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.""" - homepage = "https://cloud.r-project.org/package=GGally" - url = "https://cloud.r-project.org/src/contrib/GGally_1.3.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GGally" + cran = "GGally" + version('2.1.2', sha256='30352f36bf061bc98bdd5fa373ea0f23d007040bd908c7c018c8e627e0fb28e5') version('2.1.0', sha256='7ffb86b8a4e79543cf7e6bb1e3684d738ecd8e0ba89e8ef38991898b18dd6c53') version('1.4.0', sha256='9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe') version('1.3.2', sha256='f4143f45254fed794be991180aeffe459f6756bfa08acad963707d8e843cfd0a') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) - depends_on('r-ggplot2@3.3.0:', when='@2.1.0:', type=('build', 'run')) - depends_on('r-dplyr@1.0.0:', when='@2.1.0:', type=('build', 'run')) - depends_on('r-forcats', when='@2.1.0:', type=('build', 'run')) + depends_on('r-ggplot2@3.3.0:', type=('build', 'run'), when='@2.1.0:') + depends_on('r-ggplot2@3.3.4:', type=('build', 'run'), when='@2.1.2:') + depends_on('r-dplyr@1.0.0:', type=('build', 'run'), when='@2.1.0:') + depends_on('r-forcats', type=('build', 'run'), when='@2.1.0:') depends_on('r-gtable@0.2.0:', type=('build', 'run')) - depends_on('r-lifecycle', when='@2.1.0:', type=('build', 'run')) + depends_on('r-lifecycle', type=('build', 'run'), when='@2.1.0:') depends_on('r-plyr@1.8.3:', type=('build', 'run')) depends_on('r-progress', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-reshape@0.8.5:', type=('build', 'run')) - depends_on('r-rlang', when='@1.4.0:', type=('build', 'run')) - depends_on('r-scales@1.1.0:', when='@2.1.0:', type=('build', 'run')) - depends_on('r-tidyr', when='@2.1.0:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@1.4.0:') + depends_on('r-scales@1.1.0:', type=('build', 'run'), when='@2.1.0:') + depends_on('r-tidyr', type=('build', 'run'), when='@2.1.0:') depends_on('openssl', when='@1.4.0:') diff --git a/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py b/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py index 956e921b33..ffb21ca52f 100644 --- a/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py +++ b/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py @@ -7,11 +7,13 @@ from spack import * class RGgbeeswarm(RPackage): - """ggbeeswarm: Categorical Scatter (Violin Point) Plots""" + """Categorical Scatter (Violin Point) Plots. - homepage = "https://github.com/eclarke/ggbeeswarm" - url = "https://cloud.r-project.org/src/contrib/ggbeeswarm_0.6.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggbeeswarm" + Provides two methods of plotting categorical scatter plots such that the + arrangement of points within a category reflects the density of data at + that region, and avoids over-plotting.""" + + cran = "ggbeeswarm" version('0.6.0', sha256='bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333') diff --git a/var/spack/repos/builtin/packages/r-ggdendro/package.py b/var/spack/repos/builtin/packages/r-ggdendro/package.py index cc497d8ab5..4a665b4eac 100644 --- a/var/spack/repos/builtin/packages/r-ggdendro/package.py +++ b/var/spack/repos/builtin/packages/r-ggdendro/package.py @@ -7,20 +7,17 @@ from spack import * class RGgdendro(RPackage): - """Create Dendrograms and Tree Diagrams Using 'ggplot2' + """Create Dendrograms and Tree Diagrams Using 'ggplot2'. - This is a set of tools for dendrograms and tree plots using - 'ggplot2'. The 'ggplot2' philosophy is to clearly separate data - from the presentation. Unfortunately the plot method for - dendrograms plots directly to a plot device without exposing - the data. The 'ggdendro' package resolves this by making - available functions that extract the dendrogram plot data. - The package provides implementations for tree, rpart, as well - as diana and agnes cluster diagrams.""" + This is a set of tools for dendrograms and tree plots using 'ggplot2'. The + 'ggplot2' philosophy is to clearly separate data from the presentation. + Unfortunately the plot method for dendrograms plots directly to a plot + device without exposing the data. The 'ggdendro' package resolves this by + making available functions that extract the dendrogram plot data. The + package provides implementations for tree, rpart, as well as diana and + agnes cluster diagrams.""" - homepage = "https://cloud.r-project.org/package=ggdendro" - url = "https://cloud.r-project.org/src/contrib/ggdendro_0.1-20.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggdendro" + cran = "ggdendro" version('0.1.22', sha256='f0a65f3498c1abc3076df0fb56364b63bdf5d212d8931f85bcc6997510916b6a') version('0.1-20', sha256='125cae904fa5d426cccaf32ebe9c6297e9ef0c6fd3f19f61513834d03a0cf8ff') diff --git a/var/spack/repos/builtin/packages/r-ggforce/package.py b/var/spack/repos/builtin/packages/r-ggforce/package.py index eff0f07fc6..76c0cc2adc 100644 --- a/var/spack/repos/builtin/packages/r-ggforce/package.py +++ b/var/spack/repos/builtin/packages/r-ggforce/package.py @@ -7,7 +7,7 @@ from spack import * class RGgforce(RPackage): - """Accelerating 'ggplot2' + """Accelerating 'ggplot2'. The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' @@ -15,10 +15,9 @@ class RGgforce(RPackage): All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.""" - homepage = "https://ggforce.data-imaginist.com" - url = "https://cloud.r-project.org/src/contrib/ggforce_0.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggforce" + cran = "ggforce" + version('0.3.3', sha256='2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f') version('0.3.2', sha256='4cce8acb60ce06af44c1c76bbacd7de129eed9b51ed6a85e03a9bf55b0eff4d2') version('0.3.1', sha256='a05271da9b226c12ae5fe6bc6eddb9ad7bfe19e1737e2bfcd6d7a89631332211') diff --git a/var/spack/repos/builtin/packages/r-ggfun/package.py b/var/spack/repos/builtin/packages/r-ggfun/package.py new file mode 100644 index 0000000000..fc002e7ec3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggfun/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 RGgfun(RPackage): + """Miscellaneous Functions for 'ggplot2'. + + Useful functions to edit 'ggplot' object (e.g., setting fonts for theme and + layers, adding rounded rectangle as background for each of the legends).""" + + cran = "ggfun" + + version('0.0.5', sha256='b1e340a8932d2cffbbbf6070ce96c9356599e9955a2b6534fcb17e599c575783') + version('0.0.4', sha256='5926365f9a90baf47320baf48c40f515ef570f9c767484adea5f04219964d21e') + + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggjoy/package.py b/var/spack/repos/builtin/packages/r-ggjoy/package.py index d400e27a0d..766ba7f584 100644 --- a/var/spack/repos/builtin/packages/r-ggjoy/package.py +++ b/var/spack/repos/builtin/packages/r-ggjoy/package.py @@ -7,12 +7,12 @@ from spack import * class RGgjoy(RPackage): - """Joyplots provide a convenient way of visualizing changes in distributions - over time or space.""" + """Joyplots in 'ggplot2'. - homepage = "https://cloud.r-project.org/package=ggjoy" - url = "https://cloud.r-project.org/src/contrib/ggjoy_0.4.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggjoy" + Joyplots provide a convenient way of visualizing changes in + distributions over time or space.""" + + cran = "ggjoy" version('0.4.1', sha256='d2f778bc40203d7fbb7c81b40beed8614c36ea10448e911663cc6109aa685504') version('0.4.0', sha256='cb9ef790921ffcd3cfb6a55b409d17ccae9e8f5fdd2a28e55ea2ccfa8efd44e8') diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py index aab968955b..24a41a45b4 100644 --- a/var/spack/repos/builtin/packages/r-ggmap/package.py +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -7,14 +7,14 @@ from spack import * class RGgmap(RPackage): - """A collection of functions to visualize spatial data and models on top of + """Spatial Visualization with ggplot2. + + A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.""" - homepage = "https://github.com/dkahle/ggmap" - url = "https://cloud.r-project.org/src/contrib/ggmap_2.6.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggmap" + cran = "ggmap" version('3.0.0', sha256='96c24ffdc0710d0633ac4721d599d2c06f43a29c59d1e85c94ff0af30dfdb58d') version('2.6.2', sha256='4e9cf53ab108fc70805d971dadb69b26fe67ea289c23c38adf6e30b198379d90') @@ -22,23 +22,24 @@ class RGgmap(RPackage): depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) - depends_on('r-proto', when='@:2.6.2', type=('build', 'run')) depends_on('r-rgooglemaps', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) - depends_on('r-reshape2', when='@:2.6.2', type=('build', 'run')) depends_on('r-rjson', type=('build', 'run')) - depends_on('r-mapproj', when='@:2.6.2', type=('build', 'run')) depends_on('r-jpeg', type=('build', 'run')) - depends_on('r-geosphere', when='@:2.6.2', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) - depends_on('r-dplyr', when='@3.0.0:', type=('build', 'run')) - depends_on('r-bitops', when='@3.0.0:', type=('build', 'run')) - depends_on('r-glue', when='@3.0.0:', type=('build', 'run')) - depends_on('r-httr', when='@3.0.0:', type=('build', 'run')) - depends_on('r-stringr', when='@3.0.0:', type=('build', 'run')) - depends_on('r-purrr', when='@3.0.0:', type=('build', 'run')) - depends_on('r-magrittr', when='@3.0.0:', type=('build', 'run')) - depends_on('r-tibble', when='@3.0.0:', type=('build', 'run')) - depends_on('r-tidyr', when='@3.0.0:', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run'), when='@3.0.0:') + depends_on('r-bitops', type=('build', 'run'), when='@3.0.0:') + depends_on('r-glue', type=('build', 'run'), when='@3.0.0:') + depends_on('r-httr', type=('build', 'run'), when='@3.0.0:') + depends_on('r-stringr', type=('build', 'run'), when='@3.0.0:') + depends_on('r-purrr', type=('build', 'run'), when='@3.0.0:') + depends_on('r-magrittr', type=('build', 'run'), when='@3.0.0:') + depends_on('r-tibble', type=('build', 'run'), when='@3.0.0:') + depends_on('r-tidyr', type=('build', 'run'), when='@3.0.0:') + + depends_on('r-proto', type=('build', 'run'), when='@:2.6.2') + depends_on('r-reshape2', type=('build', 'run'), when='@:2.6.2') + depends_on('r-mapproj', type=('build', 'run'), when='@:2.6.2') + depends_on('r-geosphere', type=('build', 'run'), when='@:2.6.2') diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index b2da724ed2..69d917ce94 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -7,14 +7,13 @@ from spack import * class RGgplot2(RPackage): - """Create Elegant Data Visualisations Using the Grammar of Graphics + """Create Elegant Data Visualisations Using the Grammar of Graphics. A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.""" - homepage = "https://ggplot2.tidyverse.org/" cran = "ggplot2" version('3.3.5', sha256='b075294faf3af31b18e415f260c62d6000b218770e430484fe38819bdc3224ea') @@ -24,21 +23,22 @@ class RGgplot2(RPackage): version('2.2.1', sha256='5fbc89fec3160ad14ba90bd545b151c7a2e7baad021c0ab4b950ecd6043a8314') version('2.1.0', sha256='f2c323ae855d6c089e3a52138aa7bc25b9fe1429b8df9eae89d28ce3c0dd3969') - depends_on('r@3.1:', when='@:3.1.1', type=('build', 'run')) - depends_on('r@3.2:', when='@3.2.0:', type=('build', 'run')) - depends_on('r@3.3:', when='@3.3.4:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@3.2.0:') + depends_on('r@3.3:', type=('build', 'run'), when='@3.3.4:') depends_on('r-digest', type=('build', 'run')) - depends_on('r-glue', when='@3.3.3:', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run'), when='@3.3.3:') depends_on('r-gtable@0.1.1:', type=('build', 'run')) - depends_on('r-isoband', when='@3.3.3:', type=('build', 'run')) + depends_on('r-isoband', type=('build', 'run'), when='@3.3.3:') depends_on('r-mass', type=('build', 'run')) - depends_on('r-mgcv', when='@3.2.0:', type=('build', 'run')) - depends_on('r-rlang@0.3.0:', when='@3.0.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.10:', when='@3.3.4:', type=('build', 'run')) + depends_on('r-mgcv', type=('build', 'run'), when='@3.2.0:') + depends_on('r-rlang@0.3.0:', type=('build', 'run'), when='@3.0.0:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@3.3.4:') depends_on('r-scales@0.5.0:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) - depends_on('r-withr@2.0.0:', when='@3.0.0:', type=('build', 'run')) - depends_on('r-plyr@1.7.1:', when='@:3.1.1', type=('build', 'run')) - depends_on('r-reshape2', when='@:3.2.0', type=('build', 'run')) - depends_on('r-lazyeval', when='@:3.2.0', type=('build', 'run')) - depends_on('r-viridislite', when='@3.0.0:3.2.0', type=('build', 'run')) + depends_on('r-withr@2.0.0:', type=('build', 'run'), when='@3.0.0:') + + depends_on('r-plyr@1.7.1:', type=('build', 'run'), when='@:3.1.1') + depends_on('r-reshape2', type=('build', 'run'), when='@:3.2.0') + depends_on('r-lazyeval', type=('build', 'run'), when='@:3.2.0') + depends_on('r-viridislite', type=('build', 'run'), when='@3.0.0:3.2.0') diff --git a/var/spack/repos/builtin/packages/r-ggplotify/package.py b/var/spack/repos/builtin/packages/r-ggplotify/package.py index efc4b9bb6f..612588f420 100644 --- a/var/spack/repos/builtin/packages/r-ggplotify/package.py +++ b/var/spack/repos/builtin/packages/r-ggplotify/package.py @@ -7,7 +7,7 @@ from spack import * class RGgplotify(RPackage): - """Convert Plot to 'grob' or 'ggplot' Object + """Convert Plot to 'grob' or 'ggplot' Object. Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With @@ -15,14 +15,15 @@ class RGgplotify(RPackage): by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.""" - homepage = "https://github.com/GuangchuangYu/ggplotify" - url = "https://cloud.r-project.org/src/contrib/ggplotify_0.0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggplotify" + cran = "ggplotify" + version('0.1.0', sha256='178f73d6d3dc391c3efb1a62c95fe38587044f9e3288dffb915d3687941bb38a') version('0.0.5', sha256='035ea6a70023c4819c8a486d0fd94c2765aa4d6df318747e104eeb9829b9d65d') version('0.0.3', sha256='7e7953a2933aa7127a0bac54375e3e0219a0744cfc3249c3d7b76065f7a51892') depends_on('r@3.4.0:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-gridgraphics', type=('build', 'run')) - depends_on('r-rvcheck', type=('build', 'run')) + depends_on('r-yulab-utils', type=('build', 'run'), when='@0.1.0:') + + depends_on('r-rvcheck', type=('build', 'run'), when='@:0.0.5') diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py index 5503ca26b5..e725f3e584 100644 --- a/var/spack/repos/builtin/packages/r-ggpubr/package.py +++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py @@ -7,7 +7,7 @@ from spack import * class RGgpubr(RPackage): - """'ggplot2' Based Publication Ready Plots + """'ggplot2' Based Publication Ready Plots. The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some @@ -17,9 +17,7 @@ class RGgpubr(RPackage): provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.""" - homepage = "http://www.sthda.com/english/rpkgs/ggpubr" - url = "https://cloud.r-project.org/src/contrib/ggpubr_0.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggpubr" + cran = "ggpubr" version('0.4.0', sha256='abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675') version('0.2.2', sha256='1c93dc6d1f08680dd00a10b6842445700d1fccb11f18599fbdf51e70c6b6b364') @@ -31,17 +29,17 @@ class RGgpubr(RPackage): depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-ggrepel', type=('build', 'run')) depends_on('r-ggsci', type=('build', 'run')) - depends_on('r-tidyr', when='@0.2:', type=('build', 'run')) - depends_on('r-plyr', when='@:0.1.2', type=('build', 'run')) - depends_on('r-purrr', when='@0.2:', type=('build', 'run')) - depends_on('r-dplyr@0.7.1:', when='@0.2:', type=('build', 'run')) - depends_on('r-cowplot', when='@0.2:', type=('build', 'run')) - depends_on('r-ggsignif', when='@0.2:', type=('build', 'run')) - depends_on('r-scales', when='@0.2:', type=('build', 'run')) - depends_on('r-gridextra', when='@0.2:', type=('build', 'run')) - depends_on('r-glue', when='@0.2:', type=('build', 'run')) - depends_on('r-polynom', when='@0.2:', type=('build', 'run')) - depends_on('r-rlang', when='@0.2.2:', type=('build', 'run')) - depends_on('r-rstatix@0.6.0:', when='@0.4.0:', type=('build', 'run')) - depends_on('r-tibble', when='@0.4.0:', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run'), when='@0.2:') + depends_on('r-plyr', type=('build', 'run'), when='@:0.1.2') + depends_on('r-purrr', type=('build', 'run'), when='@0.2:') + depends_on('r-dplyr@0.7.1:', type=('build', 'run'), when='@0.2:') + depends_on('r-cowplot', type=('build', 'run'), when='@0.2:') + depends_on('r-ggsignif', type=('build', 'run'), when='@0.2:') + depends_on('r-scales', type=('build', 'run'), when='@0.2:') + depends_on('r-gridextra', type=('build', 'run'), when='@0.2:') + depends_on('r-glue', type=('build', 'run'), when='@0.2:') + depends_on('r-polynom', type=('build', 'run'), when='@0.2:') + depends_on('r-rlang', type=('build', 'run'), when='@0.2.2:') + depends_on('r-rstatix@0.6.0:', type=('build', 'run'), when='@0.4.0:') + depends_on('r-tibble', type=('build', 'run'), when='@0.4.0:') depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggraph/package.py b/var/spack/repos/builtin/packages/r-ggraph/package.py index 80f1dc74df..04c1287360 100644 --- a/var/spack/repos/builtin/packages/r-ggraph/package.py +++ b/var/spack/repos/builtin/packages/r-ggraph/package.py @@ -7,7 +7,7 @@ from spack import * class RGgraph(RPackage): - """An Implementation of Grammar of Graphics for Graphs and Networks + """An Implementation of Grammar of Graphics for Graphs and Networks. The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. @@ -15,10 +15,9 @@ class RGgraph(RPackage): and provides the same flexible approach to building up plots layer by layer.""" - homepage = "https://github.com/thomasp85/ggraph" - url = "https://cloud.r-project.org/src/contrib/ggraph_2.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggraph" + cran = "ggraph" + version('2.0.5', sha256='e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654') version('2.0.4', sha256='9c6092d9a98b7b116f9c765ba44de7a34ceff2f584e776ef7a2082ad1d717dc8') version('2.0.0', sha256='4307efe85bfc6a0496797f6b86d6b174ba196538c51b1a6b6af55de0d4e04762') @@ -37,4 +36,4 @@ class RGgraph(RPackage): depends_on('r-rlang', type=('build', 'run')) depends_on('r-tidygraph', type=('build', 'run')) depends_on('r-graphlayouts@0.5.0:', type=('build', 'run')) - depends_on('r-withr', when='@2.0.4:', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run'), when='@2.0.4:') diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py index 1138daca42..37d1952876 100644 --- a/var/spack/repos/builtin/packages/r-ggrepel/package.py +++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py @@ -7,16 +7,15 @@ from spack import * class RGgrepel(RPackage): - """Repulsive Text and Label Geoms for 'ggplot2' + """Repulsive Text and Label Geoms for 'ggplot2'. Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.""" - homepage = "https://github.com/slowkow/ggrepel" - url = "https://cloud.r-project.org/src/contrib/ggrepel_0.6.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggrepel" + cran = "ggrepel" + version('0.9.1', sha256='29fb916d4799ba6503a5dd019717ffdf154d2aaae9ff1736f03e2be24af6bdfc') version('0.9.0', sha256='4f7ca3da7dc08902487c961c539ef43516263c30abcc4ce303ff3c5580f42fda') version('0.8.1', sha256='d5d03a77ab6d8c831934bc46e840cc4e3df487272ab591fa72767ad42bcb7283') version('0.8.0', sha256='6386606e716d326354a29fcb6cd09f9b3d3b5e7c5ba0d5f7ff35416b1a4177d4') @@ -25,6 +24,6 @@ class RGgrepel(RPackage): depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-rlang@0.3.0:', when='@0.9.0:', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', type=('build', 'run'), when='@0.9.0:') depends_on('r-scales@0.3.0:', type=('build', 'run')) - depends_on('r-scales@0.5.0:', when='@0.9.0:', type=('build', 'run')) + depends_on('r-scales@0.5.0:', type=('build', 'run'), when='@0.9.0:') diff --git a/var/spack/repos/builtin/packages/r-ggridges/package.py b/var/spack/repos/builtin/packages/r-ggridges/package.py index 16e182e55c..09f90c428b 100644 --- a/var/spack/repos/builtin/packages/r-ggridges/package.py +++ b/var/spack/repos/builtin/packages/r-ggridges/package.py @@ -7,15 +7,13 @@ from spack import * class RGgridges(RPackage): - """Ridgeline Plots in 'ggplot2' + """Ridgeline Plots in 'ggplot2'. Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.""" - homepage = "https://cloud.r-project.org/package=ggridges" - url = "https://cloud.r-project.org/src/contrib/ggridges_0.4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggridges" + cran = "ggridges" version('0.5.3', sha256='f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e') version('0.5.1', sha256='01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36') @@ -25,7 +23,7 @@ class RGgridges(RPackage): depends_on('r@3.2:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) - depends_on('r-ggplot2@3.0.0:', when='@0.5.3:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run'), when='@0.5.3:') depends_on('r-plyr@1.8.0:', type=('build', 'run')) depends_on('r-scales@0.4.1:', type=('build', 'run')) - depends_on('r-withr@2.1.1:', when='@0.5.0:', type=('build', 'run')) + depends_on('r-withr@2.1.1:', type=('build', 'run'), when='@0.5.0:') diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py index 24e1ffaec1..31c0f00763 100644 --- a/var/spack/repos/builtin/packages/r-ggsci/package.py +++ b/var/spack/repos/builtin/packages/r-ggsci/package.py @@ -7,12 +7,13 @@ from spack import * class RGgsci(RPackage): - """ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for - 'ggplot2'""" + """Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'. - homepage = "https://github.com/road2stat/ggsci" - url = "https://cloud.r-project.org/src/contrib/ggsci_2.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggsci" + collection of 'ggplot2' color palettes inspired by plots in scientific + journals, data visualization libraries, science fiction movies, and TV + shows.""" + + cran = "ggsci" version('2.9', sha256='4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c') version('2.8', sha256='b4ce7adce7ef23edf777866086f98e29b2b45b58fed085bbd1ffe6ab52d74ae8') diff --git a/var/spack/repos/builtin/packages/r-ggsignif/package.py b/var/spack/repos/builtin/packages/r-ggsignif/package.py index 030b8a3e84..9f31938551 100644 --- a/var/spack/repos/builtin/packages/r-ggsignif/package.py +++ b/var/spack/repos/builtin/packages/r-ggsignif/package.py @@ -7,18 +7,20 @@ from spack import * class RGgsignif(RPackage): - """Enrich your 'ggplots' with group-wise comparisons. This package provides - an easy way to indicate if two groups are significantly different. Commonly + """Significance Brackets for 'ggplot2'. + + Enrich your 'ggplots' with group-wise comparisons. This package provides an + easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.""" - homepage = "https://github.com/const-ae/ggsignif" - url = "https://cloud.r-project.org/src/contrib/ggsignif_0.6.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggsignif" + cran = "ggsignif" + version('0.6.3', sha256='ca8545b25590e531512a90a18449a2cbab945f7434a1d60188c41f7d1839a7a9') version('0.6.0', sha256='6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e') depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) + depends_on('r-ggplot2@3.3.5:', type=('build', 'run'), when='@0.6.3:') diff --git a/var/spack/repos/builtin/packages/r-ggthemes/package.py b/var/spack/repos/builtin/packages/r-ggthemes/package.py index 3768592fff..2e6b9b712b 100644 --- a/var/spack/repos/builtin/packages/r-ggthemes/package.py +++ b/var/spack/repos/builtin/packages/r-ggthemes/package.py @@ -7,18 +7,15 @@ from spack import * class RGgthemes(RPackage): - """ggthemes: Extra Themes, Scales and Geoms for - 'ggplot2' + """Extra Themes, Scales and Geoms for 'ggplot2'. - Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes - and scales that replicate the look of plots by Edward Tufte, Stephen Few, - 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall Street - Journal', among others. Provides 'geoms' for Tufte's box plot and range - frame.""" + Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' + themes and scales that replicate the look of plots by Edward Tufte, Stephen + Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall + Street Journal', among others. Provides 'geoms' for Tufte's box plot and + range frame.""" - homepage = "https://jrnold.github.io/ggthemes/" - url = "https://cloud.r-project.org/src/contrib/ggthemes_4.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggthemes" + cran = "ggthemes" version('4.2.4', sha256='7b35168cf5b68f6f52dd533a1b345ec87e09d1a85ca68e8dc5377cdf95718567') version('4.2.0', sha256='5bb3fe94819fe2cce7865f07a6e6ea5c59d3996f78d1c0836ad406f69efb3367') diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 581588f569..d5afc7de50 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -7,15 +7,13 @@ from spack import * class RGgvis(RPackage): - """Interactive Grammar of Graphics + """Interactive Grammar of Graphics. An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework from 'shiny' and web graphics from 'vega'.""" - homepage = "https://ggvis.rstudio.com/" - url = "https://cloud.r-project.org/src/contrib/ggvis_0.4.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ggvis" + cran = "ggvis" version('0.4.7', sha256='9e6b067e11d497c796d42156570e2481afb554c5db265f42afbb74d2ae0865e3') version('0.4.4', sha256='1332ea122b768688c8a407a483be80febc4576de0ec8929077738421b27cafaf') @@ -28,7 +26,8 @@ class RGgvis(RPackage): depends_on('r-shiny@0.11.1:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-dplyr@0.4.0:', type=('build', 'run')) - depends_on('r-dplyr@0.5.0:', when='@0.4.7:', type=('build', 'run')) - depends_on('r-rlang', when='@0.4.7:', type=('build', 'run')) + depends_on('r-dplyr@0.5.0:', type=('build', 'run'), when='@0.4.7:') + depends_on('r-rlang', type=('build', 'run'), when='@0.4.7:') depends_on('r-htmltools@0.2.4:', type=('build', 'run')) - depends_on('r-lazyeval', when='@:0.4.4', type=('build', 'run')) + + depends_on('r-lazyeval', type=('build', 'run'), when='@:0.4.4') diff --git a/var/spack/repos/builtin/packages/r-gh/package.py b/var/spack/repos/builtin/packages/r-gh/package.py index 75332aa2e2..9064fca9d4 100644 --- a/var/spack/repos/builtin/packages/r-gh/package.py +++ b/var/spack/repos/builtin/packages/r-gh/package.py @@ -7,22 +7,21 @@ from spack import * class RGh(RPackage): - """'GitHub' 'API' + """'GitHub' 'API'. Minimal client to access the 'GitHub' 'API'.""" - homepage = "https://github.com/r-lib/gh#readme" - url = "https://cloud.r-project.org/src/contrib/gh_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gh" + cran = "gh" + version('1.3.0', sha256='a44039054e8ca56496f2d9c7a10cdadf4a7383bc91086e768ba7e7f1fbcaed1c') version('1.2.0', sha256='2988440ed2ba4b241c8ffbafbfdad29493574980a9aeba210521dadda91f7eff') version('1.1.0', sha256='de9faf383c3fe5e87a75391d82cf71b1331b3c80cd00c4203146a303825d89ad') version('1.0.1', sha256='f3c02b16637ae390c3599265852d94b3de3ef585818b260d00e7812595b391d2') - depends_on('r-cli', when='@1.1.0:', type=('build', 'run')) - depends_on('r-cli@2.0.1:', when='@1.2.0:', type=('build', 'run')) - depends_on('r-gitcreds', when='@1.2.0:', type=('build', 'run')) + depends_on('r-cli', type=('build', 'run'), when='@1.1.0:') + depends_on('r-cli@2.0.1:', type=('build', 'run'), when='@1.2.0:') + depends_on('r-gitcreds', type=('build', 'run'), when='@1.2.0:') depends_on('r-httr', type=('build', 'run')) - depends_on('r-httr@1.2:', when='@1.1.0:', type=('build', 'run')) + depends_on('r-httr@1.2:', type=('build', 'run'), when='@1.1.0:') depends_on('r-ini', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py index 444dfc95d6..e159d596b0 100644 --- a/var/spack/repos/builtin/packages/r-gistr/package.py +++ b/var/spack/repos/builtin/packages/r-gistr/package.py @@ -8,7 +8,7 @@ from spack import * class RGistr(RPackage): - """Work with 'GitHub' 'Gists' + """Work with 'GitHub' 'Gists'. Work with 'GitHub' 'gists' from 'R' (e.g., <https://en.wikipedia.org/wiki/GitHub#Gist>, @@ -21,9 +21,7 @@ class RGistr(RPackage): when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: <https://gist.github.com/>.""" - homepage = "https://github.com/ropensci/gistr" - url = "https://cloud.r-project.org/src/contrib/gistr_0.3.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gistr" + cran = "gistr" version('0.9.0', sha256='170ae025151ee688e7d31b9e49112086a8ddf4fef10155e9ee289ad7f28c8929') version('0.4.2', sha256='43c00c7f565732125f45f6c067724771ba1b337d6dd3a6e301639fe16e11032e') @@ -32,7 +30,7 @@ class RGistr(RPackage): depends_on('r+X', type=('build', 'run')) depends_on('r-jsonlite@1.4:', type=('build', 'run')) - depends_on('r-crul', when='@0.9.0:', type=('build', 'run')) + depends_on('r-crul', type=('build', 'run'), when='@0.9.0:') depends_on('r-httr@1.2.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py index cabbd743c5..65f0bf3854 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -7,16 +7,15 @@ from spack import * class RGit2r(RPackage): - """Provides Access to Git Repositories + """Provides Access to Git Repositories. - Interface to the 'libgit2' library, which is a pure C implementation of - the 'Git' core methods. Provides access to 'Git' repositories to extract - data and running some basic 'Git' commands.""" + Interface to the 'libgit2' library, which is a pure C implementation of the + 'Git' core methods. Provides access to 'Git' repositories to extract data + and running some basic 'Git' commands.""" - homepage = "https://github.com/ropensci/git2r" - url = "https://cloud.r-project.org/src/contrib/git2r_0.18.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/git2r" + cran = "git2r" + version('0.29.0', sha256='f8f7a181dc0ac761f2a0c4099bfd744ded01c0e0832cab32dc5b4da32accd48e') version('0.28.0', sha256='ce6d148d21d2c87757e98ef4474b2d09faded9b9b866f046bd26d4ca925e55f2') version('0.27.1', sha256='099207f180aa45ddcc443cbb22487eafd14e1cd8e5979b3476214253fd773bc0') version('0.26.1', sha256='13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435') @@ -25,6 +24,7 @@ class RGit2r(RPackage): version('0.15.0', sha256='682ab9e7f71b2ed13a9ef95840df3c6b429eeea070edeb4d21d725cf0b72ede6') depends_on('r@3.1:', type=('build', 'run')) + depends_on('libgit2') depends_on('zlib') depends_on('openssl') - depends_on('libgit2') + depends_on('libssh2') diff --git a/var/spack/repos/builtin/packages/r-gitcreds/package.py b/var/spack/repos/builtin/packages/r-gitcreds/package.py index 7339a06456..dbb7c6de4e 100644 --- a/var/spack/repos/builtin/packages/r-gitcreds/package.py +++ b/var/spack/repos/builtin/packages/r-gitcreds/package.py @@ -7,16 +7,14 @@ from spack import * class RGitcreds(RPackage): - """Query 'git' Credentials from 'R' + """Query 'git' Credentials from 'R'. Query, set, delete credentials from the 'git' credential store. Manage 'GitHub' tokens and other 'git' credentials. This package is to be used by other packages that need to authenticate to 'GitHub' and/or other 'git' repositories.""" - homepage = "https://github.com/r-lib/gitcreds" - url = "https://cloud.r-project.org/src/contrib/gitcreds_0.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gitcreds" + cran = "gitcreds" version('0.1.1', sha256='b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea') diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py index 5305ccf973..8a3e6fdc87 100644 --- a/var/spack/repos/builtin/packages/r-glmnet/package.py +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -7,26 +7,27 @@ from spack import * class RGlmnet(RPackage): - """Lasso and Elastic-Net Regularized Generalized Linear Models + """Lasso and Elastic-Net Regularized Generalized Linear Models. - Extremely efficient procedures for fitting the entire lasso or - elastic-net regularization path for linear regression, logistic and - multinomial regression models, Poisson regression and the Cox model. Two - recent additions are the multiple-response Gaussian, and the grouped - multinomial. The algorithm uses cyclical coordinate descent in a path-wise - fashion, as described in the paper linked to via the URL below.""" + Extremely efficient procedures for fitting the entire lasso or elastic-net + regularization path for linear regression, logistic and multinomial + regression models, Poisson regression and the Cox model. Two recent + additions are the multiple-response Gaussian, and the grouped multinomial. + The algorithm uses cyclical coordinate descent in a path-wise fashion, as + described in the paper linked to via the URL below.""" - homepage = "https://cloud.r-project.org/package=glmnet" - url = "https://cloud.r-project.org/src/contrib/glmnet_2.0-13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/glmnet" + cran = "glmnet" + version('4.1-3', sha256='64bc35aa40b6e580cfb8a21e649eb103e996e8747a10c476b8bb9545c846325a') version('4.1', sha256='8f0af50919f488789ecf261f6e0907f367d89fca812baa2f814054fb2d0e40cb') version('2.0-18', sha256='e8dce9d7b8105f9cc18ba981d420de64a53b09abee219660d3612915d554256b') version('2.0-13', sha256='f3288dcaddb2f7014d42b755bede6563f73c17bc87f8292c2ef7776cb9b9b8fd') version('2.0-5', sha256='2ca95352c8fbd93aa7800f3d972ee6c1a5fcfeabc6be8c10deee0cb457fd77b1') - depends_on('r@3.6.0:', when='@4.1:', type=('build', 'run')) + depends_on('r@3.6.0:', type=('build', 'run'), when='@4.1:') depends_on('r-matrix@1.0-6:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) - depends_on('r-shape', when='@4.1:', type=('build', 'run')) - depends_on('r-survival', when='@4.1:', type=('build', 'run')) + depends_on('r-shape', type=('build', 'run'), when='@4.1:') + depends_on('r-survival', type=('build', 'run'), when='@4.1:') + depends_on('r-rcpp', type=('build', 'run'), when='@4.1-3:') + depends_on('r-rcppeigen', type=('build', 'run'), when='@4.1-3:') diff --git a/var/spack/repos/builtin/packages/r-globaloptions/package.py b/var/spack/repos/builtin/packages/r-globaloptions/package.py index cf53cab0cb..ddc3cc1852 100644 --- a/var/spack/repos/builtin/packages/r-globaloptions/package.py +++ b/var/spack/repos/builtin/packages/r-globaloptions/package.py @@ -7,18 +7,16 @@ from spack import * class RGlobaloptions(RPackage): - """Generate Functions to Get or Set Global Options + """Generate Functions to Get or Set Global Options. It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.""" - homepage = "https://cloud.r-project.org/package=GlobalOptions" - url = "https://cloud.r-project.org/src/contrib/GlobalOptions_0.0.12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GlobalOptions" + cran = "GlobalOptions" version('0.1.2', sha256='47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e') version('0.1.0', sha256='567a0a51f6b7b14127302f00e6e4944befd4964c069f96a9e61256e8c3c79ef2') version('0.0.12', sha256='c09da3f9b1646d0f815056cdbeb5fff7dda29f7dd8742d245f5f6dc7066077a9') - depends_on('r@2.10:', when='@:0.0.12', type=('build', 'run')) - depends_on('r@3.3.0:', when='@0.0.13:', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.0.13:') diff --git a/var/spack/repos/builtin/packages/r-globals/package.py b/var/spack/repos/builtin/packages/r-globals/package.py index e01783ac25..8e16af438a 100644 --- a/var/spack/repos/builtin/packages/r-globals/package.py +++ b/var/spack/repos/builtin/packages/r-globals/package.py @@ -7,7 +7,7 @@ from spack import * class RGlobals(RPackage): - """Identify Global Objects in R Expressions + """Identify Global Objects in R Expressions. Identifies global ("unknown" or "free") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The @@ -15,9 +15,7 @@ class RGlobals(RPackage): global objects for the purpose of exporting them in distributed compute environments.""" - homepage = "https://github.com/HenrikBengtsson/globals" - url = "https://cloud.r-project.org/src/contrib/globals_0.12.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/globals" + cran = "globals" version('0.14.0', sha256='203dbccb829ca9cc6aedb6f5e79cb126ea31f8dd379dff9111ec66e3628c32f3') version('0.12.4', sha256='7985356ad75afa1f795f8267a20dee847020c0207252dc075c614cef55d8fe6b') diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py index 98d9bb06e6..4015badc7f 100644 --- a/var/spack/repos/builtin/packages/r-glue/package.py +++ b/var/spack/repos/builtin/packages/r-glue/package.py @@ -7,7 +7,7 @@ from spack import * class RGlue(RPackage): - """Interpreted String Literals + """Interpreted String Literals. An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> @@ -15,10 +15,10 @@ class RGlue(RPackage): Triple-Quoted String Literals <https://docs.julialang.org/en/stable/ manual/strings/#triple-quoted-string-literals>.""" - homepage = "https://github.com/tidyverse/glue" - url = "https://cloud.r-project.org/src/contrib/glue_1.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/glue" + cran = "glue" + version('1.6.1', sha256='318c2f9544f1204216009f512793c44d6bbe178ff2012f56fa5ffb5e1da978db') + version('1.6.0', sha256='77bef37ef2c47aad6188ea772880591c5763cce4b1c256e10e68e7c3ec6b4338') version('1.4.2', sha256='9f7354132a26e9a876428fa87629b9aaddcd558f9932328e6ac065b95b8ef7ad') version('1.4.1', sha256='f8b687d35cacb5ee7fcada6e9c26ea20c04d0bdc9d37e919a03abd1137513bc8') version('1.4.0', sha256='ea6c409f7141754baa090deba96cff270a11b185452cf9e6fb69cb148a9069c1') @@ -27,4 +27,5 @@ class RGlue(RPackage): version('1.2.0', sha256='19275b34ee6a1bcad05360b7eb996cebaa1402f189a5dfb084e695d423f2296e') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r@3.2:', when='@1.4.2:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@1.4.2:') + depends_on('r@3.4:', type=('build', 'run'), when='@1.6.0:') diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py index 8cd0c2ab53..2b4dd4da56 100644 --- a/var/spack/repos/builtin/packages/r-gmodels/package.py +++ b/var/spack/repos/builtin/packages/r-gmodels/package.py @@ -9,9 +9,7 @@ from spack import * class RGmodels(RPackage): """Various R programming tools for model fitting.""" - homepage = "https://www.sf.net/projects/r-gregmisc" - url = "https://cloud.r-project.org/src/contrib/gmodels_2.16.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gmodels" + cran = "gmodels" version('2.18.1', sha256='626140a34eb8c53dd0a06511a76c71bc61c48777fa76fcc5e6934c9c276a1369') version('2.16.2', sha256='ab018894bdb376c5bd6bc4fbc4fe6e86590f4106795a586ef196fbb6699ec47d') diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py index e7b401dcfc..3327d05867 100644 --- a/var/spack/repos/builtin/packages/r-gmp/package.py +++ b/var/spack/repos/builtin/packages/r-gmp/package.py @@ -7,21 +7,20 @@ from spack import * class RGmp(RPackage): - """Multiple Precision Arithmetic + """Multiple Precision Arithmetic. Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).""" - homepage = "http://mulcyber.toulouse.inra.fr/projects/gmp" - url = "https://cloud.r-project.org/src/contrib/gmp_0.5-13.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gmp" + cran = "gmp" + version('0.6-2.1', sha256='c458026346c12093a22e627e2d5707a929fe95f4de3281894db4ab988d8747d6') version('0.6-2', sha256='6bfcb45b3f1e7da27d8773f911027355cab371d150c3dabf7dbaf8fba85b7f0e') version('0.5-13.5', sha256='f681ab2ff3d1e379ba8ac44a8abddd08d08170723e885abc0b469b6fa8fe5510') version('0.5-13.4', sha256='f05605b40fc39fc589e3a4d2f526a591a649faa45eef7f95c096e1bff8775196') version('0.5-13.1', sha256='2f805374a26742cd43f6b2054130d8670eda1940070aabb9971e9e48226d0976') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.6-2:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.6-2:') depends_on('gmp@4.2.3:') diff --git a/var/spack/repos/builtin/packages/r-goftest/package.py b/var/spack/repos/builtin/packages/r-goftest/package.py index 4a5ee5270e..8fbd25d402 100644 --- a/var/spack/repos/builtin/packages/r-goftest/package.py +++ b/var/spack/repos/builtin/packages/r-goftest/package.py @@ -7,14 +7,14 @@ from spack import * class RGoftest(RPackage): - """Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for - continuous univariate distributions, using efficient algorithms. - """ + """Classical Goodness-of-Fit Tests for Univariate Distributions. - homepage = "https://cloud.r-project.org/package=goftest" - url = "https://cloud.r-project.org/src/contrib/goftest_1.2-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/goftest" + Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for + continuous univariate distributions, using efficient algorithms.""" + cran = "goftest" + + version('1.2-3', sha256='3a5f74b6ae7ece5b294781ae57782abe12375d61789c55ff5e92e4aacf347f19') version('1.2-2', sha256='e497992666b002b6c6bed73bf05047ad7aa69eb58898da0ad8f1f5b2219e7647') depends_on('r@3.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-googledrive/package.py b/var/spack/repos/builtin/packages/r-googledrive/package.py index a3b093f98f..fae27c478a 100644 --- a/var/spack/repos/builtin/packages/r-googledrive/package.py +++ b/var/spack/repos/builtin/packages/r-googledrive/package.py @@ -11,8 +11,7 @@ class RGoogledrive(RPackage): Manage Google Drive files from R.""" - homepage = "https://github.com/tidyverse/googledrive" - cran = "googledrive" + cran = "googledrive" version('2.0.0', sha256='605c469a6a086ef4b049909c2e20a35411c165ce7ce4f62d68fd39ffed8c5a26') diff --git a/var/spack/repos/builtin/packages/r-googlesheets4/package.py b/var/spack/repos/builtin/packages/r-googlesheets4/package.py index f8efe48d7d..b845405acb 100644 --- a/var/spack/repos/builtin/packages/r-googlesheets4/package.py +++ b/var/spack/repos/builtin/packages/r-googlesheets4/package.py @@ -12,13 +12,12 @@ class RGooglesheets4(RPackage): Interact with Google Sheets through the Sheets API v4 <https://developers.google.com/sheets/api>. "API" is an acronym for "application programming interface"; the Sheets API allows users to - interact with Google Sheets programmatically, instead of via a web - browser. The "v4" refers to the fact that the Sheets API is currently at - version 4. This package can read and write both the metadata and the cell - data in a Sheet.""" + interact with Google Sheets programmatically, instead of via a web browser. + The "v4" refers to the fact that the Sheets API is currently at version 4. + This package can read and write both the metadata and the cell data in a + Sheet.""" - homepage = "https://github.com/tidyverse/googlesheets4" - cran = "googlesheets4" + cran = "googlesheets4" version('1.0.0', sha256='0a107d76aac99d6db48d97ce55810c1412b2197f457b8476f676169a36c7cc7a') diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py index 4781a0ff15..260e99de9a 100644 --- a/var/spack/repos/builtin/packages/r-googlevis/package.py +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -7,7 +7,7 @@ from spack import * class RGooglevis(RPackage): - """R Interface to Google Charts + """R Interface to Google Charts. R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP @@ -15,10 +15,9 @@ class RGooglevis(RPackage): for some charts a Flash player. The data remains local and is not uploaded to Google.""" - homepage = "https://github.com/mages/googleVis#googlevis" - url = "https://cloud.r-project.org/src/contrib/googleVis_0.6.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/googleVis" + cran = "googleVis" + version('0.6.11', sha256='f8c90b6c51da7bf184bff6762d98fc24faba1b634724ecdb987161ee10987b97') version('0.6.9', sha256='0739d0a3382a73a824b5ff9a6fe329198dd05c9da5855ac051ed022d7b41b7ea') version('0.6.4', sha256='7dcaf0e9d5e5598c17e8bd474141708de37eeb2578b09788431b9d871edb7eb8') version('0.6.3', sha256='17d104c5d4e6ab7b984df229cd51be19681e4726077afec7c61a33f6e4c0b6ef') diff --git a/var/spack/repos/builtin/packages/r-goplot/package.py b/var/spack/repos/builtin/packages/r-goplot/package.py index 7047b23f8d..b7c26a62fe 100644 --- a/var/spack/repos/builtin/packages/r-goplot/package.py +++ b/var/spack/repos/builtin/packages/r-goplot/package.py @@ -6,19 +6,19 @@ from spack import * class RGoplot(RPackage): - """Implementation of multilayered visualizations for enhanced graphical - representation of functional analysis data. It combines and integrates - omics data derived from expression and functional annotation enrichment - analyses. Its plotting functions have been developed with an - hierarchical structure in mind: starting from a general overview to - identify the most enriched categories (modified bar plot, bubble plot) - to a more detailed one displaying different types of relevant - information for the molecules in a given set of categories - (circle plot, chord plot, cluster plot, Venn diagram, heatmap).""" + """Visualization of Functional Analysis Data. - homepage = "https://github.com/wencke/wencke.github.io/issues" - url = "https://cloud.r-project.org/src/contrib/GOplot_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GOplot" + Implementation of multilayered visualizations for enhanced graphical + representation of functional analysis data. It combines and integrates + omics data derived from expression and functional annotation enrichment + analyses. Its plotting functions have been developed with an hierarchical + structure in mind: starting from a general overview to identify the most + enriched categories (modified bar plot, bubble plot) to a more detailed one + displaying different types of relevant information for the molecules in a + given set of categories (circle plot, chord plot, cluster plot, Venn + diagram, heatmap).""" + + cran = "GOplot" version('1.0.2', sha256='3ddaa2b6d1297ad6daad30d18af708adf43d86e8804b1b92fa29dfbf26d80df9') diff --git a/var/spack/repos/builtin/packages/r-gower/package.py b/var/spack/repos/builtin/packages/r-gower/package.py index f116208048..a60ec14cda 100644 --- a/var/spack/repos/builtin/packages/r-gower/package.py +++ b/var/spack/repos/builtin/packages/r-gower/package.py @@ -7,15 +7,13 @@ from spack import * class RGower(RPackage): - """Gower's Distance + """Gower's Distance. Compute Gower's distance (or similarity) coefficient between records. Compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.""" - homepage = "https://github.com/markvanderloo/gower" - url = "https://cloud.r-project.org/src/contrib/gower_0.2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gower" + cran = "gower" version('0.2.2', sha256='3f022010199fafe34f6e7431730642a76893e6b4249b84e5a61012cb83483631') version('0.2.1', sha256='af3fbe91cf818c0841b2c0ec4ddf282c182a588031228c8d88f7291b2cdff100') diff --git a/var/spack/repos/builtin/packages/r-gparotation/package.py b/var/spack/repos/builtin/packages/r-gparotation/package.py index 69afb6331e..15796d1180 100644 --- a/var/spack/repos/builtin/packages/r-gparotation/package.py +++ b/var/spack/repos/builtin/packages/r-gparotation/package.py @@ -7,12 +7,12 @@ from spack import * class RGparotation(RPackage): - """Gradient Projection Algorithm Rotation for Factor Analysis. See - ?GPArotation.Intro for more details.""" + """GPA Factor Rotation. - homepage = "https://cloud.r-project.org/package=GPArotation" - url = "https://cloud.r-project.org/src/contrib/GPArotation_2014.11-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GPArotation" + Gradient Projection Algorithm Rotation for Factor Analysis. See + GPArotation.Intro for more details.""" + + cran = "GPArotation" version('2014.11-1', sha256='351bc15fc8dc6c8ea5045fbba22180d1e68314fc34d267545687748e312e5096') diff --git a/var/spack/repos/builtin/packages/r-gplots/package.py b/var/spack/repos/builtin/packages/r-gplots/package.py index ab58b1c6a3..39f92d40ad 100644 --- a/var/spack/repos/builtin/packages/r-gplots/package.py +++ b/var/spack/repos/builtin/packages/r-gplots/package.py @@ -9,27 +9,30 @@ from spack import * class RGplots(RPackage): - """Various R Programming Tools for Plotting Data - - Various R programming tools for plotting data, including: - calculating and - plotting locally smoothed summary function as ('bandplot', 'wapply'), - - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', - 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', - 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and - plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced - regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled - interface to 'stats::lowess' function ('lowess'), - displaying textual data - in plots ('textplot', 'sinkplot'), - plotting a matrix where each cell - contains a dot whose size reflects the relative magnitude of the elements - ('balloonplot'), - plotting "Venn" diagrams ('venn'), - displaying - Open-Office style plots ('ooplot'), - plotting multiple data on same - region, with separate axes ('overplot'), - plotting means and confidence - intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they - don't overlap ('space').""" - - homepage = "https://cloud.r-project.org/package=gplots" - url = "https://cloud.r-project.org/src/contrib/gplots_3.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gplots" + """Various R Programming Tools for Plotting Data. + + Various R programming tools for plotting data, including: + [1] calculating and plotting locally smoothed summary function as + ('bandplot', 'wapply'), + [2] enhanced versions of standard plots ('barplot2', 'boxplot2', + 'heatmap.2', 'smartlegend'), + [3] manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', + 'bluered', 'redblue', 'rich.colors'), + [4] calculating and plotting two-dimensional data summaries ('ci2d', + 'hist2d'), + [5] enhanced regression diagnostic plots ('lmplot2', 'residplot'), + [6] formula-enabled interface to 'stats::lowess' function ('lowess'), + [7] displaying textual data in plots ('textplot', 'sinkplot'), + [8] plotting a matrix where each cell contains a dot whose size reflects + the relative magnitude of the elements ('balloonplot'), + [9] plotting "Venn" diagrams ('venn'), + [10] displaying Open-Office style plots ('ooplot'), + [11] plotting multiple data on same region, with separate axes + ('overplot'), + [12] plotting means and confidence intervals ('plotCI', 'plotmeans'), + [13] spacing points in an x-y plot so they don't overlap ('space').""" + + cran = "gplots" version('3.1.1', sha256='f9ae19c2574b6d41adbeccaf7bc66cf56d7b2769004daba7e0038d5fbd821339') version('3.0.1.1', sha256='7db103f903a25d174cddcdfc7b946039b61e236c95084b90ad17f1a41da3770c') @@ -39,4 +42,5 @@ class RGplots(RPackage): depends_on('r-gtools', type=('build', 'run')) depends_on('r-catools', type=('build', 'run')) depends_on('r-kernsmooth', type=('build', 'run')) - depends_on('r-gdata', when='@:3.0.1.1', type=('build', 'run')) + + depends_on('r-gdata', type=('build', 'run'), when='@:3.0.1.1') diff --git a/var/spack/repos/builtin/packages/r-graphlayouts/package.py b/var/spack/repos/builtin/packages/r-graphlayouts/package.py index dd3f73e19c..7761281f67 100644 --- a/var/spack/repos/builtin/packages/r-graphlayouts/package.py +++ b/var/spack/repos/builtin/packages/r-graphlayouts/package.py @@ -15,10 +15,9 @@ class RGraphlayouts(RPackage): specific algorithms allow to emphasize hidden group structures in networks or focus on specific nodes.""" - homepage = "https://github.com/schochastics/graphlayouts" - url = "https://cloud.r-project.org/src/contrib/graphlayouts_0.5.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/graphlayouts" + cran = "graphlayouts" + version('0.8.0', sha256='d724266778e4d97ca7a762253c293ffa3d09e2627cb1c3c7a654c690819defd0') version('0.7.1', sha256='380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717') version('0.5.0', sha256='83f61ce07580c5a64c7044c12b20d98ccf138c7e78ff12855cdfc206e1fab10d') diff --git a/var/spack/repos/builtin/packages/r-grbase/package.py b/var/spack/repos/builtin/packages/r-grbase/package.py index 124ac6a6fb..37819c2ddb 100644 --- a/var/spack/repos/builtin/packages/r-grbase/package.py +++ b/var/spack/repos/builtin/packages/r-grbase/package.py @@ -7,7 +7,7 @@ from spack import * class RGrbase(RPackage): - """A Package for Graphical Modelling in R + """A Package for Graphical Modelling in R. The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms @@ -24,18 +24,16 @@ class RGrbase(RPackage): and 'RBGL' are installed from 'bioconductor'; for installation instructions please refer to the web page given below.""" - homepage = "https://people.math.aau.dk/~sorenh/software/gR/" - url = "https://cloud.r-project.org/src/contrib/gRbase_1.8-3.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gRbase" + cran = "gRbase" version('1.8-6.7', sha256='aaafc7e1b521de60e1a57c0175ac64d4283850c3273bd14774cf24dabc743388') version('1.8-3.4', sha256='d35f94c2fb7cbd4ce3991570424dfe6723a849658da32e13df29f53b6ea2cc2c') depends_on('r+X', type=('build', 'run')) depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.6.0:', when='@1.8-6.7:', type=('build', 'run')) + depends_on('r@3.6.0:', type=('build', 'run'), when='@1.8-6.7:') depends_on('r-graph', type=('build', 'run')) - depends_on('r-rgraphviz', when='@1.8-6.7:', type=('build', 'run')) + depends_on('r-rgraphviz', type=('build', 'run'), when='@1.8-6.7:') depends_on('r-rbgl', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py index 0955226afa..e0376616a0 100644 --- a/var/spack/repos/builtin/packages/r-gridbase/package.py +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -9,9 +9,7 @@ from spack import * class RGridbase(RPackage): """Integration of base and grid graphics.""" - homepage = "https://cloud.r-project.org/package=gridBase" - url = "https://cloud.r-project.org/src/contrib/gridBase_0.4-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gridBase" + cran = "gridBase" version('0.4-7', sha256='be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26') diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index 9d1f7ba36a..be385b749f 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -7,12 +7,12 @@ from spack import * class RGridextra(RPackage): - """Provides a number of user-level functions to work with "grid" graphics, + """Miscellaneous Functions for "Grid" Graphics. + + Provides a number of user-level functions to work with "grid" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.""" - homepage = "https://cloud.r-project.org/package=gridExtra" - url = "https://cloud.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gridExtras" + cran = "gridExtras" version('2.3', sha256='81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b') version('2.2.1', sha256='44fe455a5bcdf48a4ece7a542f83e7749cf251dc1df6ae7634470240398c6818') diff --git a/var/spack/repos/builtin/packages/r-gridgraphics/package.py b/var/spack/repos/builtin/packages/r-gridgraphics/package.py index b1c3a79fdc..031b56cb14 100644 --- a/var/spack/repos/builtin/packages/r-gridgraphics/package.py +++ b/var/spack/repos/builtin/packages/r-gridgraphics/package.py @@ -7,7 +7,7 @@ from spack import * class RGridgraphics(RPackage): - """Redraw Base Graphics Using 'grid' Graphics + """Redraw Base Graphics Using 'grid' Graphics. Functions to convert a page of plots drawn with the 'graphics' package into identical output drawn with the 'grid' package. The result looks like the @@ -15,9 +15,7 @@ class RGridgraphics(RPackage): that can then be manipulated with 'grid' functions (e.g., edit grobs and revisit viewports).""" - homepage = "https://github.com/pmur002/gridgraphics" - url = "https://cloud.r-project.org/src/contrib/gridGraphics_0.4-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gridGraphics" + cran = "gridGraphics" version('0.5-1', sha256='29086e94e63891884c933b186b35511aac2a2f9c56967a72e4050e2980e7da8b') version('0.4-1', sha256='b770127b71664bbf67f8853a2666c071f2b9920743eddc9f3a58ecb948b923cf') diff --git a/var/spack/repos/builtin/packages/r-gsa/package.py b/var/spack/repos/builtin/packages/r-gsa/package.py index e90aa69b54..9fb4b2d227 100644 --- a/var/spack/repos/builtin/packages/r-gsa/package.py +++ b/var/spack/repos/builtin/packages/r-gsa/package.py @@ -9,8 +9,6 @@ from spack import * class RGsa(RPackage): """Gene Set Analysis.""" - homepage = "https://www-stat.stanford.edu/~tibs/GSA" - url = "https://cloud.r-project.org/src/contrib/GSA_1.03.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GSA" + cran = "GSA" version('1.03.1', sha256='e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917') diff --git a/var/spack/repos/builtin/packages/r-gsalib/package.py b/var/spack/repos/builtin/packages/r-gsalib/package.py index 2eeb99da30..c57d076725 100644 --- a/var/spack/repos/builtin/packages/r-gsalib/package.py +++ b/var/spack/repos/builtin/packages/r-gsalib/package.py @@ -7,12 +7,12 @@ from spack import * class RGsalib(RPackage): - """This package contains utility functions used by the Genome Analysis + """Utility Functions For GATK. + + This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.""" - homepage = "https://cloud.r-project.org/package=gsalib" - url = "https://cloud.r-project.org/src/contrib/gsalib_2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gsalib" + cran = "gsalib" version('2.1', sha256='e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc') diff --git a/var/spack/repos/builtin/packages/r-gsl/package.py b/var/spack/repos/builtin/packages/r-gsl/package.py index 3a0f8b9a0c..c09dcfc540 100644 --- a/var/spack/repos/builtin/packages/r-gsl/package.py +++ b/var/spack/repos/builtin/packages/r-gsl/package.py @@ -7,15 +7,15 @@ from spack import * class RGsl(RPackage): - """An R wrapper for some of the functionality of the Gnu Scientific + """Wrapper for the Gnu Scientific Library. + + An R wrapper for some of the functionality of the Gnu Scientific Library.""" - homepage = "https://github.com/RobinHankin/gsl.git" - url = "https://cloud.r-project.org/src/contrib/gsl_2.1-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gsl" + cran = "gsl" + version('2.1-7.1', sha256='ee98d1382d37ffa77538a90ccdbf44affbf1710a9e66b8ada73fa72e67921985') version('2.1-6', sha256='f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c') depends_on('r@3.1.0:', type=('build', 'run')) - depends_on('gsl@2.1:') diff --git a/var/spack/repos/builtin/packages/r-gsodr/package.py b/var/spack/repos/builtin/packages/r-gsodr/package.py index cca5a98a39..bba48d68a0 100644 --- a/var/spack/repos/builtin/packages/r-gsodr/package.py +++ b/var/spack/repos/builtin/packages/r-gsodr/package.py @@ -7,7 +7,7 @@ from spack import * class RGsodr(RPackage): - """A Global Surface Summary of the Day (GSOD) Weather Data Client for R + """A Global Surface Summary of the Day (GSOD) Weather Data Client for R. Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from @@ -27,17 +27,18 @@ class RGsodr(RPackage): 'GSOD' 'readme.txt' file available from, <https://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.""" - homepage = "https://docs.ropensci.org/GSODR/" - url = "https://cloud.r-project.org/src/contrib/GSODR_2.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GSODR" + cran = "GSODR" + version('3.1.4', sha256='615ac4271b44a63064cb23632b887c60c86f4742957fc46f300423f8f75858c8') version('2.1.2', sha256='4fc1d084b6c21055d8cc17a6a6dc412261aa0d4ef4079bcd73b580a8c16bf74e') version('2.1.1', sha256='dba732e5bd1e367b9d710e6b8924f0c02fa4546202f049124dba02bc2e3329f5') depends_on('r@3.5.0:', type=('build', 'run')) depends_on('r-countrycode', type=('build', 'run')) depends_on('r-curl', type=('build', 'run')) - depends_on('r-data-table@1.11.6:', type=('build', 'run')) - depends_on('r-future-apply', type=('build', 'run')) + depends_on('r-data-table@1.11.6:', type=('build', 'run'), when='@:2.1.2') + depends_on('r-data-table', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-r-utils', type=('build', 'run')) + + depends_on('r-future-apply', type=('build', 'run'), when='@:2.1.2') diff --git a/var/spack/repos/builtin/packages/r-gss/package.py b/var/spack/repos/builtin/packages/r-gss/package.py index e28fbf17ae..f364b68e0f 100644 --- a/var/spack/repos/builtin/packages/r-gss/package.py +++ b/var/spack/repos/builtin/packages/r-gss/package.py @@ -7,18 +7,17 @@ from spack import * class RGss(RPackage): - """General Smoothing Splines + """General Smoothing Splines. - A comprehensive package for structural multivariate function - estimation using smoothing splines.""" + A comprehensive package for structural multivariate function estimation + using smoothing splines.""" - homepage = "https://cloud.r-project.org/package=gss" - url = "https://cloud.r-project.org/src/contrib/gss_2.1-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gss" + cran = "gss" + version('2.2-3', sha256='24306401cf4e5869f8a690eca7e17c044ece83edd66969bd2daf5976272d244b') version('2.2-2', sha256='1da4da894378ee730cff9628e8b4d2a0d7dfa344b94e5bce6953e66723c21fe4') version('2.1-10', sha256='26c47ecae6a9b7854a1b531c09f869cf8b813462bd8093e3618e1091ace61ee2') version('2.1-7', sha256='0405bb5e4c4d60b466335e5da07be4f9570045a24aed09e7bc0640e1a00f3adb') depends_on('r@2.14.0:', type=('build', 'run')) - depends_on('r@3.0.0:', when='@2.2-2:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run'), when='@2.2-2:') diff --git a/var/spack/repos/builtin/packages/r-gstat/package.py b/var/spack/repos/builtin/packages/r-gstat/package.py index 239df8e7e0..c0ae8081c1 100644 --- a/var/spack/repos/builtin/packages/r-gstat/package.py +++ b/var/spack/repos/builtin/packages/r-gstat/package.py @@ -8,17 +8,16 @@ from spack import * class RGstat(RPackage): """Spatial and Spatio-Temporal Geostatistical Modelling, Predictionand - Simulation + Simulation. Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.""" - homepage = "https://github.com/r-spatial/gstat/" - url = "https://cloud.r-project.org/src/contrib/gstat_2.0-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gstat" + cran = "gstat" + version('2.0-8', sha256='57cb9e8235a39379a96af0a5651c82e02fdd608375917939948c3dbf170668e8') version('2.0-6', sha256='6711e68aa2444cf2927879a03a976d8caeca5eac98d806b19a6a7178b90bfcab') version('2.0-3', sha256='20a93fe6bf89221a5888de273bddf9a98187806d507cd3cd6297c2b13e7acce1') diff --git a/var/spack/repos/builtin/packages/r-gsubfn/package.py b/var/spack/repos/builtin/packages/r-gsubfn/package.py index 6e72b0c933..2458ec9d92 100644 --- a/var/spack/repos/builtin/packages/r-gsubfn/package.py +++ b/var/spack/repos/builtin/packages/r-gsubfn/package.py @@ -7,23 +7,21 @@ from spack import * class RGsubfn(RPackage): - """gsubfn is like gsub but can take a replacement function or - certain other objects instead of the replacement string. Matches - and back references are input to the replacement function and - replaced by the function output. gsubfn can be used to split - strings based on content rather than delimiters and for - quasi-perl-style string interpolation. The package also has - facilities for translating formulas to functions and allowing - such formulas in function calls instead of functions. This can - be used with R functions such as apply, sapply, lapply, optim, - integrate, xyplot, Filter and any other function that expects - another function as an input argument or functions like cat or - sql calls that may involve strings where substitution is - desirable.""" + """Utilities for Strings and Function Arguments. - homepage = "https://cloud.r-project.org/package=gsubfn" - url = "https://cloud.r-project.org/src/contrib/gsubfn_0.6-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gsubfn" + gsubfn is like gsub but can take a replacement function or certain other + objects instead of the replacement string. Matches and back references are + input to the replacement function and replaced by the function output. + gsubfn can be used to split strings based on content rather than delimiters + and for quasi-perl-style string interpolation. The package also has + facilities for translating formulas to functions and allowing such formulas + in function calls instead of functions. This can be used with R functions + such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any + other function that expects another function as an input argument or + functions like cat or sql calls that may involve strings where substitution + is desirable.""" + + cran = "gsubfn" version('0.7', sha256='89351df9e65722d2862f26a0a3985666de3c86e8400808ced8a6eb6e165a4602') version('0.6-6', sha256='bbc5d29bb48e836407f81880aeb368544a54a5513dacb3411c9838180723dda4') diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py index 16460d0bf7..a16e506225 100644 --- a/var/spack/repos/builtin/packages/r-gtable/package.py +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -7,11 +7,15 @@ from spack import * class RGtable(RPackage): - """Tools to make it easier to work with "tables" of 'grobs'.""" + """Arrange 'Grobs' in Tables. - homepage = "https://cloud.r-project.org/package=gtable" - url = "https://cloud.r-project.org/src/contrib/gtable_0.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gtable" + Tools to make it easier to work with "tables" of 'grobs'. The 'gtable' + package defines a 'gtable' grob class that specifies a grid along with a + list of grobs and their placement in the grid. Further the package makes it + easy to manipulate and combine 'gtable' objects so that complex + compositions can be build up sequentially.""" + + cran = "gtable" version('0.3.0', sha256='fd386cc4610b1cc7627dac34dba8367f7efe114b968503027fb2e1265c67d6d3') version('0.2.0', sha256='801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f') diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py index becedd276c..50fb0b2936 100644 --- a/var/spack/repos/builtin/packages/r-gtools/package.py +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -7,7 +7,7 @@ from spack import * class RGtools(RPackage): - """Various R Programming Tools + """Various R Programming Tools. Functions to assist in R programming. Including: @@ -41,10 +41,9 @@ class RGtools(RPackage): [18] convert characters to/from ASCII codes; """ - homepage = "https://cloud.r-project.org/package=gtools" - url = "https://cloud.r-project.org/src/contrib/gtools_3.5.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/gtools" + cran = "gtools" + version('3.9.2', sha256='03b1898bf581f6d12fa90e23ff700cfa7c834ac10c6654bdac42d7ec943fa953') version('3.8.2', sha256='503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde') version('3.8.1', sha256='051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38') version('3.5.0', sha256='86b6a51a92ddb3c78095e0c5dc20414c67f6e28f915bf0ee11406adad3e476f6') diff --git a/var/spack/repos/builtin/packages/r-gwmodel/package.py b/var/spack/repos/builtin/packages/r-gwmodel/package.py index a62caf7799..73bca88d0d 100644 --- a/var/spack/repos/builtin/packages/r-gwmodel/package.py +++ b/var/spack/repos/builtin/packages/r-gwmodel/package.py @@ -7,7 +7,7 @@ from spack import * class RGwmodel(RPackage): - """Geographically-Weighted Models + """Geographically-Weighted Models. Techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data @@ -22,10 +22,9 @@ class RGwmodel(RPackage): <doi:10.1111/j.1538-4632.1996.tb00936.x>; some of which are provided in basic and robust (outlier resistant) forms.""" - homepage = "http://gwr.nuim.ie/" - url = "https://cloud.r-project.org/src/contrib/GWmodel_2.0-9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/GWmodel" + cran = "GWmodel" + version('2.2-8', sha256='5b1890dbf75502e89b651efd9158be77b3cfa764a5717f9889f438ed2b0a4da2') version('2.2-2', sha256='4e2b221b85fbc828ffc4f057c137ded849afcaac2a75c27d2d6d0a6db17f8a06') version('2.1-3', sha256='3e1a36fddf8e64f61d548067bb043216f8d12069d814a4cbf07a9cae0b310af6') version('2.1-1', sha256='91241b4e26d423a54c7c6784ef5159759058a5dafdff18a1ea8451faf979d1f3') @@ -35,11 +34,11 @@ class RGwmodel(RPackage): depends_on('r-maptools@0.5-2:', type=('build', 'run')) depends_on('r-robustbase', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) - depends_on('r-sp@1.4-0:', when='@2.2-2:', type=('build', 'run')) + depends_on('r-sp@1.4-0:', type=('build', 'run'), when='@2.2-2:') depends_on('r-rcpp', type=('build', 'run')) depends_on('r-spatialreg', type=('build', 'run')) depends_on('r-spacetime', type=('build', 'run')) depends_on('r-spdep', type=('build', 'run')) - depends_on('r-fnn', when='@2.1-1:', type=('build', 'run')) + depends_on('r-fnn', type=('build', 'run'), when='@2.1-1:') depends_on('r-rcpparmadillo', type=('build', 'run')) depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-haven/package.py b/var/spack/repos/builtin/packages/r-haven/package.py index 17a39cc114..81ced48957 100644 --- a/var/spack/repos/builtin/packages/r-haven/package.py +++ b/var/spack/repos/builtin/packages/r-haven/package.py @@ -7,12 +7,11 @@ from spack import * class RHaven(RPackage): - """Import and Export 'SPSS', 'Stata' and 'SAS' Files + """Import and Export 'SPSS', 'Stata' and 'SAS' Files. Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.""" - homepage = "https://haven.tidyverse.org/" cran = "haven" version('2.4.3', sha256='95b70f47e77792bed4312441787299d2e3e27d79a176f0638a37e5301b93295f') @@ -21,17 +20,17 @@ class RHaven(RPackage): version('2.1.0', sha256='c0a1cf1b039549fb3ad833f9644ed3f142790236ad755d2ee7bd3d8109e3ae74') version('1.1.0', sha256='089fb4d0955f320abc48d0a3031799f96f3a20b82492474743903fdf12001d19') - depends_on('r@3.1:', when='@:2.1.0', type=('build', 'run')) - depends_on('r@3.2:', when='@2.1.1:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@2.1.1:') depends_on('r-forcats@0.2.0:', type=('build', 'run')) depends_on('r-hms', type=('build', 'run')) depends_on('r-readr@0.1.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.0:', when='@2.3.1:', type=('build', 'run')) + depends_on('r-rlang@0.4.0:', type=('build', 'run'), when='@2.3.1:') depends_on('r-tibble', type=('build', 'run')) - depends_on('r-tidyselect', when='@2.3.1:', type=('build', 'run')) - depends_on('r-vctrs@0.3.0:', when='@2.3.1:', type=('build', 'run')) - depends_on('r-cpp11', when='@2.4:', type=('build', 'run')) + depends_on('r-tidyselect', type=('build', 'run'), when='@2.3.1:') + depends_on('r-vctrs@0.3.0:', type=('build', 'run'), when='@2.3.1:') + depends_on('r-cpp11', type=('build', 'run'), when='@2.4:') depends_on('gmake', type='build') depends_on('zlib', when='@2.4:') - depends_on('r-rcpp@0.11.4:', when='@:2.3', type=('build', 'run')) + depends_on('r-rcpp@0.11.4:', type=('build', 'run'), when='@:2.3') diff --git a/var/spack/repos/builtin/packages/r-hdf5r/package.py b/var/spack/repos/builtin/packages/r-hdf5r/package.py index 2e43abda39..4c1b462876 100644 --- a/var/spack/repos/builtin/packages/r-hdf5r/package.py +++ b/var/spack/repos/builtin/packages/r-hdf5r/package.py @@ -7,7 +7,7 @@ from spack import * class RHdf5r(RPackage): - """Interface to the 'HDF5' Binary Data Format + """Interface to the 'HDF5' Binary Data Format. 'HDF5' is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, @@ -16,12 +16,9 @@ class RHdf5r(RPackage): classes. Additionally, functionality is added so that 'HDF5' objects behave very similar to their corresponding R counterparts.""" - homepage = "https://hhoeflin.github.io/hdf5r" - url = "https://cloud.r-project.org/src/contrib/hdf5r_1.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/hdf5r" + cran = "hdf5r" - version('1.3.5', - sha256='87b75173ab226a9fbaa5b28289349f3c56b638629560a172994b8f9323c1622f') + version('1.3.5', sha256='87b75173ab226a9fbaa5b28289349f3c56b638629560a172994b8f9323c1622f') version('1.3.3', sha256='a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545') version('1.2.0', sha256='58813e334fd3f9040038345a7186e5cb02090898883ac192477a76a5b8b4fe81') diff --git a/var/spack/repos/builtin/packages/r-hdrcde/package.py b/var/spack/repos/builtin/packages/r-hdrcde/package.py index 7ec35b76a2..d59ba51b0e 100644 --- a/var/spack/repos/builtin/packages/r-hdrcde/package.py +++ b/var/spack/repos/builtin/packages/r-hdrcde/package.py @@ -5,7 +5,9 @@ class RHdrcde(RPackage): - """Computation of highest density regions in one and two + """Highest Density Regions and Conditional Density Estimation. + + Computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate,and multimodal regression.""" diff --git a/var/spack/repos/builtin/packages/r-here/package.py b/var/spack/repos/builtin/packages/r-here/package.py new file mode 100644 index 0000000000..4b11f3e46e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-here/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 RHere(RPackage): + """A Simpler Way to Find Your Files. + + Constructs paths to your project's files. Declare the relative path of a + file within your project with 'i_am()'. Use the 'here()' function as a + drop-in replacement for 'file.path()', it will always locate the files + relative to your project root.""" + + cran = "here" + + version('1.0.1', sha256='08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b') + + depends_on('r-rprojroot@2.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index f5f8339522..b5460e8190 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -8,14 +8,12 @@ from spack import * class RHexbin(RPackage): - """Hexagonal Binning Routines + """Hexagonal Binning Routines. - Binning and plotting functions for hexagonal bins. Now uses and relies - on grid graphics and formal (S4) classes and methods.""" + Binning and plotting functions for hexagonal bins. Now uses and relies on + grid graphics and formal (S4) classes and methods.""" - homepage = "https://github.com/edzer/hexbin" - url = "https://cloud.r-project.org/src/contrib/hexbin_1.27.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/hexbin" + cran = "hexbin" version('1.28.2', sha256='6241f8d3a6c6be2c1c693c3ddb99554bc103e3c6cf602d0c2787c0ce6fd1702d') version('1.27.3', sha256='7ea422a76542c2fc2840df601af1b7803aa96df4fee6d51dec456ac36940c191') diff --git a/var/spack/repos/builtin/packages/r-hh/package.py b/var/spack/repos/builtin/packages/r-hh/package.py index 8a6dc30a63..afd75fed91 100644 --- a/var/spack/repos/builtin/packages/r-hh/package.py +++ b/var/spack/repos/builtin/packages/r-hh/package.py @@ -9,25 +9,23 @@ from spack import * class RHh(RPackage): """Statistical Analysis and Data Display: Heiberger and Holland. - Support software for Statistical Analysis and Data Display (Second - Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, - Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt - Holland. This contemporary presentation of statistical methods features - extensive use of graphical displays for exploring data and for displaying - the analysis. The second edition includes redesigned graphics and - additional chapters. The authors emphasize how to construct and interpret - graphs, discuss principles of graphical design, and show how accompanying - traditional tabular results are used to confirm the visual impressions - derived directly from the graphs. Many of the graphical formats are novel - and appear here for the first time in print. All chapters have exercises. - All functions introduced in the book are in the package. R code for all - examples, both graphs and tables, in the book is included in the scripts - directory of the package.""" + Support software for Statistical Analysis and Data Display (Second Edition, + Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN + 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This + contemporary presentation of statistical methods features extensive use of + graphical displays for exploring data and for displaying the analysis. The + second edition includes redesigned graphics and additional chapters. The + authors emphasize how to construct and interpret graphs, discuss principles + of graphical design, and show how accompanying traditional tabular results + are used to confirm the visual impressions derived directly from the + graphs. Many of the graphical formats are novel and appear here for the + first time in print. All chapters have exercises. All functions introduced + in the book are in the package. R code for all examples, both graphs and + tables, in the book is included in the scripts directory of the package.""" - homepage = "https://cloud.r-project.org/package=HH" - url = "https://cloud.r-project.org/src/contrib/HH_3.1-40.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/HH" + cran = "HH" + version('3.1-47', sha256='50910ac7de49122df56c6e42413535601c74bbef9240ad8977e3267273d087c0') version('3.1-43', sha256='2ed35c8fc97092e9d2ce3439a2ec342d5d7bd93ad8f5266995cc80d88cd2235b') version('3.1-40', sha256='795924d900a98ae367e6697b2c951c3b4910a54931aebcad5024eda083d4a8a2') diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py index 7ccb419214..29f86d32be 100644 --- a/var/spack/repos/builtin/packages/r-highr/package.py +++ b/var/spack/repos/builtin/packages/r-highr/package.py @@ -3,23 +3,23 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - from spack import * class RHighr(RPackage): - """Provides syntax highlighting for R source code. Currently it supports + """Syntax Highlighting for R Source Code. + + Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.""" - homepage = "https://github.com/yihui/highr" - cran = "highr" + cran = "highr" version('0.9', sha256='beff11390d936c90fdcc00e7ed0eb72220f3de403a51b56659e3d3e0b6d8ed4d') version('0.8', sha256='4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657') version('0.7', sha256='cabba5b6f2ea82024a49c5ced5f1aa476f864bc52bc129038e319e4e26b6f3b7') version('0.6', sha256='43e152b2dea596df6e14c44398c74fcd438ece15eaae5bdb84aef8d61b213b59') - depends_on('r@3.0.2:', when='@:0.7', type=('build', 'run')) - depends_on('r@3.2.3:', when='@0.8:', type=('build', 'run')) - depends_on('r-xfun@0.18:', when='@0.9:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r@3.2.3:', type=('build', 'run'), when='@0.8:') + depends_on('r-xfun@0.18:', type=('build', 'run'), when='@0.9:') diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py index f5255a87b8..f022ca8a1f 100644 --- a/var/spack/repos/builtin/packages/r-hmisc/package.py +++ b/var/spack/repos/builtin/packages/r-hmisc/package.py @@ -7,19 +7,17 @@ from spack import * class RHmisc(RPackage): - """Harrell Miscellaneous + """Harrell Miscellaneous. - Contains many functions useful for data analysis, high-level - graphics, utility operations, functions for computing sample size - and power, importing and annotating datasets, imputing missing - values, advanced table making, variable clustering, character - string manipulation, conversion of R objects to LaTeX and html - code, and recoding variables.""" + Contains many functions useful for data analysis, high-level graphics, + utility operations, functions for computing sample size and power, + importing and annotating datasets, imputing missing values, advanced table + making, variable clustering, character string manipulation, conversion of R + objects to LaTeX and html code, and recoding variables.""" - homepage = "https://cran.r-project.org/web/packages/Hmisc/index.html" - url = "https://cloud.r-project.org/src/contrib/Hmisc_4.1-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Hmisc" + cran = "Hmisc" + version('4.6-0', sha256='2c1ce906b2333c6dc946dc7f10b74cfa552bce2b12dbebf295d143163562a1ad') version('4.4-2', sha256='490ac64dd8558868e7c6fdd9523af102e17ea536c450d62c48b04155279bfbc8') version('4.4-0', sha256='f16ecf4c5ee2202d51f426282a54f8000ffa8b9747c3e910205f34f878556ec7') version('4.2-0', sha256='9e9614673288dd00295f250fa0bf96fc9e9fed692c69bf97691081c1a01411d9') @@ -27,7 +25,7 @@ class RHmisc(RPackage): depends_on('r-lattice', type=('build', 'run')) depends_on('r-survival@2.40-1:', type=('build', 'run')) - depends_on('r-survival@3.1-6:', when='@4.4:', type=('build', 'run')) + depends_on('r-survival@3.1-6:', type=('build', 'run'), when='@4.4:') depends_on('r-formula', type=('build', 'run')) depends_on('r-ggplot2@2.2:', type=('build', 'run')) depends_on('r-latticeextra', type=('build', 'run')) @@ -42,4 +40,5 @@ class RHmisc(RPackage): depends_on('r-viridis', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-acepack', when='@:4.4-0', type=('build', 'run')) + + depends_on('r-acepack', type=('build', 'run'), when='@:4.4-0') diff --git a/var/spack/repos/builtin/packages/r-hms/package.py b/var/spack/repos/builtin/packages/r-hms/package.py index 7eade052b4..5940b3765a 100644 --- a/var/spack/repos/builtin/packages/r-hms/package.py +++ b/var/spack/repos/builtin/packages/r-hms/package.py @@ -7,12 +7,11 @@ from spack import * class RHms(RPackage): - """Pretty Time of Day + """Pretty Time of Day. Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.""" - homepage = "https://cloud.r-project.org/package=hms" cran = "hms" version('1.1.1', sha256='6b5f30db1845c70d27b5de33f31caa487cdd0787cd80a4073375e5f482269062') @@ -20,11 +19,11 @@ class RHms(RPackage): version('0.5.0', sha256='a87872665c3bf3901f597d78c152e7805f7129e4dbe27397051de4cf1a76561b') version('0.3', sha256='9368259cbc1094ce0e4cf61544875ec30088ef690d6667e6b0b564218ab3ff88') - depends_on('r-ellipsis', when='@1.0.0:', type=('build', 'run')) - depends_on('r-ellipsis@0.3.2', when='@1.1:', type=('build', 'run')) - depends_on('r-lifecycle', when='@1.0.0:', type=('build', 'run')) - depends_on('r-pkgconfig', when='@0.5.0:', type=('build', 'run')) - depends_on('r-rlang', when='@0.5.0:', type=('build', 'run')) - depends_on('r-vctrs@0.2.0:', when='@0.5.0:', type=('build', 'run')) - depends_on('r-vctrs@0.2.1:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-vctrs@0.3.8:', when='@1.1:', type=('build', 'run')) + depends_on('r-ellipsis', type=('build', 'run'), when='@1.0.0:') + depends_on('r-ellipsis@0.3.2', type=('build', 'run'), when='@1.1:') + depends_on('r-lifecycle', type=('build', 'run'), when='@1.0.0:') + depends_on('r-pkgconfig', type=('build', 'run'), when='@0.5.0:') + depends_on('r-rlang', type=('build', 'run'), when='@0.5.0:') + depends_on('r-vctrs@0.2.0:', type=('build', 'run'), when='@0.5.0:') + depends_on('r-vctrs@0.2.1:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-vctrs@0.3.8:', type=('build', 'run'), when='@1.1:') diff --git a/var/spack/repos/builtin/packages/r-hoardr/package.py b/var/spack/repos/builtin/packages/r-hoardr/package.py index b5c4264037..a1d0dec1ed 100644 --- a/var/spack/repos/builtin/packages/r-hoardr/package.py +++ b/var/spack/repos/builtin/packages/r-hoardr/package.py @@ -7,11 +7,15 @@ from spack import * class RHoardr(RPackage): - """hoardr: Manage Cached Files""" + """Manage Cached Files. - homepage = "https://cloud.r-project.org/package=hoardr" - url = "https://cloud.r-project.org/src/contrib/hoardr_0.5.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/hoardr/" + Suite of tools for managing cached files, targeting use in other R + packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to + manage cache directories, including targeting files by path or by key; + cached directories can be compressed and uncompressed easily to save disk + space.""" + + cran = "hoardr" version('0.5.2', sha256='819113f0e25da105f120a676b5173872a4144f2f6f354cad14b35f898e76dc54') diff --git a/var/spack/repos/builtin/packages/r-htmltable/package.py b/var/spack/repos/builtin/packages/r-htmltable/package.py index 9ee0cdccfb..97efa3f16f 100644 --- a/var/spack/repos/builtin/packages/r-htmltable/package.py +++ b/var/spack/repos/builtin/packages/r-htmltable/package.py @@ -7,20 +7,18 @@ from spack import * class RHtmltable(RPackage): - """Advanced Tables for Markdown/HTML + """Advanced Tables for Markdown/HTML. - Tables with state-of-the-art layout elements such as row - spanners, column spanners, table spanners, zebra striping, and - more. While allowing advanced layout, the underlying css-structure - is simple in order to maximize compatibility with word processors - such as 'MS Word' or 'LibreOffice'. The package also contains a - few text formatting functions that help outputting text - compatible with HTML/'LaTeX'.""" + Tables with state-of-the-art layout elements such as row spanners, column + spanners, table spanners, zebra striping, and more. While allowing advanced + layout, the underlying css-structure is simple in order to maximize + compatibility with word processors such as 'MS Word' or 'LibreOffice'. The + package also contains a few text formatting functions that help outputting + text compatible with HTML/'LaTeX'.""" - homepage = "https://cloud.r-project.org/package=htmlTable" - url = "https://cloud.r-project.org/src/contrib/htmlTable_1.11.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/htmlTable" + cran = "htmlTable" + version('2.4.0', sha256='4ca2b5616d77cfeee8ae5ca74307b86407d478b12d1ce17ba9c447e233b89a9d') version('2.1.0', sha256='4049339b317cbec1c8c7930e2e36cf0fc8b002516092dd270bb794d8db02f0bf') version('1.13.1', sha256='689f32b65da6a57ad500e8d9ef3309d346401dca277c6b264a46c8d7c75884d0') version('1.11.2', sha256='64a273b1cdf07a7c57b9031315ca665f95d78e70b4320d020f64a139278877d1') diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 83d2ee087a..9de35fe41a 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -7,12 +7,11 @@ from spack import * class RHtmltools(RPackage): - """Tools for HTML + """Tools for HTML. Tools for HTML generation and output.""" - homepage = "https://github.com/rstudio/htmltools" - cran = "htmltools" + cran = "htmltools" version('0.5.2', sha256='7dc7d50436e5a82a5801f85bcd2f572a06a98b4027d71aa17b4854ec9b2767fb') version('0.5.1.1', sha256='f0bfe72ffe330f3d6c9ead5857f3a4aef80e002e32558074a3e643f2ab67a4ba') @@ -22,8 +21,9 @@ class RHtmltools(RPackage): depends_on('r@2.14.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-base64enc', when='@0.5.1:', type=('build', 'run')) - depends_on('r-rlang@0.4.10:', when='@0.5.2:', type=('build', 'run')) - depends_on('r-rlang', when='@0.5.1:', type=('build', 'run')) - depends_on('r-fastmap@1.1.0:', when='@0.5.2:', type=('build', 'run')) - depends_on('r-rcpp', when=' @:0.3.6', type=('build', 'run')) + depends_on('r-base64enc', type=('build', 'run'), when='@0.5.1:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@0.5.2:') + depends_on('r-rlang', type=('build', 'run'), when='@0.5.1:') + depends_on('r-fastmap@1.1.0:', type=('build', 'run'), when='@0.5.2:') + + depends_on('r-rcpp', type=('build', 'run'), when='@:0.3.6') diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py index 186b951d0e..ac41281345 100644 --- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -7,16 +7,15 @@ from spack import * class RHtmlwidgets(RPackage): - """HTML Widgets for R + """HTML Widgets for R. A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.""" - homepage = "https://cloud.r-project.org/package=htmlwidgets" - url = "https://cloud.r-project.org/src/contrib/htmlwidgets_0.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/htmlwidgets" + cran = "htmlwidgets" + version('1.5.4', sha256='1a3fc60f40717de7f1716b754fd1c31a132e489a2560a278636ee78eba46ffc1') version('1.5.3', sha256='01a5833182cc224bd100be2815e57e67b524de9f2bb1542787b6e3d1303f0f29') version('1.3', sha256='f1e4ffabc29e6cfe857f627da095be3cfcbe0e1f02ae75e572f10b4a026c5a12') version('0.9', sha256='1154b541ccd868e41d3cf0d7f188f7275ec99f61fe2c7de21c8a05edb19b985e') diff --git a/var/spack/repos/builtin/packages/r-httpcode/package.py b/var/spack/repos/builtin/packages/r-httpcode/package.py index e77d4737a8..7077b9d115 100644 --- a/var/spack/repos/builtin/packages/r-httpcode/package.py +++ b/var/spack/repos/builtin/packages/r-httpcode/package.py @@ -7,15 +7,13 @@ from spack import * class RHttpcode(RPackage): - """httpcode: 'HTTP' Status Code Helper + """'HTTP' Status Code Helper. Find and explain the meaning of 'HTTP' status codes. Functions included for searching for codes by full or partial number, by message, and get appropriate dog and cat images for many status codes.""" - homepage = "https://github.com/sckott/httpcode" - url = "https://cloud.r-project.org/src/contrib/httpcode_0.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/httpcode" + cran = "httpcode" version('0.3.0', sha256='593a030a4f94c3df8c15576837c17344701bac023ae108783d0f06c476062f76') version('0.2.0', sha256='fbc1853db742a2cc1df11285cf27ce2ea43bc0ba5f7d393ee96c7e0ee328681a') diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index bc3217a92d..ee7fdf1618 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -7,7 +7,7 @@ from spack import * class RHttpuv(RPackage): - """HTTP and WebSocket Server Library + """HTTP and WebSocket Server Library. Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a @@ -17,10 +17,9 @@ class RHttpuv(RPackage): by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)""" - homepage = "https://github.com/rstudio/httpuv" - url = "https://cloud.r-project.org/src/contrib/httpuv_1.3.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/httpuv" + cran = "httpuv" + version('1.6.5', sha256='f5f63629ca5e9d0e396a89982d95b5286726c0cb425166f35a3ad32a60a79156') version('1.5.5', sha256='0be6c98927c7859d4bbfbbec8822c9f5e95352077d87640a76bc2ade07c83117') version('1.5.1', sha256='b5bb6b3b2f1a6d792568a70f3f357d6b3a35a5e26dd0c668c61a31f2ae8f5710') version('1.3.5', sha256='4336b993afccca2a194aca577b1975b89a35ac863423b18a11cdbb3f8470e4e9') @@ -28,8 +27,11 @@ class RHttpuv(RPackage): depends_on('r@2.15.1:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) - depends_on('r-r6', when='@1.5.0:', type=('build', 'run')) - depends_on('r-promises', when='@1.5.0:', type=('build', 'run')) - depends_on('r-later@0.8.0:', when='@1.5.0:', type=('build', 'run')) - depends_on('r-bh', when='@1.5.5:', type=('build', 'run')) + depends_on('r-rcpp@1.0.7:', type=('build', 'run'), when='@1.6.5:') + depends_on('r-r6', type=('build', 'run'), when='@1.5.0:') + depends_on('r-promises', type=('build', 'run'), when='@1.5.0:') + depends_on('r-later@0.8.0:', type=('build', 'run'), when='@1.5.0:') depends_on('gmake', type='build') + depends_on('zip') + + depends_on('r-bh', type=('build', 'run'), when='@1.5.5') diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index e56ebcb104..0c92579ffe 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -7,15 +7,13 @@ from spack import * class RHttr(RPackage): - """Tools for Working with URLs and HTTP + """Tools for Working with URLs and HTTP. - Useful tools for working with HTTP organised by HTTP verbs (GET(), - POST(), etc). Configuration functions make it easy to control additional - request components (authenticate(), add_headers() and so on).""" + Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), + etc). Configuration functions make it easy to control additional request + components (authenticate(), add_headers() and so on).""" - homepage = "https://github.com/hadley/httr" - url = "https://cloud.r-project.org/src/contrib/httr_1.2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/httr" + cran = "httr" version('1.4.2', sha256='462bed6ed0d92f811d5df4d294336025f1dbff357286999d9269bfd9c20b1ef9') version('1.4.1', sha256='675c7e07bbe82c48284ee1ab929bb14a6e653abae2860d854dc41a3c028de156') @@ -25,8 +23,8 @@ class RHttr(RPackage): version('1.1.0', sha256='d7c0cdc11b2ded3132544580f52ebe5dad2a426cde1a5029f2cc693b2f195823') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.1:', when='@1.4.0', type=('build', 'run')) - depends_on('r@3.2:', when='@1.4.1:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@1.4.0:') + depends_on('r@3.2:', type=('build', 'run'), when='@1.4.1:') depends_on('r-curl@3.0.0:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-mime', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hwriter/package.py b/var/spack/repos/builtin/packages/r-hwriter/package.py index 674a2b54ee..1905015dff 100644 --- a/var/spack/repos/builtin/packages/r-hwriter/package.py +++ b/var/spack/repos/builtin/packages/r-hwriter/package.py @@ -7,12 +7,12 @@ from spack import * class RHwriter(RPackage): - """Easy-to-use and versatile functions to + """HTML Writer - Outputs R objects in HTML format. + + Easy-to-use and versatile functions to output R objects in HTML format.""" - homepage = "https://cloud.r-project.org/package=hwriter" - url = "https://cloud.r-project.org/src/contrib/hwriter_1.3.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/hwriter" + cran = "hwriter" version('1.3.2', sha256='6b3531d2e7a239be9d6e3a1aa3256b2745eb68aa0bdffd2076d36552d0d7322b') diff --git a/var/spack/repos/builtin/packages/r-ica/package.py b/var/spack/repos/builtin/packages/r-ica/package.py index 434b917339..d8194dc1e9 100644 --- a/var/spack/repos/builtin/packages/r-ica/package.py +++ b/var/spack/repos/builtin/packages/r-ica/package.py @@ -7,13 +7,13 @@ from spack import * class RIca(RPackage): - """Independent Component Analysis (ICA) using various algorithms: FastICA, + """Independent Component Analysis. + + Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).""" - homepage = "https://cloud.r-project.org/package=ica" - url = "https://cloud.r-project.org/src/contrib/ica_1.0-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ica" + cran = "ica" version('1.0-2', sha256='e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179') version('1.0-1', sha256='98559a8bb12dd134a40ce8fd133803e2a38456b45d0e2a507d66022a8e2274ae') diff --git a/var/spack/repos/builtin/packages/r-ids/package.py b/var/spack/repos/builtin/packages/r-ids/package.py index c8b4bf9e1d..2e6f6cd88f 100644 --- a/var/spack/repos/builtin/packages/r-ids/package.py +++ b/var/spack/repos/builtin/packages/r-ids/package.py @@ -11,8 +11,7 @@ class RIds(RPackage): Generate random or human readable and pronounceable identifiers.""" - homepage = "https://github.com/richfitz/ids" - cran = "ids" + cran = "ids" version('1.0.1', sha256='b6212a186063c23116c5cbd3cca65dbb8977dd737261e4526ebee8f64852cfe8') diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py index 42c0a8dbb7..a74b7c06f3 100644 --- a/var/spack/repos/builtin/packages/r-igraph/package.py +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -7,16 +7,15 @@ from spack import * class RIgraph(RPackage): - """Network Analysis and Visualization + """Network Analysis and Visualization. - Routines for simple graphs and network analysis. It can handle large - graphs very well and provides functions for generating random and regular - graphs, graph visualization, centrality methods and much more.""" + Routines for simple graphs and network analysis. It can handle large graphs + very well and provides functions for generating random and regular graphs, + graph visualization, centrality methods and much more.""" - homepage = "https://igraph.org/" - url = "https://cloud.r-project.org/src/contrib/igraph_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/igraph" + cran = "igraph" + version('1.2.11', sha256='1c8b715eb61e6e7d9082858673929f8e84dc832c0a2a7aba7811511bbd2000de') version('1.2.6', sha256='640da72166fda84bea2c0e5eee374f1ed80cd9439c1171d056b1b1737ae6c76d') version('1.2.4.1', sha256='891acc763b5a4a4a245358a95dee69280f4013c342f14dd6a438e7bb2bf2e480') version('1.2.4', sha256='1048eb26ab6b592815bc269c1d91e974c86c9ab827ccb80ae0a40042019592cb') @@ -26,7 +25,9 @@ class RIgraph(RPackage): depends_on('r-magrittr', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-pkgconfig@2.0.0:', type=('build', 'run')) - depends_on('r-irlba', when='@:1.1.9', type=('build', 'run')) depends_on('gmp') + depends_on('gmp@4.38:', when='@1.2.11:') depends_on('libxml2') depends_on('glpk', when='@1.2.0:') + + depends_on('r-irlba', type=('build', 'run'), when='@:1.1.9') diff --git a/var/spack/repos/builtin/packages/r-imager/package.py b/var/spack/repos/builtin/packages/r-imager/package.py index 8e500da06f..be813c0b15 100644 --- a/var/spack/repos/builtin/packages/r-imager/package.py +++ b/var/spack/repos/builtin/packages/r-imager/package.py @@ -7,7 +7,7 @@ from spack import * class RImager(RPackage): - """Image Processing Library Based on 'CImg' + """Image Processing Library Based on 'CImg'. Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most @@ -16,10 +16,9 @@ class RImager(RPackage): The package wraps 'CImg', <https://cimg.eu/>, a simple, modern C++ library for image processing.""" - homepage = "https://dahtah.github.io/imager" - url = "https://cloud.r-project.org/src/contrib/imager_0.41.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/imager" + cran = "imager" + version('0.42.11', sha256='47f8b7ff8d05a5191e30ad1869f12a62bdbe3142b22b12a6032dec9b5f8532a8') version('0.42.10', sha256='01939eb03ad2e1369a4240a128c3b246a4c56f572f1ea4967f1acdc555adaeee') version('0.42.3', sha256='6fc308153df8251cef48f1e13978abd5d29ec85046fbe0b27c428801d05ebbf3') version('0.41.2', sha256='9be8bc8b3190d469fcb2883045a404d3b496a0380f887ee3caea11f0a07cd8a5') @@ -35,7 +34,8 @@ class RImager(RPackage): depends_on('r-purrr', type=('build', 'run')) depends_on('r-downloader', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) - depends_on('r-cairo', when='@:0.41.2', type=('build', 'run')) - depends_on('r-plyr', when='@:0.41.2', type=('build', 'run')) depends_on('fftw') depends_on('libtiff') + + depends_on('r-cairo', type=('build', 'run'), when='@:0.41.2') + depends_on('r-plyr', type=('build', 'run'), when='@:0.41.2') diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py index f3bd00b7e5..18f38da1c6 100644 --- a/var/spack/repos/builtin/packages/r-influencer/package.py +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -7,7 +7,9 @@ from spack import * class RInfluencer(RPackage): - """Provides functionality to compute various node centrality measures on + """Software Tools to Quantify Structural Importance of Nodes in a Network. + + Provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and effective network size (ENS) metrics, Borgatti's algorithm @@ -16,10 +18,9 @@ class RInfluencer(RPackage): with OpenMP, which may run faster on systems which have OpenMP configured.""" - homepage = "https://github.com/rcc-uchicago/influenceR" - url = "https://cloud.r-project.org/src/contrib/influenceR_0.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/influenceR" + cran = "influenceR" + version('0.1.0.1', sha256='63c46f1175fced33fb1b78d4d56e37fbee09b408945b0106dac36e3344cd4766') version('0.1.0', sha256='4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ini/package.py b/var/spack/repos/builtin/packages/r-ini/package.py index 16a62dace3..731ad9f4fc 100644 --- a/var/spack/repos/builtin/packages/r-ini/package.py +++ b/var/spack/repos/builtin/packages/r-ini/package.py @@ -7,12 +7,12 @@ from spack import * class RIni(RPackage): - """Parse simple '.ini' configuration files to an structured list. Users can + """Read and Write '.ini' Files. + + Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.""" - homepage = "https://github.com/dvdscripter/ini" - url = "https://cloud.r-project.org/src/contrib/ini_0.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ini" + cran = "ini" version('0.3.1', sha256='7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813') diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py index 312dbc9ff4..99bc0b002e 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -7,16 +7,14 @@ from spack import * class RInline(RPackage): - """Functions to Inline C, C++, Fortran Function Calls from R + """Functions to Inline C, C++, Fortran Function Calls from R. - Functionality to dynamically define R functions and S4 methods with - inlined C, C++ or Fortran code supporting .C and .Call calling - conventions.""" + Functionality to dynamically define R functions and S4 methods with inlined + C, C++ or Fortran code supporting .C and .Call calling conventions.""" - homepage = "https://cloud.r-project.org/package=inline" - url = "https://cloud.r-project.org/src/contrib/inline_0.3.14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/inline" + cran = "inline" + version('0.3.19', sha256='0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5') version('0.3.17', sha256='792857b2ebd408d6523424d2f6bb7297e241d4b28ab32372f6a9240c8cd554f3') version('0.3.15', sha256='ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68') version('0.3.14', sha256='fd34d6bf965148d26d983a022a0ff7bc1a5831f6ca066deee3f6139894dfc931') diff --git a/var/spack/repos/builtin/packages/r-insight/package.py b/var/spack/repos/builtin/packages/r-insight/package.py index 248f664752..2a0dfaf09b 100644 --- a/var/spack/repos/builtin/packages/r-insight/package.py +++ b/var/spack/repos/builtin/packages/r-insight/package.py @@ -7,7 +7,7 @@ from spack import * class RInsight(RPackage): - """Easy Access to Model Information for Various Model Objects + """Easy Access to Model Information for Various Model Objects. A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, @@ -19,9 +19,9 @@ class RInsight(RPackage): objects, where otherwise functions to access these information are missing.""" - homepage = "https://easystats.github.io/insight/" - cran = "insight" + cran = "insight" + version('0.15.0', sha256='d6a148c3e1cfcb3829e2f8950bcbf98f500ee88bebd7e2482f9b085542e93fee') version('0.14.1', sha256='0e7761997a46ee33039cdeff1779dbc210de3644e4444c6e893e4ef2f12cc129') depends_on('r@3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-intervals/package.py b/var/spack/repos/builtin/packages/r-intervals/package.py index 72e6295a21..9d8f317b01 100644 --- a/var/spack/repos/builtin/packages/r-intervals/package.py +++ b/var/spack/repos/builtin/packages/r-intervals/package.py @@ -7,13 +7,9 @@ from spack import * class RIntervals(RPackage): - """Tools for Working with Points and Intervals + """Tools for working with and comparing sets of points and intervals.""" - Tools for working with and comparing sets of points and intervals.""" - - homepage = "https://github.com/edzer/intervals" - url = "https://cloud.r-project.org/src/contrib/intervals_0.15.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/intervals" + cran = "intervals" version('0.15.2', sha256='0bd23b0ce817ddd851238233d8a5420bf3a6d29e75fd361418cbc50118777c57') version('0.15.1', sha256='9a8b3854300f2055e1492c71932cc808b02feac8c4d3dbf6cba1c7dbd09f4ae4') diff --git a/var/spack/repos/builtin/packages/r-inum/package.py b/var/spack/repos/builtin/packages/r-inum/package.py index b8289551ea..1196779b4a 100644 --- a/var/spack/repos/builtin/packages/r-inum/package.py +++ b/var/spack/repos/builtin/packages/r-inum/package.py @@ -7,13 +7,14 @@ from spack import * class RInum(RPackage): - """Enum-type representation of vectors and representation of intervals, + """Interval and Enum-Type Representation of Vectors. + + Enum-type representation of vectors and representation of intervals, including a method of coercing variables in data frames.""" - homepage = "https://cloud.r-project.org/package=inum" - url = "https://cloud.r-project.org/src/contrib/inum_1.0-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/inum" + cran = "inum" + version('1.0-4', sha256='5febef69c43a4b95b376c1418550a949d988a5f26b1383ca01c9728a94fc13ce') version('1.0-1', sha256='3c2f94c13c03607e05817e4859595592068b55e810fed94e29bc181ad248a099') depends_on('r@3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ipred/package.py b/var/spack/repos/builtin/packages/r-ipred/package.py index 0a6c41ff64..7a58fb8a0d 100644 --- a/var/spack/repos/builtin/packages/r-ipred/package.py +++ b/var/spack/repos/builtin/packages/r-ipred/package.py @@ -7,14 +7,15 @@ from spack import * class RIpred(RPackage): - """Improved predictive models by indirect classification and bagging for - classification, regression and survival problems as well as resampling + """Improved Predictors. + + Improved predictive models by indirect classification and bagging for + classification, regression and survival problems as well as resampling based estimators of prediction error.""" - homepage = "https://cloud.r-project.org/package=ipred" - url = "https://cloud.r-project.org/src/contrib/ipred_0.9-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ipred" + cran = "ipred" + version('0.9-12', sha256='d6e1535704d39415a799d7643141ffa4f6f55597f03e763f4ccd5d8106005843') version('0.9-9', sha256='0da87a70730d5a60b97e46b2421088765e7d6a7cc2695757eba0f9d31d86416f') version('0.9-8', sha256='9c1d11c3cb0d72be7870e70a216e589e403bbfee38c796fe75cd0611d878ac07') version('0.9-5', sha256='3a466417808e17c4c6cd0f2b577407355d9da79a341558b42a8b76e24b6f6ba4') diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py index e15bde6cc7..b9b72af97b 100644 --- a/var/spack/repos/builtin/packages/r-irdisplay/package.py +++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py @@ -8,14 +8,15 @@ from spack import * class RIrdisplay(RPackage): - """An interface to the rich display capabilities of Jupyter front-ends - (e.g. 'Jupyter Notebook') Designed to be used from a running IRkernel - session""" + """'Jupyter' Display Machinery. - homepage = "https://irkernel.github.io" - url = "https://cloud.r-project.org/src/contrib/IRdisplay_0.4.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/IRdisplay" + An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. + 'Jupyter Notebook') <https://jupyter.org>. Designed to be used from a + running 'IRkernel' session <https://irkernel.github.io>.""" + cran = "IRdisplay" + + version('1.1', sha256='83eb030ff91f546cb647899f8aa3f5dc9fe163a89a981696447ea49cc98e8d2b') version('0.7.0', sha256='91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089') version('0.4.4', sha256='e83a0bc52800618bf9a3ac5ef3d432512e00f392b7216fd515fca319377584a6') diff --git a/var/spack/repos/builtin/packages/r-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py index f61e687a7e..32d80184af 100644 --- a/var/spack/repos/builtin/packages/r-irkernel/package.py +++ b/var/spack/repos/builtin/packages/r-irkernel/package.py @@ -8,19 +8,31 @@ from spack import * class RIrkernel(RPackage): - """R kernel for Jupyter""" + """Native R Kernel for the 'Jupyter Notebook'. - homepage = "https://irkernel.github.io/" - git = "https://github.com/IRkernel/IRkernel.git" + The R kernel for the 'Jupyter' environment executes R code which the + front-end ('Jupyter Notebook' or other front-ends) submits to the kernel + via the network.""" - version('1.2', commit='d7f868127b876fd490aeff2a75b4254a2898f96c') - version('0.7', commit='9cdd284e03eb42d03fab18544b81f486852d5fe0') + cran = "IRkernel" - depends_on('r-repr', type=('build', 'run')) - depends_on('r-irdisplay', type=('build', 'run')) - depends_on('r-evaluate', type=('build', 'run')) + version('1.3', sha256='5a7fcbfd978dfb3cca6702a68a21c147551995fc400084ae8382ffcbbdae1903') + version('1.2', sha256='5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91') + version('0.7', + git="https://github.com/IRkernel/IRkernel.git", + commit='9cdd284e03eb42d03fab18544b81f486852d5fe0', + deprecated=True) + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-repr@0.4.99:', type=('build', 'run')) + depends_on('r-evaluate@0.10:', type=('build', 'run')) + depends_on('r-irdisplay@0.3.0.9999:', type=('build', 'run')) + depends_on('r-pbdzmq@0.2-1:', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) - depends_on('r-pbdzmq', type=('build', 'run')) - depends_on('r-devtools', type=('build', 'run')) + depends_on('r-jsonlite@0.9.6:', type=('build', 'run')) depends_on('r-uuid', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) + depends_on('py-jupyter', type='run') + + depends_on('r-evaluate@0.5.4:', type=('build', 'run'), when='@0.7') + depends_on('r-devtools', type=('build', 'run'), when='@0.7') diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py index 6a036bd1ac..d1116f9dec 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -7,17 +7,20 @@ from spack import * class RIrlba(RPackage): - """Fast and memory efficient methods for truncated singular and eigenvalue - decompositions and principal component analysis of large sparse or dense + """Fast Truncated Singular Value Decomposition and Principal Components + Analysis for Large Dense and Sparse Matrices. + + Fast and memory efficient methods for truncated singular value + decomposition and principal components analysis of large sparse and dense matrices.""" - homepage = "https://cloud.r-project.org/package=irlba" - url = "https://cloud.r-project.org/src/contrib/irlba_2.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/irlba" + cran = "irlba" + version('2.3.5', sha256='26fc8c0d36460e422ab77f43a597b8ec292eacd452628c54d34b8bf7d5269bb9') version('2.3.3', sha256='6ee233697bcd579813bd0af5e1f4e6dd1eea971e8919c748408130d970fef5c0') version('2.3.2', sha256='3fdf2d8fefa6ab14cd0992740de7958f9f501c71aca93229f5eb03c54558fc38') version('2.1.2', sha256='5183e8dd7943df11c0f44460566adf06c03d5320f142699298f516d423b06ce1') version('2.0.0', sha256='15f8d6c1107d6bb872411efd61e6077d9d7ac826f4da2d378999889a7b1ebabe') + depends_on('r@3.6.2:', type=('build', 'run'), when='@2.3.5:') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-isdparser/package.py b/var/spack/repos/builtin/packages/r-isdparser/package.py index 99a635b8f4..35a6076343 100644 --- a/var/spack/repos/builtin/packages/r-isdparser/package.py +++ b/var/spack/repos/builtin/packages/r-isdparser/package.py @@ -7,7 +7,7 @@ from spack import * class RIsdparser(RPackage): - """Parse 'NOAA' Integrated Surface Data Files + """Parse 'NOAA' Integrated Surface Data Files. Tools for parsing 'NOAA' Integrated Surface Data ('ISD') files, described at <https://www.ncdc.noaa.gov/isd>. Data includes for example, wind speed @@ -17,13 +17,11 @@ class RIsdparser(RPackage): length ASCII character strings, with most fields optional. Included are tools for parsing entire files, or individual lines of data.""" - homepage = "https://github.com/ropensci/isdparser" - url = "https://cloud.r-project.org/src/contrib/isdparser_0.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/isdparser" + cran = "isdparser" version('0.4.0', sha256='6f609e8f5ae4ce2e7904401f289d60d219b8f3a2bec9f661d10afa18ab73b317') version('0.3.0', sha256='6c9e1d7f3661802838010d659d7c77b964423dcc9a6623402df1fe3be627b7b9') depends_on('r-tibble@1.2:', type=('build', 'run')) depends_on('r-data-table@1.10.0:', type=('build', 'run')) - depends_on('r-lubridate', when='@0.4.0:', type=('build', 'run')) + depends_on('r-lubridate', type=('build', 'run'), when='@0.4.0:') diff --git a/var/spack/repos/builtin/packages/r-islr/package.py b/var/spack/repos/builtin/packages/r-islr/package.py index ed08352d9d..61da4752d7 100644 --- a/var/spack/repos/builtin/packages/r-islr/package.py +++ b/var/spack/repos/builtin/packages/r-islr/package.py @@ -7,16 +7,15 @@ from spack import * class RIslr(RPackage): - """ISLR: Data for an Introduction to Statistical Learning with Applications - in R + """Data for an Introduction to Statistical Learning with Applications in R. We provide the collection of data-sets used in the book 'An Introduction to Statistical Learning with Applications in R'.""" - homepage = "https://cloud.r-project.org/package=ISLR" - url = "https://cloud.r-project.org/src/contrib/ISLR_1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ISLR" + cran = "ISLR" + version('1.4', sha256='7151c636808198ee759cbcf22f82a7aa76580fb8d11e4cd67f69f85401c820c3') version('1.2', sha256='b00f7a06d2fb646917e629cc2dbdab71c7de3eb17a8a4d06849901a299f1caad') depends_on('r@2.10:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.4:') diff --git a/var/spack/repos/builtin/packages/r-iso/package.py b/var/spack/repos/builtin/packages/r-iso/package.py index 912af48264..d83523812f 100644 --- a/var/spack/repos/builtin/packages/r-iso/package.py +++ b/var/spack/repos/builtin/packages/r-iso/package.py @@ -7,14 +7,12 @@ from spack import * class RIso(RPackage): - """Functions to Perform Isotonic Regression + """Functions to Perform Isotonic Regression. - Linear order and unimodal order (univariate) isotonic regression; - bivariate isotonic regression with linear order on both variables.""" + Linear order and unimodal order (univariate) isotonic regression; bivariate + isotonic regression with linear order on both variables.""" - homepage = "https://cloud.r-project.org/package=Iso" - url = "https://cloud.r-project.org/src/contrib/Iso_0.0-17.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Iso" + cran = "Iso" version('0.0-18.1', sha256='2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f') version('0.0-18', sha256='2d7e8c4452653364ee086d95cea620c50378e30acfcff129b7261e1756a99504') diff --git a/var/spack/repos/builtin/packages/r-isoband/package.py b/var/spack/repos/builtin/packages/r-isoband/package.py index c28c0c9a94..3632a3a230 100644 --- a/var/spack/repos/builtin/packages/r-isoband/package.py +++ b/var/spack/repos/builtin/packages/r-isoband/package.py @@ -7,16 +7,15 @@ from spack import * class RIsoband(RPackage): - """Generate Isolines and Isobands from Regularly Spaced Elevation Grids + """Generate Isolines and Isobands from Regularly Spaced Elevation Grids. A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.""" - homepage = "https://github.com/wilkelab/isoband" - url = "https://cloud.r-project.org/src/contrib/isoband_0.2.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/isoband" + cran = "isoband" + version('0.2.5', sha256='46f53fa066f0966f02cb2bf050190c0d5e950dab2cdf565feb63fc092c886ba5') version('0.2.3', sha256='f9d3318fdf6d147dc2e2c7015ea7de42a55fa33d6232b952f982df96066b7ffe') depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-isva/package.py b/var/spack/repos/builtin/packages/r-isva/package.py index c3f4573bf7..f51408ac16 100644 --- a/var/spack/repos/builtin/packages/r-isva/package.py +++ b/var/spack/repos/builtin/packages/r-isva/package.py @@ -7,13 +7,13 @@ from spack import * class RIsva(RPackage): - """Independent Surrogate Variable Analysis: + """Independent Surrogate Variable Analysis. Independent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors (see Teschendorff AE et al 2011, <doi:10.1093/bioinformatics/btr171>).""" - cran = "isva" + cran = "isva" version('1.9', sha256='9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17') diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py index 3fe5dd40f9..b26e7624be 100644 --- a/var/spack/repos/builtin/packages/r-iterators/package.py +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -7,14 +7,12 @@ from spack import * class RIterators(RPackage): - """Provides Iterator Construct + """Provides Iterator Construct. - Support for iterators, which allow a programmer to traverse through all - the elements of a vector, list, or other collection of data.""" + Support for iterators, which allow a programmer to traverse through all the + elements of a vector, list, or other collection of data.""" - homepage = "https://cloud.r-project.org/package=iterators" - url = "https://cloud.r-project.org/src/contrib/iterators_1.0.8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/iterators" + cran = "iterators" version('1.0.13', sha256='778e30e4c292da9f94d62acc637cf55273dae258199d847e62658f44840f11a4') version('1.0.12', sha256='96bf31d60ebd23aefae105d9b7790715e63327eec0deb2ddfb3d543994ea9f4b') diff --git a/var/spack/repos/builtin/packages/r-jade/package.py b/var/spack/repos/builtin/packages/r-jade/package.py index a299cff12b..c60b7797dd 100644 --- a/var/spack/repos/builtin/packages/r-jade/package.py +++ b/var/spack/repos/builtin/packages/r-jade/package.py @@ -8,7 +8,7 @@ from spack import * class RJade(RPackage): """Blind Source Separation Methods Based on Joint Diagonalization and Some - BSS Performance Criteria: + BSS Performance Criteria. Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, @@ -16,7 +16,7 @@ class RJade(RPackage): algorithms, are given. The package is described in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.""" - cran = "JADE" + cran = "JADE" version('2.0-3', sha256='56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba') diff --git a/var/spack/repos/builtin/packages/r-janitor/package.py b/var/spack/repos/builtin/packages/r-janitor/package.py index c3948f6417..27e75ad903 100644 --- a/var/spack/repos/builtin/packages/r-janitor/package.py +++ b/var/spack/repos/builtin/packages/r-janitor/package.py @@ -7,7 +7,7 @@ from spack import * class RJanitor(RPackage): - """Simple Tools for Examining and Cleaning Dirty Data + """Simple Tools for Examining and Cleaning Dirty Data. The main janitor functions can: perfectly format data.frame column names; provide quick one- and two-variable tabulations (i.e., frequency tables and @@ -20,9 +20,7 @@ class RJanitor(RPackage): do everything covered here, but with janitor they can do it faster and save their thinking for the fun stuff.""" - homepage = "https://github.com/sfirke/janitor" - url = "https://cloud.r-project.org/src/contrib/janitor_0.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/janitor" + cran = "janitor" version('2.1.0', sha256='d60615940fbe174f67799c8abc797f27928eca4ac180418527c5897a4aaad826') version('1.2.0', sha256='5e15a2292c65c5ddd6160289dec2604b05a813651a2be0d7854ace4548a32b8c') @@ -31,14 +29,14 @@ class RJanitor(RPackage): depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-dplyr@0.7.0:', type=('build', 'run')) - depends_on('r-dplyr@1.0.0:', when='@2.1.0:', type=('build', 'run')) - depends_on('r-lifecycle', when='@2.1.0:', type=('build', 'run')) - depends_on('r-lubridate', when='@2.1.0:', type=('build', 'run')) + depends_on('r-dplyr@1.0.0:', type=('build', 'run'), when='@2.1.0:') + depends_on('r-lifecycle', type=('build', 'run'), when='@2.1.0:') + depends_on('r-lubridate', type=('build', 'run'), when='@2.1.0:') depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-purrr', when='@1.1.0:', type=('build', 'run')) - depends_on('r-rlang', when='@1.1.0:', type=('build', 'run')) - depends_on('r-stringi', when='@2.1.0:', type=('build', 'run')) - depends_on('r-stringr', when='@2.1.0:', type=('build', 'run')) - depends_on('r-snakecase@0.9.2:', when='@1.1.0:', type=('build', 'run')) - depends_on('r-tidyselect@1.0.0:', when='@2.1.0:', type=('build', 'run')) + depends_on('r-purrr', type=('build', 'run'), when='@1.1.0:') + depends_on('r-rlang', type=('build', 'run'), when='@1.1.0:') + depends_on('r-stringi', type=('build', 'run'), when='@2.1.0:') + depends_on('r-stringr', type=('build', 'run'), when='@2.1.0:') + depends_on('r-snakecase@0.9.2:', type=('build', 'run'), when='@1.1.0:') + depends_on('r-tidyselect@1.0.0:', type=('build', 'run'), when='@2.1.0:') depends_on('r-tidyr@0.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py index 84d86ea5e4..ac1ddfe6c3 100644 --- a/var/spack/repos/builtin/packages/r-jomo/package.py +++ b/var/spack/repos/builtin/packages/r-jomo/package.py @@ -7,7 +7,7 @@ from spack import * class RJomo(RPackage): - """Multilevel Joint Modelling Multiple Imputation + """Multilevel Joint Modelling Multiple Imputation. Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) @@ -16,9 +16,7 @@ class RJomo(RPackage): option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.""" - homepage = "https://cloud.r-project.org/package=jomo" - url = "https://cloud.r-project.org/src/contrib/jomo_2.6-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/jomo" + cran = "jomo" version('2.7-2', sha256='3962d5cbecc60e72670329dbef0dd74303080f5ea2a79c91e27f75db99ba6ce9') version('2.6-9', sha256='b90f47071e62b8863b00b1ae710a56ae6efbfe2baeb9963f8a91a10d6183cc9b') @@ -27,5 +25,5 @@ class RJomo(RPackage): depends_on('r-lme4', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) - depends_on('r-mass', when='@2.6-7:', type=('build', 'run')) - depends_on('r-ordinal', when='@2.6-7:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run'), when='@2.6-7:') + depends_on('r-ordinal', type=('build', 'run'), when='@2.6-7:') diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py index 284fc4896d..16c1ba6463 100644 --- a/var/spack/repos/builtin/packages/r-jpeg/package.py +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -7,16 +7,15 @@ from spack import * class RJpeg(RPackage): - """Read and write JPEG images + """Read and write JPEG images. This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.""" - homepage = "https://www.rforge.net/jpeg/" - url = "https://cloud.r-project.org/src/contrib/jpeg_0.1-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/jpeg" + cran = "jpeg" + version('0.1-9', sha256='01a175442ec209b838a56a66a3908193aca6f040d537da7838d9368e46913072') version('0.1-8.1', sha256='1db0a4976fd9b2ae27a37d3e856cca35bc2909323c7a40724846a5d3c18915a9') version('0.1-8', sha256='d032befeb3a414cefdbf70ba29a6c01541c54387cc0a1a98a4022d86cbe60a16') diff --git a/var/spack/repos/builtin/packages/r-jquerylib/package.py b/var/spack/repos/builtin/packages/r-jquerylib/package.py index a05b315527..69d14a2dad 100644 --- a/var/spack/repos/builtin/packages/r-jquerylib/package.py +++ b/var/spack/repos/builtin/packages/r-jquerylib/package.py @@ -7,7 +7,13 @@ from spack import * class RJquerylib(RPackage): - """Obtain 'jQuery' as an HTML Dependency Object.""" + """Obtain 'jQuery' as an HTML Dependency Object. + + Obtain any major version of 'jQuery' (<https://code.jquery.com/>) and use + it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', + and 'rmarkdown'). Most R users don't need to use this package directly, but + other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package + to avoid bundling redundant copies of 'jQuery'.""" cran = "jquerylib" diff --git a/var/spack/repos/builtin/packages/r-jsonify/package.py b/var/spack/repos/builtin/packages/r-jsonify/package.py new file mode 100644 index 0000000000..721d7a1f01 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-jsonify/package.py @@ -0,0 +1,23 @@ +# 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 RJsonify(RPackage): + """Convert Between 'R' Objects and Javascript Object Notation + (JSON). + + Conversions between 'R' objects and Javascript Object Notation (JSON) using + the 'rapidjsonr' library + <https://CRAN.R-project.org/package=rapidjsonr>.""" + + cran = "jsonify" + + version('1.2.1', sha256='929191ab32e34af6a02ad991e29314cc78ea40763fcf232388ef2d132137fbce') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.18:', type=('build', 'run')) + depends_on('r-rapidjsonr@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index e37f7358e9..14d758aec4 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -7,7 +7,7 @@ from spack import * class RJsonlite(RPackage): - """A Simple and Robust JSON Parser and Generator for R + """A Simple and Robust JSON Parser and Generator for R. A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of 'RJSONIO', but has been completely rewritten @@ -20,10 +20,9 @@ class RJsonlite(RPackage): package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.""" - homepage = "https://github.com/jeroenooms/jsonlite" - url = "https://cloud.r-project.org/src/contrib/jsonlite_1.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/jsonlite" + cran = "jsonlite" + version('1.7.3', sha256='720a0b5e36a5eb71677231442bba2267d077137cfa9e0700585acbee62eac558') version('1.7.2', sha256='06354b50435942f67ba264f79831e577809ef89e5f9a5a2201985396fe651fd2') version('1.6.1', sha256='74921dd249857a23afabc1ad1485a63a48828e57f240f0619deb04c60f883377') version('1.6', sha256='88c5b425229966b7409145a6cabc72db9ed04f8c37ee95901af0146bb285db53') diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py index 774136ea8c..98939d645a 100644 --- a/var/spack/repos/builtin/packages/r-kernlab/package.py +++ b/var/spack/repos/builtin/packages/r-kernlab/package.py @@ -7,16 +7,14 @@ from spack import * class RKernlab(RPackage): - """Kernel-Based Machine Learning Lab + """Kernel-Based Machine Learning Lab. Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.""" - homepage = "https://cloud.r-project.org/package=kernlab" - url = "https://cloud.r-project.org/src/contrib/kernlab_0.9-25.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/kernlab" + cran = "kernlab" version('0.9-29', sha256='c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f') version('0.9-27', sha256='f6add50ed4097f04d09411491625f8d46eafc4f003b1c1cff78a6fff8cc31dd4') diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py index adb03d7848..c11382cbcd 100644 --- a/var/spack/repos/builtin/packages/r-kernsmooth/package.py +++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py @@ -7,15 +7,14 @@ from spack import * class RKernsmooth(RPackage): - """Functions for kernel smoothing (and density estimation) + """Functions for Kernel Smoothing Supporting Wand & Jones (1995). Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".""" - homepage = "https://cloud.r-project.org/package=KernSmooth" - url = "https://cloud.r-project.org/src/contrib/KernSmooth_2.23-15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/KernSmooth" + cran = "KernSmooth" + version('2.23-20', sha256='20eb75051e2473933d41eedc9945b03c632847fd581e2207d452cf317fa5ec39') version('2.23-18', sha256='8334800c5ad2305539d2731b929ea34f50fa4269ba87277b699fd5be5b03c490') version('2.23-15', sha256='8b72d23ed121a54af188b2cda4441e3ce2646359309885f6455b82c0275210f6') diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py index 2ab4ca2d5d..2e4535acf0 100644 --- a/var/spack/repos/builtin/packages/r-kknn/package.py +++ b/var/spack/repos/builtin/packages/r-kknn/package.py @@ -7,12 +7,12 @@ from spack import * class RKknn(RPackage): - """Weighted k-Nearest Neighbors for Classification, Regression and + """Weighted k-Nearest Neighbors. + + Weighted k-Nearest Neighbors for Classification, Regression and Clustering.""" - homepage = "https://cloud.r-project.org/package=kknn" - url = "https://cloud.r-project.org/src/contrib/kknn_1.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/kknn" + cran = "kknn" version('1.3.1', sha256='22840e70ec2afa40371e274b583634c8f6d27149a87253ee411747d5db78f3db') diff --git a/var/spack/repos/builtin/packages/r-klar/package.py b/var/spack/repos/builtin/packages/r-klar/package.py index c3cd1c66dd..93712468de 100644 --- a/var/spack/repos/builtin/packages/r-klar/package.py +++ b/var/spack/repos/builtin/packages/r-klar/package.py @@ -7,7 +7,9 @@ from spack import * class RKlar(RPackage): - """Miscellaneous functions for classification and visualization, e.g. + """Classification and Visualization. + + Miscellaneous functions for classification and visualization, e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes, an interface to 'svmlight' and stepclass() wrapper variable selection for supervised classification, partimat() visualization of classification rules @@ -16,9 +18,7 @@ class RKlar(RPackage): different variable clustering models and weight of evidence preprocessing.""" - homepage = "https://cloud.r-project.org/package=klaR" - url = "https://cloud.r-project.org/src/contrib/klaR_0.6-15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/klaR" + cran = "klaR" version('0.6-15', sha256='5bfe5bc643f8a64b222317732c26e9f93be297cdc318a869f15cc9ab0d9e0fae') diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index 3223ece22d..2785669885 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -8,14 +8,14 @@ from spack import * class RKnitr(RPackage): - """A General-Purpose Package for Dynamic Report Generation in R + """A General-Purpose Package for Dynamic Report Generation in R. Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.""" - homepage = "https://yihui.org/knitr/" - cran = "knitr" + cran = "knitr" + version('1.37', sha256='39cd2a4848baebbe7fa0c0ab8200179690fb5b9190f0c1688d987c38363ad763') version('1.33', sha256='2f83332b0a880de6eae522271bda7f862c97693fba45c23ab1f772028f6c0909') version('1.30', sha256='3aabb13566a234131ba18b78d690104f9468a982dc711f81344a985318c7c93e') version('1.28', sha256='05ee01da31d715bf24793efb3e4ef3bb3101ef1e1ab2d760c645fc5b9d40232a') @@ -24,18 +24,22 @@ class RKnitr(RPackage): version('1.17', sha256='9484a2b2c7b0c2aae24ab7f4eec6db48affbceb0e42bd3d69e34d953fe92f401') version('1.14', sha256='ba6d301482d020a911390d5eff181e1771f0e02ac3f3d9853a9724b1ec041aec') - depends_on('r@2.14.1:', when='@:1.9', type=('build', 'run')) - depends_on('r@3.0.2:', when='@1.10:1.14', type=('build', 'run')) - depends_on('r@3.1.0:', when='@1.15:1.22', type=('build', 'run')) - depends_on('r@3.2.3:', when='@1.23:', type=('build', 'run')) + depends_on('r@2.14.1:', type=('build', 'run'), when='@:1.9') + depends_on('r@3.0.2:', type=('build', 'run'), when='@1.10:1.14') + depends_on('r@3.1.0:', type=('build', 'run'), when='@1.15:1.22') + depends_on('r@3.2.3:', type=('build', 'run'), when='@1.23:') depends_on('r-evaluate@0.10:', type=('build', 'run')) depends_on('r-highr', type=('build', 'run')) - depends_on('r-markdown', type=('build', 'run')) depends_on('r-stringr@0.6:', type=('build', 'run')) depends_on('r-yaml@2.1.19:', type=('build', 'run')) - depends_on('r-xfun', when='@1.23:', type=('build', 'run')) - depends_on('r-xfun@0.15:', when='@1.30', type=('build', 'run')) - depends_on('r-xfun@0.19:', when='@1.31', type=('build', 'run')) - depends_on('r-xfun@0.21:', when='@1.32:', type=('build', 'run')) - depends_on('r-digest', when='@:1.17', type=('build', 'run')) - depends_on('r-formatr', when='@:1.14', type=('build', 'run')) + depends_on('r-xfun', type=('build', 'run'), when='@1.23:') + depends_on('r-xfun@0.15:', type=('build', 'run'), when='@1.30') + depends_on('r-xfun@0.19:', type=('build', 'run'), when='@1.31') + depends_on('r-xfun@0.21:', type=('build', 'run'), when='@1.32:') + depends_on('r-xfun@0.27:', type=('build', 'run'), when='@1.37:') + depends_on('pandoc', type='build') + depends_on('py-rst2pdf', type=('build', 'run')) + + depends_on('r-digest', type=('build', 'run'), when='@:1.17') + depends_on('r-formatr', type=('build', 'run'), when='@:1.14') + depends_on('r-markdown', type=('build', 'run'), when='@:1.33') diff --git a/var/spack/repos/builtin/packages/r-kpmt/package.py b/var/spack/repos/builtin/packages/r-kpmt/package.py index 3acc0be696..6b0e6abcbc 100644 --- a/var/spack/repos/builtin/packages/r-kpmt/package.py +++ b/var/spack/repos/builtin/packages/r-kpmt/package.py @@ -7,11 +7,11 @@ from spack import * class RKpmt(RPackage): - """Known Population Median Test: + """Known Population Median Test. Functions that implement the known population median test.""" - cran = "kpmt" + cran = "kpmt" version('0.1.0', sha256='6342ad02c93bfa7a764d028821bb6115bb8bc8c55b057a5860736cc0e034a295') diff --git a/var/spack/repos/builtin/packages/r-ks/package.py b/var/spack/repos/builtin/packages/r-ks/package.py index 67bbe60322..5b4592aaab 100644 --- a/var/spack/repos/builtin/packages/r-ks/package.py +++ b/var/spack/repos/builtin/packages/r-ks/package.py @@ -7,17 +7,16 @@ from spack import * class RKs(RPackage): - """Kernel Smoothing + """Kernel Smoothing. Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.""" - homepage = "https://cloud.r-project.org/package=ks" - url = "https://cloud.r-project.org/src/contrib/ks_1.11.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ks" + cran = "ks" + version('1.13.3', sha256='defb80df665d987f1751899f7a9809cb5a770f3c74266d7fbc7b9493616dce73') version('1.11.7', sha256='6a6d9c2366e85a4c6af39b798f3798d20a42615ddfcebcedf6cf56087cdfd2b8') version('1.11.5', sha256='4f65565376391b8a6dcce76168ef628fd4859dba8496910cbdd54e4f88e8d51b') version('1.11.4', sha256='0beffaf8694819fba8c93af07a8782674a15fe00a04ad1d94d31238d0a41b134') @@ -32,3 +31,5 @@ class RKs(RPackage): depends_on('r-mgcv', type=('build', 'run')) depends_on('r-multicool', type=('build', 'run')) depends_on('r-mvtnorm@1.0-0:', type=('build', 'run')) + depends_on('r-plot3d', type=('build', 'run'), when='@1.13.3:') + depends_on('r-pracma', type=('build', 'run'), when='@1.13.3:') diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py index f8a98de25e..54d46ead1a 100644 --- a/var/spack/repos/builtin/packages/r-labeling/package.py +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -7,13 +7,11 @@ from spack import * class RLabeling(RPackage): - """Axis Labeling + """Axis Labeling. Provides a range of axis labeling algorithms.""" - homepage = "https://cloud.r-project.org/package=labeling" - url = "https://cloud.r-project.org/src/contrib/labeling_0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/labeling" + cran = "labeling" version('0.4.2', sha256='e022d79276173e0d62bf9e37d7574db65ab439eb2ae1833e460b1cff529bd165') version('0.3', sha256='0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f') diff --git a/var/spack/repos/builtin/packages/r-labelled/package.py b/var/spack/repos/builtin/packages/r-labelled/package.py index ef7184c3fd..477c10392f 100644 --- a/var/spack/repos/builtin/packages/r-labelled/package.py +++ b/var/spack/repos/builtin/packages/r-labelled/package.py @@ -7,21 +7,27 @@ from spack import * class RLabelled(RPackage): - """Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or + """Manipulating Labelled Data. + + Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or 'foreign'. This package provides useful functions to deal with "haven_labelled" and "haven_labelled_spss" classes introduced by 'haven' package.""" - homepage = "https://cloud.r-project.org/package=labelled" - url = "https://cloud.r-project.org/src/contrib/labelled_2.7.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/labelled" + cran = "labelled" + version('2.9.0', sha256='36ac0e169ee065a8bced9417efeb85d62e1504a590d4321667d8a6213285d639') version('2.7.0', sha256='b1b66b34d3ad682e492fc5bb6431780760576d29dbac40d87bef3c0960054bdb') + depends_on('r@3.0:', type=('build', 'run'), when='@2.9.0:') depends_on('r-haven@2.3.1:', type=('build', 'run')) + depends_on('r-haven@2.4.1:', type=('build', 'run'), when='@2.9.0:') depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-dplyr@1.0.0:', type=('build', 'run'), when='@2.9.0:') depends_on('r-lifecycle', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) depends_on('r-vctrs', type=('build', 'run')) - depends_on('r-pillar', type=('build', 'run')) + depends_on('r-stringr', type=('build', 'run'), when='@2.9.0:') depends_on('r-tidyr', type=('build', 'run')) + + depends_on('r-pillar', type=('build', 'run'), when='@:2.7.0') diff --git a/var/spack/repos/builtin/packages/r-lambda-r/package.py b/var/spack/repos/builtin/packages/r-lambda-r/package.py index ee612ec42a..a3285add11 100644 --- a/var/spack/repos/builtin/packages/r-lambda-r/package.py +++ b/var/spack/repos/builtin/packages/r-lambda-r/package.py @@ -7,15 +7,13 @@ from spack import * class RLambdaR(RPackage): - """Modeling Data with Functional Programming + """Modeling Data with Functional Programming. A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.""" - homepage = "https://cloud.r-project.org/package=lambda.r" - url = "https://cloud.r-project.org/src/contrib/lambda.r_1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lambda.r" + cran = "lambda.r" version('1.2.4', sha256='d252fee39065326c6d9f45ad798076522cec05e73b8905c1b30f95a61f7801d6') version('1.2.3', sha256='0cd8e37ba1a0960888016a85d492da51a57df54bd65ff920b08c79a3bfbe8631') diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py index ead6a6adbb..45217fb7ef 100644 --- a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py +++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py @@ -7,16 +7,15 @@ from spack import * class RLaplacesdemon(RPackage): - """Complete Environment for Bayesian Inference + """Complete Environment for Bayesian Inference. Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.""" - homepage = "https://github.com/LaplacesDemonR/LaplacesDemon" - url = "https://cloud.r-project.org/src/contrib/LaplacesDemon_16.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/LaplacesDemon" + cran = "LaplacesDemon" + version('16.1.6', sha256='57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7') version('16.1.4', sha256='4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db') version('16.1.1', sha256='779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77') version('16.1.0', sha256='41d99261e8fc33c977b43ecf66ebed8ef1c84d9bd46b271609e9aadddc2ca8bb') diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py index 847fe75104..2aa08c1340 100644 --- a/var/spack/repos/builtin/packages/r-lars/package.py +++ b/var/spack/repos/builtin/packages/r-lars/package.py @@ -7,12 +7,12 @@ from spack import * class RLars(RPackage): - """Efficient procedures for fitting an entire lasso sequence with the cost + """Least Angle Regression, Lasso and Forward Stagewise. + + Efficient procedures for fitting an entire lasso sequence with the cost of a single least squares fit.""" - homepage = "https://cloud.r-project.org/package=lars" - url = "https://cloud.r-project.org/src/contrib/lars_1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lars" + cran = "lars" version('1.2', sha256='64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e') version('1.1', sha256='a8e4a0efb9ca6760dec1cadf395d9a805508455a2c3ced18cc53d9b8fa70cdc0') diff --git a/var/spack/repos/builtin/packages/r-later/package.py b/var/spack/repos/builtin/packages/r-later/package.py index 50818dd743..c3bf76bc11 100644 --- a/var/spack/repos/builtin/packages/r-later/package.py +++ b/var/spack/repos/builtin/packages/r-later/package.py @@ -7,18 +7,18 @@ from spack import * class RLater(RPackage): - """Utilities for Scheduling Functions to Execute Later with Event Loops + """Utilities for Scheduling Functions to Execute Later with Event Loops. - Executes arbitrary R or C functions some time after the current time, - after the R execution stack has emptied.""" + Executes arbitrary R or C functions some time after the current time, after + the R execution stack has emptied.""" - homepage = "https://github.com/r-lib/later" - url = "https://cloud.r-project.org/src/contrib/later_0.8.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/later" + cran = "later" + version('1.3.0', sha256='08f50882ca3cfd2bb68c83f1fcfbc8f696f5cfb5a42c1448c051540693789829') version('1.1.0.1', sha256='71baa7beae774a35a117e01d7b95698511c3cdc5eea36e29732ff1fe8f1436cd') version('0.8.0', sha256='6b2a28b43c619b2c7890840c62145cd3a34a7ed65b31207fdedde52efb00e521') depends_on('r-rcpp@0.12.9:', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) - depends_on('r-bh', type=('build', 'run')) + + depends_on('r-bh', type=('build', 'run'), when='@:1.1.0.1') diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index 48c226783d..9958bc3979 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -7,17 +7,16 @@ from spack import * class RLattice(RPackage): - """Trellis Graphics for R + """Trellis Graphics for R. A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.""" - homepage = "https://lattice.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/lattice_0.20-35.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lattice" + cran = "lattice" + version('0.20-45', sha256='22388d92bdb7d3959da84d7308d9026dd8226ef07580783729e8ad2f7d7507ad') version('0.20-44', sha256='57b908e3c7ada08a38ad857ee44f44fdf9cfa59d5d9500bda2ccc9c7e96cdb9b') version('0.20-41', sha256='54ca557f0cb33df60eb10b883c2ed2847e061ddd57ed9b5dd7695149609d57b5') version('0.20-38', sha256='fdeb5e3e50dbbd9d3c5e2fa3eef865132b3eef30fbe53a10c24c7b7dfe5c0a2d') diff --git a/var/spack/repos/builtin/packages/r-latticeextra/package.py b/var/spack/repos/builtin/packages/r-latticeextra/package.py index 4128aada1c..e2a50535a0 100644 --- a/var/spack/repos/builtin/packages/r-latticeextra/package.py +++ b/var/spack/repos/builtin/packages/r-latticeextra/package.py @@ -7,23 +7,20 @@ from spack import * class RLatticeextra(RPackage): - """Extra Graphical Utilities Based on Lattice + """Extra Graphical Utilities Based on Lattice. - Building on the infrastructure provided by the lattice package, - this package provides several new high-level functions and methods, - as well as additional utilities such as panel and axis annotation - functions.""" + Building on the infrastructure provided by the lattice package, this + package provides several new high-level functions and methods, as well as + additional utilities such as panel and axis annotation functions.""" - homepage = "https://latticeextra.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/latticeExtra_0.6-28.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/latticeExtra" + cran = "latticeExtra" version('0.6-29', sha256='6cadc31d56f73d926e2e8d72e43ae17ac03607a4d1a374719999a4a231e3df11') version('0.6-28', sha256='780695323dfadac108fb27000011c734e2927b1e0f069f247d65d27994c67ec2') depends_on('r@2.10.0:', type=('build', 'run')) - depends_on('r@3.6.0:', when='@0.6-29:', type=('build', 'run')) + depends_on('r@3.6.0:', type=('build', 'run'), when='@0.6-29:') depends_on('r-lattice', type=('build', 'run')) - depends_on('r-png', when='@0.6-29:', type=('build', 'run')) - depends_on('r-jpeg', when='@0.6-29:', type=('build', 'run')) + depends_on('r-png', type=('build', 'run'), when='@0.6-29:') + depends_on('r-jpeg', type=('build', 'run'), when='@0.6-29:') depends_on('r-rcolorbrewer', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py index 8aa4cce673..43e499e381 100644 --- a/var/spack/repos/builtin/packages/r-lava/package.py +++ b/var/spack/repos/builtin/packages/r-lava/package.py @@ -7,7 +7,7 @@ from spack import * class RLava(RPackage): - """Latent Variable Models + """Latent Variable Models. A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both @@ -19,16 +19,17 @@ class RLava(RPackage): general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.""" - homepage = "https://cloud.r-project.org/package=lava" - url = "https://cloud.r-project.org/src/contrib/lava_1.4.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lava" + cran = "lava" + version('1.6.10', sha256='7a88f8a885872e2abb3011c446e9e1c4884cd4dbe6ab4cfe9207538e5560232e') version('1.6.8.1', sha256='6d243fc86c67c78ff4763502d84ff2f0889c2e55d1a59afefb7a762887473ffa') version('1.6.6', sha256='7abc84dd99cce450a45ac4f232812cde3a322e432da3472f43b057fb5c59ca59') version('1.6.4', sha256='41c6eeb96eaef9e1bfb04b31f7203e250a5ea7e7860be4d95f7f96f2a8644718') version('1.4.7', sha256='d5cbd4835a94855478efb93051eece965db116ead203f4dd4e09d9a12d52f4bf') depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-future-apply', type=('build', 'run'), when='@1.6.10:') + depends_on('r-progressr', type=('build', 'run'), when='@1.6.10:') depends_on('r-numderiv', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) - depends_on('r-squarem', when='@1.6.0:', type=('build', 'run')) + depends_on('r-squarem', type=('build', 'run'), when='@1.6.0:') diff --git a/var/spack/repos/builtin/packages/r-lavaan/package.py b/var/spack/repos/builtin/packages/r-lavaan/package.py index 44d8648a25..163a824dce 100644 --- a/var/spack/repos/builtin/packages/r-lavaan/package.py +++ b/var/spack/repos/builtin/packages/r-lavaan/package.py @@ -7,14 +7,15 @@ from spack import * class RLavaan(RPackage): - """Latent Variable Analysis: + """Latent Variable Analysis. Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.""" - homepage = "https://lavaan.ugent.be/" - cran = "lavaan" + cran = "lavaan" + version('0.6-10', sha256='4d6944eb6d5743e7a2a2c7b56aec5d5de78585a52789be235839fb9f5f468c37') + version('0.6-9', sha256='d404c4eb40686534f9c05f24f908cd954041f66d1072caea4a3adfa83a5f108a') version('0.6-8', sha256='40e204909100b7338619ae23cd87e0a4058e581c286da2327f36dbb3834b84a2') depends_on('r@3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py index 14790518e7..ecb8f0fbaf 100644 --- a/var/spack/repos/builtin/packages/r-lazyeval/package.py +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -7,13 +7,13 @@ from spack import * class RLazyeval(RPackage): - """An alternative approach to non-standard evaluation using formulas. + """Lazy (Non-Standard) Evaluation. + + An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.""" - homepage = "https://cloud.r-project.org/package=lazyeval" - url = "https://cloud.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lazyeval" + cran = "lazyeval" version('0.2.2', sha256='d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4') version('0.2.1', sha256='83b3a43e94c40fe7977e43eb607be0a3cd64c02800eae4f2774e7866d1e93f61') diff --git a/var/spack/repos/builtin/packages/r-ldheatmap/package.py b/var/spack/repos/builtin/packages/r-ldheatmap/package.py index b7c0906dfe..b3010c6984 100644 --- a/var/spack/repos/builtin/packages/r-ldheatmap/package.py +++ b/var/spack/repos/builtin/packages/r-ldheatmap/package.py @@ -7,7 +7,7 @@ from spack import * class RLdheatmap(RPackage): - """Graphical Display of Pairwise Linkage Disequilibria Between SNPs + """Graphical Display of Pairwise Linkage Disequilibria Between SNPs. Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between single nucleotide polymorphisms (SNPs). Users @@ -18,15 +18,13 @@ class RLdheatmap(RPackage): 'GenomInfoDb' and 'IRanges' are all BioConductor packages <https://bioconductor.org>.""" - homepage = "https://sfustatgen.github.io/LDheatmap/" - url = "https://cloud.r-project.org/src/contrib/LDheatmap_0.99-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/LDheatmap" + cran = "LDheatmap" version('1.0-4', sha256='07eb385f19e6a195e8e4d75be0b47c57744eabbf14045e527f0c27e1183ae5ca') version('0.99-7', sha256='aca54c839a424506d8be7153bf03b32026aeefe7ed38f534e8e19708e34212e4') depends_on('r@2.14.0:', type=('build', 'run')) - depends_on('r@4.0:', when='@1.0-4:', type=('build', 'run')) + depends_on('r@4.0:', type=('build', 'run'), when='@1.0-4:') depends_on('r-genetics', type=('build', 'run')) depends_on('r-snpstats', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leafem/package.py b/var/spack/repos/builtin/packages/r-leafem/package.py index 94e2512205..83abd933af 100644 --- a/var/spack/repos/builtin/packages/r-leafem/package.py +++ b/var/spack/repos/builtin/packages/r-leafem/package.py @@ -7,7 +7,7 @@ from spack import * class RLeafem(RPackage): - """'leaflet' Extensions for 'mapview' + """'leaflet' Extensions for 'mapview'. Provides extensions for packages 'leaflet' & 'mapdeck', many of which are used by package 'mapview'. Focus is on functionality readily available in @@ -16,13 +16,14 @@ class RLeafem(RPackage): pointer and zoom-to-layer buttons. Additionally, provides a feature type agnostic function to add points, lines, polygons to a map.""" - homepage = "https://github.com/r-spatial/leafem" - cran = "leafem" + cran = "leafem" + version('0.1.6', sha256='ca50e0a699f564449248511857a2df0d48cd07de3157e099478a19b533088156') version('0.1.3', sha256='6f123fc15efadb85d317c01003e3b7af5dc925cffe0bbe774b1b39b6bd67f304') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) + depends_on('r-geojsonsf', type=('build', 'run'), when='@0.1.6:') depends_on('r-htmltools@0.3:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-leaflet@2.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaflet-providers/package.py b/var/spack/repos/builtin/packages/r-leaflet-providers/package.py index 17ac2d6b14..dd2c61124b 100644 --- a/var/spack/repos/builtin/packages/r-leaflet-providers/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet-providers/package.py @@ -7,16 +7,14 @@ from spack import * class RLeafletProviders(RPackage): - """Leaflet Providers + """Leaflet Providers. Contains third-party map tile provider information from 'Leaflet.js', <https://github.com/leaflet-extras/leaflet-providers>, to be used with the 'leaflet' R package. Additionally, 'leaflet.providers' enables users to retrieve up-to-date provider information between package updates.""" - homepage = "https://github.com/rstudio/leaflet.providers" - url = "https://cloud.r-project.org/src/contrib/leaflet.providers_1.9.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/leaflet.providers" + cran = "leaflet.providers" version('1.9.0', sha256='9e8fc75c83313ab24663c2e718135459599549ed6e7396086cacb44e36cfd67b') diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py index fbc8ad4ea4..da95da91c5 100644 --- a/var/spack/repos/builtin/packages/r-leaflet/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -7,15 +7,13 @@ from spack import * class RLeaflet(RPackage): - """Create Interactive Web Maps with the JavaScript 'Leaflet' Library + """Create Interactive Web Maps with the JavaScript 'Leaflet' Library. Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents.""" - homepage = "https://rstudio.github.io/leaflet/" - url = "https://cloud.r-project.org/src/contrib/leaflet_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/leaflet" + cran = "leaflet" version('2.0.4.1', sha256='b0f038295f1de5d32d9ffa1d0dbc1562320190f2f1365f3a5e95863fff88901f') version('2.0.2', sha256='fa448d20940e01e953e0706fc5064b0fa347e69fa967792599eb03c52b2e3114') @@ -24,7 +22,7 @@ class RLeaflet(RPackage): depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-crosstalk', when='@2.0.0:', type=('build', 'run')) + depends_on('r-crosstalk', type=('build', 'run'), when='@2.0.0:') depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) @@ -34,5 +32,5 @@ class RLeaflet(RPackage): depends_on('r-raster', type=('build', 'run')) depends_on('r-scales@1.0.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) - depends_on('r-viridis@0.5.1:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-leaflet-providers@1.8.0:', when='@2.0.4.1:', type=('build', 'run')) + depends_on('r-viridis@0.5.1:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-leaflet-providers@1.8.0:', type=('build', 'run'), when='@2.0.4.1:') diff --git a/var/spack/repos/builtin/packages/r-leafpop/package.py b/var/spack/repos/builtin/packages/r-leafpop/package.py index 26dadc9859..912dc2c744 100644 --- a/var/spack/repos/builtin/packages/r-leafpop/package.py +++ b/var/spack/repos/builtin/packages/r-leafpop/package.py @@ -4,11 +4,12 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) # ---------------------------------------------------------------------------- + from spack import * class RLeafpop(RPackage): - """Include Tables, Images and Graphs in Leaflet Pop-Ups + """Include Tables, Images and Graphs in Leaflet Pop-Ups. Creates 'HTML' strings to embed tables, images or graphs in pop-ups of interactive maps created with packages like 'leaflet' or 'mapview'. Handles @@ -16,9 +17,9 @@ class RLeafpop(RPackage): created with 'lattice' or 'ggplot2' as well as interactive plots created with 'htmlwidgets'.""" - homepage = "https://github.com/r-spatial/leafpop" - cran = "leafpop" + cran = "leafpop" + version('0.1.0', sha256='6e546886e1db4ad93a038de6d1e8331c0d686e96a0d3f0694e7575471f7d9db1') version('0.0.6', sha256='3d9ca31d081ce8540a87790786840bde5f833543af608c53a26623c7874e722f') depends_on('r-base64enc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py index 38f4d5c546..d3d89260de 100644 --- a/var/spack/repos/builtin/packages/r-leaps/package.py +++ b/var/spack/repos/builtin/packages/r-leaps/package.py @@ -7,14 +7,11 @@ from spack import * class RLeaps(RPackage): - """Regression Subset Selection + """Regression Subset Selection. - Regression subset selection, including exhaustive search. - """ + Regression subset selection, including exhaustive search.""" - homepage = "https://cloud.r-project.org/package=leaps" - url = "https://cloud.r-project.org/src/contrib/leaps_3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/leaps" + cran = "leaps" version('3.1', sha256='3d7c3a102ce68433ecf167ece96a7ebb4207729e4defd0ac8fc00e7003f5c3b6') version('3.0', sha256='55a879cdad5a4c9bc3b5697dd4d364b3a094a49d8facb6692f5ce6af82adf285') diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py index 96da1d3198..7481f3cf8d 100644 --- a/var/spack/repos/builtin/packages/r-learnbayes/package.py +++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py @@ -7,17 +7,17 @@ from spack import * class RLearnbayes(RPackage): - """LearnBayes contains a collection of functions helpful in learning the + """Functions for Learning Bayesian Inference. + + LearnBayes contains a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing - posterior distributions defined by the user. It also contains functions - for regression models, hierarchical models, Bayesian tests, and - illustrations of Gibbs sampling.""" + posterior distributions defined by the user. It also contains functions for + regression models, hierarchical models, Bayesian tests, and illustrations + of Gibbs sampling.""" - homepage = "https://cloud.r-project.org/package=LearnBayes" - url = "https://cloud.r-project.org/src/contrib/LearnBayes_2.15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/LearnBayes" + cran = "LearnBayes" version('2.15.1', sha256='9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532') version('2.15', sha256='45c91114b4aaa0314feeb4311dbe78f5b75a3b76bb2d1ca0f8adb2e0f1cbe233') diff --git a/var/spack/repos/builtin/packages/r-leiden/package.py b/var/spack/repos/builtin/packages/r-leiden/package.py index 9a965ca42c..df4242ec64 100644 --- a/var/spack/repos/builtin/packages/r-leiden/package.py +++ b/var/spack/repos/builtin/packages/r-leiden/package.py @@ -7,19 +7,17 @@ from spack import * class RLeiden(RPackage): - """R Implementation of Leiden Clustering Algorithm + """R Implementation of Leiden Clustering Algorithm. Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: - <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain - to Leiden: guaranteeing well-connected communities. - <arXiv:1810.08473>.""" + <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to + Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.""" - homepage = "https://github.com/TomKellyGenetics/leiden" - url = "https://cloud.r-project.org/src/contrib/leiden_0.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/leiden" + cran = "leiden" + version('0.3.9', sha256='81754276e026a9a8436476365bbadf0f15a403a525a349cb56418da5d8edea0d') version('0.3.6', sha256='a7096e38c4010b1f0baf6a7e1139362520b44c0e548b0b79584cb827172822cc') version('0.3.1', sha256='17fa1e49667fdd30ef5166506181c8514ae406f68f0878a026ee111bff11f8a5') diff --git a/var/spack/repos/builtin/packages/r-lfe/package.py b/var/spack/repos/builtin/packages/r-lfe/package.py index 864700532a..50c811b112 100644 --- a/var/spack/repos/builtin/packages/r-lfe/package.py +++ b/var/spack/repos/builtin/packages/r-lfe/package.py @@ -7,7 +7,7 @@ from spack import * class RLfe(RPackage): - """Linear Group Fixed Effects + """Linear Group Fixed Effects. Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for @@ -20,10 +20,9 @@ class RLfe(RPackage): improvements are to be expected, and the package is at risk of being removed from CRAN.""" - homepage = "https://cloud.r-project.org/package=lfe" - url = "https://cloud.r-project.org/src/contrib/lfe_2.8-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lfe" + cran = "lfe" + version('2.8-7.1', sha256='d6a1efd8c43f84fa291e4959938f16e85bf5feef113515aaca1fe90075a78c50') version('2.8-6', sha256='bf5fd362e9722e871a5236f30da562c489ae6506b667609b9465eefa8f101612') version('2.8-5', sha256='fd80c573d334594db933ff38f67bd4c9f899aaf648c3bd68f19477a0059723c2') version('2.8-4', sha256='ee5f6e312214aa73e285ae84a6bdf49ba10e830f1a68ffded2fea2e532f2cd6a') diff --git a/var/spack/repos/builtin/packages/r-lhs/package.py b/var/spack/repos/builtin/packages/r-lhs/package.py index 46c18c08dc..ab36fc55d7 100644 --- a/var/spack/repos/builtin/packages/r-lhs/package.py +++ b/var/spack/repos/builtin/packages/r-lhs/package.py @@ -7,20 +7,19 @@ from spack import * class RLhs(RPackage): - """Latin Hypercube Samples + """Latin Hypercube Samples. Provides a number of methods for creating and augmenting Latin Hypercube Samples.""" - homepage = "https://lhs.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/lhs_0.16.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lhs" + cran = "lhs" + version('1.1.3', sha256='e43b8d48db1cf26013697e2a798ed1d31d1ee1790f2ebfecb280176c0e0c06d1') version('1.1.1', sha256='903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc') version('1.0.1', sha256='a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53') version('1.0', sha256='38c53482b360bdea89ddcfadf6d45476c80b99aee8902f97c5e97975903e2745') version('0.16', sha256='9cd199c3b5b2be1736d585ef0fd39a00e31fc015a053333a7a319668d0809425') - depends_on('r@3.3.0:', when='@:0.16', type=('build', 'run')) - depends_on('r@3.4.0:', when='@1.0:', type=('build', 'run')) - depends_on('r-rcpp', when='@1.0:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@1.0:') + depends_on('r-rcpp', type=('build', 'run'), when='@1.0:') diff --git a/var/spack/repos/builtin/packages/r-libcoin/package.py b/var/spack/repos/builtin/packages/r-libcoin/package.py index ad504e17b5..5064ea0e5b 100644 --- a/var/spack/repos/builtin/packages/r-libcoin/package.py +++ b/var/spack/repos/builtin/packages/r-libcoin/package.py @@ -7,18 +7,16 @@ from spack import * class RLibcoin(RPackage): - """Linear Test Statistics for Permutation Inference + """Linear Test Statistics for Permutation Inference. - Basic infrastructure for linear test statistics and permutation - inference in the framework of Strasser and Weber (1999) - <https://epub.wu.ac.at/102/>. This package must not be used by end-users. - CRAN package 'coin' implements all user interfaces and is ready to be used - by anyone.""" + Basic infrastructure for linear test statistics and permutation inference + in the framework of Strasser and Weber (1999) <https://epub.wu.ac.at/102/>. + This package must not be used by end-users. CRAN package 'coin' implements + all user interfaces and is ready to be used by anyone.""" - homepage = "https://cloud.r-project.org/package=libcoin" - url = "https://cloud.r-project.org/src/contrib/libcoin_1.0-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/libcoin" + cran = "libcoin" + version('1.0-9', sha256='2d7dd0b7c6dfc20472430570419ea36a714da7bbafd336da1fb53c5c6463d9eb') version('1.0-6', sha256='48afc1415fc89b29e4f2c8b6f6db3cffef1531580e5c806ad7cacf4afe6a4e5a') version('1.0-4', sha256='91dcbaa0ab8c2109aa54c3eda29ad0acd67c870efcda208e27acce9d641c09c5') diff --git a/var/spack/repos/builtin/packages/r-lifecycle/package.py b/var/spack/repos/builtin/packages/r-lifecycle/package.py index bed431c319..8c2b80404b 100644 --- a/var/spack/repos/builtin/packages/r-lifecycle/package.py +++ b/var/spack/repos/builtin/packages/r-lifecycle/package.py @@ -7,7 +7,7 @@ from spack import * class RLifecycle(RPackage): - """Manage the Life Cycle of your Package Functions + """Manage the Life Cycle of your Package Functions. Manage the life cycle of your exported functions with shared conventions, documentation badges, and non-invasive deprecation warnings. The @@ -18,13 +18,12 @@ class RLifecycle(RPackage): deprecated functions are signalled with increasing levels of non-invasive verbosity.""" - homepage = "https://lifecycle.r-lib.org/" cran = "lifecycle" version('1.0.1', sha256='1da76e1c00f1be96ca34e122ae611259430bf99d6a1b999fdef70c00c30f7ba0') version('0.2.0', sha256='29746e8dee05d4e36f9c612e8c7a903a4f648a36b3b94c9776e518c38a412224') depends_on('r@3.2:', type=('build', 'run')) - depends_on('r@3.3:', when='@1:', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run'), when='@1:') depends_on('r-glue', type=('build', 'run')) depends_on('r-rlang@0.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-limsolve/package.py b/var/spack/repos/builtin/packages/r-limsolve/package.py index 0ce631f290..df1fa5c3cf 100644 --- a/var/spack/repos/builtin/packages/r-limsolve/package.py +++ b/var/spack/repos/builtin/packages/r-limsolve/package.py @@ -7,7 +7,7 @@ from spack import * class RLimsolve(RPackage): - """Solving Linear Inverse Models + """Solving Linear Inverse Models. Functions that (1) find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) @@ -16,9 +16,7 @@ class RLimsolve(RPackage): Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.""" - homepage = "https://cloud.r-project.org/package=limSolve" - url = "https://cloud.r-project.org/src/contrib/limSolve_1.5.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/limSolve" + cran = "limSolve" version('1.5.6', sha256='b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0') diff --git a/var/spack/repos/builtin/packages/r-listenv/package.py b/var/spack/repos/builtin/packages/r-listenv/package.py index 6479e980b2..3dc3f4e71a 100644 --- a/var/spack/repos/builtin/packages/r-listenv/package.py +++ b/var/spack/repos/builtin/packages/r-listenv/package.py @@ -7,15 +7,13 @@ from spack import * class RListenv(RPackage): - """Environments Behaving (Almost) as Lists + """Environments Behaving (Almost) as Lists. List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting.""" - homepage = "https://github.com/HenrikBengtsson/listenv" - url = "https://cloud.r-project.org/src/contrib/listenv_0.7.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/listenv" + cran = "listenv" version('0.8.0', sha256='fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f') version('0.7.0', sha256='6126020b111870baea08b36afa82777cd578e88c17db5435cd137f11b3964555') diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index 0121997df3..a8d1d9871a 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -7,14 +7,13 @@ from spack import * class RLme4(RPackage): - """Linear Mixed-Effects Models using 'Eigen' and S4 + """Linear Mixed-Effects Models using 'Eigen' and S4. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".""" - homepage = "https://github.com/lme4/lme4/" cran = "lme4" version('1.1-27.1', sha256='25fa873e39b8192e48c15eec93db8c8bf6f03baf3bd8d5ca9188482ce8442ec5') @@ -24,15 +23,15 @@ class RLme4(RPackage): version('1.1-20', sha256='44f45f5cd20ec6a50bf96a939b1db44b1a180dbc871a5e3042baf7a107016b2c') version('1.1-12', sha256='2976b567a4a2144814ff9db987b0aa55c16122c78ecb51b9e09b87fe66a1c048') - depends_on('r@3.0.2:', when='@:1.1-15', type=('build', 'run')) - depends_on('r@3.2.0:', when='@1.1-16:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@1.1-16:') depends_on('r-matrix@1.2-1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) - depends_on('r-boot', when='@1.1-21:', type=('build', 'run')) + depends_on('r-boot', type=('build', 'run'), when='@1.1-21:') depends_on('r-nlme@3.1-123:', type=('build', 'run')) depends_on('r-minqa@1.1.15:', type=('build', 'run')) depends_on('r-nloptr@1.0.4:', type=('build', 'run')) - depends_on('r-statmod', when='@1.1-26', type=('build', 'run')) + depends_on('r-statmod', type=('build', 'run'), when='@1.1-26') depends_on('r-rcpp@0.10.5:', type=('build', 'run')) depends_on('r-rcppeigen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lmertest/package.py b/var/spack/repos/builtin/packages/r-lmertest/package.py index 94c5bb6f2c..fd5efb40d6 100644 --- a/var/spack/repos/builtin/packages/r-lmertest/package.py +++ b/var/spack/repos/builtin/packages/r-lmertest/package.py @@ -7,18 +7,16 @@ from spack import * class RLmertest(RPackage): - """Tests in Linear Mixed Effects Models + """Tests in Linear Mixed Effects Models. Provides p-values in type I, II or III anova and summary tables for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the pbkrtest package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of - linear contrasts of fixed effects are also available. - """ + linear contrasts of fixed effects are also available.""" - homepage = "https://github.com/runehaubo/lmerTestR" - cran = "lmerTest" + cran = "lmerTest" version('3.1-3', sha256='35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd') diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py index b9e94d5a56..99fe7a449e 100644 --- a/var/spack/repos/builtin/packages/r-lmtest/package.py +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -7,16 +7,15 @@ from spack import * class RLmtest(RPackage): - """Testing Linear Regression Models + """Testing Linear Regression Models. - A collection of tests, data sets, and examples for diagnostic checking - in linear regression models. Furthermore, some generic tools for inference - in parametric models are provided.""" + A collection of tests, data sets, and examples for diagnostic checking in + linear regression models. Furthermore, some generic tools for inference in + parametric models are provided.""" - homepage = "https://cloud.r-project.org/package=lmtest" - url = "https://cloud.r-project.org/src/contrib/lmtest_0.9-34.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lmtest" + cran = "lmtest" + version('0.9-39', sha256='71f8d67cbe559b33fe02910a3e98cddc60c9dcc421c64f7878c647218f07d488') version('0.9-38', sha256='32a22cea45398ffc5732d9f5c0391431d0cdd3a9e29cc7b77bea32c1eb4a216b') version('0.9-37', sha256='ddc929f94bf055974832fa4a20fdd0c1eb3a84ee11f716c287936f2141d5ca0a') version('0.9-36', sha256='be9f168d6554e9cd2be0f9d8fc3244f055dce90d1fca00f05bcbd01daa4ed56b') diff --git a/var/spack/repos/builtin/packages/r-lobstr/package.py b/var/spack/repos/builtin/packages/r-lobstr/package.py index b6eff2e242..9150c412df 100644 --- a/var/spack/repos/builtin/packages/r-lobstr/package.py +++ b/var/spack/repos/builtin/packages/r-lobstr/package.py @@ -7,19 +7,21 @@ from spack import * class RLobstr(RPackage): - """A set of tools for inspecting and understanding R data structures - inspired by str(). Includes ast() for visualizing abstract syntax trees, - ref() for showing shared references, cst() for showing call stack trees, - and obj_size() for computing object sizes.""" + """Visualize R Data Structures with Trees. - homepage = "https://lobstr.r-lib.org" - url = "https://cloud.r-project.org/src/contrib/lobstr_1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lobstr" + A set of tools for inspecting and understanding R data structures inspired + by str(). Includes ast() for visualizing abstract syntax trees, ref() for + showing shared references, cst() for showing call stack trees, and + obj_size() for computing object sizes.""" - version('1.1.1', sha256='923a384d9239d44b63dfc57f5a0309a1e59b9698ef05183f598f6f4fffb1e0fd') - version('1.0.1', sha256='f94d0a207f1b44097907d761c45130be386e908aec4ac472bf2fec6d36c74a69') - version('1.0.0', sha256='b9d5dcda36a1c1bd208ddf814f9b5a9c2c8b07730647b98505be7e296b14c883') + cran = "lobstr" - depends_on('r-rlang@0.3.0:', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + version('1.1.1', sha256='b8c9ce00095bd4f304b4883ef71da24572022f0632a18c3e1ba317814e70716e') + version('1.0.1', sha256='25fb288f73dbaf680ebbf27a50da338868c55d788501118fd33748854c5104fb') + version('1.0.0', sha256='9d24de1519c51b3bac79066a1abf623b939e884ba5b3005110bb9c2016954b3d') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@1.1.1:') depends_on('r-crayon', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-locfit/package.py b/var/spack/repos/builtin/packages/r-locfit/package.py index dc19620e8f..c351f46448 100644 --- a/var/spack/repos/builtin/packages/r-locfit/package.py +++ b/var/spack/repos/builtin/packages/r-locfit/package.py @@ -7,19 +7,16 @@ from spack import * class RLocfit(RPackage): - """Local regression, likelihood and density estimation + """Local regression, likelihood and density estimation. Local regression, likelihood and density estimation methods as described in - the 1999 book by Loader. - """ + the 1999 book by Loader.""" - homepage = "https://cloud.r-project.org/package=locfit" - url = "https://cloud.r-project.org/src/contrib/locfit_1.5-9.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/locfit" + cran = "locfit" version('1.5-9.4', sha256='d9d3665c5f3d49f698fb4675daf40a0550601e86db3dc00f296413ceb1099ced') version('1.5-9.1', sha256='f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51') depends_on('r@2.0.1:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.5-9.4:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.5-9.4:') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-log4r/package.py b/var/spack/repos/builtin/packages/r-log4r/package.py index c165b8254b..cba4266c50 100644 --- a/var/spack/repos/builtin/packages/r-log4r/package.py +++ b/var/spack/repos/builtin/packages/r-log4r/package.py @@ -7,15 +7,14 @@ from spack import * class RLog4r(RPackage): - """A Fast and Lightweight Logging System for R, Based on 'log4j' + """A Fast and Lightweight Logging System for R, Based on 'log4j'. - logr4 provides an object-oriented logging system that uses an - API roughly equivalent to log4j and its related variants.""" + logr4 provides an object-oriented logging system that uses an API roughly + equivalent to log4j and its related variants.""" - homepage = "https://cloud.r-project.org/package=log4r" - url = "https://cloud.r-project.org/src/contrib/log4r_0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/log4r" + cran = "log4r" + version('0.4.2', sha256='924a020565dcd05a2bc8283285fcae60f6b58b35e1be7c55acc0c703c7edfe34') version('0.3.2', sha256='14ba6b096283279f0accbde26a600771ab2df271db6c8eeb04d6f113107825a3') version('0.3.0', sha256='8e5d0221298410e48bee9d9a983a23e1834ce88592f9d931471bfdb05f37a691') version('0.2', sha256='321bee6babb92376b538624027a36e7d2a6c8edb360aa38ab0a6762dfea9081f') diff --git a/var/spack/repos/builtin/packages/r-loo/package.py b/var/spack/repos/builtin/packages/r-loo/package.py index 1b369445d0..dca16abbd4 100644 --- a/var/spack/repos/builtin/packages/r-loo/package.py +++ b/var/spack/repos/builtin/packages/r-loo/package.py @@ -7,7 +7,7 @@ from spack import * class RLoo(RPackage): - """Efficient Leave-One-Out Cross-Validation and WAIC for BayesianModels + """Efficient Leave-One-Out Cross-Validation and WAIC for BayesianModels. Efficient approximate leave-one-out cross-validation (LOO) for Bayesian models fit using Markov chain Monte Carlo, as described in Vehtari, @@ -20,9 +20,7 @@ class RLoo(RPackage): model weighting techniques to average Bayesian predictive distributions.""" - homepage = "https://mc-stan.org/loo" - url = "https://cloud.r-project.org/src/contrib/loo_2.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/loo" + cran = "loo" version('2.4.1', sha256='bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50') version('2.3.1', sha256='d98de21b71d9d9386131ae5ba4da051362c3ad39e0305af4f33d830f299ae08b') diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py index 8593fe9e85..cc422159b9 100644 --- a/var/spack/repos/builtin/packages/r-lpsolve/package.py +++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py @@ -7,7 +7,7 @@ from spack import * class RLpsolve(RPackage): - """Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs + """Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs. Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a @@ -15,9 +15,7 @@ class RLpsolve(RPackage): linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve""" - homepage = "https://cloud.r-project.org/package=lpSolve" - url = "https://cloud.r-project.org/src/contrib/lpSolve_5.6.13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lpSolve" + cran = "lpSolve" version('5.6.15', sha256='4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba') version('5.6.13.2', sha256='75f0c0af5cbdc219ac29c792342ecd625903632ad86e581c408879958aa88539') diff --git a/var/spack/repos/builtin/packages/r-lpsolveapi/package.py b/var/spack/repos/builtin/packages/r-lpsolveapi/package.py new file mode 100644 index 0000000000..a67d8f6a17 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lpsolveapi/package.py @@ -0,0 +1,19 @@ +# 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 RLpsolveapi(RPackage): + """R Interface to 'lp_solve' Version 5.5.2.0. + + The lpSolveAPI package provides an R interface to 'lp_solve', a Mixed + Integer Linear Programming (MILP) solver with support for pure linear, + (mixed) integer/binary, semi-continuous and special ordered sets (SOS) + models.""" + + cran = "lpSolveAPI" + + version('5.5.2.0-17.7', sha256='9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb') diff --git a/var/spack/repos/builtin/packages/r-lsei/package.py b/var/spack/repos/builtin/packages/r-lsei/package.py index 197f1324c7..37bc88bd5c 100644 --- a/var/spack/repos/builtin/packages/r-lsei/package.py +++ b/var/spack/repos/builtin/packages/r-lsei/package.py @@ -7,7 +7,8 @@ from spack import * class RLsei(RPackage): - """Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints + """Solving Least Squares or Quadratic Programming Problems under + Equality/Inequality Constraints. It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving @@ -16,9 +17,7 @@ class RLsei(RPackage): 'Fortran' program of Lawson and Hanson (1974, 1995), which is public domain and available at <http://www.netlib.org/lawson-hanson>.""" - homepage = "https://cloud.r-project.org/package=lsei" - url = "https://cloud.r-project.org/src/contrib/lsei_1.2-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/lsei" + cran = "lsei" version('1.3-0', sha256='6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6') version('1.2-0', sha256='4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6') diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 84a4616182..2357879892 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -7,7 +7,7 @@ from spack import * class RLubridate(RPackage): - """Make Dealing with Dates a Little Easier + """Make Dealing with Dates a Little Easier. Functions to work with date-times and timespans: fast and user friendly parsing of date-time data, extraction and updating of components of a @@ -16,7 +16,6 @@ class RLubridate(RPackage): a consistent and memorable syntax that makes working with dates easy and fun.""" - homepage = "https://haven.tidyverse.org/" cran = "lubridate" version('1.8.0', sha256='87d66efdb1f3d680db381d7e40a202d35645865a0542e2f270ef008a19002ba5') @@ -27,9 +26,9 @@ class RLubridate(RPackage): version('1.5.6', sha256='9b1627ba3212e132ce2b9a29d7513e250cc682ab9b4069f6788a22e84bf8d2c4') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.2:', when='@1.7.9.2:', type=('build', 'run')) - depends_on('r-generics', when='@1.7.9.2:', type=('build', 'run')) - depends_on('r-cpp11@0.2.7:', when='@1.8:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@1.7.9.2:') + depends_on('r-generics', type=('build', 'run'), when='@1.7.9.2:') + depends_on('r-cpp11@0.2.7:', type=('build', 'run'), when='@1.8:') - depends_on('r-rcpp@0.12.13:', when='@:1.7', type=('build', 'run')) - depends_on('r-stringr', when='@:1.7.4', type=('build', 'run')) + depends_on('r-rcpp@0.12.13:', type=('build', 'run'), when='@:1.7') + depends_on('r-stringr', type=('build', 'run'), when='@:1.7.4') diff --git a/var/spack/repos/builtin/packages/r-lwgeom/package.py b/var/spack/repos/builtin/packages/r-lwgeom/package.py index 55de7c2051..efab98b877 100644 --- a/var/spack/repos/builtin/packages/r-lwgeom/package.py +++ b/var/spack/repos/builtin/packages/r-lwgeom/package.py @@ -7,15 +7,15 @@ from spack import * class RLwgeom(RPackage): - """Bindings to Selected 'liblwgeom' Functions for Simple Features + """Bindings to Selected 'liblwgeom' Functions for Simple Features. Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <https://postgis.net/>.""" - homepage = "https://github.com/r-spatial/lwgeom/" - cran = "lwgeom" + cran = "lwgeom" + version('0.2-8', sha256='f48a92de222da0590b37a30d5cbf2364555044a842795f6b488afecc650b8b34') version('0.2-5', sha256='4a1d93f96c10c2aac173d8186cf7d7bef7febcb3cf066a7f45da32251496d02f') depends_on('r@3.3.0:', type=('build', 'run')) @@ -24,3 +24,4 @@ class RLwgeom(RPackage): depends_on('r-sf@0.9-3:', type=('build', 'run')) depends_on('geos@3.5.0:') depends_on('proj@4.8.0:6.999') + depends_on('sqlite', when='@0.2-8:') diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index 074035497d..fe2c4a9f25 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -7,14 +7,20 @@ from spack import * class RMagic(RPackage): - """A collection of efficient, vectorized algorithms for the creation and + """Create and Investigate Magic Squares. + + A collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned - arrays.""" + arrays. The package includes methods for creating normal magic squares of + any order greater than 2. The ultimate intention is for the package to be a + computerized embodiment all magic square knowledge, including direct + numerical verification of properties of magic squares (such as recent + results on the determinant of odd-ordered semimagic squares). Some + antimagic functionality is included. The package also serves as a rebuttal + to the often-heard comment "I thought R was just for statistics".""" - homepage = "https://cloud.r-project.org/package=magic" - url = "https://cloud.r-project.org/src/contrib/magic_1.5-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/magic" + cran = "magic" version('1.5-9', sha256='fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a') version('1.5-8', sha256='7f8bc26e05003168e9d2dadf64eb9a34b51bc41beba482208874803dee7d6c20') diff --git a/var/spack/repos/builtin/packages/r-magick/package.py b/var/spack/repos/builtin/packages/r-magick/package.py index ec16975617..075d771eb7 100644 --- a/var/spack/repos/builtin/packages/r-magick/package.py +++ b/var/spack/repos/builtin/packages/r-magick/package.py @@ -7,7 +7,7 @@ from spack import * class RMagick(RPackage): - """Advanced Graphics and Image-Processing in R + """Advanced Graphics and Image-Processing in R. Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, @@ -20,10 +20,9 @@ class RMagick(RPackage): device for creating in-memory graphics or drawing onto images using pixel coordinates.""" - homepage = "https://docs.ropensci.org/magick" - url = "https://cloud.r-project.org/src/contrib/magick_2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/magick" + cran = "magick" + version('2.7.3', sha256='83877b2e23ea43fbc1164de9c2422eafbe7858393ac384df5adf3a7eec122441') version('2.6.0', sha256='66585336e3ff18793ae9e2726af67a6672622f270468670ab5fe5e013bc48ecc') version('2.1', sha256='ef4fb8fc1c5a9cfcc36b22485a0e17d622f61e55803b1e7423fd15f0550de7df') diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py index 548c9a6d69..399b2963bb 100644 --- a/var/spack/repos/builtin/packages/r-magrittr/package.py +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -7,7 +7,7 @@ from spack import * class RMagrittr(RPackage): - """A Forward-Pipe Operator for R + """A Forward-Pipe Operator for R. Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an @@ -15,9 +15,8 @@ class RMagrittr(RPackage): support for the type of right-hand side expressions. For more information, see package vignette.""" - homepage = "https://cloud.r-project.org/package=magrittr" - url = "https://cloud.r-project.org/src/contrib/magrittr_1.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/magrittr" + cran = "magrittr" + version('2.0.2', sha256='7be6fd0d0da75b92d8bad0136076da96260ee84bf639ef632a24668acdc163a6') version('2.0.1', sha256='75c265d51cc2b34beb27040edb09823c7b954d3990a7a931e40690b75d4aad5f') version('1.5', sha256='05c45943ada9443134caa0ab24db4a962b629f00b755ccf039a2a2a7b2c92ae8') diff --git a/var/spack/repos/builtin/packages/r-maldiquant/package.py b/var/spack/repos/builtin/packages/r-maldiquant/package.py index 8cceff4584..1bf2e9eaa7 100644 --- a/var/spack/repos/builtin/packages/r-maldiquant/package.py +++ b/var/spack/repos/builtin/packages/r-maldiquant/package.py @@ -7,22 +7,23 @@ from spack import * class RMaldiquant(RPackage): - """A complete analysis pipeline for matrix-assisted laser - desorption/ionization-time-of-flight (MALDI-TOF) and other - two-dimensional mass spectrometry data. In addition to commonly used - plotting and processing methods it includes distinctive features, - namely baseline subtraction methods such as morphological filters - (TopHat) or the statistics-sensitive non-linear iterative peak-clipping - algorithm (SNIP), peak alignment using warping functions, handling of - replicated measurements as well as allowing spectra with different - resolutions.""" + """Quantitative Analysis of Mass Spectrometry Data. - homepage = "https://cloud.r-project.org/package=MALDIquant" - url = "https://cloud.r-project.org/src/contrib/MALDIquant_1.16.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/MALDIquant" + A complete analysis pipeline for matrix-assisted laser + desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional + mass spectrometry data. In addition to commonly used plotting and + processing methods it includes distinctive features, namely baseline + subtraction methods such as morphological filters (TopHat) or the + statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), + peak alignment using warping functions, handling of replicated measurements + as well as allowing spectra with different resolutions.""" + cran = "MALDIquant" + + version('1.21', sha256='0771f82034aa6a77af67f3572c900987b7e6b578d04d707c6e06689d021a2ff8') version('1.19.3', sha256='a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c') version('1.19.2', sha256='8c6efc4ae4f1af4770b079db29743049f2fd597bcdefeaeb16f623be43ddeb87') version('1.16.4', sha256='9b910dbd5dd1a739a17a7ee3f83d7e1ebad2fee89fd01a5b274415d2b6d3b0de') depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@1.21:') diff --git a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py index cbaed5d513..51d3e5ebcd 100644 --- a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py +++ b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py @@ -7,17 +7,16 @@ from spack import * class RManipulatewidget(RPackage): - """Add Even More Interactivity to Interactive Charts + """Add Even More Interactivity to Interactive Charts. Like package 'manipulate' does for static graphics, this package helps to easily add controls like sliders, pickers, checkboxes, etc. that can be used to modify the input data or the parameters of an interactive chart created with package 'htmlwidgets'.""" - homepage = "https://github.com/rte-antares-rpackage/manipulateWidget" - url = "https://cloud.r-project.org/src/contrib/manipulateWidget_0.10.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/manipulateWidget/" + cran = "manipulateWidget" + version('0.11.1', sha256='5b73728d7d6dcc32f32d861375074cd65112c03a01e4ee4fa94e21b063fdefb6') version('0.10.1', sha256='9d621192121f6b516bc7f1a18305995bfb7838c6683ac701422afc03a50e27ee') version('0.10.0', sha256='3d61a3d0cedf5c8a850a3e62ed6af38c600dc3f25b44c4ff07a5093bf9ca4ffd') version('0.9.0', sha256='5bf4bdb702263b0e156f40f3354922a06db7db544e497addcd6c98d9860bf3a3') @@ -29,6 +28,7 @@ class RManipulatewidget(RPackage): version('0.4.0', sha256='65cc7d28c2b2efc81fda35da019ac6e6058580cf0fdf5e31458cc96386c0c599') depends_on('r+X', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-shiny@1.0.3:', type=('build', 'run')) depends_on('r-miniui', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) @@ -37,3 +37,4 @@ class RManipulatewidget(RPackage): depends_on('r-base64enc', type=('build', 'run')) depends_on('r-codetools', type=('build', 'run')) depends_on('r-webshot', type=('build', 'run')) + depends_on('r-shinyjs', type=('build', 'run'), when='@0.11.1:') diff --git a/var/spack/repos/builtin/packages/r-mapplots/package.py b/var/spack/repos/builtin/packages/r-mapplots/package.py index 94d0621f8f..089713d062 100644 --- a/var/spack/repos/builtin/packages/r-mapplots/package.py +++ b/var/spack/repos/builtin/packages/r-mapplots/package.py @@ -7,11 +7,14 @@ from spack import * class RMapplots(RPackage): - """mapplots: Data Visualisation on Maps""" + """Data Visualisation on Maps. - homepage = "https://cloud.r-project.org/package=mapplots" - url = "https://cloud.r-project.org/src/contrib/mapplots_1.5.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mapplots" + Create simple maps; add sub-plots like pie plots to a map or any other + plot; format, plot and export gridded data. The package was developed for + displaying fisheries data but most functions can be used for more generic + data visualisation.""" + + cran = "mapplots" version('1.5.1', sha256='37e96d34f37922180e07bb63b4514e07d42eee5bbf0885b278286ee48cf142a3') diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py index 2a1b5c79ef..f7e0d06b6c 100644 --- a/var/spack/repos/builtin/packages/r-mapproj/package.py +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -7,14 +7,13 @@ from spack import * class RMapproj(RPackage): - """Map Projections + """Map Projections. Converts latitude/longitude into projected coordinates.""" - homepage = "https://cloud.r-project.org/package=mapproj" - url = "https://cloud.r-project.org/src/contrib/mapproj_1.2-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mapproj" + cran = "mapproj" + version('1.2.8', sha256='865f108f1ee54cda38571b86cd46063a903824d9b4eabfdf75218023d08a7781') version('1.2.7', sha256='f0081281b08bf3cc7052c4f1360d6d3c20d9063be57754448ad9b48ab0d34c5b') version('1.2.6', sha256='62a5aa97837ae95ef9f973d95fe45fe43dbbf482dfa922e9df60f3c510e7efe5') version('1.2-5', sha256='f3026a3a69a550c923b44c18b1ccc60d98e52670a438250d13f3c74cf2195f66') diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py index b66b64be60..94032ce49b 100644 --- a/var/spack/repos/builtin/packages/r-maps/package.py +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -7,15 +7,17 @@ from spack import * class RMaps(RPackage): - """Display of maps. Projection code and larger maps are in separate - packages ('mapproj' and 'mapdata').""" + """Draw Geographical Maps. - homepage = "https://cloud.r-project.org/package=maps" - url = "https://cloud.r-project.org/src/contrib/maps_3.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/maps" + Display of maps. Projection code and larger maps are in separate packages + ('mapproj' and 'mapdata').""" + cran = "maps" + + version('3.4.0', sha256='7918ccb2393ca19589d4c4e77d9ebe863dc6317ebfc1ff41869dbfaf439f5747') version('3.3.0', sha256='199afe19a4edcef966ae79ef802f5dcc15a022f9c357fcb8cae8925fe8bd2216') version('3.2.0', sha256='437abeb4fa4ad4a36af6165d319634b89bfc6bf2b1827ca86c478d56d670e714') version('3.1.1', sha256='972260e5ce9519ecc09b18e5d7a28e01bed313fadbccd7b06c571af349cb4d2a') depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.4.0:') diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py index b533c54624..89c67e6ad9 100644 --- a/var/spack/repos/builtin/packages/r-maptools/package.py +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -7,7 +7,7 @@ from spack import * class RMaptools(RPackage): - """Tools for Handling Spatial Objects + """Tools for Handling Spatial Objects. Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to @@ -15,10 +15,9 @@ class RMaptools(RPackage): exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.""" - homepage = "https://r-forge.r-project.org/projects/maptools/" - url = "https://cloud.r-project.org/src/contrib/maptools_0.8-39.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/maptools" + cran = "maptools" + version('1.1-2', sha256='3995c96e8472cd6717fe3cbd3506358ff460b6c2cf92dbe4b00f75f507514439') version('1.0-2', sha256='daac6da5817cf0cff17b9e7d4a7cdc7c329574249bd9b1bafdb6c9431e1fee49') version('0.9-5', sha256='5d9511f09fb49d57a51f28495b02239800596a4fcfad7b03ee1074d793657bdd') version('0.9-4', sha256='930875f598a516f0f9049fa2fae7391bc9bdf7e3e5db696059ab4ec2fc9ba39c') diff --git a/var/spack/repos/builtin/packages/r-mapview/package.py b/var/spack/repos/builtin/packages/r-mapview/package.py index de2735d30d..1200410162 100644 --- a/var/spack/repos/builtin/packages/r-mapview/package.py +++ b/var/spack/repos/builtin/packages/r-mapview/package.py @@ -7,16 +7,16 @@ from spack import * class RMapview(RPackage): - """Interactive Viewing of Spatial Data in R + """Interactive Viewing of Spatial Data in R. Quickly and conveniently create interactive visualisations of spatial data with or without background maps. Attributes of displayed features are fully queryable via pop-up windows. Additional functionality includes methods to visualise true- and false-color raster images and bounding boxes.""" - homepage = "https://github.com/r-spatial/mapview" - cran = "mapview" + cran = "mapview" + version('2.10.0', sha256='b597902c654b9abf1163bb9d4f1044fef85d0a52c8dc6538ca46b0024f63baaa') version('2.9.0', sha256='170cb2b5e67cbeb177f87bd2eab1ecabc44a1042addbcd95a85b2ec4a00eb690') depends_on('r+X', type=('build', 'run')) @@ -32,6 +32,7 @@ class RMapview(RPackage): depends_on('r-raster', type=('build', 'run')) depends_on('r-satellite', type=('build', 'run')) depends_on('r-scales@0.2.5:', type=('build', 'run')) + depends_on('r-servr', type=('build', 'run'), when='@2.10.0:') depends_on('r-sf', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) depends_on('r-webshot', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py index 87d622d434..9a8611505f 100644 --- a/var/spack/repos/builtin/packages/r-markdown/package.py +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -7,15 +7,15 @@ from spack import * class RMarkdown(RPackage): - """Provides R bindings to the 'Sundown' 'Markdown' rendering library + """Render Markdown with the C Library 'Sundown'. + + Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See https://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.""" - homepage = "https://cloud.r-project.org/package=markdown" - url = "https://cloud.r-project.org/src/contrib/markdown_0.7.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/markdown" + cran = "markdown" version('1.1', sha256='8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b') version('1.0', sha256='172d8072d1829644ee6cdf54282a55718e2cfe9c9915d3589ca5f9a016f8d9a6') @@ -25,4 +25,4 @@ class RMarkdown(RPackage): depends_on('r@2.11.1:', type=('build', 'run')) depends_on('r-mime@0.3:', type=('build', 'run')) - depends_on('r-xfun', when='@1.1:', type=('build', 'run')) + depends_on('r-xfun', type=('build', 'run'), when='@1.1:') diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index c99e3c847a..caea2ea9b7 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -7,15 +7,14 @@ from spack import * class RMass(RPackage): - """Support Functions and Datasets for Venables and Ripley's MASS + """Support Functions and Datasets for Venables and Ripley's MASS. Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).""" - homepage = "https://cloud.r-project.org/package=MASS" - url = "https://cloud.r-project.org/src/contrib/MASS_7.3-47.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/MASS" + cran = "MASS" + version('7.3-55', sha256='65299cbc8f3fd5e09cb3535eabcb3faad2308e01d5ba9422145cc04d7d0c31a4') version('7.3-54', sha256='b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821') version('7.3-53', sha256='41824e70ada302a620226c0f17b1b2c880c6d1a3a100b53bd6df8e8c97e64b38') version('7.3-51.5', sha256='464c0615cef01820cde2bb8457e81575d6755ae9b3ac99f3bfaaac47d43d15cc') @@ -24,3 +23,4 @@ class RMass(RPackage): version('7.3-47', sha256='ed44cdabe84fff3553122267ade61d5cc68071c435f7645d36c8f2e4e9f9c6bf') depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@7.3-55:') diff --git a/var/spack/repos/builtin/packages/r-mathjaxr/package.py b/var/spack/repos/builtin/packages/r-mathjaxr/package.py index 85ff6c8691..4ca4c069ef 100644 --- a/var/spack/repos/builtin/packages/r-mathjaxr/package.py +++ b/var/spack/repos/builtin/packages/r-mathjaxr/package.py @@ -7,13 +7,12 @@ from spack import * class RMathjaxr(RPackage): - """Using 'Mathjax' in Rd Files + """Using 'Mathjax' in Rd Files. Provides 'MathJax' and macros to enable its use within Rd files for rendering equations in the HTML help files.""" - homepage = "https://github.com/wviechtb/mathjaxr" - url = "https://cloud.r-project.org/src/contrib/mathjaxr_1.0-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mathjaxr" + cran = "mathjaxr" + version('1.4-0', sha256='ba57378236d593a39c5839054adc5473526de0c8f05b7eeb87c99438496ddc67') version('1.0-1', sha256='0d3d370c4d0c7c7c6d5541d4e0ae50170b4084ca8a66e8a43bd92c7d1c112148') diff --git a/var/spack/repos/builtin/packages/r-matlab/package.py b/var/spack/repos/builtin/packages/r-matlab/package.py index bc4573888b..f75482c96c 100644 --- a/var/spack/repos/builtin/packages/r-matlab/package.py +++ b/var/spack/repos/builtin/packages/r-matlab/package.py @@ -7,11 +7,11 @@ from spack import * class RMatlab(RPackage): - """Emulate MATLAB code using R""" + """MATLAB emulation package. - homepage = "https://cloud.r-project.org/package=matlab" - url = "https://cloud.r-project.org/src/contrib/matlab_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/matlab" + Emulate MATLAB code using R.""" + + cran = "matlab" version('1.0.2', sha256='a23dec736c51ae1864c1a53caac556a2f98e8020138a3b121badb0f5b7984154') diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py index 51f339702d..6c11f8571d 100644 --- a/var/spack/repos/builtin/packages/r-matr/package.py +++ b/var/spack/repos/builtin/packages/r-matr/package.py @@ -7,16 +7,16 @@ from spack import * class RMatr(RPackage): - """Package matR (Metagenomics Analysis Tools for R) is an analysis - client for the MG-RAST metagenome annotation engine, part of the US - Department of Energy (DOE) Systems Biology Knowledge Base (KBase). - Customized analysis and visualization tools securely access remote - data and metadata within the popular open source R language and - environment for statistical computing.""" + """Metagenomics Analysis Tools. - homepage = "https://github.com/MG-RAST/matR" - url = "https://cloud.r-project.org/src/contrib/matR_0.9.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/matR" + Package matR (Metagenomics Analysis Tools for R) is an analysis client for + the MG-RAST metagenome annotation engine, part of the US Department of + Energy (DOE) Systems Biology Knowledge Base (KBase). Customized analysis + and visualization tools securely access remote data and metadata within the + popular open source R language and environment for statistical + computing.""" + + cran = "matR" version('0.9.1', sha256='554aeff37b27d0f17ddeb62b2e1004aa1f29190300e4946b1bec1d7c2bde82e3') version('0.9', sha256='5750e6a876cf85fe66038292adefbfcb18e2584fa2e841f39dbe67f3c51b3052') diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index e07dbd1896..6a8d0d5e09 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -7,16 +7,16 @@ from spack import * class RMatrix(RPackage): - """Sparse and Dense Matrix Classes and Methods + """Sparse and Dense Matrix Classes and Methods. A rich hierarchy of matrix classes, including triangular, symmetric, and diagonal matrices, both dense and sparse and with pattern, logical and numeric entries. Numerous methods for and operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.""" - homepage = "https://matrix.r-forge.r-project.org/" cran = "Matrix" + version('1.4-0', sha256='c2b463702e4051b621f5e2b091a33f883f1caa97703d65f7a52b78caf81206f6') version('1.3-4', sha256='ab42179d44545e99bbdf44bb6d04cab051dd2aba552b1f6edd51ed71b55f6c39') version('1.3-3', sha256='f77ec8de43ae7bfa19dfdc7e76bfefbb21b3223dbc174423fcde70b44cf36a3b') version('1.3-2', sha256='950ba5d91018e711fd2743b3486a50dc47ae9c271389fce587792f0a9aab9531') @@ -27,7 +27,7 @@ class RMatrix(RPackage): version('1.2-6', sha256='4b49b639b7bf612fa3d1c1b1c68125ec7859c8cdadae0c13f499f24099fd5f20') depends_on('r@3.0.1:', type=('build', 'run')) - depends_on('r@3.2.0:', when='@1.2.13:', type=('build', 'run')) - depends_on('r@3.6.0:', when='@1.3-2:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.3-3:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@1.2.13:') + depends_on('r@3.6.0:', type=('build', 'run'), when='@1.3-2:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.3-3:') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py index 6191dbc8c9..7a776f8a56 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -7,13 +7,14 @@ from spack import * class RMatrixmodels(RPackage): - """Modelling with sparse and dense 'Matrix' matrices, using modular - prediction and response module classes.""" + """Modelling with Sparse and Dense Matrices. - homepage = "https://matrix.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/MatrixModels" + Modelling with sparse and dense 'Matrix' matrices, using modular prediction + and response module classes.""" + cran = "MatrixModels" + + version('0.5-0', sha256='a87faf1a185219f79ea2307e6787d293e1d30bf3af9398e8cfe1e079978946ed') version('0.4-1', sha256='fe878e401e697992a480cd146421c3a10fa331f6b37a51bac83b5c1119dcce33') depends_on('r@3.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py index c2692a2580..92e56e2e5e 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -7,7 +7,7 @@ from spack import * class RMatrixstats(RPackage): - """Functions that Apply to Rows and Columns of Matrices (and to Vectors) + """Functions that Apply to Rows and Columns of Matrices (and to Vectors). High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions @@ -15,7 +15,6 @@ class RMatrixstats(RPackage): memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().""" - homepage = "https://cloud.r-project.org/package=matrixStats" cran = "matrixStats" version('0.61.0', sha256='dbd3c0ec59b1ae62ff9b4c2c90c4687cbd680d1796f6fdd672319458d4d2fd9a') diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py index 1af352da9a..c3da03324b 100644 --- a/var/spack/repos/builtin/packages/r-mclust/package.py +++ b/var/spack/repos/builtin/packages/r-mclust/package.py @@ -8,17 +8,16 @@ from spack import * class RMclust(RPackage): """Gaussian Mixture Modelling for Model-Based Clustering, Classification, - and Density Estimation + and Density Estimation. Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.""" - homepage = "http://www.stat.washington.edu/mclust" - url = "https://cloud.r-project.org/src/contrib/mclust_5.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mclust" + cran = "mclust" + version('5.4.9', sha256='65f123c6af86cf5eb511c81ae0eafa60da7b2085bfea1a08bdc3116081da9568') version('5.4.7', sha256='45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23') version('5.4.5', sha256='75f2963082669485953e4306ffa93db98335ee6afdc1318b95d605d56cb30a72') version('5.4.4', sha256='ccc31b0ad445e121a447b04988e73232a085c506fcc7ebdf11a3e0754aae3e0d') diff --git a/var/spack/repos/builtin/packages/r-mcmc/package.py b/var/spack/repos/builtin/packages/r-mcmc/package.py index 01ec20d0e2..30068988cd 100644 --- a/var/spack/repos/builtin/packages/r-mcmc/package.py +++ b/var/spack/repos/builtin/packages/r-mcmc/package.py @@ -7,7 +7,7 @@ from spack import * class RMcmc(RPackage): - """Markov Chain Monte Carlo: + """Markov Chain Monte Carlo. Simulates continuous distributions of random vectors using Markov chain Monte Carlo (MCMC). Users specify the distribution by an R function that @@ -17,8 +17,7 @@ class RMcmc(RPackage): <doi:10.1214/12-AOS1048>, function morph.metrop), which achieves geometric ergodicity by change of variable.""" - homepage = "https://www.stat.umn.edu/geyer/mcmc/" - cran = "mcmc" + cran = "mcmc" version('0.9-7', sha256='b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260') diff --git a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py index 0d22fb30a6..960b213407 100644 --- a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py +++ b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py @@ -7,15 +7,16 @@ from spack import * class RMcmcglmm(RPackage): - """MCMC Generalised Linear Mixed Models + """MCMC Generalised Linear Mixed Models. - Fits Multi-response Generalised Linear Mixed Models (and related models) - using Markov chain Monte Carlo techniques.""" + Fits Multivariate Generalised Linear Mixed Models (and related models) + using Markov chain Monte Carlo techniques (Hadfield 2010 J. Stat. + Soft.).""" - homepage = "https://cloud.r-project.org/package=MCMCglmm" - url = "https://cloud.r-project.org/src/contrib/MCMCglmm_2.25.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/MCMCglmm" + cran = "MCMCglmm" + version('2.33', sha256='b56d72e799f8ed5fa2a05ecc743e5b8051f9cc2de57ad3e6de2dcb1c1715d4fc') + version('2.32', sha256='a9156e1e0d0f912f2f239476dc8765dc61c480f903381be7ec5db05bd6d3f0b3') version('2.30', sha256='714250fe6ebdd1bd3dc284f7fcb92326de1273b0c34d31e71dc825312527e042') version('2.29', sha256='13ba7837ea2049e892c04e7ec5c83d5b599a7e4820b9d875f55ec40fc2cc67b4') version('2.28', sha256='7d92e6d35638e5e060a590b92c3b1bfc02a11386276a8ab99bceec5d797bfc2a') diff --git a/var/spack/repos/builtin/packages/r-mcmcpack/package.py b/var/spack/repos/builtin/packages/r-mcmcpack/package.py index 58cfa63fae..1442458553 100644 --- a/var/spack/repos/builtin/packages/r-mcmcpack/package.py +++ b/var/spack/repos/builtin/packages/r-mcmcpack/package.py @@ -7,7 +7,7 @@ from spack import * class RMcmcpack(RPackage): - """Markov Chain Monte Carlo (MCMC) Package: + """Markov Chain Monte Carlo (MCMC) Package. Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ @@ -17,9 +17,9 @@ class RMcmcpack(RPackage): number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.""" - homepage = "https://cran.r-project.org/package=MCMCpack" - cran = "MCMCpack" + cran = "MCMCpack" + version('1.6-0', sha256='b5b9493457d11d4dca12f7732bd1b3eb1443852977c8ee78393126f13deaf29b') version('1.5-0', sha256='795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace') depends_on('r@3.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mco/package.py b/var/spack/repos/builtin/packages/r-mco/package.py index c9d5757ad7..53282a5aa0 100644 --- a/var/spack/repos/builtin/packages/r-mco/package.py +++ b/var/spack/repos/builtin/packages/r-mco/package.py @@ -7,15 +7,13 @@ from spack import * class RMco(RPackage): - """Multiple Criteria Optimization Algorithms and Related Functions + """Multiple Criteria Optimization Algorithms and Related Functions. A collection of function to solve multiple criteria optimization problems using genetic algorithms (NSGA-II). Also included is a collection of test functions.""" - homepage = "https://github.com/cran/mco" - url = "https://cloud.r-project.org/src/contrib/mco_1.0-15.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mco" + cran = "mco" version('1.15.6', sha256='17ebe279cb9c89b7cd8054ac50d3b657d2b10dadbc584b88da7e79c3a9680582') version('1.0-15.1', sha256='3c13ebc8c1f1bfa18f3f95b3998c57fde5259876e92456b6c6d4c59bef07c193') diff --git a/var/spack/repos/builtin/packages/r-mda/package.py b/var/spack/repos/builtin/packages/r-mda/package.py index f5929efa71..da4b38f635 100644 --- a/var/spack/repos/builtin/packages/r-mda/package.py +++ b/var/spack/repos/builtin/packages/r-mda/package.py @@ -7,19 +7,17 @@ from spack import * class RMda(RPackage): - """Mixture and Flexible Discriminant Analysis + """Mixture and Flexible Discriminant Analysis. Mixture and flexible discriminant analysis, multivariate adaptive regression splines (MARS), BRUTO.""" - homepage = "https://cloud.r-project.org/package=mda" - url = "https://cloud.r-project.org/src/contrib/mda_0.4-9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mda" + cran = "mda" version('0.5-2', sha256='344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3') version('0.4-10', sha256='7036bc622a8fea5b2de94fc19e6b64f5f0c27e5d743ae7646e116af08c9de6a5') version('0.4-9', sha256='b72456d2fa5b49895644489735d21cf4836d3d597f5e693e6103cce1887ffd85') depends_on('r@1.9.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.5-2:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.5-2:') depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index 08af0df1b7..84ee838dce 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -7,13 +7,18 @@ from spack import * class RMemoise(RPackage): - """Cache the results of a function so that when you call it again with the + """'Memoisation' of Functions. + + Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.""" - homepage = "https://github.com/hadley/memoise" - url = "https://cloud.r-project.org/src/contrib/memoise_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/memoise" + cran = "memoise" + + version('2.0.1', sha256='f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb') version('1.1.0', sha256='b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c') version('1.0.0', sha256='fd1b6cf12929890db7819f74a44a1dbe3d6f25c8a608a956d827f8be2f6c026b') - depends_on('r-digest@0.6.3:', type=('build', 'run')) + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@2.0.1:') + depends_on('r-cachem', type=('build', 'run'), when='@2.0.1:') + + depends_on('r-digest@0.6.3:', type=('build', 'run'), when='@:1.1.0') diff --git a/var/spack/repos/builtin/packages/r-memuse/package.py b/var/spack/repos/builtin/packages/r-memuse/package.py index c7f3acc776..0d1bbdda8c 100644 --- a/var/spack/repos/builtin/packages/r-memuse/package.py +++ b/var/spack/repos/builtin/packages/r-memuse/package.py @@ -7,18 +7,18 @@ from spack import * class RMemuse(RPackage): - """Memory Estimation Utilities + """Memory Estimation Utilities. - How much ram do you need to store a 100,000 by 100,000 matrix? How much - ram is your current R session using? How much ram do you even have? - Learn the scintillating answer to these and many more such questions - with the 'memuse' package.""" + How much ram do you need to store a 100,000 by 100,000 matrix? How much ram + is your current R session using? How much ram do you even have? Learn the + scintillating answer to these and many more such questions with the + 'memuse' package.""" - homepage = "https://github.com/shinra-dev/memuse" - cran = "memuse" + cran = "memuse" maintainers = ['dorton21'] + version('4.2-1', sha256='f5e9dbaad4efbbfe219a93f446e318a00cad5b294bfc60ca2146eca894b47cf3') version('4.1-0', sha256='58d6d1ca5d6bd481f4ed299eff6a9d5660eb0f8db1abe54c49e144093cba72ad') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-metap/package.py b/var/spack/repos/builtin/packages/r-metap/package.py index 33ccae1c0c..c7e1e68177 100644 --- a/var/spack/repos/builtin/packages/r-metap/package.py +++ b/var/spack/repos/builtin/packages/r-metap/package.py @@ -7,7 +7,7 @@ from spack import * class RMetap(RPackage): - """Meta-Analysis of Significance Values + """Meta-Analysis of Significance Values. The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for @@ -15,16 +15,16 @@ class RMetap(RPackage): Fisher, Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.""" - homepage = "http://www.dewey.myzen.co.uk/meta/meta.html" - url = "https://cloud.r-project.org/src/contrib/metap_1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/metap" + cran = "metap" + version('1.7', sha256='d9b511607d0e37de4428549061c5577a4e812b0f55bb7ed887d1b24711f58c42') version('1.4', sha256='5fac23d823d0ad4eebc3f97620364e25f7b41f8d0c3579f6c09ec059940b85a5') version('1.1', sha256='20120428672d39dc15829c7e66850fc4350a34df290d48cef0b1cc78d13f7b82') + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.7:') depends_on('r-lattice', type=('build', 'run')) depends_on('r-rdpack', type=('build', 'run')) - depends_on('r-rdpack@0.7:', when='@1.4:', type=('build', 'run')) - depends_on('r-tfisher', when='@1.4:', type=('build', 'run')) - depends_on('r-mutoss', when='@1.4:', type=('build', 'run')) - depends_on('r-mathjaxr@0.8-3:', when='@1.4:', type=('build', 'run')) + depends_on('r-rdpack@0.7:', type=('build', 'run'), when='@1.4:') + depends_on('r-tfisher', type=('build', 'run'), when='@1.4:') + depends_on('r-mutoss', type=('build', 'run'), when='@1.4:') + depends_on('r-mathjaxr@0.8-3:', type=('build', 'run'), when='@1.4:') diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index bddde369e2..ddaf2cea00 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -7,7 +7,7 @@ from spack import * class RMgcv(RPackage): - """Mixed GAM Computation Vehicle with Automatic Smoothness Estimation + """Mixed GAM Computation Vehicle with Automatic Smoothness Estimation. Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation @@ -17,7 +17,6 @@ class RMgcv(RPackage): Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.""" - homepage = "https://cloud.r-project.org/package=mgcv" cran = "mgcv" version('1.8-38', sha256='cd12ed5787d6fdcead34e782e48b62b3f9efd523616c906e2da77bd9c142ddbb') @@ -34,6 +33,6 @@ class RMgcv(RPackage): version('1.8-13', sha256='74bc819708ef59da94b777a446ef00d7f14b428eec843533e824017c29cc524b') depends_on('r@2.14.0:', type=('build', 'run')) - depends_on('r@3.6.0:', when='@1.8.34:', type=('build', 'run')) + depends_on('r@3.6.0:', type=('build', 'run'), when='@1.8.34:') depends_on('r-nlme@3.1-64:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mgraster/package.py b/var/spack/repos/builtin/packages/r-mgraster/package.py index 3d5c3e26dc..b5cbdeb516 100644 --- a/var/spack/repos/builtin/packages/r-mgraster/package.py +++ b/var/spack/repos/builtin/packages/r-mgraster/package.py @@ -7,13 +7,13 @@ from spack import * class RMgraster(RPackage): - """Convenience Functions for R Language Access to the v.1 API of the - MG-RAST Metagenome Annotation Server, part of the US Department of Energy - (DOE) Systems Biology Knowledge Base (KBase).""" + """API Client for the MG-RAST Server of the US DOE KBase. - homepage = "https://github.com/braithwaite/MGRASTer/" - url = "https://cloud.r-project.org/src/contrib/MGRASTer_0.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/MGRASTer" + Convenience Functions for R Language Access to the v.1 API of the MG-RAST + Metagenome Annotation Server, part of the US Department of Energy (DOE) + Systems Biology Knowledge Base (KBase).""" + + cran = "MGRASTer" version('0.9', sha256='f727b5270ed4bd6dcacaecb49e1ace7eb40827754be9801230db940c4012ae4a') diff --git a/var/spack/repos/builtin/packages/r-mice/package.py b/var/spack/repos/builtin/packages/r-mice/package.py index ac3f9c7b1e..2048b02682 100644 --- a/var/spack/repos/builtin/packages/r-mice/package.py +++ b/var/spack/repos/builtin/packages/r-mice/package.py @@ -7,7 +7,7 @@ from spack import * class RMice(RPackage): - """Multivariate Imputation by Chained Equations + """Multivariate Imputation by Chained Equations. Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn @@ -21,10 +21,9 @@ class RMice(RPackage): diagnostic plots are available to inspect the quality of the imputations.""" - homepage = "https://cloud.r-project.org/package=mice" - url = "https://cloud.r-project.org/src/contrib/mice_3.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mice" + cran = "mice" + version('3.14.0', sha256='f87bb73d8bfee36c6bf4f15779c59ff6b70c70ca25b1388b4ee236757276d605') version('3.12.0', sha256='575d9e650d5fc8cd66c0b5a2f1e659605052b26d61f772fff5eed81b414ef144') version('3.6.0', sha256='7bc72bdb631bc9f67d8f76ffb48a7bb275228d861075e20c24c09c736bebec5d') version('3.5.0', sha256='4fccecdf9e8d8f9f63558597bfbbf054a873b2d0b0820ceefa7b6911066b9e45') @@ -33,14 +32,16 @@ class RMice(RPackage): depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-broom', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-generics', when='@3.12.0:', type=('build', 'run')) + depends_on('r-generics', type=('build', 'run'), when='@3.12.0:') depends_on('r-lattice', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) - depends_on('r-tidyr', when='@3.12.0:', type=('build', 'run')) - depends_on('r-cpp11', when='@3.12.0:', type=('build', 'run')) - depends_on('r-mitml', when='@:3.6.0', type=('build', 'run')) - depends_on('r-nnet', when='@:3.6.0', type=('build', 'run')) - depends_on('r-rpart', when='@:3.6.0', type=('build', 'run')) - depends_on('r-survival', when='@:3.6.0', type=('build', 'run')) - depends_on('r-mass', when='@:3.6.0', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run'), when='@3.12.0:') + depends_on('r-withr', type=('build', 'run'), when='@3.14.0:') + depends_on('r-cpp11', type=('build', 'run'), when='@3.12.0:') + + depends_on('r-mitml', type=('build', 'run'), when='@:3.6.0') + depends_on('r-nnet', type=('build', 'run'), when='@:3.6.0') + depends_on('r-rpart', type=('build', 'run'), when='@:3.6.0') + depends_on('r-survival', type=('build', 'run'), when='@:3.6.0') + depends_on('r-mass', type=('build', 'run'), when='@:3.6.0') diff --git a/var/spack/repos/builtin/packages/r-microbenchmark/package.py b/var/spack/repos/builtin/packages/r-microbenchmark/package.py index 4df039664f..f12720e077 100644 --- a/var/spack/repos/builtin/packages/r-microbenchmark/package.py +++ b/var/spack/repos/builtin/packages/r-microbenchmark/package.py @@ -7,12 +7,12 @@ from spack import * class RMicrobenchmark(RPackage): - """Accurate Timing Functions + """Accurate Timing Functions. Provides infrastructure to accurately measure and compare the execution time of R expressions.""" - homepage = "https://github.com/joshuaulrich/microbenchmark/" - cran = "microbenchmark" + cran = "microbenchmark" + version('1.4.9', sha256='443d2caf370ef33e4ac2773176ad9eb86f8790f43b430968ef9647699dbbffd2') version('1.4-7', sha256='268f13c6323dd28cc2dff7e991bb78b814a8873b4a73f4a3645f40423da984f6') diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index 84d428f7fd..cf470f38c8 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -7,14 +7,14 @@ from spack import * class RMime(RPackage): - """Map Filenames to MIME Types + """Map Filenames to MIME Types. - Guesses the MIME type from a filename extension using the data derived - from /etc/mime.types in UNIX-type systems.""" + Guesses the MIME type from a filename extension using the data derived from + /etc/mime.types in UNIX-type systems.""" - homepage = "https://github.com/yihui/mime" - cran = "mime" + cran = "mime" + version('0.12', sha256='a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849') version('0.11', sha256='215427a49f0d0b0e3ab38d419c515a35d57e3bc32535805306275d8b33f8eec0') version('0.9', sha256='2ccf97d2940a09539dc051c7a9a1aee90ef04b34e9bc6c0b64b4435fb3c2fa80') version('0.7', sha256='11083ee44c92569aadbb9baf60a2e079ab7a721c849b74d102694975cc8d778b') diff --git a/var/spack/repos/builtin/packages/r-miniui/package.py b/var/spack/repos/builtin/packages/r-miniui/package.py index fea206e078..6553385170 100644 --- a/var/spack/repos/builtin/packages/r-miniui/package.py +++ b/var/spack/repos/builtin/packages/r-miniui/package.py @@ -7,12 +7,12 @@ from spack import * class RMiniui(RPackage): - """Provides UI widget and layout functions for writing Shiny apps that - work well on small screens.""" + """Shiny UI Widgets for Small Screens. - homepage = "https://cloud.r-project.org/package=miniUI" - url = "https://cloud.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/miniUI/" + Provides UI widget and layout functions for writing Shiny apps that work + well on small screens.""" + + cran = "miniUI" version('0.1.1.1', sha256='452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0') diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py index 74f36e1c5b..02482d5f06 100644 --- a/var/spack/repos/builtin/packages/r-minqa/package.py +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -7,12 +7,12 @@ from spack import * class RMinqa(RPackage): - """Derivative-free optimization by quadratic approximation based on an + """Derivative-free optimization algorithms by quadratic approximation. + + Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.""" - homepage = "https://optimizer.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/minqa_1.2.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/minqa" + cran = "minqa" version('1.2.4', sha256='cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c') diff --git a/var/spack/repos/builtin/packages/r-misc3d/package.py b/var/spack/repos/builtin/packages/r-misc3d/package.py index 1908500937..543cfc9105 100644 --- a/var/spack/repos/builtin/packages/r-misc3d/package.py +++ b/var/spack/repos/builtin/packages/r-misc3d/package.py @@ -7,14 +7,13 @@ from spack import * class RMisc3d(RPackage): - """Miscellaneous 3D Plots + """Miscellaneous 3D Plots. A collection of miscellaneous 3d plots, including isosurfaces.""" - homepage = "https://cloud.r-project.org/package=misc3d" - url = "https://cloud.r-project.org/src/contrib/misc3d_0.8-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/misc3d" + cran = "misc3d" + version('0.9-1', sha256='a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65') version('0.9-0', sha256='a1e9291d625bd1312bae5b0e26d48b9362f66a8a0fabbf48891ba1d2432e4e82') version('0.8-4', sha256='75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62') diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py index 59c7952fb8..e3451b4dd7 100644 --- a/var/spack/repos/builtin/packages/r-mitml/package.py +++ b/var/spack/repos/builtin/packages/r-mitml/package.py @@ -7,15 +7,16 @@ from spack import * class RMitml(RPackage): - """Provides tools for multiple imputation of missing data in multilevel + """Tools for Multiple Imputation in Multilevel Modeling. + + Provides tools for multiple imputation of missing data in multilevel modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo', and several functions for visualization, data management and the analysis of multiply imputed data sets.""" - homepage = "https://cloud.r-project.org/package=mitml" - url = "https://cloud.r-project.org/src/contrib/mitml_0.3-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mitml" + cran = "mitml" + version('0.4-3', sha256='49bd3eb68a60fb2a269e7ddca8b862e1e81e0651e2b29759482fb7bcad452102') version('0.3-7', sha256='c6f796d0059f1b093b599a89d955982fa257de9c45763ecc2cbbce10fdec1e7b') version('0.3-6', sha256='bc59bdc802eb882340393752535446560c716f12c6fca2b95f03c6af30d978de') version('0.3-5', sha256='8bcfeb18f3fb8a58a516348c37369eb8356af4bd3e0688c84a2366e1534608e9') diff --git a/var/spack/repos/builtin/packages/r-mitools/package.py b/var/spack/repos/builtin/packages/r-mitools/package.py index 54a89c1c0a..b5d7e243a7 100644 --- a/var/spack/repos/builtin/packages/r-mitools/package.py +++ b/var/spack/repos/builtin/packages/r-mitools/package.py @@ -7,12 +7,12 @@ from spack import * class RMitools(RPackage): - """Tools to perform analyses and combine results from multiple-imputation + """Tools for Multiple Imputation of Missing Data. + + Tools to perform analyses and combine results from multiple-imputation datasets.""" - homepage = "https://cloud.r-project.org/package=mitools" - url = "https://cloud.r-project.org/src/contrib/mitools_2.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mitools" + cran = "mitools" version('2.4', sha256='f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30') diff --git a/var/spack/repos/builtin/packages/r-mixtools/package.py b/var/spack/repos/builtin/packages/r-mixtools/package.py index 6cf536adc2..b2e583f020 100644 --- a/var/spack/repos/builtin/packages/r-mixtools/package.py +++ b/var/spack/repos/builtin/packages/r-mixtools/package.py @@ -7,7 +7,7 @@ from spack import * class RMixtools(RPackage): - """Tools for Analyzing Finite Mixture Models + """Tools for Analyzing Finite Mixture Models. Analyzes finite mixture models for various parametric and semiparametric settings. This includes mixtures of parametric distributions (normal, @@ -23,17 +23,15 @@ class RMixtools(RPackage): supported by the National Science Foundation under Grant No. SES-0518772.""" - homepage = "https://cloud.r-project.org/package=mixtools" - url = "https://cloud.r-project.org/src/contrib/mixtools_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mixtools" + cran = "mixtools" version('1.2.0', sha256='ef033ef13625209065d26767bf70d129972e6808927f755629f1d70a118b9023') version('1.1.0', sha256='543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f') version('1.0.4', sha256='62f4b0a17ce520c4f8ed50ab44f120e459143b461a9e420cd39056ee4fc8798c') depends_on('r@3.2:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.2.0:', type=('build', 'run')) - depends_on('r-kernlab', when='@1.2.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.2.0:') + depends_on('r-kernlab', type=('build', 'run'), when='@1.2.0:') depends_on('r-mass', type=('build', 'run')) depends_on('r-segmented', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlbench/package.py b/var/spack/repos/builtin/packages/r-mlbench/package.py index 1f9b2b2074..00ceddf31b 100644 --- a/var/spack/repos/builtin/packages/r-mlbench/package.py +++ b/var/spack/repos/builtin/packages/r-mlbench/package.py @@ -7,13 +7,14 @@ from spack import * class RMlbench(RPackage): - """A collection of artificial and real-world machine learning benchmark + """Machine Learning Benchmark Problems. + + A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.""" - homepage = "https://cloud.r-project.org/package=mlbench" - url = "https://cloud.r-project.org/src/contrib/mlbench_2.1-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mlbench" + cran = "mlbench" + version('2.1-3', sha256='b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194') version('2.1-1', sha256='748141d56531a39dc4d37cf0a5165a40b653a04c507e916854053ed77119e0e6') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlr/package.py b/var/spack/repos/builtin/packages/r-mlr/package.py index 774a38f09a..b96990bbeb 100644 --- a/var/spack/repos/builtin/packages/r-mlr/package.py +++ b/var/spack/repos/builtin/packages/r-mlr/package.py @@ -7,7 +7,7 @@ from spack import * class RMlr(RPackage): - """Machine Learning in R + """Machine Learning in R. Interface to a large number of classification and regression techniques, including machine-readable parameter descriptions. There is also an @@ -20,10 +20,9 @@ class RMlr(RPackage): allowing for easy nested resampling. Most operations can be parallelized.""" - homepage = "https://github.com/mlr-org/mlr/" - url = "https://cloud.r-project.org/src/contrib/mlr_2.12.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mlr" + cran = "mlr" + version('2.19.0', sha256='1149c9b453896481c85906045aa82d511d96979ddecbe5a3faf04f9f4a5e6113') version('2.18.0', sha256='c2fe74e90ed32e5f4cbb0c09a1742051688d87db2f12dd408ddad0f5afc7f8d3') version('2.15.0', sha256='a3c2c2bd65a87d90b5e5e877b1ef8e7712e76b4eb1660d3f69672a1860ca5324') version('2.14.0', sha256='1f72184400678386c7c44297c4c92a448b50148de700df5ba0438d4e486e944a') @@ -42,7 +41,7 @@ class RMlr(RPackage): depends_on('r-bbmisc@1.11:', type=('build', 'run')) depends_on('r-checkmate@1.8.2:', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) - depends_on('r-data-table@1.12.4:', when='@2.18.0:', type=('build', 'run')) + depends_on('r-data-table@1.12.4:', type=('build', 'run'), when='@2.18.0:') depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-parallelmap@1.3:', type=('build', 'run')) depends_on('r-stringi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlrmbo/package.py b/var/spack/repos/builtin/packages/r-mlrmbo/package.py index a9fa8ab8e3..ecdca83cf7 100644 --- a/var/spack/repos/builtin/packages/r-mlrmbo/package.py +++ b/var/spack/repos/builtin/packages/r-mlrmbo/package.py @@ -7,7 +7,8 @@ from spack import * class RMlrmbo(RPackage): - """Bayesian Optimization and Model-Based Optimization of Expensive Black-Box Functions + """Bayesian Optimization and Model-Based Optimization of Expensive + Black-Box Functions. Flexible and comprehensive R toolbox for model-based optimization ('MBO'), also known as Bayesian optimization. It is designed for both single- and @@ -22,9 +23,7 @@ class RMlrmbo(RPackage): modular fashion, such that single components can be easily replaced or adapted by the user for specific use cases.""" - homepage = "https://github.com/mlr-org/mlrMBO/" - url = "https://cloud.r-project.org/src/contrib/mlrMBO_1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mlrMBO" + cran = "mlrMBO" version('1.1.5', sha256='7ab9d108ad06f6c5c480fa4beca69e09ac89bb162ae6c85fe7d6d25c41f359b8') version('1.1.2', sha256='8e84caaa5d5d443d7019128f88ebb212fb095870b3a128697c9b64fe988f3efe') diff --git a/var/spack/repos/builtin/packages/r-mmwrweek/package.py b/var/spack/repos/builtin/packages/r-mmwrweek/package.py index 93b5bc7e98..00d459fe0f 100644 --- a/var/spack/repos/builtin/packages/r-mmwrweek/package.py +++ b/var/spack/repos/builtin/packages/r-mmwrweek/package.py @@ -7,18 +7,15 @@ from spack import * class RMmwrweek(RPackage): - """Convert Dates to MMWR Day, Week, and Year + """Convert Dates to MMWR Day, Week, and Year. - The first day of any MMWR week is Sunday. MMWR week numbering is - sequential beginning with 1 and incrementing with each week to a maximum - of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year - that has at least four days in the calendar year. This package provides - functionality to convert Dates to MMWR day, week, and year and the - reverse.""" + The first day of any MMWR week is Sunday. MMWR week numbering is sequential + beginning with 1 and incrementing with each week to a maximum of 52 or 53. + MMWR week #1 of an MMWR year is the first week of the year that has at + least four days in the calendar year. This package provides functionality + to convert Dates to MMWR day, week, and year and the reverse.""" - homepage = "https://cloud.r-project.org/package=MMWRweek" - url = "https://cloud.r-project.org/src/contrib/MMWRweek_0.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/MMWRweek" + cran = "MMWRweek" version('0.1.3', sha256='1aa8b687dc3340c3f277689eb0ca529e0064a4a3a66868137f2f8ab209d133d0') version('0.1.1', sha256='969fd18535f3b78dd360d62d29d5f15409fc059f4af5d345abfde711e4adbc99') diff --git a/var/spack/repos/builtin/packages/r-mnormt/package.py b/var/spack/repos/builtin/packages/r-mnormt/package.py index 5e300aafdd..41647ff47b 100644 --- a/var/spack/repos/builtin/packages/r-mnormt/package.py +++ b/var/spack/repos/builtin/packages/r-mnormt/package.py @@ -7,7 +7,8 @@ from spack import * class RMnormt(RPackage): - """The Multivariate Normal and t Distributions, and Their Truncated Versions + """The Multivariate Normal and t Distributions, and Their Truncated + Versions. Functions are provided for computing the density and the distribution function of multivariate normal and "t" random variables, and for @@ -15,12 +16,10 @@ class RMnormt(RPackage): are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.""" - homepage = "http://azzalini.stat.unipd.it/SW/Pkg-mnormt" - url = "https://cloud.r-project.org/src/contrib/mnormt_1.5-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mnormt" + cran = "mnormt" version('2.0.2', sha256='5c6aa036d3f1035ffe8f9a8e95bb908b191b126b016591cf893c50472851f334') version('1.5-5', sha256='ff78d5f935278935f1814a69e5a913d93d6dd2ac1b5681ba86b30c6773ef64ac') depends_on('r@2.2.0:', type=('build', 'run')) - depends_on('r-tmvnsim@1.0-2:', when='@2.0.2:', type=('build', 'run')) + depends_on('r-tmvnsim@1.0-2:', type=('build', 'run'), when='@2.0.2:') diff --git a/var/spack/repos/builtin/packages/r-mockery/package.py b/var/spack/repos/builtin/packages/r-mockery/package.py index e8e13d295a..b08d3327db 100644 --- a/var/spack/repos/builtin/packages/r-mockery/package.py +++ b/var/spack/repos/builtin/packages/r-mockery/package.py @@ -6,16 +6,16 @@ from spack import * class RMockery(RPackage): - """The two main functionalities of this package are creating mock - objects (functions) and selectively intercepting calls to a given - function that originate in some other function. It can be used with - any testing framework available for R. Mock objects can be injected - with either this package's own stub() function or a similar - with_mock() facility present in the 'testthat' package.""" + """Mocking Library for R. - homepage = "https://github.com/r-lib/mockery" - url = "https://cran.r-project.org/src/contrib/mockery_0.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mockery" + The two main functionalities of this package are creating mock objects + (functions) and selectively intercepting calls to a given function that + originate in some other function. It can be used with any testing framework + available for R. Mock objects can be injected with either this package's + own stub() function or a similar with_mock() facility present in the + 'testthat' package.""" + + cran = "mockery" version('0.4.2', sha256='988e249c366ee7faf277de004084cf5ca24b5c8a8c6e3842f1b1362ce2f7ea9b') version('0.4.1', sha256='959d83f8b21e9a89c06c73f310356790c2d63d5ba39b2b60c6777a4eb33909c1') diff --git a/var/spack/repos/builtin/packages/r-modelmetrics/package.py b/var/spack/repos/builtin/packages/r-modelmetrics/package.py index f30e452ef2..c09f9e8798 100644 --- a/var/spack/repos/builtin/packages/r-modelmetrics/package.py +++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py @@ -7,15 +7,13 @@ from spack import * class RModelmetrics(RPackage): - """Rapid Calculation of Model Metrics + """Rapid Calculation of Model Metrics. Collection of metrics for evaluating models written in C++ using 'Rcpp'. Popular metrics include area under the curve, log loss, root mean square error, etc.""" - homepage = "https://cloud.r-project.org/package=ModelMetrics" - url = "https://cloud.r-project.org/src/contrib/ModelMetrics_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ModelMetrics" + cran = "ModelMetrics" version('1.2.2.2', sha256='5e06f1926aebca5654e1329c66ef19b04058376b2277ebb16e3bf8c208d73457') version('1.2.2', sha256='66d6fc75658287fdbae4d437b51d26781e138b8baa558345fb9e5a2df86a0d95') @@ -24,4 +22,4 @@ class RModelmetrics(RPackage): depends_on('r@3.2.2:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-data-table', when='@1.2.0:', type=('build', 'run')) + depends_on('r-data-table', type=('build', 'run'), when='@1.2.0:') diff --git a/var/spack/repos/builtin/packages/r-modelr/package.py b/var/spack/repos/builtin/packages/r-modelr/package.py index 94c6800270..115afc3a46 100644 --- a/var/spack/repos/builtin/packages/r-modelr/package.py +++ b/var/spack/repos/builtin/packages/r-modelr/package.py @@ -7,14 +7,12 @@ from spack import * class RModelr(RPackage): - """Modelling Functions that Work with the Pipe + """Modelling Functions that Work with the Pipe. Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.""" - homepage = "https://github.com/hadley/modelr" - url = "https://cloud.r-project.org/src/contrib/modelr_0.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/modelr" + cran = "modelr" version('0.1.8', sha256='825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4') version('0.1.5', sha256='45bbee387c6ba154f9f8642e9f03ea333cce0863c324ff15d23096f33f85ce5a') @@ -22,15 +20,16 @@ class RModelr(RPackage): version('0.1.3', sha256='e536b247c17d6cacf10565dd8a1b744efc90a8815c70edd54371e413e6d1b423') version('0.1.1', sha256='25b95198d6aa23e28a0bd97dcdc78264ef168ae403928bff01e1ee81ca021ce7') - depends_on('r@3.1:', when='@:0.1.4', type=('build', 'run')) - depends_on('r@3.2:', when='@0.1.5:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@:0.1.4') + depends_on('r@3.2:', type=('build', 'run'), when='@0.1.5:') depends_on('r-broom', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-purrr@0.2.2:', type=('build', 'run')) - depends_on('r-rlang@0.2.0:', when='@0.1.3:', type=('build', 'run')) + depends_on('r-rlang@0.2.0:', type=('build', 'run'), when='@0.1.3:') depends_on('r-tibble', type=('build', 'run')) depends_on('r-tidyr@0.8.0:', type=('build', 'run')) - depends_on('r-tidyselect', when='@0.1.8:', type=('build', 'run')) - depends_on('r-vctrs', when='@0.1.8:', type=('build', 'run')) - depends_on('r-lazyeval@0.2.0:', when='@:0.1.1', type=('build', 'run')) - depends_on('r-dplyr', when='@:0.1.5', type=('build', 'run')) + depends_on('r-tidyselect', type=('build', 'run'), when='@0.1.8:') + depends_on('r-vctrs', type=('build', 'run'), when='@0.1.8:') + + depends_on('r-lazyeval@0.2.0:', type=('build', 'run'), when='@:0.1.1') + depends_on('r-dplyr', type=('build', 'run'), when='@:0.1.5') diff --git a/var/spack/repos/builtin/packages/r-modeltools/package.py b/var/spack/repos/builtin/packages/r-modeltools/package.py index 2f97c645a9..0ddfe0c986 100644 --- a/var/spack/repos/builtin/packages/r-modeltools/package.py +++ b/var/spack/repos/builtin/packages/r-modeltools/package.py @@ -7,7 +7,7 @@ from spack import * class RModeltools(RPackage): - """Tools and Classes for Statistical Models + """Tools and Classes for Statistical Models. A collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future. @@ -16,9 +16,7 @@ class RModeltools(RPackage): interesting we would be very interested in a discussion of this proposal. Contributions are more than welcome!""" - homepage = "https://cloud.r-project.org/package=modeltools" - url = "https://cloud.r-project.org/src/contrib/modeltools_0.2-21.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/modeltools" + cran = "modeltools" version('0.2-23', sha256='6b3e8d5af1a039db5c178498dbf354ed1c5627a8cea9229726644053443210ef') version('0.2-22', sha256='256a088fc80b0d9182f984f9bd3d6207fb7c1e743f72e2ecb480e6c1d4ac34e9') diff --git a/var/spack/repos/builtin/packages/r-mpm/package.py b/var/spack/repos/builtin/packages/r-mpm/package.py index 2d6beeb578..bc45ed08c8 100644 --- a/var/spack/repos/builtin/packages/r-mpm/package.py +++ b/var/spack/repos/builtin/packages/r-mpm/package.py @@ -7,13 +7,13 @@ from spack import * class RMpm(RPackage): - """Exploratory graphical analysis of multivariate data, specifically - gene expression data with different projection methods: principal - component analysis, correspondence analysis, spectral map analysis.""" + """Multivariate Projection Methods. - homepage = "https://cloud.r-project.org/package=mpm" - url = "https://cloud.r-project.org/src/contrib/mpm_1.0-22.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mpm" + Exploratory graphical analysis of multivariate data, specifically gene + expression data with different projection methods: principal component + analysis, correspondence analysis, spectral map analysis.""" + + cran = "mpm" version('1.0-22', sha256='d3ba4053cd57a189cb65c5fa20e6a4152374aead8c985254cb6e550e36e23272') diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index 68eb612376..0a3b440cf8 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -7,18 +7,17 @@ from spack import * class RMultcomp(RPackage): - """Simultaneous Inference in General Parametric Models + """Simultaneous Inference in General Parametric Models. - Simultaneous tests and confidence intervals for general linear - hypotheses in parametric models, including linear, generalized linear, - linear mixed effects, and survival models. The package includes demos - reproducing analyzes presented in the book "Multiple Comparisons Using R" - (Bretz, Hothorn, Westfall, 2010, CRC Press).""" + Simultaneous tests and confidence intervals for general linear hypotheses + in parametric models, including linear, generalized linear, linear mixed + effects, and survival models. The package includes demos reproducing + analyzes presented in the book "Multiple Comparisons Using R" (Bretz, + Hothorn, Westfall, 2010, CRC Press).""" - homepage = "https://multcomp.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/multcomp_1.4-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/multcomp" + cran = "multcomp" + version('1.4-18', sha256='107a5e65cfff158b271d7386240dc8672d8cf45313f016e0ed83767faf7c2806') version('1.4-15', sha256='9927607efb3eb84ac3d25d82daf2faef6a69e05a334b163ce43fd31c14b19bce') version('1.4-10', sha256='29bcc635c0262e304551b139cd9ee655ab25a908d9693e1cacabfc2a936df5cf') version('1.4-8', sha256='a20876619312310e9523d67e9090af501383ce49dc6113c6b4ca30f9c943a73a') diff --git a/var/spack/repos/builtin/packages/r-multicool/package.py b/var/spack/repos/builtin/packages/r-multicool/package.py index ed79d1c413..b62a29b522 100644 --- a/var/spack/repos/builtin/packages/r-multicool/package.py +++ b/var/spack/repos/builtin/packages/r-multicool/package.py @@ -7,7 +7,7 @@ from spack import * class RMulticool(RPackage): - """Permutations of multisets in cool-lex order + """Permutations of multisets in cool-lex order. A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code @@ -25,10 +25,10 @@ class RMulticool(RPackage): <https://jeromekelleher.net/tag/integer-partitions.html>. The C++ code and Python code are distributed without conditions.""" - homepage = "https://cloud.r-project.org/package=multicool" - url = "https://cloud.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/multicool/Archive/multicool" + cran = "multicool" + version('0.1-12', sha256='487d28d9c3c606be0cf56e2d8f8b0d79fb71949c68886ea9251fbb1c01664a36') + version('0.1-11', sha256='1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476') version('0.1-10', sha256='5bb0cb0d9eb64420c862877247a79bb0afadacfe23262ec8c3fa26e5e34d6ff9') version('0.1-9', sha256='bdf92571cef1b649952d155395a92b8683099ee13114f73a9d41fc5d7d49d329') diff --git a/var/spack/repos/builtin/packages/r-multitaper/package.py b/var/spack/repos/builtin/packages/r-multitaper/package.py index 56e4092c79..8654bc8f48 100644 --- a/var/spack/repos/builtin/packages/r-multitaper/package.py +++ b/var/spack/repos/builtin/packages/r-multitaper/package.py @@ -7,7 +7,7 @@ from spack import * class RMultitaper(RPackage): - """Spectral Analysis Tools using the Multitaper Methodi + """Spectral Analysis Tools using the Multitaper Method. Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted @@ -18,9 +18,7 @@ class RMultitaper(RPackage): implementation of the method described in D.J. Thomson (1982) "Spectrum estimation and harmonic analysis" <doi:10.1109/PROC.1982.12433>.""" - homepage = "https://github.com/krahim/multitaper/" - url = "https://cloud.r-project.org/src/contrib/multitaper_1.0-14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/multitaper/" + cran = "multitaper" version('1.0-15', sha256='837d71f3b46fbce2bea210449cf75e609f5363ff23b7808f5f115fdc51e6a3be') version('1.0-14', sha256='c84c122541dc2874131446e23b212259b3b00590d701efee49e6740fd74a8d13') diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index 5ce1e972d9..67cf7a43ee 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -7,15 +7,15 @@ from spack import * class RMunsell(RPackage): - """Provides easy access to, and manipulation of, the Munsell colours. + """Utilities for Using Munsell Colours. + + Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.""" - homepage = "https://cloud.r-project.org/package=munsell" - url = "https://cloud.r-project.org/src/contrib/munsell_0.4.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/munsell" + cran = "munsell" version('0.5.0', sha256='d0f3a9fb30e2b5d411fa61db56d4be5733a2621c0edf017d090bdfa5e377e199') version('0.4.3', sha256='397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49') diff --git a/var/spack/repos/builtin/packages/r-mutoss/package.py b/var/spack/repos/builtin/packages/r-mutoss/package.py index 4b5770da48..b086b39355 100644 --- a/var/spack/repos/builtin/packages/r-mutoss/package.py +++ b/var/spack/repos/builtin/packages/r-mutoss/package.py @@ -7,15 +7,13 @@ from spack import * class RMutoss(RPackage): - """Unified Multiple Testing Procedures + """Unified Multiple Testing Procedures. Designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying 'mutossGUI'.""" - homepage = "https://github.com/kornl/mutoss/" - url = "https://cloud.r-project.org/src/contrib/mutoss_0.1-12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/mutoss" + cran = "mutoss" version('0.1-12', sha256='2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa') diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index 1acff9a5aa..f465912865 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -7,12 +7,11 @@ from spack import * class RMvtnorm(RPackage): - """Multivariate Normal and t Distributions + """Multivariate Normal and t Distributions. Computes multivariate normal and t probabilities, quantiles, random deviates and densities.""" - homepage = "https://mvtnorm.r-forge.r-project.org/" cran = "mvtnorm" version('1.1-3', sha256='ff4e302139ba631280fc9c4a2ab168596bfd09e17a805974199b043697c02448') @@ -22,5 +21,5 @@ class RMvtnorm(RPackage): version('1.0-6', sha256='4a015b57b645b520151b213eb04b7331598c06442a3f652c7dc149425bd2e444') version('1.0-5', sha256='d00f9f758f0d0d4b999f259223485dc55d23cbec09004014816f180045ac81dd') - depends_on('r@1.9.0:', when='@:1.0-8', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.0-9:', type=('build', 'run')) + depends_on('r@1.9.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.0-9:') diff --git a/var/spack/repos/builtin/packages/r-nada/package.py b/var/spack/repos/builtin/packages/r-nada/package.py index 1d1472377f..b3d45a0075 100644 --- a/var/spack/repos/builtin/packages/r-nada/package.py +++ b/var/spack/repos/builtin/packages/r-nada/package.py @@ -7,14 +7,12 @@ from spack import * class RNada(RPackage): - """Nondetects and Data Analysis for Environmental Data + """Nondetects and Data Analysis for Environmental Data. Contains methods described by Dennis Helsel in his book "Nondetects And Data Analysis: Statistics for Censored Environmental Data".""" - homepage = "https://cloud.r-project.org/package=NADA" - url = "https://cloud.r-project.org/src/contrib/NADA_1.6-1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/NADA" + cran = "NADA" version('1.6-1.1', sha256='670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a') diff --git a/var/spack/repos/builtin/packages/r-nanotime/package.py b/var/spack/repos/builtin/packages/r-nanotime/package.py index e9921e0dd8..17542c7ca4 100644 --- a/var/spack/repos/builtin/packages/r-nanotime/package.py +++ b/var/spack/repos/builtin/packages/r-nanotime/package.py @@ -7,16 +7,16 @@ from spack import * class RNanotime(RPackage): - """Nanosecond-Resolution Time Support for R + """Nanosecond-Resolution Time Support for R. - Full 64-bit resolution date and time support with resolution up to - nanosecond granularity is provided, with easy transition to and from the - standard 'POSIXct' type.""" + Full 64-bit resolution date and time functionality with; nanosecond + granularity is provided, with easy transition to and from; the standard + 'POSIXct' type. Three additional classes offer interval,; period and + duration functionality for nanosecond-resolution timestamps.""" - homepage = "https://cloud.r-project.org/package=nanotime" - url = "https://cloud.r-project.org/src/contrib/nanotime_0.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nanotime" + cran = "nanotime" + version('0.3.5', sha256='44deaae58452bacea4855d018212593811401c2afc460ffb11905479013923a0') version('0.3.2', sha256='9ef53c3bca01b605a9519190117988e170e63865327007c90b05d31fe7f22b1d') version('0.2.4', sha256='2dfb7e7435fec59634b87563a215467e7793e2711e302749c0533901c74eb184') version('0.2.3', sha256='7d6df69a4223ae154f610b650e24ece38ce4aa706edfa38bec27d15473229f5d') @@ -24,7 +24,7 @@ class RNanotime(RPackage): depends_on('r-bit64', type=('build', 'run')) depends_on('r-rcppcctz@0.2.3:', type=('build', 'run')) - depends_on('r-rcppcctz@0.2.9:', when='@0.3.2:', type=('build', 'run')) + depends_on('r-rcppcctz@0.2.9:', type=('build', 'run'), when='@0.3.2:') depends_on('r-zoo', type=('build', 'run')) - depends_on('r-rcpp', when='@0.3.2:', type=('build', 'run')) - depends_on('r-rcppdate', when='@0.3.2:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run'), when='@0.3.2:') + depends_on('r-rcppdate', type=('build', 'run'), when='@0.3.2:') diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py index f4e37d5965..20c08dfbda 100644 --- a/var/spack/repos/builtin/packages/r-ncbit/package.py +++ b/var/spack/repos/builtin/packages/r-ncbit/package.py @@ -7,12 +7,12 @@ from spack import * class RNcbit(RPackage): - """Making NCBI taxonomic data locally available and searchable as an R - object.""" + """Retrieve and build NBCI taxonomic data. - homepage = "https://cloud.r-project.org/package=ncbit" - url = "https://cloud.r-project.org/src/contrib/ncbit_2013.03.29.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ncbit" + Making NCBI taxonomic data locally available and searchable as an R + object.""" + + cran = "ncbit" version('2013.03.29', sha256='4480271f14953615c8ddc2e0666866bb1d0964398ba0fab6cc29046436820738') diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index d3940dacf5..9878c5a83a 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -7,7 +7,7 @@ from spack import * class RNcdf4(RPackage): - """Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files + """Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files. Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are @@ -24,10 +24,9 @@ class RNcdf4(RPackage): packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.""" - homepage = "https://cirrus.ucsd.edu/~pierce/ncdf" - url = "https://cloud.r-project.org/src/contrib/ncdf4_1.15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ncdf4" + cran = "ncdf4" + version('1.19', sha256='cb8d139211fc7475c435ce9f6a43e47710603409dc523b053c8b7de9848dfb63') version('1.17', sha256='db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6') version('1.16.1', sha256='0dde2d6d1e8474f4abd15a61af8a2f7de564f13da00f1a01d7a479ab88587a20') version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253') diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py index 2273ecdbcf..26fe6a4610 100644 --- a/var/spack/repos/builtin/packages/r-network/package.py +++ b/var/spack/repos/builtin/packages/r-network/package.py @@ -7,21 +7,21 @@ from spack import * class RNetwork(RPackage): - """Classes for Relational Data + """Classes for Relational Data. Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.""" - homepage = "https://statnet.org" - url = "https://cloud.r-project.org/src/contrib/network_1.13.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/network" + cran = "network" + version('1.17.1', sha256='fc3c3a0014f8895a11c33994c9b44c6ef6cc49c7d026cd41ae6bba5ef63005a7') version('1.16.1', sha256='eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1') version('1.15', sha256='5cbe5c0369e5f8363e33a86f14fd33ce8727166106381627ecd13b7452e14cb3') version('1.14-377', sha256='013c02f8d97f1f87f2c421760534df9353d2a8c2277f20b46b59fb79822d3e46') version('1.13.0', sha256='7a04ea89261cdf32ccb52222810699d5fca59a849053e306b5ec9dd5c1184f87') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r-tibble', when='@1.14-377:', type=('build', 'run')) - depends_on('r-magrittr', when='@1.14-377:', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run'), when='@1.14-377:') + depends_on('r-magrittr', type=('build', 'run'), when='@1.14-377:') + depends_on('r-statnet-common@4.5:', type=('build', 'run'), when='@1.17.1:') diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py index 3cde83c042..84bf6bac8b 100644 --- a/var/spack/repos/builtin/packages/r-networkd3/package.py +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -7,12 +7,12 @@ from spack import * class RNetworkd3(RPackage): - """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs + """D3 JavaScript Network Graphs from R. + + Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.""" - homepage = "https://cloud.r-project.org/package=networkD3" - url = "https://cloud.r-project.org/src/contrib/networkD3_0.2.12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/networkD3" + cran = "networkD3" version('0.4', sha256='33b82585f1eec6233303ec14033a703d0b17def441c7a0a67bf7e6764c9c9d0b') version('0.3', sha256='6f9d6b35bb1562883df734bef8fbec166dd365e34c6e656da7be5f8a8d42343c') diff --git a/var/spack/repos/builtin/packages/r-neuralnet/package.py b/var/spack/repos/builtin/packages/r-neuralnet/package.py index 14ab2629df..bf641106ef 100644 --- a/var/spack/repos/builtin/packages/r-neuralnet/package.py +++ b/var/spack/repos/builtin/packages/r-neuralnet/package.py @@ -7,16 +7,17 @@ from spack import * class RNeuralnet(RPackage): - """Training of neural networks using backpropagation, resilient + """Training of Neural Networks. + + Training of neural networks using backpropagation, resilient backpropagation with (Riedmiller, 1994) or without weight backtracking (Riedmiller and Braun, 1993) or the modified globally convergent version by Anastasiadis et al. (2005). The package allows flexible settings through - custom-choice of error and activation function. Furthermore, the calculation of - generalized weights (Intrator O & Intrator N, 1993) is implemented.""" + custom-choice of error and activation function. Furthermore, the + calculation of generalized weights (Intrator O & Intrator N, 1993) is + implemented.""" - homepage = "https://cloud.r-project.org/package=neuralnet" - url = "https://cloud.r-project.org/src/contrib/neuralnet_1.44.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/neuralnet" + cran = "neuralnet" version('1.44.2', sha256='5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826') diff --git a/var/spack/repos/builtin/packages/r-nfactors/package.py b/var/spack/repos/builtin/packages/r-nfactors/package.py index 7f863879bb..70822c1a95 100644 --- a/var/spack/repos/builtin/packages/r-nfactors/package.py +++ b/var/spack/repos/builtin/packages/r-nfactors/package.py @@ -7,12 +7,20 @@ from spack import * class RNfactors(RPackage): - """nFactors: Parallel Analysis and Other Non Graphical Solutions to the - Cattell Scree Test""" + """Parallel Analysis and Other Non Graphical Solutions to the Cattell Scree + Test. - homepage = "https://cloud.r-project.org/package=nFactors" - url = "https://cloud.r-project.org/src/contrib/nFactors_2.4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nFactors" + Indices, heuristics and strategies to help determine the number of + factors/components to retain: 1. Acceleration factor (af with or without + Parallel Analysis); 2. Optimal Coordinates (noc with or without Parallel + Analysis); 3. Parallel analysis (components, factors and bootstrap); 4. + lambda > mean(lambda) (Kaiser, CFA and related); 5. Cattell-Nelson-Gorsuch + (CNG); 6. Zoski and Jurs multiple regression (b, t and p); 7. Zoski and + Jurs standard error of the regression coeffcient (sescree); 8. Nelson R2; + 9. Bartlett khi-2; 10. Anderson khi-2; 11. Lawley khi-2 and 12. + Bentler-Yuan khi-2.""" + + cran = "nFactors" version('2.4.1', sha256='028eb4ebd42a29f6a01297d728c7e353cabb37b46701639b4a52f17ba25a3eb6') diff --git a/var/spack/repos/builtin/packages/r-nimble/package.py b/var/spack/repos/builtin/packages/r-nimble/package.py index 47c2cccf6c..0b39896db2 100644 --- a/var/spack/repos/builtin/packages/r-nimble/package.py +++ b/var/spack/repos/builtin/packages/r-nimble/package.py @@ -7,7 +7,7 @@ from spack import * class RNimble(RPackage): - """MCMC, Particle Filtering, and Programmable Hierarchical Modeling + """MCMC, Particle Filtering, and Programmable Hierarchical Modeling. A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do @@ -24,10 +24,9 @@ class RNimble(RPackage): 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.""" - homepage = "https://cloud.r-project.org/package=nimble" - url = "https://cloud.r-project.org/src/contrib/nimble_0.9.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nimble" + cran = "nimble" + version('0.12.1', sha256='3520f3212a48c8cbe08a6a8e57b3a72180594f7c09f647d1daf417c9857867d8') version('0.10.1', sha256='11e248fda442f233c3590640efd9381c9b4b2e6fb66dce45a3391db03b70e702') version('0.9.1', sha256='ad5e8a171193cb0172e68bf61c4f94432c45c131a150101ad1c5c7318c335757') version('0.9.0', sha256='ebc28fadf933143eea73900cacaf96ff81cb3c2d607405016062b7e93afa5611') diff --git a/var/spack/repos/builtin/packages/r-nleqslv/package.py b/var/spack/repos/builtin/packages/r-nleqslv/package.py index c030bbb4fa..84ab38c6e4 100644 --- a/var/spack/repos/builtin/packages/r-nleqslv/package.py +++ b/var/spack/repos/builtin/packages/r-nleqslv/package.py @@ -7,10 +7,14 @@ from spack import * class RNleqslv(RPackage): - """nleqslv: Solve Systems of Nonlinear Equations""" + """Solve Systems of Nonlinear Equations. - homepage = "https://cloud.r-project.org/package=nleqslv" - url = "https://cloud.r-project.org/src/contrib/nleqslv_3.3.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nleqslv" + Solve a system of nonlinear equations using a Broyden or a Newton method + with a choice of global strategies such as line search and trust region. + There are options for using a numerical or user supplied Jacobian, for + specifying a banded numerical Jacobian and for allowing a singular or + ill-conditioned Jacobian.""" + + cran = "nleqslv" version('3.3.2', sha256='f54956cf67f9970bb3c6803684c84a27ac78165055745e444efc45cfecb63fed') diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index 201deb43de..decd172005 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -7,13 +7,13 @@ from spack import * class RNlme(RPackage): - """Fit and compare Gaussian linear and nonlinear mixed-effects models + """Linear and Nonlinear Mixed Effects Models. Fit and compare Gaussian linear and nonlinear mixed-effects models.""" - homepage = "https://cloud.r-project.org/package=nlme" cran = "nlme" + version('3.1-155', sha256='9f390f842852422921b5845130ea73c1f006d7bb5e988e82f728093a0cbdff4f') version('3.1-153', sha256='3d27a98edf1b16ee868949e823ac0babbf10c937a7220d648b7ef9480cd680e3') version('3.1-152', sha256='5b65d1b1f121caf29e60341acf6d85e267fd94ed517748cf42d36359f74e515e') version('3.1-151', sha256='a2c626bad68bf582663005170d1b9d844a10dca8efb13597f15ffb4b1fe886ca') @@ -22,8 +22,8 @@ class RNlme(RPackage): version('3.1-131', sha256='79daa167eb9bc7d8dba506da4b24b5250665b051d4e0a51dfccbb0087fdb564c') version('3.1-130', sha256='ec576bd906ef2e1c79b6a4382743d425846f63be2a43de1cce6aa397b40e290e') - depends_on('r@3.0.2:', when='@:3.1-131', type=('build', 'run')) - depends_on('r@3.3.0:', when='@3.1-131.1', type=('build', 'run')) - depends_on('r@3.4.0:', when='@3.1-135.5:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@3.1-134:3.1-135', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@3.1-131.1') + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.1-134:3.1-135') + depends_on('r@3.4.0:', type=('build', 'run'), when='@3.1-135.5:') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py index 0082dee121..4ee5d7484b 100644 --- a/var/spack/repos/builtin/packages/r-nloptr/package.py +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -7,27 +7,31 @@ from spack import * class RNloptr(RPackage): - """R Interface to NLopt + """R Interface to NLopt. Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See - <http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction> for more - information on the available algorithms. During installation of nloptr on - Unix-based systems, the installer checks whether the NLopt library is - installed on the system. If the NLopt library cannot be found, the code is - compiled using the NLopt source included in the nloptr package.""" - - homepage = "https://cloud.r-project.org/package=nloptr" - url = "https://cloud.r-project.org/src/contrib/nloptr_1.0.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nloptr" - + <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more + information on the available algorithms. Building from included sources + requires 'CMake'. On Linux and 'macOS', if a suitable system build of + NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from + included sources via 'CMake'. On Windows, NLopt is obtained through + 'rwinlib' for 'R <= 4.1.x' or grabbed from the 'Rtools42 toolchain' for 'R + >= 4.2.0'.""" + + cran = "nloptr" + + version('2.0.0', sha256='65ca3149cfc9ba15ac10a91f34b5d86b20f5fd693f44e3edf3e392402911619a') + version('1.2.2.3', sha256='af08b74fd5e7b4cb455fe67ed759346cbb8f3b9a4178f5f117e0092e5c9af6ff') version('1.2.2.2', sha256='e80ea9619ac18f4bfe44812198b40b9ae5c0ddf3f9cc91778f9ccc82168d1372') version('1.2.1', sha256='1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97') version('1.0.4', sha256='84225b993cb1ef7854edda9629858662cc8592b0d1344baadea4177486ece1eb') + depends_on('r-testthat', when='@2.0.0:') depends_on('nlopt@2.4.0:') + depends_on('nlopt@2.7.0:', when='@2.0.0:') def configure_args(self): include_flags = self.spec['nlopt'].headers.include_flags diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index 4faac3cbfb..d7c974d79b 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -7,7 +7,7 @@ from spack import * class RNmf(RPackage): - """Algorithms and Framework for Nonnegative Matrix Factorization (NMF) + """Algorithms and Framework for Nonnegative Matrix Factorization (NMF). Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding @@ -16,9 +16,7 @@ class RNmf(RPackage): the main interface function provides an easy way of performing parallel computations on multicore machines.""" - homepage = "https://renozao.github.io/NMF" - url = "https://cloud.r-project.org/src/contrib/NMF_0.21.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" + cran = "NMF" version('0.23.0', sha256='0f0cca01b37bf46fce90d2e951df609d3d377908aa607825083fd0c47cc24753') version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') @@ -37,5 +35,5 @@ class RNmf(RPackage): depends_on('r-doparallel', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-biocmanager', when='@0.23.0', type=('build', 'run')) - depends_on('r-biobase', when='@0.23.0', type=('build', 'run')) + depends_on('r-biocmanager', type=('build', 'run'), when='@0.23.0:') + depends_on('r-biobase', type=('build', 'run'), when='@0.23.0:') diff --git a/var/spack/repos/builtin/packages/r-nmof/package.py b/var/spack/repos/builtin/packages/r-nmof/package.py index 07393733dc..2440ea5d6d 100644 --- a/var/spack/repos/builtin/packages/r-nmof/package.py +++ b/var/spack/repos/builtin/packages/r-nmof/package.py @@ -7,7 +7,7 @@ from spack import * class RNmof(RPackage): - """Numerical Methods and Optimization in Finance + """Numerical Methods and Optimization in Finance. Functions, examples and data from the book "Numerical Methods and Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2011), @@ -17,10 +17,9 @@ class RNmof(RPackage): financial instruments, such as bonds and options, and functions that help with stochastic simulations.""" - homepage = "http://nmof.net/" - url = "https://cloud.r-project.org/src/contrib/NMOF_1.6-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/NMOF" + cran = "NMOF" + version('2.5-0', sha256='f44914c86d86c62f74cbc026179a694f0b3c2e3341b076acaf5de01de194a3c7') version('2.2-2', sha256='e64472f89023f0d779a35df753747d750174ce89644a9142312a1d2dc6f24642') version('1.6-0', sha256='5484cd43c28aaf23d560c2dde8bcd8dd440a205d2214eb50e02fe0bb42ec2755') diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py index e2f478eb1f..2a9474abbd 100644 --- a/var/spack/repos/builtin/packages/r-nnet/package.py +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -7,17 +7,16 @@ from spack import * class RNnet(RPackage): - """Feed-Forward Neural Networks and Multinomial Log-Linear Models + """Feed-Forward Neural Networks and Multinomial Log-Linear Models. - Software for feed-forward neural networks with a single hidden layer, - and for multinomial log-linear models.""" + Software for feed-forward neural networks with a single hidden layer, and + for multinomial log-linear models.""" - homepage = "https://www.stats.ox.ac.uk/pub/MASS4/" - url = "https://cloud.r-project.org/src/contrib/nnet_7.3-12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nnet" + cran = "nnet" + version('7.3-17', sha256='ee750bb8164aa058edf93823af987ab2c7ec64128dce2abeaae1b7d3661e9a67') version('7.3-14', sha256='5d1b9e9764d74d16c651f18f949aa4e9e2995ba64633cbfa2c6a7355ae30f4af') version('7.3-12', sha256='2723523e8581cc0e2215435ac773033577a16087a3f41d111757dd96b8c5559d') depends_on('r@2.14:', type=('build', 'run')) - depends_on('r@3.0.0:', when='@7.3-14:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run'), when='@7.3-14:') diff --git a/var/spack/repos/builtin/packages/r-nnls/package.py b/var/spack/repos/builtin/packages/r-nnls/package.py index 1515c83a74..dcb5ec5724 100644 --- a/var/spack/repos/builtin/packages/r-nnls/package.py +++ b/var/spack/repos/builtin/packages/r-nnls/package.py @@ -7,12 +7,12 @@ from spack import * class RNnls(RPackage): - """An R interface to the Lawson-Hanson implementation of an - algorithm for non-negative least squares (NNLS). Also allows - the combination of non-negative and non-positive constraints.""" + """The Lawson-Hanson algorithm for non-negative least squares (NNLS). - homepage = "https://cloud.r-project.org/package=nnls" - url = "https://cloud.r-project.org/src/contrib/nnls_1.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nnls" + An R interface to the Lawson-Hanson implementation of an algorithm for + non-negative least squares (NNLS). Also allows the combination of + non-negative and non-positive constraints.""" + + cran = "nnls" version('1.4', sha256='0e5d77abae12bc50639d34354f96a8e079408c9d7138a360743b73bd7bce6c1f') diff --git a/var/spack/repos/builtin/packages/r-nonnest2/package.py b/var/spack/repos/builtin/packages/r-nonnest2/package.py index 9b19943530..cb00e3b05d 100644 --- a/var/spack/repos/builtin/packages/r-nonnest2/package.py +++ b/var/spack/repos/builtin/packages/r-nonnest2/package.py @@ -7,7 +7,7 @@ from spack import * class RNonnest2(RPackage): - """Tests of Non-Nested Models: + """Tests of Non-Nested Models. Testing non-nested models via theory supplied by Vuong (1989) <doi:10.2307/1912557>. Includes tests of model distinguishability and of @@ -16,7 +16,7 @@ class RNonnest2(RPackage): and BIC. This material is partially based on work supported by the National Science Foundation under Grant Number SES-1061334.""" - cran = "nonnest2" + cran = "nonnest2" version('0.5-5', sha256='027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5') diff --git a/var/spack/repos/builtin/packages/r-nor1mix/package.py b/var/spack/repos/builtin/packages/r-nor1mix/package.py index 7884bad337..9c1c660ce2 100644 --- a/var/spack/repos/builtin/packages/r-nor1mix/package.py +++ b/var/spack/repos/builtin/packages/r-nor1mix/package.py @@ -7,15 +7,15 @@ from spack import * class RNor1mix(RPackage): - """Onedimensional Normal Mixture Models Classes, for, e.g., density - estimation or clustering algorithms research and teaching; providing - the widely used Marron-Wand densities. Efficient random number - generation and graphics; now fitting to data by ML (Maximum Likelihood) - or EM estimation.""" + """Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods). - homepage = "https://cloud.r-project.org/package=nor1mix" - url = "https://cloud.r-project.org/src/contrib/nor1mix_1.2-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nor1mix" + One dimensional Normal Mixture Models Classes, for, e.g., density + estimation or clustering algorithms research and teaching; providing the + widely used Marron-Wand densities. Efficient random number generation and + graphics; now fitting to data by ML (Maximum Likelihood) or EM + estimation.""" + + cran = "nor1mix" version('1.3-0', sha256='9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0') version('1.2-3', sha256='435e6519e832ef5229c51ccb2619640e6b50dfc7470f70f0c938d18a114273af') diff --git a/var/spack/repos/builtin/packages/r-nortest/package.py b/var/spack/repos/builtin/packages/r-nortest/package.py index 1bbcb05ec0..17e4f241d6 100644 --- a/var/spack/repos/builtin/packages/r-nortest/package.py +++ b/var/spack/repos/builtin/packages/r-nortest/package.py @@ -7,12 +7,10 @@ from spack import * class RNortest(RPackage): - """nortest: Tests for Normality + """Tests for Normality. - Five omnibus tests for testing the composite hypothesis of normality.""" + Five omnibus tests for testing the composite hypothesis of normality.""" - homepage = "https://cloud.r-project.org/package=nortest" - url = "https://cloud.r-project.org/src/contrib/nortest_1.0-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/nortest" + cran = "nortest" version('1.0-4', sha256='a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f') diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py index 8657dc5e22..7fe571d526 100644 --- a/var/spack/repos/builtin/packages/r-np/package.py +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -7,7 +7,7 @@ from spack import * class RNp(RPackage): - """Nonparametric Kernel Smoothing Methods for Mixed Data Types + """Nonparametric Kernel Smoothing Methods for Mixed Data Types. This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and @@ -17,10 +17,9 @@ class RNp(RPackage): of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).""" - homepage = "https://github.com/JeffreyRacine/R-Package-np/" - url = "https://cloud.r-project.org/src/contrib/np_0.60-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/np" + cran = "np" + version('0.60-11', sha256='a3b31b8ad70c42826076786b2b1b63b79cdbadfa55fe126773bc357686fd33a9') version('0.60-10', sha256='a27b4bbca8b83a289c98920c1c8f5e9979ba9772086893252a4297dd2698081a') version('0.60-9', sha256='fe31a8985f0b1a576a7775022b7131093b1c9a8337734136d5fcad85fa6592fc') version('0.60-8', sha256='924c342feb2a862fa3871a45db5f8434dbbfb900cfc40c001a0872108a3a069e') @@ -28,5 +27,5 @@ class RNp(RPackage): depends_on('r-boot', type=('build', 'run')) depends_on('r-cubature', type=('build', 'run')) - depends_on('r-quadprog', when='@0.60-8:', type=('build', 'run')) - depends_on('r-quantreg', when='@0.60-8:', type=('build', 'run')) + depends_on('r-quadprog', type=('build', 'run'), when='@0.60-8:') + depends_on('r-quantreg', type=('build', 'run'), when='@0.60-8:') diff --git a/var/spack/repos/builtin/packages/r-npsurv/package.py b/var/spack/repos/builtin/packages/r-npsurv/package.py index 0a02ce03d0..8d9d60e7c1 100644 --- a/var/spack/repos/builtin/packages/r-npsurv/package.py +++ b/var/spack/repos/builtin/packages/r-npsurv/package.py @@ -7,7 +7,7 @@ from spack import * class RNpsurv(RPackage): - """Nonparametric Survival Analysis + """Nonparametric Survival Analysis. Non-parametric survival analysis of exact and interval-censored observations. The methods implemented are developed by Wang (2007) @@ -16,9 +16,7 @@ class RNpsurv(RPackage): <doi:10.1007/s11222-012-9341-9> and Wang and Fani (2018) <doi:10.1007/s11222-017-9724-z>.""" - homepage = "https://www.stat.auckland.ac.nz/~yongwang" - url = "https://cloud.r-project.org/src/contrib/npsurv_0.4-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/npsurv" + cran = "npsurv" version('0.5-0', sha256='bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6') version('0.4-0', sha256='404cf7135dc40a04e9b81224a543307057a8278e11109ba1fcaa28e87c6204f3') diff --git a/var/spack/repos/builtin/packages/r-numderiv/package.py b/var/spack/repos/builtin/packages/r-numderiv/package.py index dee2be43c5..844969e018 100644 --- a/var/spack/repos/builtin/packages/r-numderiv/package.py +++ b/var/spack/repos/builtin/packages/r-numderiv/package.py @@ -7,12 +7,17 @@ from spack import * class RNumderiv(RPackage): - """Methods for calculating (usually) accurate numerical first and - second order derivatives.""" + """Accurate Numerical Derivatives. - homepage = "https://cloud.r-project.org/package=numDeriv" - url = "https://cloud.r-project.org/src/contrib/numDeriv_2016.8-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/numDeriv" + Methods for calculating (usually) accurate numerical first and second order + derivatives. Accurate calculations are done using 'Richardson"s' + extrapolation or, when applicable, a complex step derivative is available. + A simple difference method is also provided. Simple difference is (usually) + less accurate but is much quicker than 'Richardson"s' extrapolation and + provides a useful cross-check. Methods are provided for real scalar and + vector valued functions.""" + + cran = "numDeriv" version('2016.8-1.1', sha256='d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345') version('2016.8-1', sha256='1b681d273697dc780a3ac5bedabb4a257785732d9ca4ef68e4e4aac8b328d11e') diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index ec375e68f6..2c2e9abcc6 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -7,12 +7,12 @@ from spack import * class ROpenssl(RPackage): - """Toolkit for Encryption, Signatures and Certificates Based on OpenSSL + """Toolkit for Encryption, Signatures and Certificates Based on OpenSSL. - Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey - parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. - Cryptographic signatures can either be created and verified manually or via - x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric + Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. + Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic + signatures can either be created and verified manually or via x509 + certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash @@ -20,9 +20,9 @@ class ROpenssl(RPackage): generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.""" - homepage = "https://cloud.r-project.org/package=openssl" cran = "openssl" + version('1.4.6', sha256='43b832af70e71770168b997107c52c8f406f8c33e9ef9b289610bccea2f34359') version('1.4.5', sha256='4fc141aba8e94e9f5ecce6eda07e45a5e7048d8609ba909ede4f7f4933e0c1f7') version('1.4.3', sha256='342001df8ecff5df2cdf757f123d35ea4b449751045f708b91f27c1be0d48269') version('1.4.1', sha256='f7fbecc75254fc43297a95a4338c674ab9ba2ec056b59e027d16d23122161fc6') @@ -31,7 +31,7 @@ class ROpenssl(RPackage): version('0.9.6', sha256='6dd6d1cade4004962d516ad761fff0812beec0232318b385d286761423a5dc39') version('0.9.4', sha256='cb7349defa5428acc0907629a4f53f82d2519af219e5d6a41f852cf55b1feb66') - depends_on('r-askpass', when='@1.2:', type=('build', 'run')) + depends_on('r-askpass', type=('build', 'run'), when='@1.2:') depends_on('openssl@1.0.1:') def flag_handler(self, name, flags): diff --git a/var/spack/repos/builtin/packages/r-openxlsx/package.py b/var/spack/repos/builtin/packages/r-openxlsx/package.py index 8cafb9381b..30fb8dd701 100644 --- a/var/spack/repos/builtin/packages/r-openxlsx/package.py +++ b/var/spack/repos/builtin/packages/r-openxlsx/package.py @@ -7,21 +7,20 @@ from spack import * class ROpenxlsx(RPackage): - """Read, Write and Edit xlsx Files + """Read, Write and Edit xlsx Files. Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.""" - homepage = "https://github.com/awalker89/openxlsx" - url = "https://cloud.r-project.org/src/contrib/openxlsx_4.1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/openxlsx" + cran = "openxlsx" + version('4.2.5', sha256='65d06d2819b656ac30fc78437ee712a83fb5a7ab750f56268e5c9e578c582519') version('4.2.3', sha256='cdef89d826e50bef772af3e5eae935ca0316626a6e22f55f7631eac733b5e46f') version('4.1.0.1', sha256='8b7011debe14714de035ef42797c8caa923162d5dc3cc3c2a299fc10eff3d4d1') depends_on('r@3.3.0:', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-stringi', type=('build', 'run'), when='@4.2.3:') depends_on('r-zip', type=('build', 'run')) - depends_on('r-stringi', when='@4.2.3:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-optimx/package.py b/var/spack/repos/builtin/packages/r-optimx/package.py index e32576d55e..f020b19fd0 100644 --- a/var/spack/repos/builtin/packages/r-optimx/package.py +++ b/var/spack/repos/builtin/packages/r-optimx/package.py @@ -7,7 +7,7 @@ from spack import * class ROptimx(RPackage): - """Expanded Replacement and Extension of the 'optim' Function: + """Expanded Replacement and Extension of the 'optim' Function. Provides a replacement and extension of the optim() function to call to several function minimization codes in R in a single statement. These @@ -18,8 +18,9 @@ class ROptimx(RPackage): Many methods previously separate are now included here. This is the version for CRAN.""" - cran = "optimx" + cran = "optimx" + version('2021-10.12', sha256='39384c856b5efa3992cd230548b60eff936d428111ad6ad5b8fb98a3bcbb7943') version('2020-4.2', sha256='6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101') depends_on('r-numderiv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-optparse/package.py b/var/spack/repos/builtin/packages/r-optparse/package.py index 474917925a..2ecc532a3d 100644 --- a/var/spack/repos/builtin/packages/r-optparse/package.py +++ b/var/spack/repos/builtin/packages/r-optparse/package.py @@ -7,16 +7,15 @@ from spack import * class ROptparse(RPackage): - """Command Line Option Parser + """Command Line Option Parser. A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options""" - homepage = "https://cloud.r-project.org/package=optparse" - url = "https://cloud.r-project.org/src/contrib/optparse_1.6.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/optparse" + cran = "optparse" + version('1.7.1', sha256='324e304c13efd565d766766193d4ccd75e2cd949dfcfb416afc3939489071fe7') version('1.6.6', sha256='51779d497146e9354b1153713d939e81551e08948c2b00e4b117b1377c0b60d0') version('1.6.2', sha256='b5a5a49ae05005f20359868329b73daac83d50f5e088981dcf5c41399534377f') version('1.6.1', sha256='819be3eff54cb7f3f18703eed9714fc655290ab8e169f87605433d069b597e13') diff --git a/var/spack/repos/builtin/packages/r-ordinal/package.py b/var/spack/repos/builtin/packages/r-ordinal/package.py index 70f4c2993a..d083c234c7 100644 --- a/var/spack/repos/builtin/packages/r-ordinal/package.py +++ b/var/spack/repos/builtin/packages/r-ordinal/package.py @@ -7,7 +7,7 @@ from spack import * class ROrdinal(RPackage): - """Regression Models for Ordinal Data + """Regression Models for Ordinal Data. Implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models @@ -21,9 +21,7 @@ class ROrdinal(RPackage): addition to profile methods and slice methods for visualizing the likelihood function and checking convergence.""" - homepage = "https://github.com/runehaubo/ordinal" - url = "https://cloud.r-project.org/src/contrib/ordinal_2019.4-25.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ordinal" + cran = "ordinal" version('2019.12-10', sha256='7a41e7b7e852a8fa3e911f8859d36e5709ccec5ca42ee3de14a813b7aaac7725') version('2019.4-25', sha256='2812ad7a123cae5dbe053d1fe5f2d9935afc799314077eac185c844e3c9d79df') diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py index 65d81d04f9..14341f182a 100644 --- a/var/spack/repos/builtin/packages/r-packrat/package.py +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -7,10 +7,12 @@ from spack import * class RPackrat(RPackage): - """Manage the R packages your project depends on in an isolated, portable, - and reproducible way.""" + """A Dependency Management System for Projects and their R Package + Dependencies. + + Manage the R packages your project depends on in an isolated, portable, and + reproducible way.""" - homepage = "https://github.com/rstudio/packrat/" cran = "packrat" version('0.7.0', sha256='e8bce1fd78f28f3a7bf56e65a2ae2c6802e69bf55466c24e1d1a4b8a5f83dcc2') diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py index 20419aa15e..4b35b19433 100644 --- a/var/spack/repos/builtin/packages/r-pacman/package.py +++ b/var/spack/repos/builtin/packages/r-pacman/package.py @@ -7,20 +7,21 @@ from spack import * class RPacman(RPackage): - """Tools to more conveniently perform tasks associated with add-on + """Package Management Tool. + + Tools to more conveniently perform tasks associated with add-on packages. pacman conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.""" - homepage = "https://cloud.r-project.org/package=pacman" - url = "https://cloud.r-project.org/src/contrib/pacman_0.4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pacman" + cran = "pacman" version('0.5.1', sha256='9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c') version('0.5.0', sha256='61294757212ab0aa0153219d7d031f58be6f30ead88d84859001d58caa76603d') version('0.4.1', sha256='fffa72307912cbd5aa5bee0a9b65931500483036ccffb1791dd808eb5eb70362') depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.5.0:', type=('build', 'run')) - depends_on('r-devtools', when='@:0.4.6', type=('build', 'run')) - depends_on('r-remotes', when='@0.5.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.5.0:') + depends_on('r-remotes', type=('build', 'run'), when='@0.5.0:') + + depends_on('r-devtools', type=('build', 'run'), when='@:0.4.6') diff --git a/var/spack/repos/builtin/packages/r-paleotree/package.py b/var/spack/repos/builtin/packages/r-paleotree/package.py index 96fcb07503..54e61b5fbc 100644 --- a/var/spack/repos/builtin/packages/r-paleotree/package.py +++ b/var/spack/repos/builtin/packages/r-paleotree/package.py @@ -8,14 +8,12 @@ from spack import * class RPaleotree(RPackage): - """Paleontological and Phylogenetic Analyses of Evolution + """Paleontological and Phylogenetic Analyses of Evolution. Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages""" - homepage = "https://github.com/dwbapst/paleotree" - url = "https://cloud.r-project.org/src/contrib/paleotree_3.1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/paleotree" + cran = "paleotree" version('3.3.25', sha256='aa64b9120075581229439227a12db776d052b03eb5f9721692a16a9402ac8712') version('3.3.0', sha256='f8f6b0228dd5290b251cad3a8626689442b5aa793d8f072c8c2c7813a063df90') @@ -25,6 +23,6 @@ class RPaleotree(RPackage): depends_on('r-ape@4.1:', type=('build', 'run')) depends_on('r-phangorn@2.0.0:', type=('build', 'run')) depends_on('r-phytools@0.6-00:', type=('build', 'run')) - depends_on('r-jsonlite', when='@3.3.0:', type=('build', 'run')) - depends_on('r-png', when='@3.3.0:', type=('build', 'run')) - depends_on('r-rcurl', when='@3.3.0:', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run'), when='@3.3.0:') + depends_on('r-png', type=('build', 'run'), when='@3.3.0:') + depends_on('r-rcurl', type=('build', 'run'), when='@3.3.0:') diff --git a/var/spack/repos/builtin/packages/r-pamr/package.py b/var/spack/repos/builtin/packages/r-pamr/package.py index 189b63bf64..530f024966 100644 --- a/var/spack/repos/builtin/packages/r-pamr/package.py +++ b/var/spack/repos/builtin/packages/r-pamr/package.py @@ -7,11 +7,11 @@ from spack import * class RPamr(RPackage): - """Some functions for sample classification in microarrays.""" + """Pam: Prediction Analysis for Microarrays - homepage = "https://cloud.r-project.org/package=pamr" - url = "https://cloud.r-project.org/src/contrib/pamr_1.55.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pamr" + Some functions for sample classification in microarrays.""" + + cran = "pamr" version('1.56.1', sha256='d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779') version('1.55', sha256='ed910194937a6097ec79234d84777856fd520b111a7c79f7c86dc607169cc3c3') diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py index 2bd38ff8ed..15f3a58b5f 100644 --- a/var/spack/repos/builtin/packages/r-pan/package.py +++ b/var/spack/repos/builtin/packages/r-pan/package.py @@ -7,11 +7,16 @@ from spack import * class RPan(RPackage): - """Multiple imputation for multivariate panel or clustered data.""" + """Multiple imputation for multivariate panel or clustered data. - homepage = "https://cloud.r-project.org/package=pan" - url = "https://cloud.r-project.org/src/contrib/pan_1.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pan" + It provides functions and examples for maximum likelihood estimation for + generalized linear mixed models and Gibbs sampler for multivariate linear + mixed models with incomplete data, as described in Schafer JL (1997) + "Imputation of missing covariates under a multivariate linear mixed model". + Technical report 97-04, Dept. of Statistics, The Pennsylvania State + University.""" + + cran = "pan" version('1.6', sha256='adc0df816ae38bc188bce0aef3aeb71d19c0fc26e063107eeee71a81a49463b6') version('1.4', sha256='e6a83f0799cc9714f5052f159be6e82ececd013d1626f40c828cda0ceb8b76dc') diff --git a/var/spack/repos/builtin/packages/r-parallelly/package.py b/var/spack/repos/builtin/packages/r-parallelly/package.py index c9cba212be..68bf7eef7e 100644 --- a/var/spack/repos/builtin/packages/r-parallelly/package.py +++ b/var/spack/repos/builtin/packages/r-parallelly/package.py @@ -7,7 +7,7 @@ from spack import * class RParallelly(RPackage): - """Enhancing the 'parallel' Package + """Enhancing the 'parallel' Package. Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, @@ -20,8 +20,8 @@ class RParallelly(RPackage): job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.""" - homepage = "https://github.com/HenrikBengtsson/parallelly" cran = "parallelly" + version('1.30.0', sha256='aab080cb709bab232b2d808053efb2391eeb30a2de9497cbe474c99df89f9f3b') version('1.28.1', sha256='f4ae883b18409adb83c561ed69427e740e1b50bf85ef57f48c3f2edf837cc663') version('1.23.0', sha256='376ce2381587380a4da60f9563710d63084a605f93aa364e9349f2523e83bc08') diff --git a/var/spack/repos/builtin/packages/r-parallelmap/package.py b/var/spack/repos/builtin/packages/r-parallelmap/package.py index e35576305e..ae08766914 100644 --- a/var/spack/repos/builtin/packages/r-parallelmap/package.py +++ b/var/spack/repos/builtin/packages/r-parallelmap/package.py @@ -7,7 +7,7 @@ from spack import * class RParallelmap(RPackage): - """Unified Interface to Parallelization Back-Ends + """Unified Interface to Parallelization Back-Ends. Unified parallelization framework for multiple back-end, designed for internal package and interactive usage. The main operation is a parallel @@ -16,10 +16,9 @@ class RParallelmap(RPackage): later selected by the user to switch on parallel execution for exactly this operation.""" - homepage = "https://github.com/berndbischl/parallelMap" - url = "https://cloud.r-project.org/src/contrib/parallelMap_1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/parallelMap" + cran = "parallelMap" + version('1.5.1', sha256='c108a634a335ed47b0018f532a52b032487e239c5061f939ba32355dfefde7e1') version('1.5.0', sha256='4afa727f4786279718cc799e45e91859a46f5cbc1ee652b0f47ae3b9f9d45e4e') version('1.4', sha256='fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b') version('1.3', sha256='a52d93572c1b85281e41d8e3c2db97dda5fce96c222e04171b4489ec5000cd08') diff --git a/var/spack/repos/builtin/packages/r-paramhelpers/package.py b/var/spack/repos/builtin/packages/r-paramhelpers/package.py index 5d4d6fd179..4f329fb305 100644 --- a/var/spack/repos/builtin/packages/r-paramhelpers/package.py +++ b/var/spack/repos/builtin/packages/r-paramhelpers/package.py @@ -7,7 +7,8 @@ from spack import * class RParamhelpers(RPackage): - """Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning + """Helpers for Parameters in Black-Box Optimization, Tuning and Machine + Learning. Functions for parameter descriptions and operations in black-box optimization, tuning and machine learning. Parameters can be described @@ -15,16 +16,14 @@ class RParamhelpers(RPackage): general be programmed on. A useful OptPath object (archive) to log function evaluations is also provided.""" - homepage = "https://github.com/berndbischl/ParamHelpers" - url = "https://cloud.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ParamHelpers" + cran = "ParamHelpers" version('1.14', sha256='b17652d0a69de3241a69f20be4ad1bfe02c413328a17f3c1ac7b73886a6ba2eb') version('1.12', sha256='b54db9e6608ba530345c380c757a60cb2b78ab08992a890b1a41914ce7abcc14') version('1.11', sha256='1614f4c0842cf822befc01228ab7263417f3423dd6a1dc24347b14f8491637a0') version('1.10', sha256='80629ba62e93b0b706bf2e451578b94fbb9c5b95ff109ecfb5b011bfe0a0fa5b') - depends_on('r-backports', when='@1.11:', type=('build', 'run')) + depends_on('r-backports', type=('build', 'run'), when='@1.11:') depends_on('r-bbmisc@1.10:', type=('build', 'run')) depends_on('r-checkmate@1.8.2:', type=('build', 'run')) - depends_on('r-fastmatch', when='@1.11:', type=('build', 'run')) + depends_on('r-fastmatch', type=('build', 'run'), when='@1.11:') diff --git a/var/spack/repos/builtin/packages/r-party/package.py b/var/spack/repos/builtin/packages/r-party/package.py index 5fd479dc0c..3b09830939 100644 --- a/var/spack/repos/builtin/packages/r-party/package.py +++ b/var/spack/repos/builtin/packages/r-party/package.py @@ -7,7 +7,7 @@ from spack import * class RParty(RPackage): - """A Laboratory for Recursive Partytioning + """A Laboratory for Recursive Partytioning. A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed @@ -26,17 +26,16 @@ class RParty(RPackage): <doi:10.1198/106186008X319331> and Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.""" - homepage = "https://cloud.r-project.org/package=party" - url = "https://cloud.r-project.org/src/contrib/party_1.1-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/party" + cran = "party" + version('1.3-9', sha256='29a1fefdb86369285ebf5d48ab51268a83e2011fb9d9f609a2250b5f0b169089') version('1.3-5', sha256='1c3a35d3fe56498361542b3782de2326561c14a8fa1b76f3c9f13beb1fd51364') version('1.3-3', sha256='9f72eea02d43a4cee105790ae7185b0478deb6011ab049cc9d31a0df3abf7ce9') version('1.3-2', sha256='9f350fa21114151c49bccc3d5f8536dbc5a608cfd88f60461c9805a4c630510b') version('1.1-2', sha256='c3632b4b02dc12ec949e2ee5b24004e4a4768b0bc9737432e9a85acbc2ed0e74') - depends_on('r@2.14.0:', when='@:1.2-2', type=('build', 'run')) - depends_on('r@3.0.0:', when='@1.2-3:', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run'), when='@1.2-3:') depends_on('r-mvtnorm@1.0-2:', type=('build', 'run')) depends_on('r-modeltools@0.2-21:', type=('build', 'run')) depends_on('r-strucchange', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py index f9bd323880..3d9c8d0e8c 100644 --- a/var/spack/repos/builtin/packages/r-partykit/package.py +++ b/var/spack/repos/builtin/packages/r-partykit/package.py @@ -8,7 +8,7 @@ from spack import * class RPartykit(RPackage): - """A Toolkit for Recursive Partytioning + """A Toolkit for Recursive Partytioning. A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This @@ -21,20 +21,19 @@ class RPartykit(RPackage): published by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.""" - homepage = "https://partykit.r-forge.r-project.org/partykit" - url = "https://cloud.r-project.org/src/contrib/partykit_1.1-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/partykit" + cran = "partykit" + version('1.2-15', sha256='b2e9454b2f4b9a39c9581c5871462f00acef4eeee5696ce3e32cfa1468d1e3ac') version('1.2-11', sha256='3a83332d782a235cfb5ba60cc8f1c51d46ca5477b22979a614f514d1c951c602') version('1.2-5', sha256='f48e30790f93fa5d03e68e8ce71ce33d009d107d46d45d85da2016b38b27629c') version('1.2-3', sha256='56749b246e283f94ac2ad2cdcfc0a477e05cd44b5e8f6e462c26f4dff818da35') version('1.1-1', sha256='d9f4762690cd85ee4e3dc44f5a14069d10a1900afdfbcdc284d2a94b4a8e8332') depends_on('r@3.1.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.2-11:', type=('build', 'run')) - depends_on('r-libcoin@1.0-0:', when='@1.2-0:', type=('build', 'run')) - depends_on('r-mvtnorm', when='@1.2-0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.2-11:') + depends_on('r-libcoin@1.0-0:', type=('build', 'run'), when='@1.2-0:') + depends_on('r-mvtnorm', type=('build', 'run'), when='@1.2-0:') depends_on('r-survival', type=('build', 'run')) depends_on('r-formula@1.2-1:', type=('build', 'run')) - depends_on('r-inum@1.0-0:', when='@1.2-0:', type=('build', 'run')) - depends_on('r-rpart@4.1-11:', when='@1.2-0:', type=('build', 'run')) + depends_on('r-inum@1.0-0:', type=('build', 'run'), when='@1.2-0:') + depends_on('r-rpart@4.1-11:', type=('build', 'run'), when='@1.2-0:') diff --git a/var/spack/repos/builtin/packages/r-patchwork/package.py b/var/spack/repos/builtin/packages/r-patchwork/package.py index 213bf52d18..8f70d94ed6 100644 --- a/var/spack/repos/builtin/packages/r-patchwork/package.py +++ b/var/spack/repos/builtin/packages/r-patchwork/package.py @@ -7,7 +7,7 @@ from spack import * class RPatchwork(RPackage): - """The Composer of Plots + """The Composer of Plots. The 'ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. @@ -16,9 +16,7 @@ class RPatchwork(RPackage): operators for combining multiple plots. Other packages that try to address this need (but with a different approach) are 'gridExtra' and 'cowplot'.""" - homepage = "https://patchwork.data-imaginist.com/" - url = "https://cloud.r-project.org/src/contrib/patchwork_1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/patchwork" + cran = "patchwork" version('1.1.1', sha256='cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481') diff --git a/var/spack/repos/builtin/packages/r-pbapply/package.py b/var/spack/repos/builtin/packages/r-pbapply/package.py index 3ca72c8c47..0d36943f6a 100644 --- a/var/spack/repos/builtin/packages/r-pbapply/package.py +++ b/var/spack/repos/builtin/packages/r-pbapply/package.py @@ -7,7 +7,7 @@ from spack import * class RPbapply(RPackage): - """Adding Progress Bar to '*apply' Functions + """Adding Progress Bar to '*apply' Functions. A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where @@ -15,10 +15,9 @@ class RPbapply(RPackage): progress bar (with percentages or remaining time) can be set through options. Supports several parallel processing backends.""" - homepage = "https://cloud.r-project.org/package=pbapply" - url = "https://cloud.r-project.org/src/contrib/pbapply_1.3-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pbapply" + cran = "pbapply" + version('1.5-0', sha256='effdfee286e5ba9534dc2ac3cee96590a37f5cd2af28c836d00c25ca9f070a55') version('1.4-3', sha256='8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21') version('1.4-1', sha256='b3633349181db944e1dfc4422b4728a6562e454117a232cbb51633906cd27cad') version('1.3-4', sha256='cdfdaf9b8aecbe48daac858aecaf65a766b74a363d1eb7cd6ebf27c0549f6552') diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index 479c346828..c1e31ced80 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -8,27 +8,27 @@ from spack import * class RPbdzmq(RPackage): - """Programming with Big Data -- Interface to 'ZeroMQ' + """Programming with Big Data -- Interface to 'ZeroMQ'. 'ZeroMQ' is a well-known library for high-performance asynchronous - messaging in scalable, distributed applications. This package provides - high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus - on interactive client/server programming frameworks. For convenience, a - minimal 'ZeroMQ' library (4.1.0 rc1) is shipped with 'pbdZMQ', which can - be used if no system installation of 'ZeroMQ' is available. A few wrapper + messaging in scalable, distributed applications. This package provides high + level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on + interactive client/server programming frameworks. For convenience, a + minimal 'ZeroMQ' library (4.1.0 rc1) is shipped with 'pbdZMQ', which can be + used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.""" - homepage = "http://r-pbd.org/" - url = "https://cloud.r-project.org/src/contrib/pbdZMQ_0.2-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pbdZMQ" + cran = "pbdZMQ" + version('0.3-6', sha256='9944c8c44221aed1dbd7763ad9ec52c0ad2611d37bee25971ca16f02e8e8c37b') version('0.3-4', sha256='07794bd6858e093f8b6b879ddd5ab0195449b47a41b70cab2f60603f0a53b129') version('0.3-3', sha256='ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca') version('0.3-2', sha256='ece2a2881c662f77126e4801ba4e01c991331842b0d636ce5a2b591b9de3fc37') version('0.2-4', sha256='bfacac88b0d4156c70cf63fc4cb9969a950693996901a4fa3dcd59949ec065f6') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.3-4:', type=('build', 'run')) - depends_on('r-r6', when='@:0.2-6', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@0.2-6:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.3-4:') depends_on('libzmq@4.0.4:') + + depends_on('r-r6', type=('build', 'run'), when='@:0.2-6') diff --git a/var/spack/repos/builtin/packages/r-pbivnorm/package.py b/var/spack/repos/builtin/packages/r-pbivnorm/package.py index be913dce0c..68f10e7a3c 100644 --- a/var/spack/repos/builtin/packages/r-pbivnorm/package.py +++ b/var/spack/repos/builtin/packages/r-pbivnorm/package.py @@ -7,12 +7,11 @@ from spack import * class RPbivnorm(RPackage): - """ Vectorized Bivariate Normal CDF: + """Vectorized Bivariate Normal CDF. Provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.""" - homepage = "https://github.com/brentonk/pbivnorm" - cran = "pbivnorm" + cran = "pbivnorm" version('0.6.0', sha256='07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16') diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index 05e6af8a8a..e367ef099f 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -8,7 +8,7 @@ from spack import * class RPbkrtest(RPackage): """Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for - Test in Mixed Models + Test in Mixed Models. Test in mixed effects models. Attention is on mixed effects models as implemented in the 'lme4' package. For linear mixed models, this package @@ -20,9 +20,7 @@ class RPbkrtest(RPackage): paper by Halehoh and Hojsgaard, (2012, <doi:10.18637/jss.v059.i09>). Please see 'citation("pbkrtest")' for citation details.""" - homepage = "https://cran.r-project.org/web/packages/pbkrtest/index.html" - url = "https://cloud.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pbkrtest" + cran = "pbkrtest" version('0.5.1', sha256='b2a3452003d93890f122423b3f2487dcb6925440f5b8a05578509e98b6aec7c5') version('0.5-0.1', sha256='f56525488c6efe4a5cbf849bf9a82747041478605b166c29bad54e464e46f469') @@ -31,13 +29,13 @@ class RPbkrtest(RPackage): version('0.4-4', sha256='a685392ef3fca0ddc2254f6cc9bba6bc22b298fa823359fc4515e64e753abd31') depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.2.3:', when='@0.4-6:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.5-0.1:', type=('build', 'run')) + depends_on('r@3.2.3:', type=('build', 'run'), when='@0.4-6:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.5-0.1:') depends_on('r-lme4@1.1-10:', type=('build', 'run')) - depends_on('r-broom', when='@0.5-0.1:', type=('build', 'run')) - depends_on('r-dplyr', when='@0.5-0.1:', type=('build', 'run')) - depends_on('r-magrittr', when='@0.5-0.1:', type=('build', 'run')) + depends_on('r-broom', type=('build', 'run'), when='@0.5-0.1:') + depends_on('r-dplyr', type=('build', 'run'), when='@0.5-0.1:') + depends_on('r-magrittr', type=('build', 'run'), when='@0.5-0.1:') depends_on('r-mass', type=('build', 'run')) depends_on('r-matrix@1.2.3:', type=('build', 'run')) - depends_on('r-numderiv', when='@0.5-0.1:', type=('build', 'run')) - depends_on('r-knitr', when='@0.5-0.1:', type=('build', 'run')) + depends_on('r-numderiv', type=('build', 'run'), when='@0.5-0.1:') + depends_on('r-knitr', type=('build', 'run'), when='@0.5-0.1:') diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py index 5d87ed716d..4a5808f0eb 100644 --- a/var/spack/repos/builtin/packages/r-pcapp/package.py +++ b/var/spack/repos/builtin/packages/r-pcapp/package.py @@ -7,12 +7,16 @@ from spack import * class RPcapp(RPackage): - """Provides functions for robust PCA by projection pursuit.""" + """Provides functions for robust PCA by projection pursuit. - homepage = "https://cloud.r-project.org/package=pcaPP" - url = "https://cloud.r-project.org/src/contrib/pcaPP_1.9-72.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pcaPP" + Provides functions for robust PCA by projection pursuit. The methods are + described in Croux et al. (2006) <doi:10.2139/ssrn.968376>, Croux et al. + (2013) <doi:10.1080/00401706.2012.727746>, Todorov and Filzmoser (2013) + <doi:10.1007/978-3-642-33042-1_31>.""" + cran = "pcaPP" + + version('1.9-74', sha256='50837b434d67e4b5fcec34c689a9e30c7a9fb94c561b39f24e68a1456ff999b6') version('1.9-73', sha256='ca4566b0babfbe83ef9418283b08a12b3420dc362f93c6562f265df7926b53fc') version('1.9-72.1', sha256='a9e39ee15a650930c07672092f9f0c431807869b68b5471037eb7290a4d65bd5') version('1.9-72', sha256='58bd0bfb5931aecd734801654bac95f28dab6d30fd043c66c5b719b497104844') diff --git a/var/spack/repos/builtin/packages/r-pegas/package.py b/var/spack/repos/builtin/packages/r-pegas/package.py index a1390303a3..300d517161 100644 --- a/var/spack/repos/builtin/packages/r-pegas/package.py +++ b/var/spack/repos/builtin/packages/r-pegas/package.py @@ -7,24 +7,23 @@ from spack import * class RPegas(RPackage): - """Population and Evolutionary Genetics Analysis System + """Population and Evolutionary Genetics Analysis System. - Functions for reading, writing, plotting, analysing, and - manipulating allelic and haplotypic data, including from VCF files, - and for the analysis of population nucleotide sequences and - micro-satellites including coalescent analyses, linkage - disequilibrium, population structure (Fst, Amova) and equilibrium - (HWE), haplotype networks, minimum spanning tree and network, and - median-joining networks.""" + Functions for reading, writing, plotting, analysing, and manipulating + allelic and haplotypic data, including from VCF files, and for the analysis + of population nucleotide sequences and micro-satellites including + coalescent analyses, linkage disequilibrium, population structure (Fst, + Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and + network, and median-joining networks.""" - homepage = "http://ape-package.ird.fr/pegas.html" - url = "https://cloud.r-project.org/src/contrib/pegas_0.14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pegas" + cran = "pegas" maintainers = ['dorton21'] + version('1.1', sha256='87ba91a819496dfc3abdcc792ff853a6d49caae6335598a24c23e8851505ed59') version('0.14', sha256='7df90e6c4a69e8dbed2b3f68b18f1975182475bf6f86d4159256b52fd5332053') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-ape@5.3-11:', type=('build', 'run')) - depends_on('r-adegenet', type=('build', 'run')) + + depends_on('r-adegenet', type=('build', 'run'), when='@:0.14') diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py index f069d817ae..de581bd0e0 100644 --- a/var/spack/repos/builtin/packages/r-permute/package.py +++ b/var/spack/repos/builtin/packages/r-permute/package.py @@ -7,18 +7,19 @@ from spack import * class RPermute(RPackage): - """A set of restricted permutation designs for freely exchangeable, line + """Functions for Generating Restricted Permutations of Data. + + A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be - freely-exchangeable or one of the restricted designs. The 'permute' - package is modelled after the permutation schemes of 'Canoco 3.1' - (and later) by Cajo ter Braak.""" + freely-exchangeable or one of the restricted designs. The 'permute' package + is modelled after the permutation schemes of 'Canoco 3.1' (and later) by + Cajo ter Braak.""" - homepage = "https://github.com/gavinsimpson/permute" - url = "https://cloud.r-project.org/src/contrib/permute_0.9-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/permute" + cran = "permute" + version('0.9-7', sha256='eff88ffb579aaeb994e9f8609b776b2d9d9d56bc2879ddf180e3a2ad19f48dc0') version('0.9-5', sha256='d2885384a07497e8df273689d6713fc7c57a7c161f6935f3572015e16ab94865') version('0.9-4', sha256='a541a5f5636ddd67fd856d3e11224f15bc068e96e23aabe3e607a7e7c2fc1cf1') diff --git a/var/spack/repos/builtin/packages/r-phangorn/package.py b/var/spack/repos/builtin/packages/r-phangorn/package.py index 57e0cd8bf4..f87ac2dcc8 100644 --- a/var/spack/repos/builtin/packages/r-phangorn/package.py +++ b/var/spack/repos/builtin/packages/r-phangorn/package.py @@ -7,24 +7,30 @@ from spack import * class RPhangorn(RPackage): - """Package contains methods for estimation of phylogenetic trees and - networks using Maximum Likelihood, Maximum Parsimony, distance methods - and Hadamard conjugation. Allows to compare trees, models selection and - offers visualizations for trees and split networks.""" + """Phylogenetic Reconstruction and Analysis. - homepage = "https://cloud.r-project.org/package=phangorn" - url = "https://cloud.r-project.org/src/contrib/phangorn_2.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/phangorn" + Allows for estimation of phylogenetic trees and networks using Maximum + Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. + Offers methods for tree comparison, model selection and visualization of + phylogenetic networks as described in Schliep et al. (2017) + <doi:10.1111/2041-210X.12760>.""" + cran = "phangorn" + + version('2.8.1', sha256='6d471410ae29775104a94746936e8c1c54c7273dd289333973ec06dad489dc75') version('2.5.5', sha256='c58dc1ace26cb4358619a15da3ea4765dbdde1557acccc5103c85589a7571346') version('2.5.3', sha256='a306585a0aabe7360a2adaf9116ae2993fb5ceff641b198f2e01e4329d3768af') version('2.3.1', sha256='518c31f5b2c5f0a655d02a3c71b00c30caea2794dfc31f9d63f3d505bd7863eb') depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@4.1.0:', type=('build', 'run'), when='@2.8.1:') depends_on('r-ape@5.0:', type=('build', 'run')) - depends_on('r-quadprog', type=('build', 'run')) + depends_on('r-ape@5.5:', type=('build', 'run'), when='@2.8.1:') + depends_on('r-fastmatch', type=('build', 'run')) depends_on('r-igraph@1.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) - depends_on('r-fastmatch', type=('build', 'run')) - depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-rcpp@0.12.0:', type=('build', 'run')) + depends_on('r-quadprog', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + + depends_on('r-rcpp@0.12.0:', type=('build', 'run'), when='@:2.5.5') + depends_on('r-magrittr', type=('build', 'run'), when='@:2.5.5') diff --git a/var/spack/repos/builtin/packages/r-pheatmap/package.py b/var/spack/repos/builtin/packages/r-pheatmap/package.py index e125943bb5..0a07af4629 100644 --- a/var/spack/repos/builtin/packages/r-pheatmap/package.py +++ b/var/spack/repos/builtin/packages/r-pheatmap/package.py @@ -7,14 +7,12 @@ from spack import * class RPheatmap(RPackage): - """Pretty Heatmaps + """Pretty Heatmaps. Implementation of heatmaps that offers more control over dimensions and appearance.""" - homepage = "https://cloud.r-project.org/package=pheatmap" - url = "https://cloud.r-project.org/src/contrib/pheatmap_1.0.12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pheatmap" + cran = "pheatmap" version('1.0.12', sha256='579d96ee0417203b85417780eca921969cda3acc210c859bf9dfeff11539b0c1') diff --git a/var/spack/repos/builtin/packages/r-philentropy/package.py b/var/spack/repos/builtin/packages/r-philentropy/package.py index 5f92cee6b4..1a46d949b7 100644 --- a/var/spack/repos/builtin/packages/r-philentropy/package.py +++ b/var/spack/repos/builtin/packages/r-philentropy/package.py @@ -7,7 +7,9 @@ from spack import * class RPhilentropy(RPackage): - """Computes 46 optimized distance and similarity measures for comparing + """Similarity and Distance Quantification Between Probability Functions. + + Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of @@ -16,10 +18,9 @@ class RPhilentropy(RPackage): information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.""" - homepage = "https://github.com/HajkD/philentropy" - url = "https://cloud.r-project.org/src/contrib/philentropy_0.4.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/philentropy" + cran = "philentropy" + version('0.5.0', sha256='b39e9a825458f3377e23b2a133180566780e89019e9d22a6a5b7ca87c49c412f') version('0.4.0', sha256='bfd30bf5635aab6a82716299a87d44cf96c7ab7f4ee069843869bcc85c357127') depends_on('r@3.1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phylobase/package.py b/var/spack/repos/builtin/packages/r-phylobase/package.py index a81113eaac..9279cac7a6 100644 --- a/var/spack/repos/builtin/packages/r-phylobase/package.py +++ b/var/spack/repos/builtin/packages/r-phylobase/package.py @@ -7,15 +7,12 @@ from spack import * class RPhylobase(RPackage): - """phylobase: Base Package for Phylogenetic Structures and Comparative - Data. + """Base Package for Phylogenetic Structures and Comparative Data. - Provides a base S4 class for comparative methods, incorporating one or - more trees and trait data.""" + Provides a base S4 class for comparative methods, incorporating one or more + trees and trait data.""" - homepage = "https://github.com/fmichonneau/phylobase" - url = "https://cloud.r-project.org/src/contrib/phylobase_0.8.10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/phylobase" + cran = "phylobase" version('0.8.10', sha256='5a44380ff49bab333a56f6f96157324ade8afb4af0730e013194c4badb0bf94b') diff --git a/var/spack/repos/builtin/packages/r-phytools/package.py b/var/spack/repos/builtin/packages/r-phytools/package.py index 2642ae71aa..a9c6f95ba8 100644 --- a/var/spack/repos/builtin/packages/r-phytools/package.py +++ b/var/spack/repos/builtin/packages/r-phytools/package.py @@ -7,7 +7,7 @@ from spack import * class RPhytools(RPackage): - """Phylogenetic Tools for Comparative Biology (and Other Things) + """Phylogenetic Tools for Comparative Biology (and Other Things). A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes @@ -28,23 +28,21 @@ class RPhytools(RPackage): range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.""" - homepage = "https://github.com/liamrevell/phytools" - url = "https://cloud.r-project.org/src/contrib/phytools_0.6-60.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/phytools/" + cran = "phytools" + version('1.0-1', sha256='b7bf5d35ec4205115112481f6761de3e276e6b086a3e5249621ad63aa23a1ac8') version('0.7-70', sha256='e3432c3b006e5cc6f1292bebd81ebc20044edf1f56c3d27a3497f738eb99f0d3') version('0.6-99', sha256='2ef532cba77c5f73803bd34582bef05709705311a0b50e42316e69944567390f') version('0.6-60', sha256='55cad759510d247ebbf03a53a46caddadd3bf87584ccf7fcd6dd06d44516b377') depends_on('r@3.2.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.7-70:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.7-70:') depends_on('r-ape@4.0:', type=('build', 'run')) depends_on('r-maps', type=('build', 'run')) depends_on('r-clustergeneration', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) depends_on('r-combinat', type=('build', 'run')) depends_on('r-expm', type=('build', 'run')) - depends_on('r-gtools', when='@0.6-99:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-mnormt', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) @@ -52,4 +50,6 @@ class RPhytools(RPackage): depends_on('r-phangorn@2.3.1:', type=('build', 'run')) depends_on('r-plotrix', type=('build', 'run')) depends_on('r-scatterplot3d', type=('build', 'run')) - depends_on('r-animation', when='@:0.6-99', type=('build', 'run')) + + depends_on('r-animation', type=('build', 'run'), when='@:0.6-99') + depends_on('r-gtools', type=('build', 'run'), when='@0.6-99:0.7-70') diff --git a/var/spack/repos/builtin/packages/r-picante/package.py b/var/spack/repos/builtin/packages/r-picante/package.py index 570ac8b70b..8b59aa9b0d 100644 --- a/var/spack/repos/builtin/packages/r-picante/package.py +++ b/var/spack/repos/builtin/packages/r-picante/package.py @@ -7,7 +7,7 @@ from spack import * class RPicante(RPackage): - """R tools for integrating phylogenies and ecology + """R tools for integrating phylogenies and ecology. Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including @@ -18,9 +18,7 @@ class RPicante(RPackage): functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.""" - homepage = "https://cloud.r-project.org/package=picante" - url = "https://cloud.r-project.org/src/contrib/picante_1.6-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/picante" + cran = "picante" version('1.8.2', sha256='56565ca7f7c37f49c961372a816724967c21a4f5025cd69b8b671122bfdc4aa7') version('1.8', sha256='81a6308dbb53c9cdab30c1f9ac727abee76314351823b3a2142c21ed8e1498ad') diff --git a/var/spack/repos/builtin/packages/r-pillar/package.py b/var/spack/repos/builtin/packages/r-pillar/package.py index 86c4e07031..c169783c5b 100644 --- a/var/spack/repos/builtin/packages/r-pillar/package.py +++ b/var/spack/repos/builtin/packages/r-pillar/package.py @@ -7,14 +7,14 @@ from spack import * class RPillar(RPackage): - """Coloured Formatting for Columns + """Coloured Formatting for Columns. Provides a 'pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals.""" - homepage = "https://cloud.r-project.org/package=pillar" cran = "pillar" + version('1.6.5', sha256='22fbf1ba0677fbd15cb35729fe4e97fab751a4c1de3eb8a4694f86b2be411bdb') version('1.6.4', sha256='033a92a271ddeec2a17323d070de8257b9ca4d57f5be6181e2ad35fe7e1ea19e') version('1.4.7', sha256='cdedb2b2a4854e917f43b0c6379efefda9d7ff4e58dec2a3159a80ee8288f298') version('1.4.2', sha256='bababb76b6db06dc32ccd947dbad6c164a1749ff5b558c6783ad03570f010825') @@ -31,12 +31,13 @@ class RPillar(RPackage): depends_on('r-cli', type=('build', 'run')) depends_on('r-crayon@1.3.4:', type=('build', 'run')) - depends_on('r-ellipsis', when='@1.4.7:', type=('build', 'run')) - depends_on('r-ellipsis@0.3.2', when='@1.6.1:', type=('build', 'run')) + depends_on('r-ellipsis', type=('build', 'run'), when='@1.4.7:') + depends_on('r-ellipsis@0.3.2', type=('build', 'run'), when='@1.6.1:') depends_on('r-fansi', type=('build', 'run')) - depends_on('r-lifecycle', when='@1.4.7:', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run'), when='@1.6.5:') + depends_on('r-lifecycle', type=('build', 'run'), when='@1.4.7:') depends_on('r-rlang@0.3.0:', type=('build', 'run')) depends_on('r-utf8@1.1.0:', type=('build', 'run')) - depends_on('r-vctrs', when='@1.4.0:', type=('build', 'run')) - depends_on('r-vctrs@0.2.0:', when='@1.4.7:', type=('build', 'run')) - depends_on('r-vctrs@0.3.8:', when='@1.6.1:', type=('build', 'run')) + depends_on('r-vctrs', type=('build', 'run'), when='@1.4.0:') + depends_on('r-vctrs@0.2.0:', type=('build', 'run'), when='@1.4.7:') + depends_on('r-vctrs@0.3.8:', type=('build', 'run'), when='@1.6.1:') diff --git a/var/spack/repos/builtin/packages/r-pinfsc50/package.py b/var/spack/repos/builtin/packages/r-pinfsc50/package.py index 3418399b47..1862162073 100644 --- a/var/spack/repos/builtin/packages/r-pinfsc50/package.py +++ b/var/spack/repos/builtin/packages/r-pinfsc50/package.py @@ -8,15 +8,14 @@ from spack import * class RPinfsc50(RPackage): """Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for 17 - Samples of 'P. Infestans" and 1 'P. Mirabilis' + Samples of 'P. Infestans" and 1 'P. Mirabilis'. - Genomic data for the plant pathogen "Phytophthora infestans." It includes - a variant file ('VCF'), a sequence file ('FASTA') and an annotation file + Genomic data for the plant pathogen "Phytophthora infestans." It includes a + variant file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data.""" - homepage = "https://cloud.r-project.org/web/packages/pinfsc50/index.html" - cran = "pinfsc50" + cran = "pinfsc50" maintainers = ['dorton21'] diff --git a/var/spack/repos/builtin/packages/r-pixmap/package.py b/var/spack/repos/builtin/packages/r-pixmap/package.py index 6619389163..dfbe6aacaf 100644 --- a/var/spack/repos/builtin/packages/r-pixmap/package.py +++ b/var/spack/repos/builtin/packages/r-pixmap/package.py @@ -7,13 +7,12 @@ from spack import * class RPixmap(RPackage): - """Bitmap Images ("Pixel Maps") + """Bitmap Images ("Pixel Maps"). Functions for import, export, plotting and other manipulations of bitmapped images.""" - homepage = "https://cloud.r-project.org/package=pixmap" - url = "https://cloud.r-project.org/src/contrib/pixmap_0.4-11.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pixmap" + cran = "pixmap" + version('0.4-12', sha256='893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec') version('0.4-11', sha256='6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412') diff --git a/var/spack/repos/builtin/packages/r-pkgbuild/package.py b/var/spack/repos/builtin/packages/r-pkgbuild/package.py index 46194da749..7869f0d6a0 100644 --- a/var/spack/repos/builtin/packages/r-pkgbuild/package.py +++ b/var/spack/repos/builtin/packages/r-pkgbuild/package.py @@ -7,24 +7,23 @@ from spack import * class RPkgbuild(RPackage): - """Find Tools Needed to Build R Packages + """Find Tools Needed to Build R Packages. Provides functions used to build R packages. Locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.""" - homepage = "https://cloud.r-project.org/package=pkgbuild" - url = "https://cloud.r-project.org/src/contrib/pkgbuild_1.0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgbuild/" + cran = "pkgbuild" + version('1.3.1', sha256='7c6a82d1e6b19e136a7d16095743c50cd7b6340eeda594e4a8e14d74972ddb48') version('1.2.0', sha256='2e19308d3271fefd5e118c6d132d6a2511253b903620b5417892c72d2010a963') version('1.0.8', sha256='b149fcf3e98ef148945ff9f4272512cd03e21408c235ec6c0548167fd41219a1') version('1.0.4', sha256='2934efa5ff9ccfe1636d360aedec36713f3bb3128a493241dbb728d842ea3b5f') version('1.0.3', sha256='c93aceb499886e42bcd61eb7fb59e47a76c9ba5ab5349a426736d46c8ce21f4d') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r-callr@2.0.0:', when='@:1.0.3', type=('build', 'run')) - depends_on('r-callr@3.2.0:', when='@1.0.4:', type=('build', 'run')) + depends_on('r-callr@2.0.0:', type=('build', 'run')) + depends_on('r-callr@3.2.0:', type=('build', 'run'), when='@1.0.4:') depends_on('r-cli', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) depends_on('r-desc', type=('build', 'run')) @@ -32,3 +31,4 @@ class RPkgbuild(RPackage): depends_on('r-r6', type=('build', 'run')) depends_on('r-rprojroot', type=('build', 'run')) depends_on('r-withr@2.1.2:', type=('build', 'run')) + depends_on('r-withr@2.3.0:', type=('build', 'run'), when='@1.3.1:') diff --git a/var/spack/repos/builtin/packages/r-pkgcache/package.py b/var/spack/repos/builtin/packages/r-pkgcache/package.py new file mode 100644 index 0000000000..bedd98d3d1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pkgcache/package.py @@ -0,0 +1,35 @@ +# 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 RPkgcache(RPackage): + """Cache 'CRAN'-Like Metadata and R Packages. + + Metadata and package cache for CRAN-like repositories. This is a utility + package to be used by package management tools that want to take advantage + of caching.""" + + cran = "pkgcache" + + version('1.3.0', sha256='bd5f460a3bee9fc1298cf9f747bc59a6b9fbed90e92454bc6ea6bf82c15b9471') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-assertthat', type=('build', 'run')) + depends_on('r-callr@2.0.4.9000:', type=('build', 'run')) + depends_on('r-cli@2.0.0:', type=('build', 'run')) + depends_on('r-curl@3.2:', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-filelock', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-prettyunits', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-processx@3.3.0.9001:', type=('build', 'run')) + depends_on('r-rappdirs', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-uuid', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgconfig/package.py b/var/spack/repos/builtin/packages/r-pkgconfig/package.py index 6aa35856ae..09967bed00 100644 --- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py @@ -7,14 +7,12 @@ from spack import * class RPkgconfig(RPackage): - """Private Configuration for 'R' Packages + """Private Configuration for 'R' Packages. Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.""" - homepage = "https://cloud.r-project.org/package=pkgconfig" - url = "https://cloud.r-project.org/src/contrib/pkgconfig_2.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgconfig" + cran = "pkgconfig" version('2.0.3', sha256='330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850') version('2.0.2', sha256='25997754d1adbe7a251e3bf9879bb52dced27dd8b84767d558f0f644ca8d69ca') diff --git a/var/spack/repos/builtin/packages/r-pkgdepends/package.py b/var/spack/repos/builtin/packages/r-pkgdepends/package.py new file mode 100644 index 0000000000..bb4c27a029 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pkgdepends/package.py @@ -0,0 +1,44 @@ +# 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 RPkgdepends(RPackage): + """Package Dependency Resolution and Downloads. + + Find recursive dependencies of 'R' packages from various sources. Solve the + dependencies to obtain a consistent set of packages to install. Download + packages, and install them. It supports packages on 'CRAN', 'Bioconductor' + and other 'CRAN-like' repositories, 'GitHub', package 'URLs', and local + package trees and files. It caches metadata and package files via the + 'pkgcache' package, and performs all 'HTTP' requests, downloads, builds and + installations in parallel. 'pkgdepends' is the workhorse of the 'pak' + package.""" + + cran = "pkgdepends" + + version('0.2.0', sha256='59afdbe0e59663088ba4facac5cd011a0a05b0b9c540103fb8b9f0a673bf4d94') + + depends_on('r-callr@3.3.1:', type=('build', 'run')) + depends_on('r-cli@2.1.0:', type=('build', 'run')) + depends_on('r-crayon', type=('build', 'run')) + depends_on('r-curl', type=('build', 'run')) + depends_on('r-desc@1.2.0:', type=('build', 'run')) + depends_on('r-filelock@1.0.2:', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-lpsolve', type=('build', 'run')) + depends_on('r-pkgbuild@1.0.2:', type=('build', 'run')) + depends_on('r-pkgcache@1.3.0:', type=('build', 'run')) + depends_on('r-prettyunits@1.1.1:', type=('build', 'run')) + depends_on('r-processx@3.4.2:', type=('build', 'run')) + depends_on('r-ps', type=('build', 'run')) + depends_on('r-rematch2', type=('build', 'run')) + depends_on('r-rprojroot', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-withr@2.1.1:', type=('build', 'run')) + depends_on('r-zip@2.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgload/package.py b/var/spack/repos/builtin/packages/r-pkgload/package.py index 1f0cb4049c..5f31c309fd 100644 --- a/var/spack/repos/builtin/packages/r-pkgload/package.py +++ b/var/spack/repos/builtin/packages/r-pkgload/package.py @@ -7,24 +7,24 @@ from spack import * class RPkgload(RPackage): - """Simulate Package Installation and Attach + """Simulate Package Installation and Attach. Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.""" - homepage = "https://cloud.r-project.org/package=pkgload" - url = "https://cloud.r-project.org/src/contrib/pkgload_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgload/" + cran = "pkgload" + version('1.2.4', sha256='d6912bc824a59ccc9b2895c3cf3b08a3ff310a333888bb8e90d1a6ce754dd90f') version('1.1.0', sha256='189d460dbba2b35fa15dd59ce832df252dfa654a5acee0c9a8471b4d70477b0d') version('1.0.2', sha256='3186564e690fb05eabe76e1ac0bfd4312562c3ac8794b29f8850399515dcf27c') - depends_on('r-cli', when='@1.1.0:', type=('build', 'run')) - depends_on('r-crayon', when='@1.1.0:', type=('build', 'run')) + depends_on('r-cli', type=('build', 'run'), when='@1.1.0:') + depends_on('r-crayon', type=('build', 'run'), when='@1.1.0:') depends_on('r-desc', type=('build', 'run')) - depends_on('r-pkgbuild', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) depends_on('r-rprojroot', type=('build', 'run')) depends_on('r-rstudioapi', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) + + depends_on('r-pkgbuild', type=('build', 'run'), when='@:1.1.0') diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index 9cab569abd..fbcc879341 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -7,7 +7,7 @@ from spack import * class RPkgmaker(RPackage): - """Development Utilities for R Packages + """Development Utilities for R Packages. This package provides some low-level utilities to use for package development. It currently provides managers for multiple package specific @@ -17,9 +17,7 @@ class RPkgmaker(RPackage): eventually be packaged separately. It is still under heavy development and changes in the interface(s) are more than likely to happen.""" - homepage = "https://renozao.github.io/pkgmaker" - url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.27.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" + cran = "pkgmaker" version('0.32.2', sha256='ce45b22def771a9c90a414093823e6befe7e23489c500eeccee5154b44d3ef91') version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') @@ -31,7 +29,8 @@ class RPkgmaker(RPackage): depends_on('r-stringr', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) - depends_on('r-assertthat', when='@0.32.2:', type=('build', 'run')) - depends_on('r-stringi', when='@:0.27', type=('build', 'run')) - depends_on('r-magrittr', when='@:0.27', type=('build', 'run')) - depends_on('r-bibtex@0.4:', when='@:0.27', type=('build', 'run')) + depends_on('r-assertthat', type=('build', 'run'), when='@0.32.2:') + + depends_on('r-stringi', type=('build', 'run'), when='@:0.27') + depends_on('r-magrittr', type=('build', 'run'), when='@:0.27') + depends_on('r-bibtex@0.4:', type=('build', 'run'), when='@:0.27') diff --git a/var/spack/repos/builtin/packages/r-plogr/package.py b/var/spack/repos/builtin/packages/r-plogr/package.py index 4361223f74..5464c7c169 100644 --- a/var/spack/repos/builtin/packages/r-plogr/package.py +++ b/var/spack/repos/builtin/packages/r-plogr/package.py @@ -7,13 +7,12 @@ from spack import * class RPlogr(RPackage): - """A simple header-only logging library for C++. Add - 'LinkingTo: plogr' to 'DESCRIPTION', and '#include <plogr.h>' - in your C++ modules to use it.""" + """The 'plog' C++ Logging Library. - homepage = "https://cloud.r-project.org/package=plogr" - url = "https://cloud.r-project.org/src/contrib/plogr_0.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/plogr" + A simple header-only logging library for C++. Add 'LinkingTo: plogr' to + 'DESCRIPTION', and '#include <plogr.h>' in your C++ modules to use it.""" + + cran = "plogr" version('0.2.0', sha256='0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29') version('0.1-1', sha256='22755c93c76c26252841f43195df31681ea865e91aa89726010bd1b9288ef48f') diff --git a/var/spack/repos/builtin/packages/r-plot3d/package.py b/var/spack/repos/builtin/packages/r-plot3d/package.py index dac3f2d77a..c3a75f4499 100644 --- a/var/spack/repos/builtin/packages/r-plot3d/package.py +++ b/var/spack/repos/builtin/packages/r-plot3d/package.py @@ -7,16 +7,15 @@ from spack import * class RPlot3d(RPackage): - """Plotting Multi-Dimensional Data + """Plotting Multi-Dimensional Data. Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.""" - homepage = "https://cloud.r-project.org/package=plot3D" - url = "https://cloud.r-project.org/src/contrib/plot3D_1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/plot3D" + cran = "plot3D" + version('1.4', sha256='d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0') version('1.3', sha256='b9e4ec2789e34ad249318900e186868650e1a33466b385cb492a45466db3dfc9') version('1.1.1', sha256='f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632') diff --git a/var/spack/repos/builtin/packages/r-plotly/package.py b/var/spack/repos/builtin/packages/r-plotly/package.py index 675cfe7b8c..3e5698e2b8 100644 --- a/var/spack/repos/builtin/packages/r-plotly/package.py +++ b/var/spack/repos/builtin/packages/r-plotly/package.py @@ -7,16 +7,15 @@ from spack import * class RPlotly(RPackage): - """Create Interactive Web Graphics via 'plotly.js' + """Create Interactive Web Graphics via 'plotly.js'. Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.""" - homepage = "https://cloud.r-project.org/package=plotly" - url = "https://cloud.r-project.org/src/contrib/plotly_4.7.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/plotly" + cran = "plotly" + version('4.10.0', sha256='bd995c654dbc8c09a84adaba8def99766919e3894caf18b551bb26b2f591389a') version('4.9.3', sha256='d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120') version('4.9.0', sha256='f761148338231f210fd7fe2f8325ffe9cfdaaaeddd7b933b65c44ebb4f85e2cf') version('4.8.0', sha256='78f90282c831bbbb675ed4811fb506a98dd05e37251fabd42ebc263c80bae8a6') @@ -30,7 +29,7 @@ class RPlotly(RPackage): depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) - depends_on('r-httr@1.3.0:', when='@4.9.3:', type=('build', 'run')) + depends_on('r-httr@1.3.0:', type=('build', 'run'), when='@4.9.3:') depends_on('r-jsonlite@1.6:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) @@ -38,16 +37,19 @@ class RPlotly(RPackage): depends_on('r-base64enc', type=('build', 'run')) depends_on('r-htmltools@0.3.6:', type=('build', 'run')) depends_on('r-htmlwidgets@1.3:', type=('build', 'run')) - depends_on('r-htmlwidgets@1.5.2.9001:', when='@4.9.3:', type=('build', 'run')) + depends_on('r-htmlwidgets@1.5.2.9001:', type=('build', 'run'), when='@4.9.3:') depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-rcolorbrewer', when='@4.6.0:', type=('build', 'run')) + depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@4.10.0:') + depends_on('r-rcolorbrewer', type=('build', 'run'), when='@4.6.0:') depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-vctrs', when='@4.9.3:', type=('build', 'run')) + depends_on('r-vctrs', type=('build', 'run'), when='@4.9.3:') depends_on('r-tibble', type=('build', 'run')) depends_on('r-lazyeval@0.2.0:', type=('build', 'run')) - depends_on('r-rlang', when='@4.8.0:', type=('build', 'run')) - depends_on('r-crosstalk', when='@4.6.0:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@4.8.0:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@4.10.0:') + depends_on('r-crosstalk', type=('build', 'run'), when='@4.6.0:') depends_on('r-purrr', type=('build', 'run')) - depends_on('r-data-table', when='@4.7.0:', type=('build', 'run')) - depends_on('r-promises', when='@4.8.0:', type=('build', 'run')) - depends_on('r-hexbin', when='@:4.9.0', type=('build', 'run')) + depends_on('r-data-table', type=('build', 'run'), when='@4.7.0:') + depends_on('r-promises', type=('build', 'run'), when='@4.8.0:') + + depends_on('r-hexbin', type=('build', 'run'), when='@:4.9.0') diff --git a/var/spack/repos/builtin/packages/r-plotmo/package.py b/var/spack/repos/builtin/packages/r-plotmo/package.py index 29cba0110c..d00c376382 100644 --- a/var/spack/repos/builtin/packages/r-plotmo/package.py +++ b/var/spack/repos/builtin/packages/r-plotmo/package.py @@ -13,10 +13,9 @@ class RPlotmo(RPackage): plots and other techniques. Also plot model residuals and other information on the model.""" - homepage = "http://www.milbo.users.sonic.net/" - url = "https://cloud.r-project.org/src/contrib/plotmo_3.5.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/plotmo" + cran = "plotmo" + version('3.6.1', sha256='245a0c87f0cca08746c6fdc60da2e3856cd69b1a2b7b5641293c620d4ae04343') version('3.6.0', sha256='c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3') version('3.5.6', sha256='78f08dc897136d21fa8ade2acb6290351b569d29eb0592c7074c0be3cf2aa594') diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index 88721cc64a..67f155cee2 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -7,18 +7,17 @@ from spack import * class RPlotrix(RPackage): - """Various Plotting Functions + """Various Plotting Functions. Lots of plots, various labeling, axis and color scaling functions.""" - homepage = "https://cloud.r-project.org/package=plotrix" - url = "https://cloud.r-project.org/src/contrib/plotrix_3.6-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/plotrix" + cran = "plotrix" + version('3.8-2', sha256='bb72953102889cea41cd6521874e35d2458ebd10aab97ba6f262e102cac0bc1f') version('3.7-8', sha256='8ccd1f7e656413b9956cea614c986ce9cc61366deba356afb38cee6672a59480') version('3.7-6', sha256='83d5f7574592953288b4fe39c4c0dd7670d097598ad7f6bddbb0687a32954e46') version('3.7-5', sha256='b22f3f9d93961d23ad46e41597d1e45d2665ced04dcad8c40f6806a67cded14c') version('3.6-4', sha256='883b7d0a00c1b2b418f9167c72ed9e86eca3c9865d34158a7a6ad0b9bf95bff3') version('3.6-3', sha256='217164bdd04405c3280a0c8b2691f289287f9851fa8248648a5ae38f54962741') - depends_on('r@3.5.0:', when='@3.7-6:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.7-6:') diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py index ccf6918d30..13dd0d1f49 100644 --- a/var/spack/repos/builtin/packages/r-pls/package.py +++ b/var/spack/repos/builtin/packages/r-pls/package.py @@ -7,16 +7,15 @@ from spack import * class RPls(RPackage): - """Partial Least Squares and Principal Component Regression + """Partial Least Squares and Principal Component Regression. Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).""" - homepage = "https://cloud.r-project.org/package=pls" - url = "https://cloud.r-project.org/src/contrib/pls_2.6-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pls" + cran = "pls" + version('2.8-0', sha256='eff3a92756ca34cdc1661fa36d2bf7fc8e9f4132d2f1ef9ed0105c83594618bf') version('2.7-3', sha256='8f1d960ab74f05fdd11c4c7a3d30ff9e263fc658f5690b67278ca7c045d0742c') version('2.7-1', sha256='f8fd817fc2aa046970c49a9a481489a3a2aef8b6f09293fb1f0218f00bfd834b') version('2.7-0', sha256='5ddc1249a14d69a7a39cc4ae81595ac8c0fbb1e46c911af67907baddeac35875') diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index dcf19b3f3a..197005cbbc 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -7,7 +7,7 @@ from spack import * class RPlyr(RPackage): - """Tools for Splitting, Applying and Combining Data + """Tools for Splitting, Applying and Combining Data. A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put @@ -17,9 +17,7 @@ class RPlyr(RPackage): development of 'plyr' has been generously supported by 'Becton Dickinson'.""" - homepage = "http://had.co.nz/plyr" - url = "https://cloud.r-project.org/src/contrib/plyr_1.8.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/plyr" + cran = "plyr" version('1.8.6', sha256='ea55d26f155443e9774769531daa5d4c20a0697bb53abd832e891b126c935287') version('1.8.4', sha256='60b522d75961007658c9806f8394db27989f1154727cb0bb970062c96ec9eac5') diff --git a/var/spack/repos/builtin/packages/r-pmcmr/package.py b/var/spack/repos/builtin/packages/r-pmcmr/package.py index 46d361f904..147c4f059f 100644 --- a/var/spack/repos/builtin/packages/r-pmcmr/package.py +++ b/var/spack/repos/builtin/packages/r-pmcmr/package.py @@ -7,24 +7,18 @@ from spack import * class RPmcmr(RPackage): - """The Kruskal and Wallis one-way analysis of variance by ranks or van - der Waerden's normal score test can be employed, if the data do not - meet the assumptions for one-way ANOVA. Provided that significant - differences were detected by the omnibus test, one may be interested - in applying post-hoc tests for pairwise multiple comparisons (such as - Nemenyi's test, Dunn's test, Conover's test, van der Waerden's test). - Similarly, one-way ANOVA with repeated measures that is also referred - to as ANOVA with unreplicated block design can also be conducted via - the Friedman-Test or the Quade-test. The consequent post-hoc pairwise - multiple comparison tests according to Nemenyi, Conover and Quade are - also provided in this package. Finally Durbin's test for a two-way - balanced incomplete block design (BIBD) is also given in this - package.""" + """Calculate Pairwise Multiple Comparisons of Mean Rank Sums. - homepage = "https://cloud.r-project.org/package=PMCMR" - url = "https://cloud.r-project.org/src/contrib/PMCMR_4.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/PMCMR" + Note, that the 'PMCMR' package is superset by the novel 'PMCMRplus' + package. The 'PMCMRplus' package contains all functions from 'PMCMR' and + many more parametric and non-parametric multiple comparison procedures, + one-factorial trend tests, as well as improved method functions, such as + print, summary and plot. The 'PMCMR' package is no longer maintained, but + kept for compatibility of reverse depending packages for some time.""" + cran = "PMCMR" + + version('4.4', sha256='e7b4d9d595a879a62c9b3bb44c1f95432ad75a6607f84ce6bfc6395fee1dc116') version('4.3', sha256='328a2880dd614dc412e8dca21d29ed9d5eea29ccbe0eff98c8068100856c7b25') version('4.1', sha256='6c164e2976c59ddd27297433a34fa61b1e70b9e26265abdf9c8af1b639d2d555') diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py index 7ac0fe9cb6..5d4f03e5d7 100644 --- a/var/spack/repos/builtin/packages/r-png/package.py +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -7,13 +7,13 @@ from spack import * class RPng(RPackage): - """This package provides an easy and simple way to read, write and display + """Read and write PNG images. + + This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.""" - homepage = "https://www.rforge.net/png/" - url = "https://cloud.r-project.org/src/contrib/png_0.1-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/png" + cran = "png" version('0.1-7', sha256='e269ff968f04384fc9421d17cfc7c10cf7756b11c2d6d126e9776f5aca65553c') diff --git a/var/spack/repos/builtin/packages/r-polspline/package.py b/var/spack/repos/builtin/packages/r-polspline/package.py index f03e5c8dd4..6d036dc33f 100644 --- a/var/spack/repos/builtin/packages/r-polspline/package.py +++ b/var/spack/repos/builtin/packages/r-polspline/package.py @@ -7,15 +7,13 @@ from spack import * class RPolspline(RPackage): - """Polynomial Spline Routines + """Polynomial Spline Routines. Routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars, by C. Kooperberg and co-authors.""" - homepage = "https://cloud.r-project.org/package=polspline" - url = "https://cloud.r-project.org/src/contrib/polspline_1.1.18.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/polspline" + cran = "polspline" version('1.1.19', sha256='953e3c4d007c3ef86ac2af3c71b272a99e8e35b194bdd58575785558c6711f66') version('1.1.18', sha256='df250ee144bfff154249ba50308f46863107ef3efb2333ad908e599ed0eb0102') diff --git a/var/spack/repos/builtin/packages/r-polyclip/package.py b/var/spack/repos/builtin/packages/r-polyclip/package.py index 631d8c6f78..e201f632ec 100644 --- a/var/spack/repos/builtin/packages/r-polyclip/package.py +++ b/var/spack/repos/builtin/packages/r-polyclip/package.py @@ -7,11 +7,17 @@ from spack import * class RPolyclip(RPackage): - """polyclip: Polygon Clipping""" + """Polygon Clipping. - homepage = "https://cloud.r-project.org/package=polyclip" - url = "https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/polyclip" + R port of Angus Johnson's open source library Clipper. Performs polygon + clipping operations (intersection, union, set minus, set difference) for + polygonal regions of arbitrary complexity, including holes. Computes offset + polygons (spatial buffer zones, morphological dilations, Minkowski + dilations) for polygonal regions and polygonal lines. Computes Minkowski + Sum of general polygons. There is a function for removing + self-intersections from polygon data.""" + + cran = "polyclip" version('1.10-0', sha256='74dabc0dfe5a527114f0bb8f3d22f5d1ae694e6ea9345912909bae885525d34b') diff --git a/var/spack/repos/builtin/packages/r-polynom/package.py b/var/spack/repos/builtin/packages/r-polynom/package.py index 06465843bd..ef20f15b9f 100644 --- a/var/spack/repos/builtin/packages/r-polynom/package.py +++ b/var/spack/repos/builtin/packages/r-polynom/package.py @@ -10,8 +10,6 @@ class RPolynom(RPackage): """A collection of functions to implement a class for univariate polynomial manipulations.""" - homepage = "https://cloud.r-project.org/package=polynom" - url = "https://cloud.r-project.org/src/contrib/polynom_1.4-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/polynom" + cran = "polynom" version('1.4-0', sha256='c5b788b26f7118a18d5d8e7ba93a0abf3efa6603fa48603c70ed63c038d3d4dd') diff --git a/var/spack/repos/builtin/packages/r-pool/package.py b/var/spack/repos/builtin/packages/r-pool/package.py index 5322115339..97aa33a1a4 100644 --- a/var/spack/repos/builtin/packages/r-pool/package.py +++ b/var/spack/repos/builtin/packages/r-pool/package.py @@ -7,14 +7,13 @@ from spack import * class RPool(RPackage): - """Object Pooling + """Object Pooling. Enables the creation of object pools, which make it less computationally expensive to fetch a new object. Currently the only supported pooled objects are 'DBI' connections.""" - homepage = "https://github.com/rstudio/pool" - cran = "pool" + cran = "pool" version('0.1.6', sha256='cdbe5f6c7f757c01893dc9870df0fb8d300829da0e427f6c2559b01caa52d9e1') diff --git a/var/spack/repos/builtin/packages/r-popgenome/package.py b/var/spack/repos/builtin/packages/r-popgenome/package.py index b6ab3286f0..2d03c4536a 100644 --- a/var/spack/repos/builtin/packages/r-popgenome/package.py +++ b/var/spack/repos/builtin/packages/r-popgenome/package.py @@ -7,7 +7,7 @@ from spack import * class RPopgenome(RPackage): - """An Efficient Swiss Army Knife for Population Genomic Analyses + """An Efficient Swiss Army Knife for Population Genomic Analyses. Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome @@ -16,9 +16,7 @@ class RPopgenome(RPackage): algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.""" - homepage = "https://popgenome.weebly.com" - url = "https://cloud.r-project.org/src/contrib/PopGenome_2.6.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/PopGenome" + cran = "PopGenome" version('2.7.5', sha256='d627b8ac87b4db6038d7349b2df20648d2fcfd48e2dafcd7f4731d1b607cbc75') version('2.7.1', sha256='a84903b151528fa026ccaba42ada22cd89babbc1824afd40269b7204e488a5fa') diff --git a/var/spack/repos/builtin/packages/r-popvar/package.py b/var/spack/repos/builtin/packages/r-popvar/package.py index 45f14f2b87..7234c19ad7 100644 --- a/var/spack/repos/builtin/packages/r-popvar/package.py +++ b/var/spack/repos/builtin/packages/r-popvar/package.py @@ -7,16 +7,26 @@ from spack import * class RPopvar(RPackage): - """PopVar: Genomic Breeding Tools: Genetic Variance Prediction andCross- - Validation""" + """Genomic Breeding Tools: Genetic Variance Prediction and + Cross-Validation. - homepage = "https://cloud.r-project.org/package=PopVar" - url = "https://cloud.r-project.org/src/contrib/PopVar_1.2.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/PopVar" + The main attribute of 'PopVar' is the prediction of genetic variance in + bi-parental populations, from which the package derives its name. 'PopVar' + contains a set of functions that use phenotypic and genotypic data from a + set of candidate parents to 1) predict the mean, genetic variance, and + superior progeny value of all, or a defined set of pairwise bi-parental + crosses, and 2) perform cross-validation to estimate genome-wide prediction + accuracy of multiple statistical models. More details are available in + Mohammadi, Tiede, and Smith (2015, <doi:10.2135/cropsci2015.01.0030>). A + dataset 'think_barley.rda' is included for reference and examples.""" + cran = "PopVar" + + version('1.3.0', sha256='3145c41c9aa1588d47aaf76c082e6b1c2fd95cf5014b98bd2867cbf2cec782f9') version('1.2.1', sha256='5e3df79634ab63708a431e4b8e6794675972ac6c58d2bc615726aa0f142f5f25') depends_on('r@3.1.1:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.3.0:') depends_on('r-bglr', type=('build', 'run')) depends_on('r-qtl', type=('build', 'run')) depends_on('r-rrblup', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-posterior/package.py b/var/spack/repos/builtin/packages/r-posterior/package.py index c0725f41dc..e64678ff2c 100644 --- a/var/spack/repos/builtin/packages/r-posterior/package.py +++ b/var/spack/repos/builtin/packages/r-posterior/package.py @@ -19,9 +19,9 @@ class RPosterior(RPackage): lightweight implementations of state of the art posterior inference diagnostics. References: Vehtari et al. (2021) <doi:10.1214/20-BA1221>.""" - homepage = "https://mc-stan.org/posterior/" - cran = "posterior" + cran = "posterior" + version('1.2.0', sha256='2ba01711a98448acc939cf506d22e8ee4cf680cdcea873226671fa8ae6934386') version('1.1.0', sha256='eff6262dbcc1bf18337f535b0c75ba2fe360322e8b170c466e24ed3ee76cf4d2') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-powerlaw/package.py b/var/spack/repos/builtin/packages/r-powerlaw/package.py index d577b1afc1..594a5da50c 100644 --- a/var/spack/repos/builtin/packages/r-powerlaw/package.py +++ b/var/spack/repos/builtin/packages/r-powerlaw/package.py @@ -7,22 +7,21 @@ from spack import * class RPowerlaw(RPackage): - """Analysis of Heavy Tailed Distributions + """Analysis of Heavy Tailed Distributions. An implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.""" - homepage = "https://github.com/csgillespie/poweRlaw" - url = "https://cloud.r-project.org/src/contrib/poweRlaw_0.70.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/poweRlaw" + cran = "poweRlaw" version('0.70.6', sha256='efc091449c5c6494c1c13c85a8eb95625d1c55ffffebe86c7ea16e4abbafa191') version('0.70.2', sha256='240f1454389b1a00ad483fb63e5b53243cc9367f21a3e7253ab2c293673459ab') version('0.70.1', sha256='15b1b8dadeb550c01b9f1308cfa64720be6fbf56afb80f6a096987d6a0055913') - depends_on('r@3.1.0:', when='@:0.70.1', type=('build', 'run')) - depends_on('r@3.4.0:', when='@0.70.2:', type=('build', 'run')) - depends_on('r-pracma', when='@0.70.6:', type=('build', 'run')) - depends_on('r-vgam', when='@:0.70.2', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@0.70.2:') + depends_on('r-pracma', type=('build', 'run'), when='@0.70.6:') + + depends_on('r-vgam', type=('build', 'run'), when='@:0.70.2') diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py index cccd8acd1b..7ffc7cb535 100644 --- a/var/spack/repos/builtin/packages/r-prabclus/package.py +++ b/var/spack/repos/builtin/packages/r-prabclus/package.py @@ -7,8 +7,8 @@ from spack import * class RPrabclus(RPackage): - """prabclus: Functions for Clustering of Presence-Absence, Abundance and - Multilocus Genetic Data + """Functions for Clustering of Presence-Absence, Abundance and Multilocus + Genetic Data. Distance-based parametric bootstrap tests for clustering with spatial neighborhood information. Some distance measures, Clustering of @@ -17,9 +17,7 @@ class RPrabclus(RPackage): between communities. Tests whether various distance-based regressions are equal. Try package?prabclus for on overview.""" - homepage = "https://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cloud.r-project.org/src/contrib/prabclus_2.2-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/prabclus" + cran = "prabclus" version('2.3-2', sha256='f421bcbcb557281e0de4a06b15f9a496adb5c640e883c0f7bb12051efc69e441') version('2.3-1', sha256='ef3294767d43bc3f72478fdaf0d1f13c8de18881bf9040c9f1add68af808b3c0') diff --git a/var/spack/repos/builtin/packages/r-pracma/package.py b/var/spack/repos/builtin/packages/r-pracma/package.py index 1653c54a14..c2439bed99 100644 --- a/var/spack/repos/builtin/packages/r-pracma/package.py +++ b/var/spack/repos/builtin/packages/r-pracma/package.py @@ -7,17 +7,16 @@ from spack import * class RPracma(RPackage): - """Practical Numerical Math Functions + """Practical Numerical Math Functions. Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.""" - homepage = "https://cloud.r-project.org/package=pracma" - url = "https://cloud.r-project.org/src/contrib/pracma_2.2.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pracma" + cran = "pracma" + version('2.3.6', sha256='17ac83fd48c9155e00dc3f0433f95723505dc73d046860afd9001866d699b8de') version('2.2.9', sha256='0cea0ff5e88643df121e07b9aebfe57084c61e11801680039752f371fe87bf1e') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py index ac8a1bbefb..eb452fc575 100644 --- a/var/spack/repos/builtin/packages/r-praise/package.py +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -7,11 +7,11 @@ from spack import * class RPraise(RPackage): - """Build friendly R packages that praise their users if they have done + """Praise Users. + + Build friendly R packages that praise their users if they have done something good, or they just need it to feel better.""" - homepage = "https://github.com/gaborcsardi/praise" - url = "https://cloud.r-project.org/src/contrib/praise_1.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/praise" + cran = "praise" version('1.0.0', sha256='5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd') diff --git a/var/spack/repos/builtin/packages/r-prettydoc/package.py b/var/spack/repos/builtin/packages/r-prettydoc/package.py index 3964d4bd22..0a1dd61a4f 100644 --- a/var/spack/repos/builtin/packages/r-prettydoc/package.py +++ b/var/spack/repos/builtin/packages/r-prettydoc/package.py @@ -7,15 +7,14 @@ from spack import * class RPrettydoc(RPackage): - """Creating Pretty Documents from R Markdown: + """Creating Pretty Documents from R Markdown. Creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the 'html_pretty' output format as an alternative to the 'html_document' and 'html_vignette' engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.""" - homepage = "https://github.com/yixuan/prettydoc" - cran = "prettydoc" + cran = "prettydoc" version('0.4.1', sha256='1094a69b026238d149435472b4f41c75151c7370a1be6c6332147c88ad4c4829') diff --git a/var/spack/repos/builtin/packages/r-prettyunits/package.py b/var/spack/repos/builtin/packages/r-prettyunits/package.py index 9d5d485e33..414c6041ab 100644 --- a/var/spack/repos/builtin/packages/r-prettyunits/package.py +++ b/var/spack/repos/builtin/packages/r-prettyunits/package.py @@ -7,18 +7,16 @@ from spack import * class RPrettyunits(RPackage): - """Pretty, Human Readable Formatting of Quantities + """Pretty, Human Readable Formatting of Quantities. Pretty, human readable formatting of quantities. Time intervals: 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.""" - homepage = "https://cloud.r-project.org/package=prettyunits" - url = "https://cloud.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/prettyunits" + cran = "prettyunits" version('1.1.1', sha256='9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5') version('1.0.2', sha256='35a4980586c20650538ae1e4fed4d80fdde3f212b98546fc3c7d9469a1207f5c') - depends_on('r-magrittr', when='@:1.0.2', type=('build', 'run')) - depends_on('r-assertthat', when='@:1.0.2', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run'), when='@:1.0.2') + depends_on('r-assertthat', type=('build', 'run'), when='@:1.0.2') diff --git a/var/spack/repos/builtin/packages/r-proc/package.py b/var/spack/repos/builtin/packages/r-proc/package.py index c89e7c6370..a66ba3e94f 100644 --- a/var/spack/repos/builtin/packages/r-proc/package.py +++ b/var/spack/repos/builtin/packages/r-proc/package.py @@ -7,17 +7,16 @@ from spack import * class RProc(RPackage): - """Display and Analyze ROC Curves + """Display and Analyze ROC Curves. Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.""" - homepage = "https://expasy.org/tools/pROC/" - url = "https://cloud.r-project.org/src/contrib/pROC_1.17.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pROC" + cran = "pROC" + version('1.18.0', sha256='d5ef54b384176ece6d6448014ba40570a98181b58fee742f315604addb5f7ba9') version('1.17.0.1', sha256='221c726ffb81b04b999905effccfd3a223cd73cae70d7d86688e2dd30e51a6bd') depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-processx/package.py b/var/spack/repos/builtin/packages/r-processx/package.py index b9d5c290c8..6022618084 100644 --- a/var/spack/repos/builtin/packages/r-processx/package.py +++ b/var/spack/repos/builtin/packages/r-processx/package.py @@ -7,7 +7,7 @@ from spack import * class RProcessx(RPackage): - """Execute and Control System Processes + """Execute and Control System Processes. Tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get @@ -16,7 +16,6 @@ class RProcessx(RPackage): connections. 'processx' can poll a process for standard output or error, with a timeout. It can also poll several processes at once.""" - homepage = "https://github.com/r-lib/processx" cran = "processx" version('3.5.2', sha256='ed6f2d1047461c6061e6ed58fb6de65a289b56009867892abad76c6bba46fc2b') @@ -29,9 +28,9 @@ class RProcessx(RPackage): version('2.0.0.1', sha256='8f61b2952d0f2d13c74465bfba174ce11eee559475c2f7b9be6bcb9e2e1d827b') version('2.0.0', sha256='8325b56a60a276909228756281523cda9256bc754c5f3ca03b41c5c17cc398ad') - depends_on('r-ps@1.2.0:', when='@3.2.0:', type=('build', 'run')) + depends_on('r-ps@1.2.0:', type=('build', 'run'), when='@3.2.0:') depends_on('r-r6', type=('build', 'run')) - depends_on('r-assertthat', when='@:3.2.9', type=('build', 'run')) - depends_on('r-crayon', when='@:3.2.9', type=('build', 'run')) - depends_on('r-debugme', when='@:3.0.9', type=('build', 'run')) + depends_on('r-assertthat', type=('build', 'run'), when='@:3.2.9') + depends_on('r-crayon', type=('build', 'run'), when='@:3.2.9') + depends_on('r-debugme', type=('build', 'run'), when='@:3.0.9') diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py index b3c8c7b25f..f6da27db74 100644 --- a/var/spack/repos/builtin/packages/r-prodlim/package.py +++ b/var/spack/repos/builtin/packages/r-prodlim/package.py @@ -7,15 +7,13 @@ from spack import * class RProdlim(RPackage): - """Product-Limit Estimation for Censored Event History Analysis + """Product-Limit Estimation for Censored Event History Analysis. - Product-Limit Estimation for Censored Event History Analysis. Fast and - user friendly implementation of nonparametric estimators for censored event + Product-Limit Estimation for Censored Event History Analysis. Fast and user + friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.""" - homepage = "https://cloud.r-project.org/package=prodlim" - url = "https://cloud.r-project.org/src/contrib/prodlim_1.5.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/prodlim" + cran = "prodlim" version('2019.11.13', sha256='6809924f503a14681de84730489cdaf9240d7951c64f5b98ca37dc1ce7809b0f') version('2018.04.18', sha256='4b22b54fdf712439309be0ff74f63cde9080464667b00e19823372ac0fc254ab') diff --git a/var/spack/repos/builtin/packages/r-progress/package.py b/var/spack/repos/builtin/packages/r-progress/package.py index 858356abed..97e5a0e352 100644 --- a/var/spack/repos/builtin/packages/r-progress/package.py +++ b/var/spack/repos/builtin/packages/r-progress/package.py @@ -7,15 +7,14 @@ from spack import * class RProgress(RPackage): - """Configurable Progress bars, they may include percentage, elapsed time, - and/or the estimated completion time. They work in terminals, in - 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. - The package also provides a 'C++' 'API', that works with or without - 'Rcpp'.""" + """Terminal Progress Bars. - homepage = "https://cloud.r-project.org/package=progress" - url = "https://cloud.r-project.org/src/contrib/progress_1.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/progress" + Configurable Progress bars, they may include percentage, elapsed time, + and/or the estimated completion time. They work in terminals, in 'Emacs' + 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package + also provides a 'C++' 'API', that works with or without 'Rcpp'.""" + + cran = "progress" version('1.2.2', sha256='b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35') version('1.2.1', sha256='7401e86ff76bef4d26508b74ee8bd169a0377b2738d9ec79ebff0b7fd5c55326') @@ -23,5 +22,5 @@ class RProgress(RPackage): depends_on('r-r6', type=('build', 'run')) depends_on('r-prettyunits', type=('build', 'run')) - depends_on('r-hms', when='@1.2.0:', type=('build', 'run')) - depends_on('r-crayon', when='@1.2.0:', type=('build', 'run')) + depends_on('r-hms', type=('build', 'run'), when='@1.2.0:') + depends_on('r-crayon', type=('build', 'run'), when='@1.2.0:') diff --git a/var/spack/repos/builtin/packages/r-progressr/package.py b/var/spack/repos/builtin/packages/r-progressr/package.py new file mode 100644 index 0000000000..b395c73a89 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-progressr/package.py @@ -0,0 +1,35 @@ +# 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 RProgressr(RPackage): + """An Inclusive, Unifying API for Progress Updates. + + A minimal, unifying API for scripts and packages to report progress updates + from anywhere including when using parallel processing. The package is + designed such that the developer can to focus on what progress should be + reported on without having to worry about how to present it. The end user + has full control of how, where, and when to render these progress updates, + e.g. in the terminal using utils::txtProgressBar() or + progress::progress_bar(), in a graphical user interface using + utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), + via the speakers using beep::beepr(), or on a file system via the size of a + file. Anyone can add additional, customized, progression handlers. The + 'progressr' package uses R's condition framework for signaling progress + updated. Because of this, progress can be reported from almost anywhere in + R, e.g. from classical for and while loops, from map-reduce API:s like the + lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will also + work with parallel processing via the 'future' framework, e.g. + future.apply::future_lapply(), furrr::future_map(), and 'foreach' with + 'doFuture'. The package is compatible with Shiny applications.""" + + cran = "progressr" + + version('0.10.0', sha256='4c95dc11c50c792440fa17f4538d59f1f3012bf6ef462a5a141609f87319badc') + + depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-proj/package.py b/var/spack/repos/builtin/packages/r-proj/package.py index 8d872852e1..120de9680f 100644 --- a/var/spack/repos/builtin/packages/r-proj/package.py +++ b/var/spack/repos/builtin/packages/r-proj/package.py @@ -7,17 +7,15 @@ from spack import * class RProj(RPackage): - """Generic Coordinate System Transformations Using 'PROJ' + """Generic Coordinate System Transformations Using 'PROJ'. Currently non-operational, a harmless wrapper to allow package 'reproj' to install and function while relying on the 'proj4' package.""" - homepage = "https://github.com/hypertidy/PROJ" - url = "https://cloud.r-project.org/src/contrib/PROJ_0.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/PROJ" + cran = "PROJ" version('0.4.0', sha256='dde90cfeca83864e61a7422e1573d2d55bb0377c32b9a8f550f47b8631121ce7') version('0.1.0', sha256='5186f221335e8092bbcd4d82bd323ee7e752c7c9cf83d3f94e4567e0b407aa6f') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r@3.0.2:', when='@0.4.0:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run'), when='@0.4.0:') diff --git a/var/spack/repos/builtin/packages/r-proj4/package.py b/var/spack/repos/builtin/packages/r-proj4/package.py index 89a57a4044..71ddd17051 100644 --- a/var/spack/repos/builtin/packages/r-proj4/package.py +++ b/var/spack/repos/builtin/packages/r-proj4/package.py @@ -7,18 +7,22 @@ from spack import * class RProj4(RPackage): - """A simple interface to the PROJ.4 cartographic projections library + """A simple interface to the PROJ.4 cartographic projections library. - A simple interface to lat/long projection and datum transformation of - the PROJ.4 cartographic projections library. It allows transformation of + A simple interface to lat/long projection and datum transformation of the + PROJ.4 cartographic projections library. It allows transformation of geographic coordinates from one projection and/or datum to another.""" - homepage = "https://www.rforge.net/proj4/" - url = "https://cloud.r-project.org/src/contrib/proj4_1.0-8.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/proj4" + cran = "proj4" + version('1.0-11', sha256='c5f186530267005d53cc2e86849613b254ca4515a8b10310146f712d45a1d11d') + version('1.0-10.1', sha256='66857cbe5cba4930b18621070f9a7263ea0d8ddc3e5a035a051a1496e4e1da19') version('1.0-10', sha256='5f396f172a17cfa9821a390f11ff7d3bff3c92ccf585572116dec459c621d1d0') version('1.0-8.1', sha256='a3a2a8f0014fd79fa34b5957440fd38299d8e97f1a802a61a068a6c6cda10a7e') depends_on('r@2.0.0:', type=('build', 'run')) - depends_on('proj@4.4.6:5') + depends_on('proj@4.4.6:7', when='@:1.0-8') + depends_on('proj@4.4.6:') + + # This is needed because the configure script links to sqlite3 + depends_on('sqlite', when='@1.0-10.1:') diff --git a/var/spack/repos/builtin/packages/r-projpred/package.py b/var/spack/repos/builtin/packages/r-projpred/package.py index 64d22609aa..bde772b6ec 100644 --- a/var/spack/repos/builtin/packages/r-projpred/package.py +++ b/var/spack/repos/builtin/packages/r-projpred/package.py @@ -7,7 +7,7 @@ from spack import * class RProjpred(RPackage): - """Projection Predictive Feature Selection: + """Projection Predictive Feature Selection. Performs projection predictive feature selection for generalized linear models and generalized linear and additive multilevel models (see, @@ -17,8 +17,7 @@ class RProjpred(RPackage): 'rstanarm' and 'brms' packages, but other reference models can also be used. See the package vignette for more information and examples.""" - homepage = "https://mc-stan.org/projpred/" - cran = "projpred" + cran = "projpred" version('2.0.2', sha256='af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b') diff --git a/var/spack/repos/builtin/packages/r-promises/package.py b/var/spack/repos/builtin/packages/r-promises/package.py index 14f5d709d0..dca9d202b0 100644 --- a/var/spack/repos/builtin/packages/r-promises/package.py +++ b/var/spack/repos/builtin/packages/r-promises/package.py @@ -7,18 +7,17 @@ from spack import * class RPromises(RPackage): - """Abstractions for Promise-Based Asynchronous Programming + """Abstractions for Promise-Based Asynchronous Programming. - Provides fundamental abstractions for doing asynchronous programming in - R using promises. Asynchronous programming is useful for allowing a single - R process to orchestrate multiple tasks in the background while also + Provides fundamental abstractions for doing asynchronous programming in R + using promises. Asynchronous programming is useful for allowing a single R + process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.""" - homepage = "https://rstudio.github.io/promises" - url = "https://cloud.r-project.org/src/contrib/promises_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/promises" + cran = "promises" + version('1.2.0.1', sha256='8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7') version('1.1.1', sha256='3718c6eb2c3362cbe89389e613118f783f9977dbf24757f85026e661199c5800') version('1.0.1', sha256='c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558') diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py index 13a2d2176f..406df2ae0e 100644 --- a/var/spack/repos/builtin/packages/r-proto/package.py +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -7,12 +7,12 @@ from spack import * class RProto(RPackage): - """An object oriented system using object-based, also called - prototype-based, rather than class-based object oriented ideas.""" + """Prototype Object-Based Programming. - homepage = "https://cran.r-project.org/web/packages/proto/index.html" - url = "https://cloud.r-project.org/src/contrib/proto_0.3-10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/proto" + An object oriented system using object-based, also called prototype-based, + rather than class-based object oriented ideas.""" + + cran = "proto" version('1.0.0', sha256='9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1') version('0.3-10', sha256='d0d941bfbf247879b3510c8ef3e35853b1fbe83ff3ce952e93d3f8244afcbb0e') diff --git a/var/spack/repos/builtin/packages/r-proxy/package.py b/var/spack/repos/builtin/packages/r-proxy/package.py index d60c6033fa..e992e3522e 100644 --- a/var/spack/repos/builtin/packages/r-proxy/package.py +++ b/var/spack/repos/builtin/packages/r-proxy/package.py @@ -7,18 +7,17 @@ from spack import * class RProxy(RPackage): - """Distance and Similarity Measures + """Distance and Similarity Measures. Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.""" - homepage = "https://cloud.r-project.org/package=proxy" - url = "https://cloud.r-project.org/src/contrib/proxy_0.4-19.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/proxy" + cran = "proxy" + version('0.4-26', sha256='676bad821343974e0297a0566c4bf0cf0ea890104906a745b87d3b5989c81a4d') version('0.4-24', sha256='8cff9bf036475941a7c44ba9bb5e2f6d4777d49ab3daaeb52d23f4b2af6d9c7c') version('0.4-23', sha256='9dd4eb0978f40e4fcb55c8a8a26266d32eff9c63ac9dfe70cf1f664ca9c3669d') version('0.4-19', sha256='6b27e275018366e6024382704da9a9757c8878535dbcd7d450824b70e2e34d51') depends_on('r@3.3.2:', type=('build', 'run')) - depends_on('r@3.4.0:', when='@0.4-21:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@0.4-21:') diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py index 548696ef21..575716a986 100644 --- a/var/spack/repos/builtin/packages/r-pryr/package.py +++ b/var/spack/repos/builtin/packages/r-pryr/package.py @@ -8,18 +8,20 @@ from spack import * class RPryr(RPackage): - """Useful tools to pry back the covers of R and understand the language - at a deeper level.""" + """Tools for Computing on the Language. - homepage = "https://github.com/hadley/pryr" - url = "https://cloud.r-project.org/src/contrib/pryr_0.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pryr" + Useful tools to pry back the covers of R and understand the language at a + deeper level.""" + cran = "pryr" + + version('0.1.5', sha256='7b1653ec51850f4633cee8e2eb7d0b2724fb587b801539488b426cf88f0f770b') version('0.1.4', sha256='d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b') version('0.1.3', sha256='6acd88341dde4fe247a5cafd3949b281dc6742b7d60f68b57c1feb84b96739ac') version('0.1.2', sha256='65c2b7c9f96e2aa683ac9cdab3c215fd3039ecd66a2ba7002a8e77881428c3c6') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-codetools', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-lobstr', type=('build', 'run'), when='@0.1.5:') diff --git a/var/spack/repos/builtin/packages/r-ps/package.py b/var/spack/repos/builtin/packages/r-ps/package.py index 8a2479fb83..1d58d5f8f3 100644 --- a/var/spack/repos/builtin/packages/r-ps/package.py +++ b/var/spack/repos/builtin/packages/r-ps/package.py @@ -7,15 +7,14 @@ from spack import * class RPs(RPackage): - """List, Query, Manipulate System Processes + """List, Query, Manipulate System Processes. List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.""" - homepage = "https://github.com/r-lib/ps" - url = "https://cloud.r-project.org/src/contrib/ps_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ps" + cran = "ps" + version('1.6.0', sha256='89ad7ddc5e0818bccacfd0673ddf2da0892ac2a3b4d3a821e40884ab1e96bf31') version('1.5.0', sha256='7461a196f55557feda569a9791ad851c884f9a2dd71671655ed17cb048fafe96') version('1.3.0', sha256='289193d0ccd2db0b6fe8702e8c5711e935219b17f90f01a6e9684982413e98d1') version('1.2.1', sha256='bd7207164e6557a9e4213c4b00dc5dc23d7705ab290569765998640b16a3beff') diff --git a/var/spack/repos/builtin/packages/r-pscbs/package.py b/var/spack/repos/builtin/packages/r-pscbs/package.py index 1ce479d042..5b7fbcc7e5 100644 --- a/var/spack/repos/builtin/packages/r-pscbs/package.py +++ b/var/spack/repos/builtin/packages/r-pscbs/package.py @@ -7,23 +7,31 @@ from spack import * class RPscbs(RPackage): - """Segmentation of allele-specific DNA copy number data and detection of + """Analysis of Parent-Specific DNA Copy Numbers. + + Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.""" - homepage = "https://github.com/HenrikBengtsson/PSCBS" - url = "https://cloud.r-project.org/src/contrib/PSCBS_0.65.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/PSCBS" + cran = "PSCBS" + version('0.66.0', sha256='58805636e55e0fd3f57bd4a0e296a8bb3d57a7bdd0fdd5868a73ddc83d173a93') version('0.65.0', sha256='3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) + depends_on('r-r-methodss3@1.8.1:', type=('build', 'run'), when='@0.66.0:') depends_on('r-r-oo@1.22.1:', type=('build', 'run')) + depends_on('r-r-oo@1.24.0:', type=('build', 'run'), when='@0.66.0:') depends_on('r-r-utils@2.8.0:', type=('build', 'run')) + depends_on('r-r-utils@2.11.0:', type=('build', 'run'), when='@0.66.0:') depends_on('r-r-cache@0.13.0:', type=('build', 'run')) + depends_on('r-r-cache@0.15.0:', type=('build', 'run'), when='@0.66.0:') depends_on('r-matrixstats@0.54.0:', type=('build', 'run')) + depends_on('r-matrixstats@0.61.0:', type=('build', 'run'), when='@0.66.0:') depends_on('r-aroma-light@2.4.0:', type=('build', 'run')) depends_on('r-dnacopy@1.42.0:', type=('build', 'run')) depends_on('r-listenv@0.7.0:', type=('build', 'run')) + depends_on('r-listenv@0.8.0:', type=('build', 'run'), when='@0.66.0:') depends_on('r-future@1.12.0:', type=('build', 'run')) + depends_on('r-future@1.22.1:', type=('build', 'run'), when='@0.66.0:') diff --git a/var/spack/repos/builtin/packages/r-pspline/package.py b/var/spack/repos/builtin/packages/r-pspline/package.py index d63f44d723..0fa9be5598 100644 --- a/var/spack/repos/builtin/packages/r-pspline/package.py +++ b/var/spack/repos/builtin/packages/r-pspline/package.py @@ -7,11 +7,11 @@ from spack import * class RPspline(RPackage): - """Smoothing splines with penalties on order m derivatives.""" + """Penalized Smoothing Splines. - homepage = "https://cloud.r-project.org/package=pspline" - url = "https://cloud.r-project.org/src/contrib/pspline_1.0-18.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pspline" + Smoothing splines with penalties on order m derivatives.""" + + cran = "pspline" version('1.0-18', sha256='f71cf293bd5462e510ac5ad16c4a96eda18891a0bfa6447dd881c65845e19ac7') diff --git a/var/spack/repos/builtin/packages/r-psych/package.py b/var/spack/repos/builtin/packages/r-psych/package.py index ddee749d82..7d2c7d102e 100644 --- a/var/spack/repos/builtin/packages/r-psych/package.py +++ b/var/spack/repos/builtin/packages/r-psych/package.py @@ -7,7 +7,7 @@ from spack import * class RPsych(RPackage): - """Procedures for Psychological, Psychometric, and Personality Research + """Procedures for Psychological, Psychometric, and Personality Research. A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis @@ -25,10 +25,9 @@ class RPsych(RPackage): research. For more information, see the <http://personality-project.org/r> web page.""" - homepage = "https://personality-project.org/r/psych" - url = "https://cloud.r-project.org/src/contrib/psych_1.7.8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/psych" + cran = "psych" + version('2.1.9', sha256='1475e03a17f1ae6837834f01c2472aed68887c89d90a84a3e09a532ce218500c') version('2.0.12', sha256='8a71d4a1d8bc8c96703f9b4515cfb497e1947c6e017cb08270a7cfb36ce1ad4c') version('1.8.12', sha256='6e175e049bc1ee5b79a9e51ccafb22b962b4e6c839ce5c9cfa1ad83967037743') version('1.8.10', sha256='e8901ddab14729bfccbd82a8824fbb6523c10c2cd8fb7199b1ca56a7ffcb6e58') @@ -37,4 +36,5 @@ class RPsych(RPackage): depends_on('r-mnormt', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) - depends_on('r-foreign', when='@:1.8.12', type=('build', 'run')) + + depends_on('r-foreign', type=('build', 'run'), when='@:1.8.12') diff --git a/var/spack/repos/builtin/packages/r-ptw/package.py b/var/spack/repos/builtin/packages/r-ptw/package.py index 35d7785dbf..c58fbdeb71 100644 --- a/var/spack/repos/builtin/packages/r-ptw/package.py +++ b/var/spack/repos/builtin/packages/r-ptw/package.py @@ -7,7 +7,7 @@ from spack import * class RPtw(RPackage): - """Parametric Time Warping + """Parametric Time Warping. Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal @@ -21,12 +21,12 @@ class RPtw(RPackage): directory of the source package - the vignette source can be found on the package github site.""" - homepage = "https://cloud.r-project.org/package=ptw" - url = "https://cloud.r-project.org/src/contrib/ptw_1.9-12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ptw" + cran = "ptw" + version('1.9-16', sha256='7e87c34b9eeaeabe3bfb937162e6cda4dd48d6bd6a97b9db8bb8303d131caa66') version('1.9-15', sha256='22fa003f280bc000f46bca88d69bf332b29bc68435115ba8044533b70bfb7b46') version('1.9-13', sha256='7855e74a167db3d3eba9df9d9c3daa25d7cf487cbcfe8b095f16d96eba862f46') version('1.9-12', sha256='cdb1752e04e661e379f11867b0a17e2177e9ee647c54bbcc37d39d6b8c062b84') depends_on('r-nloptr', type=('build', 'run')) + depends_on('r-rcppde', type=('build', 'run'), when='@1.9-16:') diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py index 87787622f5..aaee25474b 100644 --- a/var/spack/repos/builtin/packages/r-purrr/package.py +++ b/var/spack/repos/builtin/packages/r-purrr/package.py @@ -7,11 +7,11 @@ from spack import * class RPurrr(RPackage): - """A complete and consistent functional programming toolkit for R.""" + """Functional Programming Tools. - homepage = "https://purrr.tidyverse.org/" - url = "https://cloud.r-project.org/src/contrib/purrr_0.2.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/purrr" + A complete and consistent functional programming toolkit for R.""" + + cran = "purrr" version('0.3.4', sha256='23ebc93bc9aed9e7575e8eb9683ff4acc0270ef7d6436cc2ef4236a9734840b2') version('0.3.2', sha256='27c74dd9e4f6f14bf442473df22bcafc068822f7f138f0870326532f143a9a31') @@ -19,7 +19,8 @@ class RPurrr(RPackage): version('0.2.4', sha256='ed8d0f69d29b95c2289ae52be08a0e65f8171abb6d2587de7b57328bf3b2eb71') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r@3.2:', when='@0.3.3:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@0.3.3:') depends_on('r-magrittr@1.5:', type=('build', 'run')) depends_on('r-rlang@0.3.1:', type=('build', 'run')) - depends_on('r-tibble', when='@:0.2.9', type=('build', 'run')) + + depends_on('r-tibble', type=('build', 'run'), when='@:0.2.9') diff --git a/var/spack/repos/builtin/packages/r-pvclust/package.py b/var/spack/repos/builtin/packages/r-pvclust/package.py index b712dd29de..aad55c22bb 100644 --- a/var/spack/repos/builtin/packages/r-pvclust/package.py +++ b/var/spack/repos/builtin/packages/r-pvclust/package.py @@ -7,17 +7,15 @@ from spack import * class RPvclust(RPackage): - """pvclust: Hierarchical Clustering with P-Values via Multiscale Bootstrap - Resampling + """Hierarchical Clustering with P-Values via Multiscale Bootstrap + Resampling. An implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides SI (selective inference) p-value, AU (approximately unbiased) p-value and BP (bootstrap probability) value for each cluster in a dendrogram.""" - homepage = "https://cloud.r-project.org/package=pvclust" - url = "https://cloud.r-project.org/src/contrib/pvclust_2.2-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/pvclust" + cran = "pvclust" version('2.2-0', sha256='7892853bacd413b5a921006429641ad308a344ca171b3081c15e4c522a8b0201') diff --git a/var/spack/repos/builtin/packages/r-qs/package.py b/var/spack/repos/builtin/packages/r-qs/package.py index 809535c147..78141b337d 100644 --- a/var/spack/repos/builtin/packages/r-qs/package.py +++ b/var/spack/repos/builtin/packages/r-qs/package.py @@ -7,20 +7,21 @@ from spack import * class RQs(RPackage): - """Quick Serialization of R Objects + """Quick Serialization of R Objects. - Provides functions for quickly writing and reading any R object - to and from disk.""" + Provides functions for quickly writing and reading any R object to and from + disk.""" - homepage = "https://cloud.r-project.org/web/packages/qs/index.html" - url = "https://cloud.r-project.org/src/contrib/qs_0.23.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/qs" + cran = "qs" maintainers = ['dorton21'] + version('0.25.2', sha256='fe428ae5dc46f88fdf454ca74c4a073f5ac288d6d039080a3c0d66c4ebbd5cbf') version('0.23.6', sha256='c6e958e9741ee981bf2388c91b8f181718ffb0f32283cd7ebcd2d054817280e4') depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run'), when='@0.25.2:') depends_on('r-rcpp', type=('build', 'run')) depends_on('r-rapiserialize', type=('build', 'run')) depends_on('r-stringfish@0.14.1:', type=('build', 'run')) + depends_on('r-stringfish@0.15.1:', type=('build', 'run'), when='@0.25.2:') diff --git a/var/spack/repos/builtin/packages/r-qtl/package.py b/var/spack/repos/builtin/packages/r-qtl/package.py index 493c568caa..94ccccd7f6 100644 --- a/var/spack/repos/builtin/packages/r-qtl/package.py +++ b/var/spack/repos/builtin/packages/r-qtl/package.py @@ -7,16 +7,15 @@ from spack import * class RQtl(RPackage): - """Tools for Analyzing QTL Experiments + """Tools for Analyzing QTL Experiments. Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.""" - homepage = "https://rqtl.org" - url = "https://cloud.r-project.org/src/contrib/qtl_1.44-9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/qtl" + cran = "qtl" + version('1.50', sha256='2d38656f04dc4187aefe56c29a8f915b8c7e222d76b84afe7045d272294f9ed5') version('1.47-9', sha256='6ba4e7b40d946b3ab68d54624599284b1d352c86fb50d31b134826be758ece41') version('1.44-9', sha256='315063f0c3fbb95cd2169eb4109ade0339e8f3c28670b38c3167214b9bdf950e') diff --git a/var/spack/repos/builtin/packages/r-quadprog/package.py b/var/spack/repos/builtin/packages/r-quadprog/package.py index 5957d24c35..0a0e46a7c2 100644 --- a/var/spack/repos/builtin/packages/r-quadprog/package.py +++ b/var/spack/repos/builtin/packages/r-quadprog/package.py @@ -7,14 +7,12 @@ from spack import * class RQuadprog(RPackage): - """Functions to Solve Quadratic Programming Problems + """Functions to Solve Quadratic Programming Problems. This package contains routines and documentation for solving quadratic programming problems.""" - homepage = "https://cloud.r-project.org/package=quadprog" - url = "https://cloud.r-project.org/src/contrib/quadprog_1.5-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/quadprog" + cran = "quadprog" version('1.5-8', sha256='22128dd6b08d3516c44ff89276719ad4fe46b36b23fdd585274fa3a93e7a49cd') version('1.5-7', sha256='1af41e57df6f2d08ee8b72a1a5ada137beadb36c7ec9ab9bdb7c05226e8ae76d') diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py index 64e12dc424..2c5b12290d 100644 --- a/var/spack/repos/builtin/packages/r-quantmod/package.py +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -7,14 +7,12 @@ from spack import * class RQuantmod(RPackage): - """Quantitative Financial Modelling Framework + """Quantitative Financial Modelling Framework. Specify, build, trade, and analyse quantitative financial trading strategies.""" - homepage = "https://www.quantmod.com/" - url = "https://cloud.r-project.org/src/contrib/quantmod_0.4-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/quantmod" + cran = "quantmod" version('0.4.18', sha256='aa40448e93a1facf399213ac691784007731e869ad243fe762381ab099cd6c35') version('0.4-15', sha256='7ef2e798d4d8e4d2af0a5b2b9fecebec30568087afbd24bfd923cdeb8b53df53') @@ -22,7 +20,7 @@ class RQuantmod(RPackage): version('0.4-10', sha256='030040aa567adaba1ea4a1f05eb45712dbdaabbabca72733e7fb2984051f688b') version('0.4-5', sha256='c7889eb55a21296e7bda1242c46e734a0a8bd6dcbf5726aafae5313354eec893') - depends_on('r@3.2.0:', when='@0.4-11:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@0.4-11:') depends_on('r-xts@0.9-0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) depends_on('r-ttr@0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py index 170cc91961..b220ae06e0 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -7,18 +7,20 @@ from spack import * class RQuantreg(RPackage): - """Quantile Regression + """Quantile Regression. Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection - methods based on expected shortfall risk are also now included.""" + methods based on expected shortfall risk are also now included. See Koenker + (2006) <doi:10.1017/CBO9780511754098> and Koenker et al. (2017) + <doi:10.1201/9781315120256>.""" - homepage = "https://cloud.r-project.org/package=quantreg" - url = "https://cloud.r-project.org/src/contrib/quantreg_5.29.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/quantreg" + cran = "quantreg" + version('5.87', sha256='9ad7ef09e5f53b89ef09dea3a1aa25cfda9f3f2528994f874ec1cd9ca7fda38e') + version('5.86', sha256='71d1c829af7574ca00575cc0375376ac3ecd54b3d6d36e8eecd71ed8acb9d605') version('5.82', sha256='eac34e1e34d00a24ed7cb6981af258a3afc561843c00501de3206b4540548c07') version('5.51', sha256='df1330d245f66ee6d924b209bd4c15d44ff8cce52667959ec0d299975428bdb1') version('5.42.1', sha256='4cc2b0883c52694e58fcfde83e30e4a54be9f4d9cbcf6138f6498cc8e0b3ccab') @@ -30,4 +32,5 @@ class RQuantreg(RPackage): depends_on('r-sparsem', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-matrixmodels', type=('build', 'run')) - depends_on('r-conquer', when='@5.82:', type=('build', 'run')) + + depends_on('r-conquer', type=('build', 'run'), when='@5.82:5.86') diff --git a/var/spack/repos/builtin/packages/r-questionr/package.py b/var/spack/repos/builtin/packages/r-questionr/package.py index bf8b6d3776..9485cae149 100644 --- a/var/spack/repos/builtin/packages/r-questionr/package.py +++ b/var/spack/repos/builtin/packages/r-questionr/package.py @@ -7,22 +7,25 @@ from spack import * class RQuestionr(RPackage): - """Set of functions to make the processing and analysis of surveys easier : + """Functions to Make Surveys Processing Easier. + + Set of functions to make the processing and analysis of surveys easier: interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.""" - homepage = "https://cloud.r-project.org/package=questionr" - url = "https://cloud.r-project.org/src/contrib/questionr_0.7.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/questionr" + cran = "questionr" + version('0.7.7', sha256='ce24c40bd98dbeca615b9eb2a9cd2da26852821dc3840f8394eeecb0739dfd56') + version('0.7.6', sha256='4b71d049d9e032157e12a7809dbfa2a39262b49d0c7a03ed434791a66f0cee5e') version('0.7.4', sha256='818ad87723aa7ebe466b3a639c9e86b7f77e6a341c8d9a933073925a21d4555c') - depends_on('r@3.5.0:', type=('build', 'run')) - depends_on('r-shiny@1.0.5:', type=('build', 'run')) - depends_on('r-miniui', type=('build', 'run')) - depends_on('r-rstudioapi', type=('build', 'run')) - depends_on('r-highr', type=('build', 'run')) - depends_on('r-styler', type=('build', 'run')) - depends_on('r-classint', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r-shiny@1.0.5:', type=('build', 'run')) + depends_on('r-miniui', type=('build', 'run')) + depends_on('r-rstudioapi', type=('build', 'run')) + depends_on('r-highr', type=('build', 'run')) + depends_on('r-styler', type=('build', 'run')) + depends_on('r-classint', type=('build', 'run')) + depends_on('r-htmltools', type=('build', 'run')) depends_on('r-labelled@2.6.0:', type=('build', 'run')) + depends_on('xclip', when='platform=linux') diff --git a/var/spack/repos/builtin/packages/r-quickplot/package.py b/var/spack/repos/builtin/packages/r-quickplot/package.py index 103b1cd47f..c3d2c41df7 100644 --- a/var/spack/repos/builtin/packages/r-quickplot/package.py +++ b/var/spack/repos/builtin/packages/r-quickplot/package.py @@ -7,16 +7,14 @@ from spack import * class RQuickplot(RPackage): - """A System of Plotting Optimized for Speed and Modularity + """A System of Plotting Optimized for Speed and Modularity. - A high-level plotting system, built using 'grid' graphics, that - is optimized for speed and modularity. This has great utility - for quick visualizations when testing code, with the key benefit - that visualizations are updated independently of one another.""" + A high-level plotting system, built using 'grid' graphics, that is + optimized for speed and modularity. This has great utility for quick + visualizations when testing code, with the key benefit that visualizations + are updated independently of one another.""" - homepage = "https://quickplot.predictiveecology.org/" - url = "https://cloud.r-project.org/src/contrib/quickPlot_0.1.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/quickPlot" + cran = "quickPlot" maintainers = ['dorton21'] diff --git a/var/spack/repos/builtin/packages/r-r-cache/package.py b/var/spack/repos/builtin/packages/r-r-cache/package.py index 9e86cf7a76..45d6c31ac1 100644 --- a/var/spack/repos/builtin/packages/r-r-cache/package.py +++ b/var/spack/repos/builtin/packages/r-r-cache/package.py @@ -7,23 +7,28 @@ from spack import * class RRCache(RPackage): - """Memoization can be used to speed up repetitive and computational - expensive function calls. The first time a function that implements - memoization is called the results are stored in a cache memory. The next - time the function is called with the same set of parameters, the results - are momentarily retrieved from the cache avoiding repeating the - calculations. With this package, any R object can be cached in a key-value - storage where the key can be an arbitrary set of R objects. The cache - memory is persistent (on the file system).""" + """Fast and Light-Weight Caching (Memoization) of Objects and Results to + Speed Up Computations. - homepage = "https://github.com/HenrikBengtsson/R.cache" - url = "https://cloud.r-project.org/src/contrib/R.cache_0.14.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/R.cache" + Memoization can be used to speed up repetitive and computational expensive + function calls. The first time a function that implements memoization is + called the results are stored in a cache memory. The next time the function + is called with the same set of parameters, the results are momentarily + retrieved from the cache avoiding repeating the calculations. With this + package, any R object can be cached in a key-value storage where the key + can be an arbitrary set of R objects. The cache memory is persistent (on + the file system).""" + cran = "R.cache" + + version('0.15.0', sha256='adb4d3b08f7917e10fe6188c7b90a3318701a974c58eaa09943b929382bdf126') version('0.14.0', sha256='18af4e372440b9f28b4b71346c8ed9de220232f9903730ccee2bfb3c612c16d9') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) + depends_on('r-r-methodss3@1.8.1:', type=('build', 'run'), when='@0.15.0:') depends_on('r-r-oo@1.23.0:', type=('build', 'run')) + depends_on('r-r-oo@1.24.0:', type=('build', 'run'), when='@0.15.0:') depends_on('r-r-utils@2.8.0:', type=('build', 'run')) + depends_on('r-r-utils@2.10.1:', type=('build', 'run'), when='@0.15.0:') depends_on('r-digest@0.6.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r-methodss3/package.py b/var/spack/repos/builtin/packages/r-r-methodss3/package.py index 04f6383ee8..3c2db2cfa7 100644 --- a/var/spack/repos/builtin/packages/r-r-methodss3/package.py +++ b/var/spack/repos/builtin/packages/r-r-methodss3/package.py @@ -7,21 +7,18 @@ from spack import * class RRMethodss3(RPackage): - """S3 Methods Simplified + """S3 Methods Simplified. - Methods that simplify the setup of S3 generic functions and - S3 methods. Major effort has been made in making definition of - methods as simple as possible with a minimum of maintenance for - package developers. For example, generic functions are created - automatically, if missing, and naming conflict are automatically - solved, if possible. The method setMethodS3() is a good start - for those who in the future may want to migrate to S4. This is - a cross-platform package implemented in pure R that generates - standard S3 methods.""" + Methods that simplify the setup of S3 generic functions and S3 methods. + Major effort has been made in making definition of methods as simple as + possible with a minimum of maintenance for package developers. For example, + generic functions are created automatically, if missing, and naming + conflict are automatically solved, if possible. The method setMethodS3() is + a good start for those who in the future may want to migrate to S4. This is + a cross-platform package implemented in pure R that generates standard S3 + methods.""" - homepage = "https://cloud.r-project.org/package=R.methodsS3" - url = "https://cloud.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/R.methodsS3" + cran = "R.methodsS3" version('1.8.1', sha256='8a98fb81bcfa78193450f855f614f6f64e6c65daf115f301d97d1f474f5e619b') version('1.7.1', sha256='44b840399266cd27f8f9157777b4d9d85ab7bd31bfdc143b3fc45079a2d8e687') diff --git a/var/spack/repos/builtin/packages/r-r-oo/package.py b/var/spack/repos/builtin/packages/r-r-oo/package.py index 5acc4267db..990c5b11cd 100644 --- a/var/spack/repos/builtin/packages/r-r-oo/package.py +++ b/var/spack/repos/builtin/packages/r-r-oo/package.py @@ -7,19 +7,16 @@ from spack import * class RROo(RPackage): - """R Object-Oriented Programming with or without References + """R Object-Oriented Programming with or without References. - Methods and classes for object-oriented programming in R with - or without references. Large effort has been made on making - definition of methods as simple as possible with a minimum of - maintenance for package developers. The package has been developed - since 2001 and is now considered very stable. This is a - cross-platform package implemented in pure R that defines + Methods and classes for object-oriented programming in R with or without + references. Large effort has been made on making definition of methods as + simple as possible with a minimum of maintenance for package developers. + The package has been developed since 2001 and is now considered very + stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.""" - homepage = "https://github.com/HenrikBengtsson/R.oo" - url = "https://cloud.r-project.org/src/contrib/R.oo_1.21.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/R.oo" + cran = "R.oo" version('1.24.0', sha256='37a1dab8dd668ceba69a1ba36c0c60e9809e29b74bd56d1e8ed519e19c8e3bb6') version('1.23.0', sha256='f5124ce3dbb0a62e8ef1bfce2de2d1dc2f776e8c48fd8cac358f7f5feb592ea1') @@ -28,4 +25,4 @@ class RROo(RPackage): depends_on('r@2.13.0:', type=('build', 'run')) depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) - depends_on('r-r-methodss3@1.8.0:', when='@1.24.0:', type=('build', 'run')) + depends_on('r-r-methodss3@1.8.0:', type=('build', 'run'), when='@1.24.0:') diff --git a/var/spack/repos/builtin/packages/r-r-utils/package.py b/var/spack/repos/builtin/packages/r-r-utils/package.py index d50adae3a7..d176f3698c 100644 --- a/var/spack/repos/builtin/packages/r-r-utils/package.py +++ b/var/spack/repos/builtin/packages/r-r-utils/package.py @@ -7,21 +7,21 @@ from spack import * class RRUtils(RPackage): - """Various Programming Utilities + """Various Programming Utilities. - Utility functions useful when programming and - developing R packages.""" + Utility functions useful when programming and developing R packages.""" - homepage = "https://github.com/HenrikBengtsson/R.utils" - url = "https://cloud.r-project.org/src/contrib/R.utils_2.5.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/R.utils" + cran = "R.utils" + version('2.11.0', sha256='622860f995f78be3a6e439f29d945874c5cb0866f6a73a9b43ac1d4d7f23fed8') version('2.10.1', sha256='957a4f51998c79403a50f6a46266e6553bbf08757b26bf80603a423bceb45abf') version('2.9.0', sha256='b2aacc5a55d3ea86c41ac576d2583e446af145f4cb1103ad7b6f95b09ab09ff0') version('2.5.0', sha256='1ae1a0f0c6a4972bb2369a2dbccd29ade87d747255ff9cb5a0bd784a5be1039f') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-r-oo@1.22.0:', type=('build', 'run')) - depends_on('r-r-oo@1.23.0:', when='@2.10.1:', type=('build', 'run')) + depends_on('r-r-oo@1.23.0:', type=('build', 'run'), when='@2.10.1:') + depends_on('r-r-oo@1.24.0:', type=('build', 'run'), when='@2.11.0:') depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) - depends_on('r-r-methodss3@1.8.0:', when='@2.10.1:', type=('build', 'run')) + depends_on('r-r-methodss3@1.8.0:', type=('build', 'run'), when='@2.10.1:') + depends_on('r-r-methodss3@1.8.1:', type=('build', 'run'), when='@2.11.0:') diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py index 8a9282ace4..104c2fc447 100644 --- a/var/spack/repos/builtin/packages/r-r6/package.py +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -7,7 +7,7 @@ from spack import * class RR6(RPackage): - """Encapsulated Classes with Reference Semantics + """Encapsulated Classes with Reference Semantics. The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, @@ -16,7 +16,6 @@ class RR6(RPackage): public and private members, and they support inheritance, even when the classes are defined in different packages.""" - homepage = "https://github.com/wch/R6/" cran = "R6" version('2.5.1', sha256='8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48') diff --git a/var/spack/repos/builtin/packages/r-rainbow/package.py b/var/spack/repos/builtin/packages/r-rainbow/package.py index 9b102edec1..e1edd5b498 100644 --- a/var/spack/repos/builtin/packages/r-rainbow/package.py +++ b/var/spack/repos/builtin/packages/r-rainbow/package.py @@ -5,7 +5,9 @@ class RRainbow(RPackage): - """Visualizing functional data and identifying functional outliers.""" + """Bagplots, Boxplots and Rainbow Plots for Functional Data. + + Visualizing functional data and identifying functional outliers.""" cran = 'rainbow' diff --git a/var/spack/repos/builtin/packages/r-randomfields/package.py b/var/spack/repos/builtin/packages/r-randomfields/package.py index 2df91f1fd5..316bb241ea 100644 --- a/var/spack/repos/builtin/packages/r-randomfields/package.py +++ b/var/spack/repos/builtin/packages/r-randomfields/package.py @@ -7,27 +7,25 @@ from spack import * class RRandomfields(RPackage): - """Simulation and Analysis of Random Fields + """Simulation and Analysis of Random Fields. Methods for the inference on and the simulation of Gaussian fields are - provided, as well as methods for the simulation of extreme value random - fields. Main geostatistical parts are based on the books by Christian - Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre - Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie - <doi:10.1002/9781119115151>. For the extreme value random fields see - Oesting, Schlather, Schillings (2019) <doi.org/10.1002/sta4.228> and - Schlather (2002) <doi.org/10.1023/A:1020977924878>.""" + provided. Furthermore, methods for the simulation of extreme value random + fields are provided. Main geostatistical parts are based among others on + the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>.""" - homepage = "https://cloud.r-project.org/package=RandomFields" - url = "https://cloud.r-project.org/src/contrib/RandomFields_3.1.50.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFields" + cran = "RandomFields" + version('3.3.14', sha256='242600b9bf93af9d49a06c00ff2398054a882d644a4653ea348533410c3db930') + version('3.3.13', sha256='dbf82a8a39a79ca1b53665c2375cdd58f7accb38062063bbd9854d13493d3f49') version('3.3.8', sha256='8a08e2fdae428e354a29fb6818ae781cc56235a6849a0d29574dc756f73199d0') version('3.3.6', sha256='51b7bfb4e5bd7fd0ce1207c77f428508a6cd3dfc9de01545a8724dfd9c050213') version('3.3.4', sha256='a340d4f3ba7950d62acdfa19b9724c82e439d7b1a9f73340124038b7c90c73d4') version('3.1.50', sha256='2d6a07c3a716ce20f9c685deb59e8fcc64fd52c8a50b0f04baf451b6b928e848') depends_on('r@3.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@3.3.8:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.3.8:') depends_on('r-sp', type=('build', 'run')) depends_on('r-randomfieldsutils@0.5.1:', type=('build', 'run')) + depends_on('r-randomfieldsutils@0.5.5:', type=('build', 'run'), when='@3.3.13:') + depends_on('r-randomfieldsutils@1.1:', type=('build', 'run'), when='@3.3.14:') diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index b6f4a0cebd..adb16cfc08 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -7,15 +7,17 @@ from spack import * class RRandomfieldsutils(RPackage): - """Various utilities are provided that might be used in spatial statistics - and elsewhere. It delivers a method for solving linear equations that - checks the sparsity of the matrix before any algorithm is used. - Furthermore, it includes the Struve functions.""" + """Utilities for the Simulation and Analysis of Random Fields and Genetic + Data. - homepage = "https://cloud.r-project.org/package=RandomFieldsUtils" - url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.5.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFieldsUtils" + Various utilities are provided that might be used in spatial statistics and + elsewhere. It delivers a method for solving linear equations that checks + the sparsity of the matrix before any algorithm is used.""" + cran = "RandomFieldsUtils" + + version('1.1.0', sha256='f472602fed449a505a2e5787ab8a6c8c1b764335980adaeeb7b1f24069124a9d') + version('0.5.6', sha256='07f484443dffab53fb530e56f1e36e7a59e77768638555975587b6a1e619480b') version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') version('0.5.1', sha256='a95aab4e2025c4247503ff513570a65aa3c8e63cb7ce2979c9317a2798dfaca2') diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py index 6e621f72dd..9d781f19bd 100644 --- a/var/spack/repos/builtin/packages/r-randomforest/package.py +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -7,15 +7,15 @@ from spack import * class RRandomforest(RPackage): - """Classification and regression based on a forest of trees using random + """Breiman and Cutler's Random Forests for Classification and Regression. + + Classification and regression based on a forest of trees using random inputs.""" - homepage = "https://www.stat.berkeley.edu/~breiman/RandomForests/" - url = "https://cloud.r-project.org/src/contrib/randomForest_4.6-12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/randomForest" + cran = "randomForest" version('4.6-14', sha256='f4b88920419eb0a89d0bc5744af0416d92d112988702dc726882394128a8754d') version('4.6-12', sha256='6e512f8f88a51c01a918360acba61f1f39432f6e690bc231b7864218558b83c4') - depends_on('r@2.5.0:', when='@:4.6-12', type=('build', 'run')) - depends_on('r@3.2.2:', when='@4.6-14:', type=('build', 'run')) + depends_on('r@2.5.0:', type=('build', 'run')) + depends_on('r@3.2.2:', type=('build', 'run'), when='@4.6-14:') diff --git a/var/spack/repos/builtin/packages/r-randomglm/package.py b/var/spack/repos/builtin/packages/r-randomglm/package.py index f5810f415f..b1e71b8a10 100644 --- a/var/spack/repos/builtin/packages/r-randomglm/package.py +++ b/var/spack/repos/builtin/packages/r-randomglm/package.py @@ -7,15 +7,16 @@ from spack import * class RRandomglm(RPackage): - """randomGLM: Random General Linear Model Prediction""" + """Random General Linear Model Prediction. - homepage = "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/" - url = "https://cloud.r-project.org/src/contrib/randomGLM_1.02-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/randomGLM" + The package implements a bagging predictor based on general linear + models.""" + + cran = "randomGLM" version('1.02-1', sha256='3bf7c1dbdacc68125f8ae3014b9bc546dd3328d04ad015d154781bdf3f1a230c') depends_on('r@2.14.0:', type=('build', 'run')) - depends_on('r-doparallel', type=('build', 'run')) - depends_on('r-foreach', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) + depends_on('r-foreach', type=('build', 'run')) + depends_on('r-doparallel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ranger/package.py b/var/spack/repos/builtin/packages/r-ranger/package.py index 6cd2fc0f60..dd79e0774a 100644 --- a/var/spack/repos/builtin/packages/r-ranger/package.py +++ b/var/spack/repos/builtin/packages/r-ranger/package.py @@ -7,19 +7,18 @@ from spack import * class RRanger(RPackage): - """A Fast Implementation of Random Forests + """A Fast Implementation of Random Forests. A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' - (R package 'Matrix') can be directly analyzed.""" + (R package 'Matrix') can be directly analyzed.""" - homepage = "https://cloud.r-project.org/package=ranger" - url = "https://cloud.r-project.org/src/contrib/ranger_0.8.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ranger" + cran = "ranger" + version('0.13.1', sha256='60934f0accc21edeefddbb4ddebfdd7cd10a3d3e90b31aa2e6e4b7f50d632d0a') version('0.12.1', sha256='fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef') version('0.11.2', sha256='13ac8a9433fdd92f62f66de44abc52477dcbb436b2045c1947951a266bffbeeb') version('0.11.1', sha256='999fb114602e27601ff0fe8ab461c39d667c6f5e8434e7feb3d21c7caf0dcffb') diff --git a/var/spack/repos/builtin/packages/r-rann/package.py b/var/spack/repos/builtin/packages/r-rann/package.py index 707d5c6044..76482217de 100644 --- a/var/spack/repos/builtin/packages/r-rann/package.py +++ b/var/spack/repos/builtin/packages/r-rann/package.py @@ -7,15 +7,15 @@ from spack import * class RRann(RPackage): - """Finds the k nearest neighbours for every point in a given dataset in O(N + """Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric. + + Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.""" - homepage = "https://github.com/jefferis/RANN" - url = "https://cloud.r-project.org/src/contrib/RANN_2.6.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RANN" + cran = "RANN" version('2.6.1', sha256='b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182') diff --git a/var/spack/repos/builtin/packages/r-rapidjsonr/package.py b/var/spack/repos/builtin/packages/r-rapidjsonr/package.py new file mode 100644 index 0000000000..e639095a96 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rapidjsonr/package.py @@ -0,0 +1,19 @@ +# 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 RRapidjsonr(RPackage): + """'Rapidjson' C++ Header Files. + + Provides JSON parsing capability through the 'Rapidjson' 'C++' header-only + library.""" + + cran = "rapidjsonr" + + version('1.2.0', sha256='62c94fcdcf5d0fbdfa2f6168affe526bf547c37c16d94e2e1b78d7bf608eed1f') + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rapiserialize/package.py b/var/spack/repos/builtin/packages/r-rapiserialize/package.py index 9d2006f65f..545e80ec90 100644 --- a/var/spack/repos/builtin/packages/r-rapiserialize/package.py +++ b/var/spack/repos/builtin/packages/r-rapiserialize/package.py @@ -7,20 +7,18 @@ from spack import * class RRapiserialize(RPackage): - """R API Serialization + """R API Serialization. This package provides other packages with access to the internal R - serialization code. Access to this code is provided at the C function - level by using the registration of native function mechanism. Client - packages simply include a single header file RApiSerializeAPI.h provided - by this package. This packages builds on the Rhpc package by Junji Nakano - and Ei-ji Nakama which also includes a (partial) copy of the file - src/main/serialize.c from R itself. The R Core group is the original - author of the serialization code made available by this package.""" + serialization code. Access to this code is provided at the C function level + by using the registration of native function mechanism. Client packages + simply include a single header file RApiSerializeAPI.h provided by this + package. This packages builds on the Rhpc package by Junji Nakano and Ei-ji + Nakama which also includes a (partial) copy of the file + src/main/serialize.c from R itself. The R Core group is the original author + of the serialization code made available by this package.""" - homepage = "https://cloud.r-project.org/web/packages/RApiSerialize/index.html" - url = "https://cloud.r-project.org/src/contrib/RApiSerialize_0.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RApiSerialize" + cran = "RApiSerialize" maintainers = ['dorton21'] diff --git a/var/spack/repos/builtin/packages/r-rappdirs/package.py b/var/spack/repos/builtin/packages/r-rappdirs/package.py index 41756949b4..84566e6a60 100644 --- a/var/spack/repos/builtin/packages/r-rappdirs/package.py +++ b/var/spack/repos/builtin/packages/r-rappdirs/package.py @@ -7,15 +7,16 @@ from spack import * class RRappdirs(RPackage): - """An easy way to determine which directories on the users computer - you should use to save data, caches and logs. A port of Python's - 'Appdirs' to R.""" + """Application Directories: Determine Where to Save Data, Caches, and Logs. + + An easy way to determine which directories on the users computer you should + use to save data, caches and logs. A port of Python's 'Appdirs' + (<https://github.com/ActiveState/appdirs>) to R.""" - homepage = "https://cloud.r-project.org/package=rappdirs" cran = "rappdirs" version('0.3.3', sha256='49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184') version('0.3.1', sha256='2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a') depends_on('r@2.14:', type=('build', 'run')) - depends_on('r@3.2:', when='@0.3.2:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@0.3.2:') diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py index 0fee2b2648..20d72d54c1 100644 --- a/var/spack/repos/builtin/packages/r-raster/package.py +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -7,24 +7,27 @@ from spack import * class RRaster(RPackage): - """Geographic Data Analysis and Modeling + """Geographic Data Analysis and Modeling. Reading, writing, manipulating, analyzing and modeling of spatial data. The package implements basic and high-level functions for raster data and for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.""" - homepage = "https://cloud.r-project.org/package=raster" - url = "https://cloud.r-project.org/src/contrib/raster_2.5-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/raster" + cran = "raster" + version('3.5-15', sha256='29c7d3c5d34284f8b5a2ddc9989fbcf092ce209d5eb5310ebc772b5ebdfdd685') + version('3.5-11', sha256='e6c4823925260c65fe98585d7a0d47778616ae2e4eb1a1782b219580a9db61a3') version('3.4-5', sha256='c6620d790b3aba1b64aec31325f726e63f26a14a1b48c1a0f9167a0b1a64e4a5') version('2.9-23', sha256='90aaec9e3b1e3e6015d9993ea7491e008f2f71990f8abb8610f979c4e28b38af') version('2.9-22', sha256='8107d95f1aa85cea801c8101c6aa391becfef4b5b915d9bc7a323531fee26128') version('2.5-8', sha256='47992abd783450513fbce3770298cc257030bf0eb77e42aa3a4b3924b16264cc') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@3.4-5:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.4-5:') depends_on('r-sp@1.2-0:', type=('build', 'run')) - depends_on('r-sp@1.4.1:', when='@3.4-5:', type=('build', 'run')) + depends_on('r-sp@1.4.1:', type=('build', 'run'), when='@3.4-5:') + depends_on('r-sp@1.4.5:', type=('build', 'run'), when='@3.5-11:') depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-terra@1.4-11:', type=('build', 'run'), when='@3.5-11:') + depends_on('r-terra@1.5-12:', type=('build', 'run'), when='@3.5-15:') diff --git a/var/spack/repos/builtin/packages/r-rbibutils/package.py b/var/spack/repos/builtin/packages/r-rbibutils/package.py index 390972d974..8351ab50ab 100644 --- a/var/spack/repos/builtin/packages/r-rbibutils/package.py +++ b/var/spack/repos/builtin/packages/r-rbibutils/package.py @@ -7,17 +7,16 @@ from spack import * class RRbibutils(RPackage): - """Convert Between Bibliography Formats + """Convert Between Bibliography Formats. Converts between a number of bibliography formats, including 'BibTeX', 'BibLaTeX' and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all bibliography formats and character encodings implemented in 'bibutils'.""" - homepage = "https://geobosh.github.io/rbibutils/" - url = "https://cloud.r-project.org/src/contrib/rbibutils_2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rbibutils" + cran = "rbibutils" + version('2.2.7', sha256='7c9e6719556b8caa9fb58743b717e89f45e8e7018371bf16f07dc3c1f96a55c5') version('2.0', sha256='03d13abee321decb88bc4e7c9f27276d62a4a880fa72bb6b86be91885010cfed') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py index 4cf22ee653..1f3d49576a 100644 --- a/var/spack/repos/builtin/packages/r-rbokeh/package.py +++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py @@ -8,16 +8,15 @@ from spack import * class RRbokeh(RPackage): - """R Interface for Bokeh + """R Interface for Bokeh. A native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the Bokeh visualization library <https://bokeh.pydata.org/>.""" - homepage = "https://hafen.github.io/rbokeh" - url = "https://cloud.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rbokeh" + cran = "rbokeh" + version('0.5.2', sha256='d8c47dbd978efce04e5676a3a91d511517a9bb8fe1859c404bfc9ee0f0bf4ec0') version('0.5.1', sha256='48eba3b238cea2b9aa408d8a48c663564292e76f2ab3f603bc671315a4a75a88') version('0.5.0', sha256='499c3224a7dcaeb4bb60fd645b3ef528a20e59437747a073713941b80cbcebd2') @@ -30,6 +29,7 @@ class RRbokeh(RPackage): depends_on('r-lazyeval', type=('build', 'run')) depends_on('r-pryr', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-gistr', type=('build', 'run')) + + depends_on('r-ggplot2', type=('build', 'run'), when='@:0.5.1') diff --git a/var/spack/repos/builtin/packages/r-rcmdcheck/package.py b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py index 73e9c50ee1..9c05ff7535 100644 --- a/var/spack/repos/builtin/packages/r-rcmdcheck/package.py +++ b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py @@ -7,19 +7,21 @@ from spack import * class RRcmdcheck(RPackage): - """Run 'R CMD check' from 'R' and capture the results of the individual + """Run 'R CMD check' from 'R' and Capture Results. + + Run 'R CMD check' from 'R' and capture the results of the individual checks. Supports running checks in the background, timeouts, pretty printing and comparing check results.""" - homepage = "https://github.com/r-Lib/rcmdcheck#readme" - url = "https://cloud.r-project.org/src/contrib/rcmdcheck_1.3.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rcmdcheck" + cran = "rcmdcheck" + version('1.4.0', sha256='bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0') version('1.3.3', sha256='1ab679eb1976d74cd3be5bcad0af7fcc673dbdfd4406bbce32591c8fddfb93b4') depends_on('r-callr@3.1.1.9000:', type=('build', 'run')) depends_on('r-cli@1.1.0:', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) + depends_on('r-cli@3.0.0:', type=('build', 'run'), when='@1.4.0:') + depends_on('r-curl', type=('build', 'run'), when='@1.4.0:') depends_on('r-desc@1.2.0:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-pkgbuild', type=('build', 'run')) @@ -29,3 +31,5 @@ class RRcmdcheck(RPackage): depends_on('r-sessioninfo@1.1.1:', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) depends_on('r-xopen', type=('build', 'run')) + + depends_on('r-crayon', type=('build', 'run'), when='@:1.3.3') diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py index aebe520de2..b57da787f7 100644 --- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -7,12 +7,12 @@ from spack import * class RRcolorbrewer(RPackage): - """Provides color schemes for maps (and other graphics) designed by Cynthia + """ColorBrewer Palettes. + + Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at https://colorbrewer2.org/""" - homepage = "https://colorbrewer2.org" - url = "https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RColorBrewer" + cran = "RColorBrewer" version('1.1-2', sha256='f3e9781e84e114b7a88eb099825936cc5ae7276bbba5af94d35adb1b3ea2ccdd') diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 066c2210da..22493cd9e2 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -7,7 +7,7 @@ from spack import * class RRcpp(RPackage): - """Seamless R and C++ Integration + """Seamless R and C++ Integration. The 'Rcpp' package provides R functions as well as C++ classes which; offer a seamless integration of R and C++. Many R data types and objects can be; @@ -21,9 +21,9 @@ class RRcpp(RPackage): (2018,; <doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.""" - homepage = "https://dirk.eddelbuettel.com/code/rcpp.html" cran = "Rcpp" + version('1.0.8', sha256='879f9296bc045ac4ed464578723bd37fcabbbdaa30aaaf070cf953e329f678ee') version('1.0.7', sha256='15e5a4732216daed16263c79fb37017c2ada84a2d4e785e3b76445d0eba3dc1d') version('1.0.6', sha256='c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012') version('1.0.4.6', sha256='45af675ddbbe155e671453b2e84fe32250bb98d4ccb4342b61c1e25cff10b302') diff --git a/var/spack/repos/builtin/packages/r-rcppannoy/package.py b/var/spack/repos/builtin/packages/r-rcppannoy/package.py index 440e8d1618..4d42070520 100644 --- a/var/spack/repos/builtin/packages/r-rcppannoy/package.py +++ b/var/spack/repos/builtin/packages/r-rcppannoy/package.py @@ -7,7 +7,8 @@ from spack import * class RRcppannoy(RPackage): - """'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors + """'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest + Neighbors. 'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. @@ -17,12 +18,12 @@ class RRcppannoy(RPackage): under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.""" - homepage = "https://cloud.r-project.org/package=RcppAnnoy" - url = "https://cloud.r-project.org/src/contrib/RcppAnnoy_0.0.12.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppAnnoy" + cran = "RcppAnnoy" + version('0.0.19', sha256='89b209900516f3096b53c90937081fb8965c605c867aa465f1b3b68092b7688a') version('0.0.18', sha256='e4e7ddf071109b47b4fdf285db6d2155618ed73da829c30d8e64fc778e63c858') version('0.0.12', sha256='8f736cbbb4a32c80cb08ba4e81df633846d725f27867e983af2012966eac0eac') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r-rcpp@0.11.3:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.3:', type=('build', 'run'), when='@:0.0.12') diff --git a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py index a9790d92ce..79e6b364d6 100644 --- a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py +++ b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py @@ -7,7 +7,7 @@ from spack import * class RRcpparmadillo(RPackage): - """'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library + """'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library. 'Armadillo' is a templated C++ linear algebra library (by Conrad; Sanderson) that aims towards a good balance between speed and ease of; use. @@ -21,14 +21,15 @@ class RRcpparmadillo(RPackage): under licensed as MPL; 2.0 from version 3.800.0 onwards and LGPL-3 prior to that""" - homepage = "https://cloud.r-project.org/package=RcppArmadillo" cran = "RcppArmadillo" + version('0.10.8.1.0', sha256='efa415afb38514648456d1feab247c556735573673986a4fb0f512960b9af5f4') + version('0.10.7.5.0', sha256='7c061e6371c3c068d17744fd7f764dfd02f25393c3f5d534aa7d9e62ac912614') version('0.10.7.3.0', sha256='3710b767708e3b9408723eedb98391daa8651fda53a2c6b033273265512f6262') version('0.10.1.2.2', sha256='38323703fcf2b61f46f2984aafdd3ddf17c3c993d1d27a8f0f4ba5012b99d069') version('0.9.600.4.0', sha256='2057b7aa965a4c821dd734276d8e6a01cd59a1b52536b65cb815fa7e8c114f1e') version('0.9.400.3.0', sha256='56936d501fe8e6f8796ae1a6badb9294d7dad98a0b557c3b3ce6bd4ecaad13b0') version('0.8.100.1.0', sha256='97ca929b34d84d99d7cadc3612b544632cdd0c43ed962933a3d47caa27854fa7') - depends_on('r@3.3.0:', when='@0.8.500.0:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.8.500.0:') depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppblaze/package.py b/var/spack/repos/builtin/packages/r-rcppblaze/package.py index 8b34ef4348..b990b3653b 100644 --- a/var/spack/repos/builtin/packages/r-rcppblaze/package.py +++ b/var/spack/repos/builtin/packages/r-rcppblaze/package.py @@ -8,35 +8,32 @@ from spack import * class RRcppblaze(RPackage): """'Blaze' is an open-source, high-performance C++ math library for dense - and sparse arithmetic. + and sparse arithmetic. - With its state-of-the-art Smart Expression Template implementation - 'Blaze' combines the elegance and ease of use of a domain-specific - language with 'HPC'-grade performance, making it one of the most - intuitive and fastest C++ math libraries available. The 'Blaze' - library offers: - high performance through the integration of - 'BLAS' libraries and manually tuned 'HPC' math kernels - vectorization - by 'SSE', 'SSE2', 'SSE3', 'SSSE3', 'SSE4', 'AVX', 'AVX2', 'AVX-512', - 'FMA', and 'SVML' - parallel execution by 'OpenMP', C++11 threads and - 'Boost' threads ('Boost' threads are disabled in 'RcppBlaze') - the - intuitive and easy to use API of a domain specific language - unified - arithmetic with dense and sparse vectors and matrices - thoroughly - tested matrix and vector arithmetic - completely portable, high quality - C++ source code. The 'RcppBlaze' package includes the header files from - the 'Blaze' library with disabling some functionalities related to link - to the thread and system libraries which make 'RcppBlaze' be a - header-only library. Therefore, users do not need to install 'Blaze' - and the dependency 'Boost'. 'Blaze' is licensed under the New (Revised) - BSD license, while 'RcppBlaze' (the 'Rcpp' bindings/bridge to 'Blaze') - is licensed under the GNU GPL version 2 or later, as is the rest of - 'Rcpp'. Note that since 'Blaze' has committed to 'C++14' commit to - 'C++14' which does not used by most R users from version 3.0, we will - use the version 2.6 of 'Blaze' which is 'C++98' compatible to support - the most compilers and system.""" + With its state-of-the-art Smart Expression Template implementation 'Blaze' + combines the elegance and ease of use of a domain-specific language with + 'HPC'-grade performance, making it one of the most intuitive and fastest + C++ math libraries available. The 'Blaze' library offers: - high + performance through the integration of 'BLAS' libraries and manually tuned + 'HPC' math kernels - vectorization by 'SSE', 'SSE2', 'SSE3', 'SSSE3', + 'SSE4', 'AVX', 'AVX2', 'AVX-512', 'FMA', and 'SVML' - parallel execution by + 'OpenMP', C++11 threads and 'Boost' threads ('Boost' threads are disabled + in 'RcppBlaze') - the intuitive and easy to use API of a domain specific + language - unified arithmetic with dense and sparse vectors and matrices - + thoroughly tested matrix and vector arithmetic - completely portable, high + quality C++ source code. The 'RcppBlaze' package includes the header files + from the 'Blaze' library with disabling some functionalities related to + link to the thread and system libraries which make 'RcppBlaze' be a + header-only library. Therefore, users do not need to install 'Blaze' and + the dependency 'Boost'. 'Blaze' is licensed under the New (Revised) BSD + license, while 'RcppBlaze' (the 'Rcpp' bindings/bridge to 'Blaze') is + licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. + Note that since 'Blaze' has committed to 'C++14' commit to 'C++14' which + does not used by most R users from version 3.0, we will use the version 2.6 + of 'Blaze' which is 'C++98' compatible to support the most compilers and + system.""" - homepage = "https://github.com/Chingchuan-chen/RcppBlaze" - url = "https://cloud.r-project.org/src/contrib/RcppBlaze_0.2.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppBlaze" + cran = "RcppBlaze" version('0.2.2', sha256='67550ed8aea12a219047af61b41e5b9f991608a21ce9a8fbf7ac55da0f7c2742') diff --git a/var/spack/repos/builtin/packages/r-rcppcctz/package.py b/var/spack/repos/builtin/packages/r-rcppcctz/package.py index 945011b5e8..bc343f32a3 100644 --- a/var/spack/repos/builtin/packages/r-rcppcctz/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcctz/package.py @@ -7,7 +7,7 @@ from spack import * class RRcppcctz(RPackage): - """'Rcpp' Bindings for the 'CCTZ' Library + """'Rcpp' Bindings for the 'CCTZ' Library. 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of @@ -15,10 +15,9 @@ class RRcppcctz(RPackage): is included in this package. See <https://github.com/google/cctz> for more details.""" - homepage = "https://github.com/eddelbuettel/rcppcctz" - url = "https://cloud.r-project.org/src/contrib/RcppCCTZ_0.2.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppCCTZ" + cran = "RcppCCTZ" + version('0.2.10', sha256='3a78188ec771270c87d5ccb8237506adac1827220c694df2f683f64002e2444a') version('0.2.9', sha256='723f45eca1be08903234e339523daca35748fe65c1a9d59afcb583d3a17bcaae') version('0.2.6', sha256='0e9a76055d29da24cd4c4069c78c1f44998f3461be60c7a6c3e7a35059fb79ae') version('0.2.4', sha256='98b6867d38abe03957fe803e88b6cc2d122b85a68ef07fa86f7e1009d6c00819') diff --git a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py index 3dd1c25fd1..4266a58645 100644 --- a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py @@ -7,11 +7,16 @@ from spack import * class RRcppcnpy(RPackage): - """Rcpp bindings for NumPy files.""" + """Read-Write Support for 'NumPy' Files via 'Rcpp'. - homepage = "https://github.com/eddelbuettel/rcppcnpy" - url = "https://cloud.r-project.org/src/contrib/RcppCNPy_0.2.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppCNPy" + The 'cnpy' library written by Carl Rogers provides read and write + facilities for files created with (or for) the 'NumPy' extension for + 'Python'. Vectors and matrices of numeric types can be read or written to + and from files as well as compressed files. Support for integer files is + available if the package has been built with -std=c++11 which should be the + default on all platforms since the release of R 3.3.0.""" + + cran = "RcppCNPy" version('0.2.10', sha256='77d6fbc86520a08da40d44c0b82767099f8f719ca95870d91efff1a9cab1ab9c') version('0.2.9', sha256='733f004ad1a8b0e5aafbf547c4349d2df3118afd57f1ff99f20e39135c6edb30') diff --git a/var/spack/repos/builtin/packages/r-rcppdate/package.py b/var/spack/repos/builtin/packages/r-rcppdate/package.py index b5def212da..48f39fb548 100644 --- a/var/spack/repos/builtin/packages/r-rcppdate/package.py +++ b/var/spack/repos/builtin/packages/r-rcppdate/package.py @@ -7,7 +7,7 @@ from spack import * class RRcppdate(RPackage): - """'date' C++ Header Library for Date and Time Functionality + """'date' C++ Header Library for Date and Time Functionality. 'date' is a C++ header library offering extensive date and time functionality for the C++11, C++14 and C++17 standards written by Howard @@ -17,8 +17,7 @@ class RRcppdate(RPackage): other R packages can use them in their C++ code. At present, few of the types have explicit 'Rcpp' wrapper though these may be added as needed.""" - homepage = "https://github.com/eddelbuettel/rcppdate" - url = "https://cloud.r-project.org/src/contrib/RcppDate_0.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppDate" + cran = "RcppDate" + version('0.0.3', sha256='9c5ee7cf76d63cd51e8faff831f5f865762868d7d705395960c0f22e9b238bdb') version('0.0.1', sha256='117721fc677dfb4209200a7ff894fbbb8ee1b652d01b3878b11c3253733b4a5f') diff --git a/var/spack/repos/builtin/packages/r-rcppde/package.py b/var/spack/repos/builtin/packages/r-rcppde/package.py new file mode 100644 index 0000000000..c093147c56 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcppde/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 RRcppde(RPackage): + """Global Optimization by Differential Evolution in C++. + + An efficient C++ based implementation of the 'DEoptim' function which + performs global optimization by differential evolution. Its creation was + motivated by trying to see if the old approximation "easier, shorter, + faster: pick any two" could in fact be extended to achieving all three + goals while moving the code from plain old C to modern C++. The initial + version did in fact do so, but a good part of the gain was due to an + implicit code review which eliminated a few inefficiencies which have since + been eliminated in 'DEoptim'.""" + + cran = "RcppDE" + + version('0.1.6', sha256='c9386709f72cdc33505b3ac675c173013fe098434b7c21bc09eb625b529132c5') + + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpparmadillo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index 7970198fe3..adbda4c47a 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -7,25 +7,23 @@ from spack import * class RRcppeigen(RPackage): - """'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library + """'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library. - R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template - library for linear algebra: matrices, vectors, numerical solvers and - related algorithms. It supports dense and sparse matrices on integer, - floating point and complex numbers, decompositions of such matrices, and - solutions of linear systems. Its performance on many algorithms is - comparable with some of the best implementations based on 'Lapack' and - level-3 'BLAS'. The 'RcppEigen' package includes the header files from the - 'Eigen' C++ template library (currently version 3.2.8). Thus users do not - need to install 'Eigen' itself in order to use 'RcppEigen'. Since version - 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); - earlier version were licensed under the GNU LGPL version 3 or later. - 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the - GNU GPL version 2 or later, as is the rest of 'Rcpp'.""" + R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library + for linear algebra: matrices, vectors, numerical solvers and related + algorithms. It supports dense and sparse matrices on integer, floating + point and complex numbers, decompositions of such matrices, and solutions + of linear systems. Its performance on many algorithms is comparable with + some of the best implementations based on 'Lapack' and level-3 'BLAS'. The + 'RcppEigen' package includes the header files from the 'Eigen' C++ template + library (currently version 3.2.8). Thus users do not need to install + 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is + licensed under the Mozilla Public License (version 2); earlier version were + licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' + bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or + later, as is the rest of 'Rcpp'.""" - homepage = "https://eigen.tuxfamily.org/" - url = "https://cloud.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppEigen" + cran = "RcppEigen" version('0.3.3.9.1', sha256='8a0486249b778a4275a1168fc89fc7fc49c2bb031cb14b50a50089acae7fe962') version('0.3.3.5.0', sha256='e5c6af17770c5f57b7cf2fba04ad1a519901b446e8138bfff221952458207f05') diff --git a/var/spack/repos/builtin/packages/r-rcpphnsw/package.py b/var/spack/repos/builtin/packages/r-rcpphnsw/package.py index e69be5a828..18e353349e 100644 --- a/var/spack/repos/builtin/packages/r-rcpphnsw/package.py +++ b/var/spack/repos/builtin/packages/r-rcpphnsw/package.py @@ -8,16 +8,14 @@ from spack import * class RRcpphnsw(RPackage): """'Rcpp' Bindings for 'hnswlib', a Library for Approximate - NearestNeighbors + NearestNeighbors. 'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This ; package provides a minimal R interface by relying on the 'Rcpp' package. See ; <https://github.com/nmslib/hnswlib> for more on 'hnswlib'. 'hnswlib' is ; released under Version 2.0 of the Apache License.""" - homepage = "https://cloud.r-project.org/package=RcppHNSW" - url = "https://cloud.r-project.org/src/contrib/RcppHNSW_0.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppHNSW" + cran = "RcppHNSW" version('0.3.0', sha256='a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007') version('0.1.0', sha256='75a54c30953845dec685764c7b3b4cd7315197c91aef4ab3b4eb0a6293010a95') diff --git a/var/spack/repos/builtin/packages/r-rcppparallel/package.py b/var/spack/repos/builtin/packages/r-rcppparallel/package.py index 54458338b8..52241335dc 100644 --- a/var/spack/repos/builtin/packages/r-rcppparallel/package.py +++ b/var/spack/repos/builtin/packages/r-rcppparallel/package.py @@ -7,21 +7,21 @@ from spack import * class RRcppparallel(RPackage): - """Parallel Programming Tools for 'Rcpp' + """Parallel Programming Tools for 'Rcpp'. - High level functions for parallel programming with 'Rcpp'. For example, - the 'parallelFor()' function can be used to convert the work of a standard + High level functions for parallel programming with 'Rcpp'. For example, the + 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.""" - homepage = "https://rcppcore.github.io/RcppParallel" - url = "https://cloud.r-project.org/src/contrib/RcppParallel_4.4.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppParallel" + cran = "RcppParallel" + version('5.1.5', sha256='6396322b3b6d6f7019aac808ceb74707bc5c4ed01677fab408372c2a5508c2ea') version('5.0.2', sha256='8ca200908c6365aafb2063be1789f0894969adc03c0f523c6cc45434b8236f81') version('4.4.3', sha256='7a04929ecab97e46c0b09fe5cdbac9d7bfa17ad7d111f1a9787a9997f45fa0fa') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('gmake', type='build') + depends_on('tbb', when='@5.1.5:') patch('asclang.patch', when='%fj') diff --git a/var/spack/repos/builtin/packages/r-rcppprogress/package.py b/var/spack/repos/builtin/packages/r-rcppprogress/package.py index 9c0821926d..b5ca017f40 100644 --- a/var/spack/repos/builtin/packages/r-rcppprogress/package.py +++ b/var/spack/repos/builtin/packages/r-rcppprogress/package.py @@ -7,15 +7,13 @@ from spack import * class RRcppprogress(RPackage): - """An Interruptible Progress Bar with OpenMP Support for C++ in R Packages + """An Interruptible Progress Bar with OpenMP Support for C++ in R Packages. Allows to display a progress bar in the R console for long running - computations taking place in c++ code, and support for interrupting - those computations even in multithreaded code, typically using OpenMP.""" + computations taking place in c++ code, and support for interrupting those + computations even in multithreaded code, typically using OpenMP.""" - homepage = "https://cloud.r-project.org/package=RcppProgress" - url = "https://cloud.r-project.org/src/contrib/RcppProgress_0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppProgress" + cran = "RcppProgress" version('0.4.2', sha256='b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48') version('0.4.1', sha256='11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a') @@ -25,4 +23,4 @@ class RRcppprogress(RPackage): version('0.2', sha256='ca32624739058f1b5aab18b09dc4c613ecfd18a3ace39f3b97790232db829481') version('0.1', sha256='04f71d3391b7dfab997afadf7ffdd87b88037f7fbc751bea544ad2a65e2872bf') - depends_on('r-rcpp@0.9.4:', when='@:0.4', type=('build', 'run')) + depends_on('r-rcpp@0.9.4:', type=('build', 'run'), when='@:0.4') diff --git a/var/spack/repos/builtin/packages/r-rcpptoml/package.py b/var/spack/repos/builtin/packages/r-rcpptoml/package.py new file mode 100644 index 0000000000..05fee75b56 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcpptoml/package.py @@ -0,0 +1,23 @@ +# 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 RRcpptoml(RPackage): + """'Rcpp' Bindings to Parser for Tom's Obvious Markup Language. + + The configuration format defined by 'TOML' (which expands to "Tom's Obvious + Markup Language") specifies an excellent format (described at + <https://toml.io/en/>) suitable for both human editing as well as the + common uses of a machine-readable format. This package uses 'Rcpp' to + connect the 'cpptoml' parser written by Chase Geigle (in C++11) to R.""" + + cran = "RcppTOML" + + version('0.1.7', sha256='2f09f00cbee6c6eeff5d5f0195c10de0155496de15fbe8189c18627ee3090541') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcurl/package.py b/var/spack/repos/builtin/packages/r-rcurl/package.py index 48a0b8cf56..d59fbc0309 100644 --- a/var/spack/repos/builtin/packages/r-rcurl/package.py +++ b/var/spack/repos/builtin/packages/r-rcurl/package.py @@ -7,27 +7,27 @@ from spack import * class RRcurl(RPackage): - """A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/> Provides - functions to allow one to compose general HTTP requests and provides - convenient functions to fetch URIs, get & post forms, etc. and process - the results returned by the Web server. This provides a great deal of - control over the HTTP/FTP/... connection and the form of the request - while providing a higher-level interface than is available just using - R socket connections. Additionally, the underlying implementation is - robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), - SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, - authentication, etc.""" + """General Network (HTTP/FTP/...) Client Interface for R. - homepage = "https://cloud.r-project.org/package=RCurl" - url = "https://cloud.r-project.org/src/contrib/RCurl_1.95-4.8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RCurl" + A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/> Provides functions + to allow one to compose general HTTP requests and provides convenient + functions to fetch URIs, get & post forms, etc. and process the results + returned by the Web server. This provides a great deal of control over the + HTTP/FTP/... connection and the form of the request while providing a + higher-level interface than is available just using R socket connections. + Additionally, the underlying implementation is robust and extensive, + supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, + ldap, and also supports cookies, redirects, authentication, etc.""" + cran = "RCurl" + + version('1.98-1.5', sha256='73187c9a039188ffdc255fb7fa53811a6abfb31e6375a51eae8c763b37dd698d') version('1.98-1.2', sha256='5d74a0cdc3c5684b0348b959f67039e3c2a5da2bbb6176f6800a94124895a7a8') version('1.95-4.12', sha256='393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4') version('1.95-4.8', sha256='e72243251bbbec341bc5864305bb8cc23d311d19c5d0d9310afec7eb35aa2bfb') - depends_on('r@3.4.0:', when='@1.98:', type=('build', 'run')) depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@1.98:') depends_on('r-bitops', type=('build', 'run')) depends_on('curl') depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rda/package.py b/var/spack/repos/builtin/packages/r-rda/package.py index 0ee90bd287..03580dbf96 100644 --- a/var/spack/repos/builtin/packages/r-rda/package.py +++ b/var/spack/repos/builtin/packages/r-rda/package.py @@ -7,12 +7,12 @@ from spack import * class RRda(RPackage): - """Shrunken Centroids Regularized Discriminant Analysis for the - classification purpose in high dimensional data.""" + """Shrunken Centroids Regularized Discriminant Analysis. - homepage = "https://cloud.r-project.org/package=rda" - url = "https://cloud.r-project.org/src/contrib/rda_1.0.2-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rda" + Shrunken Centroids Regularized Discriminant Analysis for the classification + purpose in high dimensional data.""" + + cran = "rda" # Note: Package 'rda' was removed from the CRAN repository. # The latest archived version is below diff --git a/var/spack/repos/builtin/packages/r-rdpack/package.py b/var/spack/repos/builtin/packages/r-rdpack/package.py index 8dada315d5..89ec7e0e34 100644 --- a/var/spack/repos/builtin/packages/r-rdpack/package.py +++ b/var/spack/repos/builtin/packages/r-rdpack/package.py @@ -7,24 +7,24 @@ from spack import * class RRdpack(RPackage): - """Update and Manipulate Rd Documentation Objects + """Update and Manipulate Rd Documentation Objects. - Functions for manipulation of R documentation objects, including - functions reprompt() and ereprompt() for updating 'Rd' documentation for - functions, methods and classes; 'Rd' macros for citations and import of - references from 'bibtex' files for use in 'Rd' files and 'roxygen2' - comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and - the results of its evaluation or creating graphics on the fly; and many - functions for manipulation of references and Rd files.""" + Functions for manipulation of R documentation objects, including functions + reprompt() and ereprompt() for updating 'Rd' documentation for functions, + methods and classes; 'Rd' macros for citations and import of references + from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' + macros for evaluating and inserting snippets of 'R' code and the results of + its evaluation or creating graphics on the fly; and many functions for + manipulation of references and Rd files.""" - homepage = "https://github.com/GeoBosh/Rdpack" - url = "https://cloud.r-project.org/src/contrib/Rdpack_0.11-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Rdpack" + cran = "Rdpack" + version('2.1.3', sha256='8381a8866b9acf5acb2c80069684339c3921f1b45fa202719e8f6852fb4d55b8') version('2.1', sha256='26e094fe3c077fb2a99e95c5bd94015a5f993a4a5f5d217829b4872ff004bfce') version('0.11-0', sha256='8fb449c80fbe931cdce51f728fb03a1978009ccce66fd6b9edacdc6ff4118d85') depends_on('r@2.15.0:', type=('build', 'run')) - depends_on('r-gbrd', type=('build', 'run')) - depends_on('r-rbibutils@1.3:', when='@2.1:', type=('build', 'run')) - depends_on('r-bibtex@0.4.0:', when='@:0.11-0', type=('build', 'run')) + depends_on('r-rbibutils@1.3:', type=('build', 'run'), when='@2.1:') + + depends_on('r-bibtex@0.4.0:', type=('build', 'run'), when='@:0.11-0') + depends_on('r-gbrd', type=('build', 'run'), when='@:2.1') diff --git a/var/spack/repos/builtin/packages/r-readbitmap/package.py b/var/spack/repos/builtin/packages/r-readbitmap/package.py index c5c9af6ee0..b28986d58d 100644 --- a/var/spack/repos/builtin/packages/r-readbitmap/package.py +++ b/var/spack/repos/builtin/packages/r-readbitmap/package.py @@ -7,15 +7,14 @@ from spack import * class RReadbitmap(RPackage): - """Identifies and reads Windows BMP, JPEG, PNG, and TIFF format bitmap - images. Identification defaults to the use of the magic number embedded in - the file rather than the file extension. Reading of JPEG and PNG image - depends on libjpg and libpng libraries. See file INSTALL for details if - necessary.""" + """Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF). - homepage = "https://github.com/jefferis/readbitmap" - url = "https://cloud.r-project.org/src/contrib/readbitmap_0.1.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/readbitmap" + Identifies and reads Windows BMP, JPEG, PNG, and TIFF format bitmap images. + Identification defaults to the use of the magic number embedded in the file + rather than the file extension. Reading of JPEG and PNG image depends on + libjpg and libpng libraries. See file INSTALL for details if necessary.""" + + cran = "readbitmap" version('0.1.5', sha256='737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291') @@ -23,6 +22,5 @@ class RReadbitmap(RPackage): depends_on('r-jpeg', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-tiff', type=('build', 'run')) - depends_on('jpeg') depends_on('libpng') diff --git a/var/spack/repos/builtin/packages/r-readr/package.py b/var/spack/repos/builtin/packages/r-readr/package.py index c1922637ee..96a80ec3c1 100644 --- a/var/spack/repos/builtin/packages/r-readr/package.py +++ b/var/spack/repos/builtin/packages/r-readr/package.py @@ -7,36 +7,39 @@ from spack import * class RReadr(RPackage): - """Read Rectangular Text Data + """Read Rectangular Text Data. The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.""" - homepage = "https://cloud.r-project.org/package=readr" cran = "readr" + version('2.1.2', sha256='94afd03a1fa4abcf2985ec903bbf5995d7c590e1a50512ed80d081ef4fe10c1b') + version('2.1.1', sha256='03937918a547e3a1587295f5e5f8c7f6865a4d04047d2b20c8d0f0701f1cbc84') version('2.0.2', sha256='98b05ed751dda2bcf7a29d070ce3d3e8475e0138a3e3ec68941dc45218db7615') version('1.4.0', sha256='02b1188aab8b2bc3f3d2bba5b946bd299610e87f3f7660c88b60b444093c46b9') version('1.3.1', sha256='33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3') version('1.1.1', sha256='1a29b99009a06f2cee18d08bc6201fd4985b6d45c76cefca65084dcc1a2f7cb3') - depends_on('r@3.0.2:', when='@:1.2.1', type=('build', 'run')) - depends_on('r@3.1:', when='@1.3.0:', type=('build', 'run')) - depends_on('r-cli', when='@1.4.0:', type=('build', 'run')) - depends_on('r-clipr', when='@1.2.0:', type=('build', 'run')) - depends_on('r-crayon', when='@1.3.1:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-cli', type=('build', 'run'), when='@1.4.0:') + depends_on('r-cli@3.0.0:', type=('build', 'run'), when='@2.1.2:') + depends_on('r-clipr', type=('build', 'run'), when='@1.2.0:') + depends_on('r-crayon', type=('build', 'run'), when='@1.3.1:') depends_on('r-hms@0.4.1:', type=('build', 'run')) - depends_on('r-rlang', when='@1.4.0:', type=('build', 'run')) + depends_on('r-lifecycle', type=('build', 'run'), when='@1.4.0:') + depends_on('r-lifecycle@0.2.0:', type=('build', 'run'), when='@2:') depends_on('r-r6', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@1.4.0:') depends_on('r-tibble', type=('build', 'run')) - depends_on('r-vroom@1.5.2:', when='@2.0.0', type=('build', 'run')) - depends_on('r-vroom@1.5.4:', when='@2.0.1:', type=('build', 'run')) - depends_on('r-lifecycle', when='@1.4.0:', type=('build', 'run')) - depends_on('r-lifecycle@0.2.0:', when='@2:', type=('build', 'run')) - depends_on('r-cpp11', when='@1.4.0:', type=('build', 'run')) - depends_on('r-tzdb@0.1.1:', when='@2:', type=('build', 'run')) - - depends_on('r-bh', when='@:1', type=('build', 'run')) - depends_on('r-rcpp@0.12.0.5:', when='@:1.3.1', type=('build', 'run')) + depends_on('r-vroom@1.5.2:', type=('build', 'run'), when='@2.0.0') + depends_on('r-vroom@1.5.4:', type=('build', 'run'), when='@2.0.1:') + depends_on('r-vroom@1.5.6:', type=('build', 'run'), when='@2.1.1:') + depends_on('r-cpp11', type=('build', 'run'), when='@1.4.0:') + depends_on('r-tzdb@0.1.1:', type=('build', 'run'), when='@2:') + + depends_on('r-bh', type=('build', 'run'), when='@:1') + depends_on('r-rcpp@0.12.0.5:', type=('build', 'run'), when='@:1.3.1') diff --git a/var/spack/repos/builtin/packages/r-readxl/package.py b/var/spack/repos/builtin/packages/r-readxl/package.py index f6aa28642d..01e2543563 100644 --- a/var/spack/repos/builtin/packages/r-readxl/package.py +++ b/var/spack/repos/builtin/packages/r-readxl/package.py @@ -7,15 +7,14 @@ from spack import * class RReadxl(RPackage): - """Import excel files into R. Supports '.xls' via the embedded - 'libxls' C library <https://sourceforge.net/projects/libxls/> and - '.xlsx' via the embedded 'RapidXML' C++ library - <https://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux - without external dependencies.""" + """Read Excel Files. - homepage = "https://readxl.tidyverse.org/" - url = "https://cloud.r-project.org/src/contrib/readxl_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/readxl" + Import excel files into R. Supports '.xls' via the embedded 'libxls' C + library <https://sourceforge.net/projects/libxls/> and '.xlsx' via the + embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net>. Works + on Windows, Mac and Linux without external dependencies.""" + + cran = "readxl" version('1.3.1', sha256='24b441713e2f46a3e7c6813230ad6ea4d4ddf7e0816ad76614f33094fbaaaa96') version('1.3.0', sha256='8379d1026dcfc662d073eb1c69ed1d90aa6439d6cb3c6fc1b5d1db4f51b3fadc') @@ -25,4 +24,4 @@ class RReadxl(RPackage): depends_on('r-tibble@1.3.1:', type=('build', 'run')) depends_on('r-rcpp@0.12.18:', type=('build', 'run')) depends_on('r-cellranger', type=('build', 'run')) - depends_on('r-progress', when='@1.2.0:', type=('build', 'run')) + depends_on('r-progress', type=('build', 'run'), when='@1.2.0:') diff --git a/var/spack/repos/builtin/packages/r-reams/package.py b/var/spack/repos/builtin/packages/r-reams/package.py index 515e86d8a4..2179d290a8 100644 --- a/var/spack/repos/builtin/packages/r-reams/package.py +++ b/var/spack/repos/builtin/packages/r-reams/package.py @@ -7,11 +7,13 @@ from spack import * class RReams(RPackage): - """reams: Resampling-Based Adaptive Model Selection""" + """Resampling-Based Adaptive Model Selection. - homepage = "https://cloud.r-project.org/package=reams" - url = "https://cloud.r-project.org/src/contrib/reams_0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/reams" + Resampling methods for adaptive linear model selection. These can be + thought of as extensions of the Akaike information criterion that account + for searching among candidate models.""" + + cran = "reams" version('0.1', sha256='ac24ea875b24bd18152afd87538b1f807f442cf2bd1c6ac1a365cf543c88181e') diff --git a/var/spack/repos/builtin/packages/r-recipes/package.py b/var/spack/repos/builtin/packages/r-recipes/package.py index a4d9fa4922..c72291cf11 100644 --- a/var/spack/repos/builtin/packages/r-recipes/package.py +++ b/var/spack/repos/builtin/packages/r-recipes/package.py @@ -7,29 +7,30 @@ from spack import * class RRecipes(RPackage): - """Preprocessing Tools to Create Design Matrices + """Preprocessing Tools to Create Design Matrices. - An extensible framework to create and preprocess design matrices. - Recipes consist of one or more data manipulation and analysis "steps". - Statistical parameters for the steps can be estimated from an initial data - set and then applied to other data sets. The resulting design matrices can - then be used as inputs into statistical or machine learning models.""" + An extensible framework to create and preprocess design matrices. Recipes + consist of one or more data manipulation and analysis "steps". Statistical + parameters for the steps can be estimated from an initial data set and then + applied to other data sets. The resulting design matrices can then be used + as inputs into statistical or machine learning models.""" - homepage = "https://github.com/tidymodels/recipes" - url = "https://cloud.r-project.org/src/contrib/recipes_0.1.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/recipes" + cran = "recipes" + version('0.1.17', sha256='ed20ba0ea0165310e31864ed7d2e005a2a37b76c7913977fd124d8b567616d3d') version('0.1.15', sha256='808ad2f4d68ae03aa27332437f037597e9c1bebd65ed4ebfab1d243ea6022e76') version('0.1.6', sha256='51e0db72de171d58d13ad8ffcf1dea402ab8f82100d161722041b6fd014cbfd9') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-ellipsis', type=('build', 'run'), when='@0.1.17:') depends_on('r-generics', type=('build', 'run')) - depends_on('r-generics@0.1.0:', when='@0.1.15:', type=('build', 'run')) + depends_on('r-generics@0.1.0:', type=('build', 'run'), when='@0.1.15:') depends_on('r-glue', type=('build', 'run')) depends_on('r-gower', type=('build', 'run')) depends_on('r-ipred', type=('build', 'run')) - depends_on('r-lifecycle', when='@0.1.15:', type=('build', 'run')) + depends_on('r-ipred@0.9-12:', type=('build', 'run'), when='@0.1.17:') + depends_on('r-lifecycle', type=('build', 'run'), when='@0.1.15:') depends_on('r-lubridate', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) @@ -37,8 +38,9 @@ class RRecipes(RPackage): depends_on('r-rlang@0.4.0:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-tidyr@1.0.0:', when='@0.1.15:', type=('build', 'run')) + depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@0.1.15:') depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) - depends_on('r-tidyselect@1.1.0:', when='@0.1.15:', type=('build', 'run')) + depends_on('r-tidyselect@1.1.0:', type=('build', 'run'), when='@0.1.15:') depends_on('r-timedate', type=('build', 'run')) + depends_on('r-vctrs', type=('build', 'run'), when='@0.1.17:') depends_on('r-withr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py index b0b2dde6a9..ac90b09ae7 100644 --- a/var/spack/repos/builtin/packages/r-registry/package.py +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -7,11 +7,11 @@ from spack import * class RRegistry(RPackage): - """Provides a generic infrastructure for creating and using registries.""" + """Infrastructure for R Package Registries. - homepage = "https://cloud.r-project.org/package=registry" - url = "https://cloud.r-project.org/src/contrib/registry_0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/registry" + Provides a generic infrastructure for creating and using registries.""" + + cran = "registry" version('0.5-1', sha256='dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc') version('0.5', sha256='5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb') diff --git a/var/spack/repos/builtin/packages/r-rematch/package.py b/var/spack/repos/builtin/packages/r-rematch/package.py index 2ec612bbb6..89fabf91ed 100644 --- a/var/spack/repos/builtin/packages/r-rematch/package.py +++ b/var/spack/repos/builtin/packages/r-rematch/package.py @@ -7,12 +7,11 @@ from spack import * class RRematch(RPackage): - """A small wrapper on 'regexpr' to extract the matches and - captured groups from the match of a regular expression to a - character vector.""" + """Match Regular Expressions with a Nicer 'API'. - homepage = "https://cloud.r-project.org/package=rematch" - url = "https://cloud.r-project.org/src/contrib/rematch_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rematch" + A small wrapper on 'regexpr' to extract the matches and captured groups + from the match of a regular expression to a character vector.""" + + cran = "rematch" version('1.0.1', sha256='a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578') diff --git a/var/spack/repos/builtin/packages/r-rematch2/package.py b/var/spack/repos/builtin/packages/r-rematch2/package.py index 98fde2d516..42e67d721d 100644 --- a/var/spack/repos/builtin/packages/r-rematch2/package.py +++ b/var/spack/repos/builtin/packages/r-rematch2/package.py @@ -7,13 +7,12 @@ from spack import * class RRematch2(RPackage): - """Wrappers on 'regexpr' and 'gregexpr' to return - the match results in tidy data frames. - """ + """Tidy Output from Regular Expression Matching. - homepage = "https://cloud.r-project.org/package=rematch2" - url = "https://cloud.r-project.org/src/contrib/rematch2_2.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rematch2" + Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy + data frames.""" + + cran = "rematch2" version('2.1.2', sha256='fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb') version('2.1.1', sha256='d0423a418e8b46ac3a4819af7a7d19c39ca7c8c862c1e9a1c1294aa19152518f') diff --git a/var/spack/repos/builtin/packages/r-remotes/package.py b/var/spack/repos/builtin/packages/r-remotes/package.py index 5b49e3b3d9..2c354ea3c1 100644 --- a/var/spack/repos/builtin/packages/r-remotes/package.py +++ b/var/spack/repos/builtin/packages/r-remotes/package.py @@ -7,17 +7,16 @@ from spack import * class RRemotes(RPackage): - """R Package Installation from Remote Repositories, Including 'GitHub' + """R Package Installation from Remote Repositories, Including 'GitHub'. - Download and install R packages stored in 'GitHub', 'BitBucket', or - plain 'subversion' or 'git' repositories. This package provides the - 'install_*' functions in 'devtools'. Indeed most of the code was copied - over from 'devtools'. """ + Download and install R packages stored in 'GitHub', 'BitBucket', or plain + 'subversion' or 'git' repositories. This package provides the 'install_*' + functions in 'devtools'. Indeed most of the code was copied over from + 'devtools'. """ - homepage = "https://github.com/r-lib/remotes#readme" - url = "https://cloud.r-project.org/src/contrib/remotes_2.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/remotes" + cran = "remotes" + version('2.4.2', sha256='f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516') version('2.2.0', sha256='12f234fd8c46f4ac54e06a3c60e4015ed2193a32762ca4dd6854f120136f33b8') version('2.1.1', sha256='4e590746fce618094089372b185e1ea234b3337b23c44c44118e942d0fb5118b') version('2.1.0', sha256='8944c8f6fc9f0cd0ca04d6cf1221b716eee08facef9f4b4c4d91d0346d6d68a7') diff --git a/var/spack/repos/builtin/packages/r-renv/package.py b/var/spack/repos/builtin/packages/r-renv/package.py index c26fb7b817..a0f22846af 100644 --- a/var/spack/repos/builtin/packages/r-renv/package.py +++ b/var/spack/repos/builtin/packages/r-renv/package.py @@ -7,7 +7,7 @@ from spack import * class RRenv(RPackage): - """Project Environments for R packages: + """Project Environments for R packages. A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a @@ -15,7 +15,8 @@ class RRenv(RPackage): tools can help make your projects more isolated, portable, and reproducible.""" - homepage = "https://rstudio.github.io/renv/" - cran = "renv" + cran = "renv" + version('0.15.2', sha256='d07effd329f6d653fec9cb517bc8adf3cd6b711758e439055b6d2f06c88765db') + version('0.15.1', sha256='36e8c8df4af50f2341053aa567798dfca6852ade10fa70f9dc146fe9f96f9b5b') version('0.13.2', sha256='41f208ed957e27c50cbd8b0fff77a434bad963707df85e462419e2edb6719a4a') diff --git a/var/spack/repos/builtin/packages/r-reordercluster/package.py b/var/spack/repos/builtin/packages/r-reordercluster/package.py index c7bd7b2912..c75d6bd9d6 100644 --- a/var/spack/repos/builtin/packages/r-reordercluster/package.py +++ b/var/spack/repos/builtin/packages/r-reordercluster/package.py @@ -7,13 +7,13 @@ from spack import * class RReordercluster(RPackage): - """Tools for performing the leaf reordering for the dendrogram - that preserves the hierarchical clustering result and at the - same time tries to group instances from the same class together.""" + """Reordering the dendrogram according to the class labels. - homepage = "https://cloud.r-project.org/package=ReorderCluster" - url = "https://cloud.r-project.org/src/contrib/ReorderCluster_1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ReorderCluster" + Tools for performing the leaf reordering for the dendrogram that preserves + the hierarchical clustering result and at the same time tries to group + instances from the same class together.""" + + cran = "ReorderCluster" version('1.0', sha256='a87898faa20380aac3e06a52eedcb2f0eb2b35ab74fdc3435d40ee9f1d28476b') diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py index d87dcdd948..18a63bdc73 100644 --- a/var/spack/repos/builtin/packages/r-repr/package.py +++ b/var/spack/repos/builtin/packages/r-repr/package.py @@ -8,22 +8,21 @@ from spack import * class RRepr(RPackage): - """Serializable Representations + """Serializable Representations. - String and binary representations of objects for several formats and - mime types.""" + String and binary representations of objects for several formats and mime + types.""" - homepage = "https://github.com/IRkernel/repr" - url = "https://cloud.r-project.org/src/contrib/repr_0.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/repr" + cran = "repr" + version('1.1.4', sha256='6f799ca83e0940618dd8c22e62ffdce5ec11ba3366c5306ae58b55b53c097040') version('1.1.0', sha256='743fe018f9e3e54067a970bc38b6b8c0c0498b43f88d179ac4a959c2013a5f96') version('1.0.1', sha256='ecde22c17fd800e1ff5c2b2962689119aa486fba40fbc6f2c50e8d4cc61bc44b') version('1.0.0', sha256='98b2eb1058c1cb2caa8f98708b63726f5564b45de03d38b95ff6b963a8261f49') version('0.9', sha256='24cac6e98f2a7e5483cf87aaffcb37611702099b63d3783e319441b4ecd0264b') depends_on('r@3.0.1:', type=('build', 'run')) - depends_on('r-htmltools', when='@0.13:', type=('build', 'run')) - depends_on('r-jsonlite', when='@0.19.1:', type=('build', 'run')) - depends_on('r-pillar@1.4.0:', when='@1.0.0:', type=('build', 'run')) - depends_on('r-base64enc', when='@0.13:', type=('build', 'run')) + depends_on('r-htmltools', type=('build', 'run'), when='@0.13:') + depends_on('r-jsonlite', type=('build', 'run'), when='@0.19.1:') + depends_on('r-pillar@1.4.0:', type=('build', 'run'), when='@1.0.0:') + depends_on('r-base64enc', type=('build', 'run'), when='@0.13:') diff --git a/var/spack/repos/builtin/packages/r-reprex/package.py b/var/spack/repos/builtin/packages/r-reprex/package.py index 6eba6a5181..c1d1b26d31 100644 --- a/var/spack/repos/builtin/packages/r-reprex/package.py +++ b/var/spack/repos/builtin/packages/r-reprex/package.py @@ -10,14 +10,13 @@ class RReprex(RPackage): """Prepare Reproducible Example Code via the Clipboard. Convenience wrapper that uses the 'rmarkdown' package to render small - snippets of code to target formats that include both code and output. - The goal is to encourage the sharing of small, reproducible, and - runnable examples on code-oriented websites, such as - <https://stackoverflow.com/> and <https://github.com>, or in email. - 'reprex' also extracts clean, runnable R code from various common - formats, such as copy/paste from an R session.""" - - homepage = "https://github.com/jennybc/reprex" + snippets of code to target formats that include both code and output. The + goal is to encourage the sharing of small, reproducible, and runnable + examples on code-oriented websites, such as <https://stackoverflow.com/> + and <https://github.com>, or in email. 'reprex' also extracts clean, + runnable R code from various common formats, such as copy/paste from an R + session.""" + cran = "reprex" version('2.0.1', sha256='0e6d8667cacb63135476a766fba3a4f91e5ad86274ea66d2b1e6d773b5ca6426') @@ -27,25 +26,25 @@ class RReprex(RPackage): depends_on('r+X', type=('build', 'run')) depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.1:', when='@0.2.0:', type=('build', 'run')) - depends_on('r@3.3:', when='@1:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@0.2.0:') + depends_on('r@3.3:', type=('build', 'run'), when='@1:') depends_on('r-callr@2.0.0:', type=('build', 'run')) - depends_on('r-callr@3.3.1:', when='@1:', type=('build', 'run')) - depends_on('r-callr@3.6.0:', when='@2:', type=('build', 'run')) - depends_on('r-cli', when='@1:', type=('build', 'run')) - depends_on('r-cli@2.3.1:', when='@2:', type=('build', 'run')) + depends_on('r-callr@3.3.1:', type=('build', 'run'), when='@1:') + depends_on('r-callr@3.6.0:', type=('build', 'run'), when='@2:') + depends_on('r-cli', type=('build', 'run'), when='@1:') + depends_on('r-cli@2.3.1:', type=('build', 'run'), when='@2:') depends_on('r-clipr@0.4.0:', type=('build', 'run')) - depends_on('r-fs', when='@0.2.1:', type=('build', 'run')) - depends_on('r-glue', when='@1:', type=('build', 'run')) - depends_on('r-knitr', when='@:0.1.9', type=('build', 'run')) - depends_on('r-knitr@1.23:', when='@1:', type=('build', 'run')) - depends_on('r-rlang', when='@0.2.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.0:', when='@1:', type=('build', 'run')) + depends_on('r-fs', type=('build', 'run'), when='@0.2.1:') + depends_on('r-glue', type=('build', 'run'), when='@1:') + depends_on('r-knitr', type=('build', 'run'), when='@:0.1.9') + depends_on('r-knitr@1.23:', type=('build', 'run'), when='@1:') + depends_on('r-rlang', type=('build', 'run'), when='@0.2.0:') + depends_on('r-rlang@0.4.0:', type=('build', 'run'), when='@1:') depends_on('r-rmarkdown', type=('build', 'run')) - depends_on('r-rstudioapi', when='@2:', type=('build', 'run')) - depends_on('r-withr', when='@0.2.0:', type=('build', 'run')) - depends_on('r-withr@2.3.0:', when='@1:', type=('build', 'run')) + depends_on('r-rstudioapi', type=('build', 'run'), when='@2:') + depends_on('r-withr', type=('build', 'run'), when='@0.2.0:') + depends_on('r-withr@2.3.0:', type=('build', 'run'), when='@1:') depends_on('pandoc@1.12.3:') depends_on('pandoc@2:', when='@2:') - depends_on('r-whisker', when='@:0', type=('build', 'run')) + depends_on('r-whisker', type=('build', 'run'), when='@:0') diff --git a/var/spack/repos/builtin/packages/r-reproducible/package.py b/var/spack/repos/builtin/packages/r-reproducible/package.py index f89f5c7f53..8029ed28b6 100644 --- a/var/spack/repos/builtin/packages/r-reproducible/package.py +++ b/var/spack/repos/builtin/packages/r-reproducible/package.py @@ -7,34 +7,33 @@ from spack import * class RReproducible(RPackage): - """A Set of Tools that Enhance Reproducibility Beyond Package Management - - Collection of high-level, machine- and OS-independent tools for - making deeply reproducible and reusable content in R. The two - workhorse functions are Cache and prepInputs; these allow for: - nested caching, robust to environments, and objects with - environments (like functions); and data retrieval and processing - in continuous workflow environments. In all cases, efforts are - made to make the first and subsequent calls of functions have - the same result, but vastly faster at subsequent times by way of - checksums and digesting. Several features are still under active - development, including cloud storage of cached objects, allowing - for sharing between users. Several advanced options are - available, see ?reproducibleOptions.""" - - homepage = "https://reproducible.predictiveecology.org/" - url = "https://cloud.r-project.org/src/contrib/reproducible_1.2.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/reproducible" + """A Set of Tools that Enhance Reproducibility Beyond Package Management. + + Collection of high-level, machine- and OS-independent tools for making + deeply reproducible and reusable content in R. The two workhorse functions + are Cache and prepInputs; these allow for: nested caching, robust to + environments, and objects with environments (like functions); and data + retrieval and processing in continuous workflow environments. In all cases, + efforts are made to make the first and subsequent calls of functions have + the same result, but vastly faster at subsequent times by way of checksums + and digesting. Several features are still under active development, + including cloud storage of cached objects, allowing for sharing between + users. Several advanced options are available, see ?reproducibleOptions.""" + + cran = "reproducible" maintainers = ['dorton21'] + version('1.2.8', sha256='6f453016404f6a2a235cb4d951a29aa7394dc3bd0b9cfc338dc85fb3d5045dd5') version('1.2.4', sha256='0525deefa6a0713c3fe2da8bfc529f62d6352bebf2ef08866503b4853412f149') depends_on('r@3.5:', type=('build', 'run')) + depends_on('r@3.6:', type=('build', 'run'), when='@1.2.8:') depends_on('r-data-table@1.10.4:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-fpcompare', type=('build', 'run')) + depends_on('r-gdalutilities', type=('build', 'run'), when='@1.2.8:') depends_on('r-glue', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-require', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-require/package.py b/var/spack/repos/builtin/packages/r-require/package.py index 9361c542cb..d802b5ecfb 100644 --- a/var/spack/repos/builtin/packages/r-require/package.py +++ b/var/spack/repos/builtin/packages/r-require/package.py @@ -7,23 +7,23 @@ from spack import * class RRequire(RPackage): - """Installing and Loading R Packages for Reproducible Workflows + """Installing and Loading R Packages for Reproducible Workflows. A single key function, 'Require' that wraps 'install.packages', 'remotes::install_github', 'versions::install.versions', and - 'base::require' that allows for reproducible workflows. As with - other functions in a reproducible workflow, this package - emphasizes functions that return the same result whether it is - the first or subsequent times running the function. Maturing.""" + 'base::require' that allows for reproducible workflows. As with other + functions in a reproducible workflow, this package emphasizes functions + that return the same result whether it is the first or subsequent times + running the function. Maturing.""" - homepage = "https://require.predictiveecology.org/" - url = "https://cloud.r-project.org/src/contrib/Require_0.0.10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Require" + cran = "Require" maintainers = ['dorton21'] + version('0.0.13', sha256='ad9cb167694abe70beadc972c2c25086f0ac8e7e5802bf9606c1868e01be2526') version('0.0.10', sha256='2087c3bb4d660d205962e241c1fc4a366dada5a1ed090d545c52188490567f8d') depends_on('r@3.5:', type=('build', 'run')) + depends_on('r@3.6:', type=('build', 'run'), when='@0.0.13:') depends_on('r-data-table@1.10.4:', type=('build', 'run')) depends_on('r-remotes', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reshape/package.py b/var/spack/repos/builtin/packages/r-reshape/package.py index b5b94fb43b..f035125a97 100644 --- a/var/spack/repos/builtin/packages/r-reshape/package.py +++ b/var/spack/repos/builtin/packages/r-reshape/package.py @@ -7,12 +7,12 @@ from spack import * class RReshape(RPackage): - """Flexibly restructure and aggregate data using just two functions: melt - and cast.""" + """Flexibly Reshape Data. - homepage = "https://cloud.r-project.org/package=reshape" - url = "https://cloud.r-project.org/src/contrib/reshape_0.8.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/reshape" + Flexibly restructure and aggregate data using just two functions: melt and + cast.""" + + cran = "reshape" version('0.8.8', sha256='4d5597fde8511e8fe4e4d1fd7adfc7ab37ff41ac68c76a746f7487d7b106d168') version('0.8.7', sha256='2fa6c87d1e89f182e51bc5a4fcda3d42d83b8fb4474ca525fa7a8db5081f3992') diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index 3875cf9875..b1287e17a7 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -7,21 +7,19 @@ from spack import * class RReshape2(RPackage): - """Flexibly Reshape Data: A Reboot of the Reshape Package + """Flexibly Reshape Data: A Reboot of the Reshape Package. - Flexibly restructure and aggregate data using just two functions: melt - and dcast (or acast).""" + Flexibly restructure and aggregate data using just two functions: melt and + dcast (or acast).""" - homepage = "https://github.com/hadley/reshape" - url = "https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/reshape2" + cran = "reshape2" version('1.4.4', sha256='d88dcf9e2530fa9695fc57d0c78adfc5e361305fe8919fe09410b17da5ca12d8') version('1.4.3', sha256='8aff94c935e75032344b52407593392ddd4e16a88bb206984340c816d42c710e') version('1.4.2', sha256='6d3783610379be4c5676d9236cf66276a166b5b96c18f2759e9b219758959b6b') version('1.4.1', sha256='fbd49f75a5b0b7266378515af98db310cf6c772bf6e68bed01f38ee99b408042') - depends_on('r@3.1:', when='@1.4.3:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@1.4.3:') depends_on('r-plyr@1.8.1:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reticulate/package.py b/var/spack/repos/builtin/packages/r-reticulate/package.py index 3a59ac8437..3367073a83 100644 --- a/var/spack/repos/builtin/packages/r-reticulate/package.py +++ b/var/spack/repos/builtin/packages/r-reticulate/package.py @@ -7,7 +7,7 @@ from spack import * class RReticulate(RPackage): - """Interface to 'Python' + """Interface to 'Python'. Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent @@ -15,17 +15,21 @@ class RReticulate(RPackage): converted back to R types. Compatible with all versions of 'Python' >= 2.7.""" - homepage = "https://github.com/rstudio/reticulate" - url = "https://cloud.r-project.org/src/contrib/reticulate_1.13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/reticulate" + cran = "reticulate" + version('1.24', sha256='b918c5204916601f757ad0fc629b2ae1eabab7cdf7f6aa2e219d26e506d916cc') + version('1.23', sha256='fea04a3ff33c71f1910d65000a93c6882180ca03f8657ee118ea9e79786c36d6') version('1.18', sha256='b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513') version('1.15', sha256='47db3e9c9424263ade15287da8e74f6ba261a936b644b197dba6772853b7b50d') version('1.13', sha256='adbe41d556b667c4419d563680f8608a56b0f792b8bc427b3bf4c584ff819de3') depends_on('r@3.0:', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) - depends_on('r-rappdirs', when='@1.15:', type=('build', 'run')) depends_on('r-rcpp@0.12.7:', type=('build', 'run', 'link')) + depends_on('r-rcpptoml', type=('build', 'run', 'link'), when='@1.23:') + depends_on('r-here', type=('build', 'run', 'link'), when='@1.23:') + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-png', type=('build', 'run', 'link'), when='@1.23:') + depends_on('r-rappdirs', type=('build', 'run'), when='@1.15:') + depends_on('r-withr', type=('build', 'run', 'link'), when='@1.23:') depends_on('python@2.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rex/package.py b/var/spack/repos/builtin/packages/r-rex/package.py index 7926e5d889..94f1ec56c4 100644 --- a/var/spack/repos/builtin/packages/r-rex/package.py +++ b/var/spack/repos/builtin/packages/r-rex/package.py @@ -7,16 +7,16 @@ from spack import * class RRex(RPackage): - """Friendly Regular Expressions + """Friendly Regular Expressions. A friendly interface for the construction of regular expressions.""" - homepage = "https://cloud.r-project.org/package=rex" - url = "https://cloud.r-project.org/src/contrib/rex_1.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rex" + cran = "rex" + version('1.2.1', sha256='af42e649c06e4bbdba94d5a1870a7e8347903571c90cd5e5ca40f52307a3bfd6') version('1.2.0', sha256='06b491f1469078862e40543fd74e1d38b2e0fb61fdf01c8083add4b11ac2eb54') version('1.1.2', sha256='bd3c74ceaf335336f5dd04314d0a791f6311e421a2158f321f5aab275f539a2a') depends_on('r-lazyeval', type=('build', 'run')) - depends_on('r-magrittr', when='@:1.1.2', type=('build', 'run')) + + depends_on('r-magrittr', type=('build', 'run'), when='@:1.1.2') diff --git a/var/spack/repos/builtin/packages/r-rferns/package.py b/var/spack/repos/builtin/packages/r-rferns/package.py index c9409273e5..535231dfc5 100644 --- a/var/spack/repos/builtin/packages/r-rferns/package.py +++ b/var/spack/repos/builtin/packages/r-rferns/package.py @@ -7,16 +7,15 @@ from spack import * class RRferns(RPackage): - """Random Ferns Classifier + """Random Ferns Classifier. Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.""" - homepage = "https://cloud.r-project.org/package=rFerns" - url = "https://cloud.r-project.org/src/contrib/rFerns_3.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rFerns" + cran = "rFerns" + version('5.0.0', sha256='78da671e18dc1fb499eddcc6db7eedd69cef673ba0b46c873bd95615cbb583fb') version('4.0.0', sha256='cc8cea0893390bf5db0fb0f59748d5bf6f29537d68bedca900268fd551489128') version('3.0.0', sha256='35e7e31a6497e415a0fe578678cf9b2f537b21319e4c015a1e2dade00310227c') diff --git a/var/spack/repos/builtin/packages/r-rgdal/package.py b/var/spack/repos/builtin/packages/r-rgdal/package.py index c013c4103f..6e45bea3b6 100644 --- a/var/spack/repos/builtin/packages/r-rgdal/package.py +++ b/var/spack/repos/builtin/packages/r-rgdal/package.py @@ -7,7 +7,7 @@ from spack import * class RRgdal(RPackage): - """Bindings for the 'Geospatial' Data Abstraction Library + """Bindings for the 'Geospatial' Data Abstraction Library. Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' @@ -21,10 +21,9 @@ class RRgdal(RPackage): and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.""" - homepage = "https://cloud.r-project.org/package=rgdal" - url = "https://cloud.r-project.org/src/contrib/rgdal_1.3-9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rgdal" + cran = "rgdal" + version('1.5-28', sha256='7f54432cfa8c0db463f68e8856c3ca0a90671dc841ac5203af049eb318e261a2') version('1.5-19', sha256='6fbfd71b19e7b8d9dbddc91cb1eef8890c74a1e2bf8f619da165ff51bf1231b2') version('1.5-18', sha256='53467c19bc93d8ea311458eaa281c8c456168ab75e84d76ef5cc6c00f53122df') version('1.4-4', sha256='2532e76e0af27d145f799d70006a5dbecb2d3be698e3d0bbf580f4c41a34c5d7') @@ -32,8 +31,11 @@ class RRgdal(RPackage): version('1.2-16', sha256='017fefea4f9a6d4540d128c707197b7025b55e4aff98fc763065366b025b03c9') depends_on('r@3.3.0:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.5:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.5:') depends_on('r-sp@1.1-0:', type=('build', 'run')) depends_on('gdal@1.11.4:') depends_on('proj@4.8.0:5', when='@:1.3-9') depends_on('proj@4.8.0:', when='@1.4-2:') + + conflicts('^proj@:5', when='^gdal@3:') + conflicts('^proj@6:', when='^gdal@:2') diff --git a/var/spack/repos/builtin/packages/r-rgenoud/package.py b/var/spack/repos/builtin/packages/r-rgenoud/package.py index 61014e09b0..032299d76f 100644 --- a/var/spack/repos/builtin/packages/r-rgenoud/package.py +++ b/var/spack/repos/builtin/packages/r-rgenoud/package.py @@ -7,11 +7,11 @@ from spack import * class RRgenoud(RPackage): - """A genetic algorithm plus derivative optimizer.""" + """R Version of GENetic Optimization Using Derivatives. - homepage = "https://sekhon.berkeley.edu/rgenoud/" - url = "https://cloud.r-project.org/src/contrib/rgenoud_5.8-1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rgenoud" + A genetic algorithm plus derivative optimizer.""" + + cran = "rgenoud" version('5.8-3.0', sha256='9beb11b5edab3ab3aa6001daa39668b240a8e0328be9d55db4e23ff88ce3235d') version('5.8-2.0', sha256='106c4f6a6df5159578e929a0141b3cfbaa88141a70703ff59a1fc48a27e2d239') diff --git a/var/spack/repos/builtin/packages/r-rgeos/package.py b/var/spack/repos/builtin/packages/r-rgeos/package.py index 3c8f119a67..c83777e470 100644 --- a/var/spack/repos/builtin/packages/r-rgeos/package.py +++ b/var/spack/repos/builtin/packages/r-rgeos/package.py @@ -7,7 +7,7 @@ from spack import * class RRgeos(RPackage): - """Interface to Geometry Engine - Open Source ('GEOS') + """Interface to Geometry Engine - Open Source ('GEOS'). Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the @@ -28,14 +28,14 @@ class RRgeos(RPackage): 'gMakeValid()', which may, however, return a collection of geometries of different types.""" - homepage = "https://cloud.r-project.org/package=rgeos" - url = "https://cloud.r-project.org/src/contrib/rgeos_0.3-26.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rgeos" + cran = "rgeos" + version('0.5-9', sha256='ab90cbfe6a3680a9d2eed5e655064a075adc66788e304468969ab7cc2df0e3d4') version('0.5-5', sha256='4baa0dfe6ff76e87ddb67a030fc14fe963d28b518485a4d71058923b2606d420') version('0.5-1', sha256='8408973e7fe5648e39aa53f3d4bfe800638021a146a4e06f86496c0132e05488') version('0.3-26', sha256='98524a0b8113abe6c3d0ecc1f2f66e7ab6d40c783a76158cfc017e1ab1e3f433') depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-sp@1.1-0:', type=('build', 'run')) - depends_on('geos@3.2.0:3.8.0') + depends_on('geos@3.2.0:3.8.0', when='@:0.5-1') + depends_on('geos@3.2.0:') diff --git a/var/spack/repos/builtin/packages/r-rgexf/package.py b/var/spack/repos/builtin/packages/r-rgexf/package.py index 7d4d60bb6f..b2d68391fa 100644 --- a/var/spack/repos/builtin/packages/r-rgexf/package.py +++ b/var/spack/repos/builtin/packages/r-rgexf/package.py @@ -7,25 +7,24 @@ from spack import * class RRgexf(RPackage): - """Build, Import and Export GEXF Graph Files + """Build, Import and Export GEXF Graph Files. - Create, read and write GEXF (Graph Exchange XML Format) graph files - (used in Gephi and others). Using the XML package, it allows the user to - easily build/read graph files including attributes, GEXF viz attributes - (such as color, size, and position), network dynamics (for both edges and - nodes) and edge weighting. Users can build/handle graphs element-by-element - or massively through data-frames, visualize the graph on a web browser - through "sigmajs" (a javascript library) and interact with the igraph - package.""" + Create, read and write GEXF (Graph Exchange XML Format) graph files (used + in Gephi and others). Using the XML package, it allows the user to easily + build/read graph files including attributes, GEXF viz attributes (such as + color, size, and position), network dynamics (for both edges and nodes) and + edge weighting. Users can build/handle graphs element-by-element or + massively through data-frames, visualize the graph on a web browser through + "sigmajs" (a javascript library) and interact with the igraph package.""" - homepage = "https://bitbucket.org/gvegayon/rgexf" - url = "https://cloud.r-project.org/src/contrib/rgexf_0.15.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rgexf" + cran = "rgexf" + version('0.16.2', sha256='6ee052b0de99d0c7492366b991d345a51b3d0cc890d10a68b8670e1bd4fc8201') version('0.16.0', sha256='2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee') version('0.15.3', sha256='2e8a7978d1fb977318e6310ba65b70a9c8890185c819a7951ac23425c6dc8147') depends_on('r-xml', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) - depends_on('r-servr', when='@0.16.0:', type=('build', 'run')) - depends_on('r-rook', when='@:0.15.3', type=('build', 'run')) + depends_on('r-servr', type=('build', 'run'), when='@0.16.0:') + + depends_on('r-rook', type=('build', 'run'), when='@:0.15.3') diff --git a/var/spack/repos/builtin/packages/r-rgl/package.py b/var/spack/repos/builtin/packages/r-rgl/package.py index 36993ccf2b..e6f1694cf5 100644 --- a/var/spack/repos/builtin/packages/r-rgl/package.py +++ b/var/spack/repos/builtin/packages/r-rgl/package.py @@ -7,19 +7,18 @@ from spack import * class RRgl(RPackage): - """3D Visualization Using OpenGL + """3D Visualization Using OpenGL. Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), - etc.). Output may be on screen using OpenGL, or to various standard - 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, + etc.). Output may be on screen using OpenGL, or to various standard 3D file + formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.""" - homepage = "https://r-forge.r-project.org/projects/rgl" - url = "https://cloud.r-project.org/src/contrib/rgl_0.99.16.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rgl" + cran = "rgl" + version('0.108.3', sha256='89f96eb462cacfcc796ad351d7dac0480a7eb9f80e9bd75e58c5a79f0ee8133b') version('0.104.16', sha256='b82d2e2b965e76d6cc55bbd15ee0f79c36913ab09ce5436d2104551563462a99') version('0.100.26', sha256='e1889c2723ad458b39fdf9366fdaf590d7657d3762748f8534a8491ef754e740') version('0.100.24', sha256='1233a7bdc5a2b908fc64d5f56e92a0e123e8f7c0b9bac93dfd005608b78fa35a') @@ -29,14 +28,14 @@ class RRgl(RPackage): depends_on('r+X', type=('build', 'run')) depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.108.3:') depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-knitr', type=('build', 'run')) + depends_on('r-knitr@1.33:', type=('build', 'run'), when='@0.108.3:') depends_on('r-jsonlite@0.9.20:', type=('build', 'run')) - depends_on('r-shiny', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-crosstalk', when='@0.99.16:', type=('build', 'run')) - depends_on('r-manipulatewidget@0.9.0:', when='@0.99.16:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run'), when='@0.108.3:') depends_on('libx11') depends_on('gl') depends_on('glu') @@ -45,6 +44,10 @@ class RRgl(RPackage): depends_on('freetype', type='link') depends_on('pandoc@1.14:', type='build') + depends_on('r-shiny', type=('build', 'run'), when='@:0.104.16') + depends_on('r-crosstalk', type=('build', 'run'), when='@0.99.16:0.104.16') + depends_on('r-manipulatewidget@0.9.0:', type=('build', 'run'), when='@0.99.16:0.104.16') + def configure_args(self): args = ['--x-includes=%s' % self.spec['libx11'].prefix.include, '--x-libraries=%s' % self.spec['libx11'].prefix.lib, diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py index 563cb1cb8e..b0118c2dcf 100644 --- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -7,16 +7,14 @@ from spack import * class RRgooglemaps(RPackage): - """Overlays on Static Maps + """Overlays on Static Maps. - This package serves two purposes: (i) Provide a comfortable R interface - to query the Google server for static maps, and (ii) Use the map as a + This package serves two purposes: (i) Provide a comfortable R interface to + query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.""" - homepage = "https://cloud.r-project.org/package=RgoogleMaps" - url = "https://cloud.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RgoogleMaps" + cran = "RgoogleMaps" version('1.4.5.3', sha256='d1d5ad8db841754af175d4104a05c5c31e5cc445be314a3ac70483c31798680b') version('1.4.3', sha256='44cb62bcd23e5b4807e91c5825352eb8d38aaaeb3b38a8271ca9f21c1e1d4b19') @@ -25,5 +23,6 @@ class RRgooglemaps(RPackage): depends_on('r@2.10:', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) - depends_on('r-sp', when='@1.4.5.3:', type=('build', 'run')) - depends_on('r-rjsonio', when='@1.2.0.5:1.2.0.7', type=('build', 'run')) + depends_on('r-sp', type=('build', 'run'), when='@1.4.5.3:') + + depends_on('r-rjsonio', type=('build', 'run'), when='@1.2.0.5:1.2.0.7') diff --git a/var/spack/repos/builtin/packages/r-rhmmer/package.py b/var/spack/repos/builtin/packages/r-rhmmer/package.py index c2360dc4b4..7580726475 100644 --- a/var/spack/repos/builtin/packages/r-rhmmer/package.py +++ b/var/spack/repos/builtin/packages/r-rhmmer/package.py @@ -7,11 +7,13 @@ from spack import * class RRhmmer(RPackage): - """rhmmer: Utilities Parsing 'HMMER' Results""" + """Utilities Parsing 'HMMER' Results. - homepage = "https://cloud.r-project.org/package=rhmmer" - url = "https://cloud.r-project.org/src/contrib/rhmmer_0.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rhmmer/" + 'HMMER' is a profile hidden Markov model tool used primarily for sequence + analysis in bioinformatics (<http://hmmer.org/>). 'rhmmer' provides + utilities for parsing the 'HMMER' output into tidy data frames.""" + + cran = "rhmmer" version('0.1.0', sha256='5022cefc9ba335160c1ad8d1b614610ae0ad48287c9fdbaf8f8966149358e520') diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py index 4205a7ce51..dbd780af7c 100644 --- a/var/spack/repos/builtin/packages/r-rinside/package.py +++ b/var/spack/repos/builtin/packages/r-rinside/package.py @@ -7,26 +7,24 @@ from spack import * class RRinside(RPackage): - """C++ Classes to Embed R in C++ (and C) Applications + """C++ Classes to Embed R in C++ (and C) Applications. - C++ classes to embed R in C++ applications The 'RInside' packages makes - it easier to have "R inside" your C++ application by providing a C++ - wrapperclass providing the R interpreter. As R itself is embedded into - your application, a shared library build of R is required. This works on - Linux, OS X and even on Windows provided you use the same tools used to - build R itself. Numerous examples are provided in the eight subdirectories - of the examples/ directory of the installed package: standard, mpi (for - parallel computing) qt (showing how to embed 'RInside' inside a Qt GUI - application), wt (showing how to build a "web-application" using the Wt - toolkit), armadillo (for 'RInside' use with 'RcppArmadillo') and eigen (for - 'RInside' use with 'RcppEigen'). The example use GNUmakefile(s) with GNU - extensions, so a GNU make is required (and will use the GNUmakefile - automatically). Doxygen-generated documentation of the C++ classes is - available at the 'RInside' website as well.""" + C++ classes to embed R in C++ applications The 'RInside' packages makes it + easier to have "R inside" your C++ application by providing a C++ + wrapperclass providing the R interpreter. As R itself is embedded into your + application, a shared library build of R is required. This works on Linux, + OS X and even on Windows provided you use the same tools used to build R + itself. Numerous examples are provided in the eight subdirectories of the + examples/ directory of the installed package: standard, mpi (for parallel + computing) qt (showing how to embed 'RInside' inside a Qt GUI application), + wt (showing how to build a "web-application" using the Wt toolkit), + armadillo (for 'RInside' use with 'RcppArmadillo') and eigen (for 'RInside' + use with 'RcppEigen'). The example use GNUmakefile(s) with GNU extensions, + so a GNU make is required (and will use the GNUmakefile automatically). + Doxygen-generated documentation of the C++ classes is available at the + 'RInside' website as well.""" - homepage = "https://dirk.eddelbuettel.com/code/rinside.html" - url = "https://cloud.r-project.org/src/contrib/RInside_0.2.15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RInside" + cran = "RInside" version('0.2.16', sha256='7ae4ade128ea05f37068d59e610822ff0b277f9d39d8900f7eb31759ad5a2a0e') version('0.2.15', sha256='1e1d87a3584961f3aa4ca6acd4d2f3cda26abdab027ff5be2fd5cd76a98af02b') diff --git a/var/spack/repos/builtin/packages/r-rio/package.py b/var/spack/repos/builtin/packages/r-rio/package.py index d5e95eeead..851aa29cb4 100644 --- a/var/spack/repos/builtin/packages/r-rio/package.py +++ b/var/spack/repos/builtin/packages/r-rio/package.py @@ -18,7 +18,6 @@ class RRio(RPackage): where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.""" - homepage = "https://github.com/leeper/rio" cran = "rio" version('0.5.29', sha256='9fa63187e1814053e6ed2a164665b4924e08c3453adccb78f7211d403dcc5412') @@ -26,7 +25,7 @@ class RRio(RPackage): depends_on('r@2.15.0:', type=('build', 'run')) depends_on('r-foreign', type=('build', 'run')) - depends_on('r-haven@1.1.2:', when='@0.5.26:', type=('build', 'run')) + depends_on('r-haven@1.1.2:', type=('build', 'run'), when='@0.5.26:') depends_on('r-haven@1.1.0:', type=('build', 'run')) depends_on('r-curl@0.6:', type=('build', 'run')) depends_on('r-data-table@1.9.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rjags/package.py b/var/spack/repos/builtin/packages/r-rjags/package.py index b1e6fc49be..927ba100d6 100644 --- a/var/spack/repos/builtin/packages/r-rjags/package.py +++ b/var/spack/repos/builtin/packages/r-rjags/package.py @@ -8,14 +8,13 @@ from spack import * class RRjags(RPackage): - """Bayesian Graphical Models using MCMC + """Bayesian Graphical Models using MCMC. Interface to the JAGS MCMC library.""" - homepage = "https://cloud.r-project.org/package=rjags" - url = "https://cloud.r-project.org/src/contrib/rjags_4-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rjags/" + cran = "rjags" + version('4-12', sha256='b91f34c3f9ebf78fa44bd661346fbb6f28a01693a7203ac133c98392dd273e10') version('4-10', sha256='bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada') version('4-8', sha256='1529827ab11493fb5f05552e239d700ae2f818995d86d3c9e4c92523f594b59f') version('4-6', sha256='cf24bb1e7c8445bafb49097089ad33e5bd5d8efbccf16fc7e32ad230f05f89ad') diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index 334c8006cb..7d2d095117 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -7,20 +7,20 @@ from spack import * class RRjava(RPackage): - """Low-Level R to Java Interface + """Low-Level R to Java Interface. - Low-level interface to Java VM very much like .C/.Call and friends. - Allows creation of objects, calling methods and accessing fields.""" + Low-level interface to Java VM very much like .C/.Call and friends. Allows + creation of objects, calling methods and accessing fields.""" - homepage = "https://www.rforge.net/rJava/" - url = "https://cloud.r-project.org/src/contrib/rJava_0.9-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rJava" + cran = "rJava" + version('1.0-6', sha256='e290d0493317a5d6c452793e92baa914e37ef03faef19b2e436329b4ec8658c6') version('0.9-13', sha256='5b1688f5044476b34f71d868b222ac5fce3a088f0c2b9e4591c1e48f3d8c75f4') version('0.9-11', sha256='c28ae131456a98f4d3498aa8f6eac9d4df48727008dacff1aa561fc883972c69') version('0.9-8', sha256='dada5e031414da54eb80b9024d51866c20b92d41d68da65789fe0130bc54bd8a') depends_on('r@2.5:', type=('build', 'run')) + depends_on('r@3.6.0:', type=('build', 'run'), when='@1.0-6:') depends_on('java@2:') depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py index c2213c74f4..6573287b09 100644 --- a/var/spack/repos/builtin/packages/r-rjson/package.py +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -7,14 +7,16 @@ from spack import * class RRjson(RPackage): - """Converts R object into JSON objects and vice-versa.""" + """JSON for R. - homepage = "https://cloud.r-project.org/package=rjson" - url = "https://cloud.r-project.org/src/contrib/rjson_0.2.15.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rjson" + Converts R object into JSON objects and vice-versa.""" + cran = "rjson" + + version('0.2.21', sha256='982b56d35ccc0c7db0b20c1d3eab5f5f47c620309646fdc278ff1cc3433ea2e2') version('0.2.20', sha256='3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c') version('0.2.19', sha256='5c2672461986f2b715416cab92ed262abe9875f31299bc8a1a072ef7c6dd49bc') version('0.2.15', sha256='77d00d8f6a1c936329b46f3b8b0be79a165f8c5f1989497f942ecc53dcf6f2ef') depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@0.2.21:') diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py index 25e9d18598..3d73444cd7 100644 --- a/var/spack/repos/builtin/packages/r-rjsonio/package.py +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -7,7 +7,7 @@ from spack import * class RRjsonio(RPackage): - """Serialize R Objects to JSON, JavaScript Object Notation + """Serialize R Objects to JSON, JavaScript Object Notation. This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into @@ -25,10 +25,9 @@ class RRjsonio(RPackage): aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.""" - homepage = "https://cloud.r-project.org/package=RJSONIO" - url = "https://cloud.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RJSONIO" + cran = "RJSONIO" + version('1.3-1.6', sha256='82d1c9ea7758b2a64ad683f9c46223dcba9aa8146b43c1115bf9aa76a657a09f') version('1.3-1.4', sha256='54142c931e15eca278a02dad5734026bb49d960471eb085008af825352953190') version('1.3-1.2', sha256='550e18f7c04186376d67747b8258f529d205bfc929da9194fe45ec384e092d7e') version('1.3-1.1', sha256='c72493b441758cd1e3e9d91296b9ea31068e71104649f46ad84c854a02c09693') diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py index 38bc3b56dd..1699506b0c 100644 --- a/var/spack/repos/builtin/packages/r-rlang/package.py +++ b/var/spack/repos/builtin/packages/r-rlang/package.py @@ -7,14 +7,14 @@ from spack import * class RRlang(RPackage): - """Functions for Base Types and Core R and 'Tidyverse' Features + """Functions for Base Types and Core R and 'Tidyverse' Features. A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.""" - homepage = "https://cloud.r-project.org/package=rlang" cran = "rlang" + version('1.0.0', sha256='ab6134c97b3100613ba2a15792fde5341f485ba85432a81370c6270c73396e6a') version('0.4.12', sha256='2a26915738be120a56ec93e781bcb50ffa1031e11904544198b4a15c35029915') version('0.4.10', sha256='07530270c4c199f2b7efc5d57a476d99babd9d0c3388a02bb7d57fe312da3576') version('0.4.6', sha256='3a81b107765fd6ac0ad716c428d01878775ded9208ba125d43c890c73d2533ca') @@ -28,6 +28,6 @@ class RRlang(RPackage): version('0.1.2', sha256='90cfcd88cae6fff044fca64b24a8e6bdc09fc276163b518ff2d90268b0c785f9') version('0.1.1', sha256='5901f95d68728a7d9bb1c2373a20ce6e4ad222f66e397e7735e9eff987c73c3f') - depends_on('r@3.1.0:', when='@:0.3.4', type=('build', 'run')) - depends_on('r@3.2.0:', when='@0.4.0:', type=('build', 'run')) - depends_on('r@3.3.0:', when='@0.4.10:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@0.4.0:') + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.4.10:') diff --git a/var/spack/repos/builtin/packages/r-rle/package.py b/var/spack/repos/builtin/packages/r-rle/package.py index be364e6ba3..dbcc32319c 100644 --- a/var/spack/repos/builtin/packages/r-rle/package.py +++ b/var/spack/repos/builtin/packages/r-rle/package.py @@ -7,14 +7,12 @@ from spack import * class RRle(RPackage): - """Common Functions for Run-Length Encoded Vectors + """Common Functions for Run-Length Encoded Vectors. Common 'base' and 'stats' methods for 'rle' objects, aiming to make it possible to treat them transparently as vectors.""" - homepage = "https://cloud.r-project.org/package=rle" - url = "https://cloud.r-project.org/src/contrib/rle_0.9.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rle" + cran = "rle" version('0.9.2', sha256='803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69') diff --git a/var/spack/repos/builtin/packages/r-rmariadb/package.py b/var/spack/repos/builtin/packages/r-rmariadb/package.py index 9431d1e244..cbc29161f2 100644 --- a/var/spack/repos/builtin/packages/r-rmariadb/package.py +++ b/var/spack/repos/builtin/packages/r-rmariadb/package.py @@ -7,29 +7,31 @@ from spack import * class RRmariadb(RPackage): - """Database Interface and 'MariaDB' Driver + """Database Interface and 'MariaDB' Driver. Implements a 'DBI'-compliant interface to 'MariaDB' (<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>) databases.""" - homepage = "https://rmariadb.r-dbi.org/" - url = "https://cloud.r-project.org/src/contrib/RMariaDB_1.0.8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RMariaDB" + cran = "RMariaDB" + version('1.2.1', sha256='c9176a096854ce33a98ce0faef0065c50b5d356174f90cea742c70e130cf5f0c') version('1.1.0', sha256='9ffa63a15052876a51a7996ca4e6a5b7b937f594b5cc7ca5a86f43789e22a956') version('1.0.8', sha256='3c8aedc519dc063ceb068535a3700bc5caf26f867078cc5a228aa8961e2d99f5') depends_on('r@2.8.0:', type=('build', 'run')) depends_on('r-bit64', type=('build', 'run')) + depends_on('r-blob', type=('build', 'run'), when='@1.2.1:') depends_on('r-dbi@1.1.0:', type=('build', 'run')) depends_on('r-hms@0.5.0:', type=('build', 'run')) - depends_on('r-lubridate', when='@1.1.0:', type=('build', 'run')) + depends_on('r-lubridate', type=('build', 'run'), when='@1.1.0:') depends_on('r-rcpp@0.12.4:', type=('build', 'run')) - depends_on('r-bh', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@1.2.1:') depends_on('r-plogr', type=('build', 'run')) depends_on('mariadb-client') + depends_on('r-bh', type=('build', 'run'), when='@:1.1.0') + # Set the library explicitly to prevent configure from finding a system # mysql-client def configure_vars(self): diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py index b38a16b7b1..8cfa1b1a06 100644 --- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py +++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py @@ -8,12 +8,11 @@ from spack import * class RRmarkdown(RPackage): - """Dynamic Documents for R + """Dynamic Documents for R. Convert R Markdown documents into a variety of formats.""" - homepage = "https://rmarkdown.rstudio.com/" - cran = "rmarkdown" + cran = "rmarkdown" version('2.11', sha256='9371255300e7ea4cd936978ad2ca3d205d8605e09f4913cb0d4725005a7a9775') version('2.9', sha256='6ce5af8b9a7c282619f74d3999d27ec4de12d3f93cde8fd12cc4c19f02ea8668') @@ -30,16 +29,16 @@ class RRmarkdown(RPackage): depends_on('r-htmltools@0.3.5:', type=('build', 'run')) depends_on('r-evaluate@0.13:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-tinytex@0.11:', when='@1.10:', type=('build', 'run')) - depends_on('r-tinytex@0.31:', when='@2.8:', type=('build', 'run')) - depends_on('r-xfun', when='@1.13:', type=('build', 'run')) - depends_on('r-xfun@0.15:', when='@2.6:', type=('build', 'run')) - depends_on('r-xfun@0.21:', when='@2.8:', type=('build', 'run')) - depends_on('r-jquerylib', when='@2.11:', type=('build', 'run')) - depends_on('r-stringr@1.2.0:', when='@1.6:', type=('build', 'run')) - depends_on('r-rprojroot', when='@1.3:1.7', type=('build', 'run')) - depends_on('r-mime', when='@1.8:1.14', type=('build', 'run')) - depends_on('r-catools', when='@:1.7', type=('build', 'run')) - depends_on('r-base64enc', when='@:1.14', type=('build', 'run')) + depends_on('r-tinytex@0.11:', type=('build', 'run'), when='@1.10:') + depends_on('r-tinytex@0.31:', type=('build', 'run'), when='@2.8:') + depends_on('r-xfun', type=('build', 'run'), when='@1.13:') + depends_on('r-xfun@0.15:', type=('build', 'run'), when='@2.6:') + depends_on('r-xfun@0.21:', type=('build', 'run'), when='@2.8:') + depends_on('r-jquerylib', type=('build', 'run'), when='@2.11:') + depends_on('r-stringr@1.2.0:', type=('build', 'run'), when='@1.6:') + depends_on('r-rprojroot', type=('build', 'run'), when='@1.3:1.7') + depends_on('r-mime', type=('build', 'run'), when='@1.8:1.14') + depends_on('r-catools', type=('build', 'run'), when='@:1.7') + depends_on('r-base64enc', type=('build', 'run'), when='@:1.14') depends_on('pandoc@1.12.3:') depends_on('pandoc@1.14:', when='@2.6:') diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py index 2fbe71d0f4..da511c44a9 100644 --- a/var/spack/repos/builtin/packages/r-rminer/package.py +++ b/var/spack/repos/builtin/packages/r-rminer/package.py @@ -7,7 +7,7 @@ from spack import * class RRminer(RPackage): - """Data Mining Classification and Regression Methods + """Data Mining Classification and Regression Methods. Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short @@ -25,9 +25,7 @@ class RRminer(RPackage): 1.2 - new input importance methods via improved Importance() function; 1.0 - first version.""" - homepage = "http://www3.dsi.uminho.pt/pcortez/rminer.html" - url = "https://cloud.r-project.org/src/contrib/rminer_1.4.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rminer" + cran = "rminer" version('1.4.6', sha256='1f8bf7b3fbc887fd766568c1ec1f861021c962259354bd8967a61c1d0761cdf7') version('1.4.2', sha256='64444dcedcd17f2f26129819d6bd2f84d4bb59c8f65328b6054ef32cb9624fc2') diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py index 3bd78e15be..215a42cffe 100644 --- a/var/spack/repos/builtin/packages/r-rmpfr/package.py +++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py @@ -7,7 +7,7 @@ from spack import * class RRmpfr(RPackage): - """R MPFR - Multiple Precision Floating-Point Reliable + """R MPFR - Multiple Precision Floating-Point Reliable. Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, @@ -15,20 +15,20 @@ class RRmpfr(RPackage): Reliable) Library which itself is based on the GMP (GNU Multiple Precision) Library.""" - homepage = "https://rmpfr.r-forge.r-project.org" - url = "https://cloud.r-project.org/src/contrib/Rmpfr_0.6-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Rmpfr" + cran = "Rmpfr" + version('0.8-7', sha256='93c2db785ff705dcfc6fa7f0373c2426cdc2ef72ceb5b294edeb2952775f57d2') version('0.8-2', sha256='74f6af1738b2cd21e7f2564b4cc2c84d5473a3745ba88ec76355d07fdd61f700') version('0.7-2', sha256='ec1da6ec5292ea6ac95495c6a299591d367e520ae324719817fb884c865603ff') version('0.7-1', sha256='9b3021617a22b0710b0f1acc279290762317ff123fd9e8fd03f1449f4bbfe204') version('0.6-1', sha256='bf50991055e9336cd6a110d711ae8a91a0551b96f9eaab5fef8c05f578006e1c') depends_on('r@3.0.1:', type=('build', 'run')) - depends_on('r@3.1.0:', when='@0.7-0', type=('build', 'run')) - depends_on('r@3.3.0:', when='@0.7-1:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.8-2:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@0.7-0') + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.7-1:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.8-2:') depends_on('r-gmp@0.5-8:', type=('build', 'run')) - depends_on('r-gmp@0.6-1:', when='@0.8-2:', type=('build', 'run')) + depends_on('r-gmp@0.6-1:', type=('build', 'run'), when='@0.8-2:') depends_on('gmp@4.2.3:') depends_on('mpfr@3.0.0:') + depends_on('texlive', type='build') diff --git a/var/spack/repos/builtin/packages/r-rmpi/package.py b/var/spack/repos/builtin/packages/r-rmpi/package.py index 17931cbc61..baeb12d66d 100644 --- a/var/spack/repos/builtin/packages/r-rmpi/package.py +++ b/var/spack/repos/builtin/packages/r-rmpi/package.py @@ -7,13 +7,14 @@ from spack import * class RRmpi(RPackage): - """An interface (wrapper) to MPI APIs. It also provides interactive R - manager and worker environment.""" + """Interface (Wrapper) to MPI (Message-Passing Interface). - homepage = "https://cran.r-project.org/web/packages/Rmpi/index.html" - url = "https://cloud.r-project.org/src/contrib/Rmpi_0.6-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Rmpi" + An interface (wrapper) to MPI APIs. It also provides interactive R manager + and worker environment.""" + cran = "Rmpi" + + version('0.6-9.2', sha256='358ac1af97402e676f209261a231f36a35e60f0301edf8ca53dac11af3c3bd1a') version('0.6-9', sha256='b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6') version('0.6-8', sha256='9b453ce3bd7284eda33493a0e47bf16db6719e3c48ac5f69deac6746f5438d96') version('0.6-6', sha256='d8fc09ad38264697caa86079885a7a1098921a3116d5a77a62022b9508f8a63a') diff --git a/var/spack/repos/builtin/packages/r-rms/package.py b/var/spack/repos/builtin/packages/r-rms/package.py index dc87dd9398..961080be9d 100644 --- a/var/spack/repos/builtin/packages/r-rms/package.py +++ b/var/spack/repos/builtin/packages/r-rms/package.py @@ -7,7 +7,7 @@ from spack import * class RRms(RPackage): - """Regression Modeling Strategies + """Regression Modeling Strategies. Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. @@ -23,10 +23,9 @@ class RRms(RPackage): for serially or spatially correlated observations, generalized linear models, and quantile regression.""" - homepage = "https://cloud.r-project.org/package=rms" - url = "https://cloud.r-project.org/src/contrib/rms_5.1-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rms" + cran = "rms" + version('6.2-0', sha256='10d58cbfe39fb434223834e29e5248c9384cded23e6267cfc99367d0f5ee24b6') version('6.1-0', sha256='b89ec3b9211a093bfe83a2a8107989b5ce3b7b7c323b88a5d887d99753289f52') version('5.1-4', sha256='38f5844c4944a95b2adebea6bb1d163111270b8662399ea0349c45c0758076a6') version('5.1-3.1', sha256='0946d9547a4e3ff020a61ab3fce38f88aa9545729683e2bfefeb960edec82b37') @@ -37,7 +36,7 @@ class RRms(RPackage): depends_on('r@3.5.0:', type=('build', 'run')) depends_on('r-hmisc@4.3-0:', type=('build', 'run')) depends_on('r-survival@3.1-6:', type=('build', 'run')) - depends_on('r-survival@3.1-12:', when='@6.1-0:', type=('build', 'run')) + depends_on('r-survival@3.1-12:', type=('build', 'run'), when='@6.1-0:') depends_on('r-lattice', type=('build', 'run')) depends_on('r-ggplot2@2.2:', type=('build', 'run')) depends_on('r-sparsem', type=('build', 'run')) @@ -48,6 +47,6 @@ class RRms(RPackage): depends_on('r-multcomp', type=('build', 'run')) depends_on('r-htmltable@1.11.0:', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) - depends_on('r-mass', when='@6.1-0:', type=('build', 'run')) - depends_on('r-cluster', when='@6.1-0:', type=('build', 'run')) - depends_on('r-digest', when='@6.1-0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run'), when='@6.1-0:') + depends_on('r-cluster', type=('build', 'run'), when='@6.1-0:') + depends_on('r-digest', type=('build', 'run'), when='@6.1-0:') diff --git a/var/spack/repos/builtin/packages/r-rmutil/package.py b/var/spack/repos/builtin/packages/r-rmutil/package.py index fb762ad282..ada5f5b391 100644 --- a/var/spack/repos/builtin/packages/r-rmutil/package.py +++ b/var/spack/repos/builtin/packages/r-rmutil/package.py @@ -7,16 +7,14 @@ from spack import * class RRmutil(RPackage): - """Utilities for Nonlinear Regression and Repeated MeasurementsModels + """Utilities for Nonlinear Regression and Repeated MeasurementsModels. A toolkit of functions for nonlinear regression and repeated measurements not to be used by itself but called by other Lindsey packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event' (available at <https://www.commanster.eu/rcode.html>).""" - homepage = "https://www.commanster.eu/rcode.html" - url = "https://cloud.r-project.org/src/contrib/rmutil_1.1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rmutil" + cran = "rmutil" version('1.1.5', sha256='6077e643d6daeba6edcf49d928320b54cc6aa6ff59934f9e9e6071a2f9afb2f6') version('1.1.3', sha256='7abaf41e99d1c4a0e4082c4594964ac1421c53b4268116c82fa55aa8bc0582da') diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 6072a41afa..d020170d06 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -7,16 +7,15 @@ from spack import * class RRmysql(RPackage): - """Database Interface and 'MySQL' Driver for R + """Database Interface and 'MySQL' Driver for R. Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package.""" - homepage = "https://github.com/rstats-db/rmysql" - url = "https://cloud.r-project.org/src/contrib/RMySQL_0.10.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RMySQL" + cran = "RMySQL" + version('0.10.23', sha256='f4ac7ed4fba83749819c07ce32d53ee024cf1cedebbda3b832644bff9edf4a15') version('0.10.21', sha256='3a6bf06d32d66c7c958d4f89ed517614171a7fd254ef6f4d40f4c5982c2d6b31') version('0.10.17', sha256='754df4fce159078c1682ef34fc96aa5ae30981dc91f4f2bada8d1018537255f5') version('0.10.9', sha256='41289c743dc8ee2e0dea8b8f291d65f0a7cd11e799b713d94840406ff296fd42') diff --git a/var/spack/repos/builtin/packages/r-rncl/package.py b/var/spack/repos/builtin/packages/r-rncl/package.py index 06ebc5b26a..2f19835d08 100644 --- a/var/spack/repos/builtin/packages/r-rncl/package.py +++ b/var/spack/repos/builtin/packages/r-rncl/package.py @@ -7,7 +7,7 @@ from spack import * class RRncl(RPackage): - """rncl: An Interface to the Nexus Class Library. + """An Interface to the Nexus Class Library. An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of @@ -15,9 +15,7 @@ class RRncl(RPackage): 'phylo' or phylobase's 'phylo4(d)'. This functionality is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.""" - homepage = "https://github.com/fmichonneau/rncl" - url = "https://cloud.r-project.org/src/contrib/rncl_0.8.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rncl" + cran = "rncl" version('0.8.4', sha256='6b19d0dd9bb08ecf99766be5ad684bcd1894d1cd9291230bdd709dbd3396496b') diff --git a/var/spack/repos/builtin/packages/r-rnexml/package.py b/var/spack/repos/builtin/packages/r-rnexml/package.py index ce09a68b50..e617b6d193 100644 --- a/var/spack/repos/builtin/packages/r-rnexml/package.py +++ b/var/spack/repos/builtin/packages/r-rnexml/package.py @@ -7,16 +7,14 @@ from spack import * class RRnexml(RPackage): - """RNeXML: Semantically Rich I/O for the 'NeXML' Format. + """Semantically Rich I/O for the 'NeXML' Format. Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.""" - homepage = "https://github.com/ropensci/RNeXML" - url = "https://cloud.r-project.org/src/contrib/RNeXML_2.4.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RNeXML" + cran = "RNeXML" version('2.4.5', sha256='2b667ecb6400e4c0c125ca73a98cde81330cde3a85b764261f77159e702754f3') diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index acfe844462..7af3db7edf 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -7,7 +7,7 @@ from spack import * class RRngtools(RPackage): - """Utility Functions for Working with Random Number Generators + """Utility Functions for Working with Random Number Generators. Provides a set of functions for working with Random Number Generators (RNGs). In particular, a generic S4 framework is defined for @@ -15,17 +15,17 @@ class RRngtools(RPackage): for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.""" - homepage = "https://renozao.github.io/rngtools" - url = "https://cloud.r-project.org/src/contrib/rngtools_1.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rngtools" + cran = "rngtools" + version('1.5.2', sha256='7f8c76ca4c7851b69a86e27be09b02ddc86357f0388659ef8787634682e8a74d') version('1.5', sha256='8274873b73f7acbe0ce007e62893bf4d369d2aab8768754a60da46b3f078f575') version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') version('1.3.1.1', sha256='99e1a8fde6b81128d0946746c1ef84ec5b6c2973ad843a080098baf73aa3364c') version('1.3.1', sha256='763fc493cb821a4d3e514c0dc876d602a692c528e1d67f295dde70c77009e224') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.2.0:', when='@1.4:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@1.4:') depends_on('r-digest', type=('build', 'run')) - depends_on('r-pkgmaker@0.20:', when='@:1.4', type=('build', 'run')) - depends_on('r-stringr', when='@:1.4', type=('build', 'run')) + + depends_on('r-pkgmaker@0.20:', type=('build', 'run'), when='@:1.4') + depends_on('r-stringr', type=('build', 'run'), when='@:1.4') diff --git a/var/spack/repos/builtin/packages/r-rnoaa/package.py b/var/spack/repos/builtin/packages/r-rnoaa/package.py index e63699f84f..df40001dda 100644 --- a/var/spack/repos/builtin/packages/r-rnoaa/package.py +++ b/var/spack/repos/builtin/packages/r-rnoaa/package.py @@ -7,7 +7,7 @@ from spack import * class RRnoaa(RPackage): - """'NOAA' Weather Data from R + """'NOAA' Weather Data from R. Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each @@ -18,10 +18,9 @@ class RRnoaa(RPackage): storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.""" - homepage = "https://github.com/ropensci/rnoaa" - url = "https://cloud.r-project.org/src/contrib/rnoaa_0.8.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rnoaa" + cran = "rnoaa" + version('1.3.8', sha256='57974b48162637e98888f041d6f0e580d3c60bd5008af2d2bc659491f0deb98a') version('1.3.0', sha256='4c421ad6e4c2b25e4dea5351c338aed70bea6e382562412d1dad825a50b0d161') version('0.8.4', sha256='fb9ae771111dd5f638c1eff3290abad2ff9cc7e68a6678bf2414433ebed2dbbf') @@ -29,16 +28,17 @@ class RRnoaa(RPackage): depends_on('r-lubridate', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-tidyselect', when='@1.3.0:', type=('build', 'run')) + depends_on('r-tidyselect', type=('build', 'run'), when='@1.3.0:') depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) depends_on('r-xml2', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-rappdirs', type=('build', 'run')) depends_on('r-gridextra', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-isdparser@0.2.0:', type=('build', 'run')) depends_on('r-geonames', type=('build', 'run')) depends_on('r-hoardr@0.5.2:', type=('build', 'run')) - depends_on('r-data-table', when='@1.3.0:', type=('build', 'run')) + depends_on('r-data-table', type=('build', 'run'), when='@1.3.0:') + + depends_on('r-rappdirs', type=('build', 'run'), when='@:1.3.0') diff --git a/var/spack/repos/builtin/packages/r-robust/package.py b/var/spack/repos/builtin/packages/r-robust/package.py index c453d7ce6c..491dbe7aca 100644 --- a/var/spack/repos/builtin/packages/r-robust/package.py +++ b/var/spack/repos/builtin/packages/r-robust/package.py @@ -8,15 +8,14 @@ from spack import * class RRobust(RPackage): - """Port of the S+ Robust Library + """Port of the S+ Robust Library. Methods for robust statistics, a state of the art in the early 2000s, notably for robust regression and robust multivariate analysis.""" - homepage = "https://cloud.r-project.org/package=robust" - url = "https://cloud.r-project.org/src/contrib/robust_0.4-18.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/robust/" + cran = "robust" + version('0.6-1', sha256='496fd225f6bc6f734e338308f18475125aaf691b39e25308bddb284d3106117d') version('0.5-0.0', sha256='82f0b50028938966f807a4c4da5c345a3a64ccafd9a31c64a22cda852ed345cf') version('0.4-18.1', sha256='de31901882873ef89748bb6863caf55734431df5b3eb3c6663ed17ee2e4a4077') version('0.4-18', sha256='e4196f01bb3b0d768759d4411d524238b627eb8dc213d84cb30014e75480f8ac') diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py index d3631fa653..3c253dff58 100644 --- a/var/spack/repos/builtin/packages/r-robustbase/package.py +++ b/var/spack/repos/builtin/packages/r-robustbase/package.py @@ -7,7 +7,7 @@ from spack import * class RRobustbase(RPackage): - """Basic Robust Statistics + """Basic Robust Statistics. "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections @@ -15,15 +15,15 @@ class RRobustbase(RPackage): Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.""" - homepage = "https://robustbase.r-forge.r-project.org" - url = "https://cloud.r-project.org/src/contrib/robustbase_0.92-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/robustbase" + cran = "robustbase" + version('0.93-9', sha256='d75fb5075463fec61d063bced7003936e9198492328b6fae15f67e8415713c45') version('0.93-7', sha256='8911d2d0fdca5e2627033e046279f9d106e25ce98d588f9ccc4d8e4b42680956') version('0.93-5', sha256='bde564dbd52f04ab32f9f2f9dd09b9578f3ccd2541cf5f8ff430da42a55e7f56') version('0.93-4', sha256='ea9e03d484ef52ea805803477ffc48881e4c8c86ffda4eea56109f8b23f0a6e0') version('0.92-7', sha256='fcbd6ccbb0291b599fe6a674a91344511e0a691b9cadba0a9d40037faa22bf8f') - depends_on('r@3.0.2:', when='@:0.93-1.1', type=('build', 'run')) - depends_on('r@3.1.0:', when='@0.93-2:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@0.93-2:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.93-9:') depends_on('r-deoptimr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rocr/package.py b/var/spack/repos/builtin/packages/r-rocr/package.py index f126aed5c6..2521443206 100644 --- a/var/spack/repos/builtin/packages/r-rocr/package.py +++ b/var/spack/repos/builtin/packages/r-rocr/package.py @@ -7,31 +7,27 @@ from spack import * class RRocr(RPackage): - """Visualizing the Performance of Scoring Classifiers + """Visualizing the Performance of Scoring Classifiers. - ROC graphs, sensitivity/specificity curves, lift charts, - and precision/recall plots are popular examples of trade-off - visualizations for specific pairs of performance measures. ROCR - is a flexible tool for creating cutoff-parameterized 2D performance - curves by freely combining two from over 25 performance measures - (new performance measures can be added using a standard interface). - Curves from different cross-validation or bootstrapping runs can - be averaged by different methods, and standard deviations, standard - errors or box plots can be used to visualize the variability across - the runs. The parameterization can be visualized by printing cutoff - values at the corresponding curve positions, or by coloring the - curve according to cutoff. All components of a performance plot - can be quickly adjusted using a flexible parameter dispatching - mechanism. Despite its flexibility, ROCR is easy to use, with only - three commands and reasonable default values for all optional - parameters.""" + ROC graphs, sensitivity/specificity curves, lift charts, and + precision/recall plots are popular examples of trade-off visualizations for + specific pairs of performance measures. ROCR is a flexible tool for + creating cutoff-parameterized 2D performance curves by freely combining two + from over 25 performance measures (new performance measures can be added + using a standard interface). Curves from different cross-validation or + bootstrapping runs can be averaged by different methods, and standard + deviations, standard errors or box plots can be used to visualize the + variability across the runs. The parameterization can be visualized by + printing cutoff values at the corresponding curve positions, or by coloring + the curve according to cutoff. All components of a performance plot can be + quickly adjusted using a flexible parameter dispatching mechanism. Despite + its flexibility, ROCR is easy to use, with only three commands and + reasonable default values for all optional parameters.""" - homepage = "https://cloud.r-project.org/package=ROCR" - url = "https://cloud.r-project.org/src/contrib/ROCR_1.0-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ROCR" + cran = "ROCR" version('1.0-11', sha256='57385a773220a3aaef5b221a68b2d9c2a94794d4f9e9fc3c1eb9521767debb2a') version('1.0-7', sha256='e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9') - depends_on('r@3.6:', when='@1.0-11:', type=('build', 'run')) + depends_on('r@3.6:', type=('build', 'run'), when='@1.0-11:') depends_on('r-gplots', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index 563acfbc36..54054d2dad 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -7,19 +7,17 @@ from spack import * class RRodbc(RPackage): - """ODBC Database Access + """ODBC Database Access. An ODBC database interface.""" - homepage = "https://cloud.r-project.org/package=RODBC" - url = "https://cloud.r-project.org/src/contrib/RODBC_1.3-13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RODBC/" + cran = "RODBC" + version('1.3-19', sha256='3afcbd6877cd8b7c8df4a94bacd041a51e5ac607810acb88efd380b45d2d4efe') version('1.3-17', sha256='469fc835f65c344d5c3eaa097ff278ee8e9f12f845722a9aad340115faa704f7') version('1.3-15', sha256='c43e5a2f0aa2f46607e664bfc0bb3caa230bbb779f4ff084e01727642da136e1') version('1.3-13', sha256='e8ea7eb77a07be36fc2d824c28bb426334da7484957ffbc719140373adf1667c') - depends_on('unixodbc') - depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@4.0.0:', when='@1.3-17:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@1.3-17:') + depends_on('unixodbc') diff --git a/var/spack/repos/builtin/packages/r-rook/package.py b/var/spack/repos/builtin/packages/r-rook/package.py index 0c8360222f..d4d782b3ff 100644 --- a/var/spack/repos/builtin/packages/r-rook/package.py +++ b/var/spack/repos/builtin/packages/r-rook/package.py @@ -7,13 +7,13 @@ from spack import * class RRook(RPackage): - """This package contains the Rook specification and convenience software - for building and running Rook applications. To get started, be sure and - read the 'Rook' help file first.""" + """Rook - a web server interface for R. - homepage = "https://cloud.r-project.org/package=Rook" - url = "https://cloud.r-project.org/src/contrib/Rook_1.1-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Rook" + This package contains the Rook specification and convenience software for + building and running Rook applications. To get started, be sure and read + the 'Rook' help file first.""" + + cran = "Rook" version('1.1-1', sha256='00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903') diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py index 6ee7349a4e..468611453d 100644 --- a/var/spack/repos/builtin/packages/r-roxygen2/package.py +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -7,36 +7,38 @@ from spack import * class RRoxygen2(RPackage): - """In-Line Documentation for R + """In-Line Documentation for R. Generate your Rd documentation, 'NAMESPACE' file, and collation field using specially formatted comments. Writing documentation in-line with code makes it easier to keep your documentation up-to-date as your requirements change. 'Roxygen2' is inspired by the 'Doxygen' system for C++.""" - homepage = "https://github.com/klutometis/roxygen" - url = "https://cloud.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/roxygen2" + cran = "roxygen2" + version('7.1.2', sha256='b3693d1eb57bb1c27134447ea7f64c353c085dd2237af7cfacc75fca3d2fc5fd') version('7.1.1', sha256='bdc55ded037d4366f4d25a0d69e880dacc0fa22bee20f595d45855eef8548861') version('7.1.0', sha256='7e9b36f6e7c01a5c8c4747340b3d0c064ce2e48c93fcfbfe45139854fae74103') version('6.1.1', sha256='ed46b7e062e0dfd8de671c7a5f6d120fb2b720982e918dbeb01e6985694c0273') version('5.0.1', sha256='9f755ddd08358be436f08b02df398e50e7508b856131aeeed235099bb3a7eba5') depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.1:', when='@6.1.0:', type=('build', 'run')) - depends_on('r@3.2:', when='@7.1.0:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@6.1.0:') + depends_on('r@3.2:', type=('build', 'run'), when='@7.1.0:') + depends_on('r@3.3:', type=('build', 'run'), when='@7.1.2:') depends_on('r-brew', type=('build', 'run')) depends_on('r-commonmark', type=('build', 'run')) depends_on('r-desc@1.2.0:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-knitr', when='@7.1.0:', type=('build', 'run')) + depends_on('r-knitr', type=('build', 'run'), when='@7.1.0:') depends_on('r-pkgload@1.0.2:', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-purrr@0.3.3:', when='@7.1.0:', type=('build', 'run')) + depends_on('r-purrr@0.3.3:', type=('build', 'run'), when='@7.1.0:') depends_on('r-r6@2.1.2:', type=('build', 'run')) - depends_on('r-rcpp@0.11.0:', type=('build', 'run')) - depends_on('r-rlang', when='@7.1.0:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@7.1.0:') depends_on('r-stringi', type=('build', 'run')) depends_on('r-stringr@1.0.0:', type=('build', 'run')) depends_on('r-xml2', type=('build', 'run')) + depends_on('r-cpp11', type=('build', 'run'), when='@7.1.2:') + + depends_on('r-rcpp@0.11.0:', type=('build', 'run'), when='@:7.1.1') diff --git a/var/spack/repos/builtin/packages/r-rpart-plot/package.py b/var/spack/repos/builtin/packages/r-rpart-plot/package.py index b46a55e925..37519fcd59 100644 --- a/var/spack/repos/builtin/packages/r-rpart-plot/package.py +++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py @@ -7,21 +7,20 @@ from spack import * class RRpartPlot(RPackage): - """Plot 'rpart' Models: An Enhanced Version of 'plot.rpart' + """Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'. - Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the - 'rpart' package.""" + Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' + package.""" - homepage = "https://cloud.r-project.org/package=rpart.plot" - url = "https://cloud.r-project.org/src/contrib/rpart.plot_2.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rpart.plot" + cran = "rpart.plot" + version('3.1.0', sha256='2aaba0c0cabbc17aca9085248b0ad74ee7ff2b8f729e020e84b3917de174c15e') version('3.0.9', sha256='1150f5e9899b3b31b17160617cd99c3ad340c8361aeb229264a7a3a3a28015a4') version('3.0.7', sha256='04e7fcadfa907507b74529c3ecfae4a0c782badf55e87d9c62dbd9a536ea9144') version('3.0.6', sha256='1c584290c8f58ded5c3f0638790a0da63408eca3ecd5d5c4d8c46954de9f4b02') version('2.1.0', sha256='17686da1883f97cb8f44be0d9cb915b366a3cb7313cd131b96497ab09f727436') - depends_on('r@3.2.0:', when='@2.1.2:3.0.6', type=('build', 'run')) - depends_on('r@3.4.0:', when='@3.0.7:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@3.0.7:') depends_on('r-rpart@4.1-10:', type=('build', 'run')) - depends_on('r-rpart@4.1-15:', when='@3.0.9:', type=('build', 'run')) + depends_on('r-rpart@4.1-15:', type=('build', 'run'), when='@3.0.9:') diff --git a/var/spack/repos/builtin/packages/r-rpart/package.py b/var/spack/repos/builtin/packages/r-rpart/package.py index 513bcd1875..2a207ee2be 100644 --- a/var/spack/repos/builtin/packages/r-rpart/package.py +++ b/var/spack/repos/builtin/packages/r-rpart/package.py @@ -7,13 +7,15 @@ from spack import * class RRpart(RPackage): - """Recursive partitioning for classification, regression and - survival trees.""" + """Recursive Partitioning and Regression Trees. - homepage = "https://cloud.r-project.org/package=rpart" - url = "https://cloud.r-project.org/src/contrib/rpart_4.1-10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rpart" + Recursive partitioning for classification, regression and survival trees. + An implementation of most of the functionality of the 1984 book by Breiman, + Friedman, Olshen and Stone.""" + cran = "rpart" + + version('4.1.16', sha256='27ec75258a5a3459ad999f5f36760ead974930744249605bf8465f234f31425c') version('4.1-15', sha256='2b8ebe0e9e11592debff893f93f5a44a6765abd0bd956b0eb1f70e9394cfae5c') version('4.1-13', sha256='8e11a6552224e0fbe23a85aba95acd21a0889a3fe48277f3d345de3147c7494c') version('4.1-11', sha256='38ab80959f59bcdd2c4c72860e8dd0deab0307668cbbf24f96014d7a2496ad98') diff --git a/var/spack/repos/builtin/packages/r-rpmm/package.py b/var/spack/repos/builtin/packages/r-rpmm/package.py index 549d7e1048..8588840d97 100644 --- a/var/spack/repos/builtin/packages/r-rpmm/package.py +++ b/var/spack/repos/builtin/packages/r-rpmm/package.py @@ -7,14 +7,14 @@ from spack import * class RRpmm(RPackage): - """Recursively Partitioned Mixture Model: + """Recursively Partitioned Mixture Model. Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures. This is a model-based clustering algorithm that returns a hierarchy of classes, similar to hierarchical clustering, but also similar to finite mixture models.""" - cran = "RPMM" + cran = "RPMM" version('1.25', sha256='f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8') diff --git a/var/spack/repos/builtin/packages/r-rpostgres/package.py b/var/spack/repos/builtin/packages/r-rpostgres/package.py index a6d06234c2..9da3523be4 100644 --- a/var/spack/repos/builtin/packages/r-rpostgres/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgres/package.py @@ -7,14 +7,14 @@ from spack import * class RRpostgres(RPackage): - """'Rcpp' Interface to 'PostgreSQL' + """'Rcpp' Interface to 'PostgreSQL'. Fully 'DBI'-compliant 'Rcpp'-backed interface to 'PostgreSQL' <https://www.postgresql.org/>, an open-source relational database.""" - homepage = "https://rpostgres.r-dbi.org/" - cran = "RPostgres" + cran = "RPostgres" + version('1.4.3', sha256='a5be494a54b6e989fadafdc6ee2dc5c4c15bb17bacea9ad540b175c693331be2') version('1.3.1', sha256='f68ab095567317ec32d3faa10e5bcac400aee5aeca8d7132260d4e90f82158ea') depends_on('r@3.1.0:', type=('build', 'run')) @@ -22,9 +22,12 @@ class RRpostgres(RPackage): depends_on('r-blob@1.2.0:', type=('build', 'run')) depends_on('r-dbi@1.1.0:', type=('build', 'run')) depends_on('r-hms@0.5.0:', type=('build', 'run')) + depends_on('r-hms@1.0.0:', type=('build', 'run'), when='@1.4.3:') depends_on('r-lubridate', type=('build', 'run')) depends_on('r-rcpp@0.11.4.2:', type=('build', 'run')) + depends_on('r-rcpp@1.0.7:', type=('build', 'run'), when='@1.4.3:') depends_on('r-withr', type=('build', 'run')) - depends_on('r-bh', type=('build', 'run')) depends_on('r-plogr@0.2.0:', type=('build', 'run')) depends_on('postgresql@9.0:') + + depends_on('r-bh', type=('build', 'run'), when='@:1.3.1') diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index de6806b1c5..88bf94ba7b 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -7,7 +7,9 @@ from spack import * class RRpostgresql(RPackage): - """Database interface and PostgreSQL driver for R This package provides a + """R Interface to the 'PostgreSQL' Database System. + + Database interface and PostgreSQL driver for R This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems. In order to build and install this package from source, PostgreSQL itself must be present your system to provide PostgreSQL @@ -17,10 +19,9 @@ class RRpostgresql(RPackage): issue tracking system for the package are available at Google Code at https://code.google.com/p/rpostgresql/.""" - homepage = "https://cran.r-project.org/web/packages/RPostgreSQL/index.html" - url = "https://cloud.r-project.org/src/contrib/RPostgreSQL_0.4-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RPostgreSQL" + cran = "RPostgreSQL" + version('0.7-3', sha256='bdbca10329aeb357f05364772964716dfb5ce2470f7eb4a33770862b6ded71b9') version('0.6-2', sha256='080118647208bfa2621bcaac0d324891cc513e07618fa22e3c50ec2050e1b0d5') version('0.4-1', sha256='6292e37fa841670a3fb1a0950ceb83d15beb4631c3c532c8ce279d1c0d10bf79') diff --git a/var/spack/repos/builtin/packages/r-rprojroot/package.py b/var/spack/repos/builtin/packages/r-rprojroot/package.py index 5e6687b897..714c713d9b 100644 --- a/var/spack/repos/builtin/packages/r-rprojroot/package.py +++ b/var/spack/repos/builtin/packages/r-rprojroot/package.py @@ -7,19 +7,18 @@ from spack import * class RRprojroot(RPackage): - """Finding Files in Project Subdirectories + """Finding Files in Project Subdirectories. - Robust, reliable and flexible paths to files below a project root. - The 'root' of a project is defined as a directory that matches a - certain criterion, e.g., it contains a certain regular file.""" + Robust, reliable and flexible paths to files below a project root. The + 'root' of a project is defined as a directory that matches a certain + criterion, e.g., it contains a certain regular file.""" - homepage = "https://cloud.r-project.org/package=rprojroot" - url = "https://cloud.r-project.org/src/contrib/rprojroot_1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rprojroot" + cran = "rprojroot" version('2.0.2', sha256='5fa161f0d4ac3b7a99dc6aa2d832251001dc92e93c828593a51fe90afd019e1f') version('1.3-2', sha256='df5665834941d8b0e377a8810a04f98552201678300f168de5f58a587b73238b') version('1.2', sha256='28b4d235ce67314528a0c1cc7e98faed42437b42e07fca18a59a80fdc3eefeb9') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r-backports', when='@:1.3-2', type=('build', 'run')) + + depends_on('r-backports', type=('build', 'run'), when='@:1.3-2') diff --git a/var/spack/repos/builtin/packages/r-rpsychi/package.py b/var/spack/repos/builtin/packages/r-rpsychi/package.py index 4023ea141f..dbf9264aaf 100644 --- a/var/spack/repos/builtin/packages/r-rpsychi/package.py +++ b/var/spack/repos/builtin/packages/r-rpsychi/package.py @@ -5,16 +5,17 @@ class RRpsychi(RPackage): - """The rpsychi offers a number of functions for psychiatry, - psychiatric nursing, clinical psychology. Functions are primarily - for statistical significance testing using published work. For - example, you can conduct a factorial analysis of variance (ANOVA), - which requires only the mean, standard deviation, and sample size - for each cell, rather than the individual data. This package - covers fundamental statistical tests such as t-test, chi-square - test, analysis of variance, and multiple regression analysis. With - some exceptions, you can obtain effect size and its confidence - interval. These functions help you to obtain effect size from + """Statistics for psychiatric research. + + The rpsychi offers a number of functions for psychiatry, psychiatric + nursing, clinical psychology. Functions are primarily for statistical + significance testing using published work. For example, you can conduct a + factorial analysis of variance (ANOVA), which requires only the mean, + standard deviation, and sample size for each cell, rather than the + individual data. This package covers fundamental statistical tests such as + t-test, chi-square test, analysis of variance, and multiple regression + analysis. With some exceptions, you can obtain effect size and its + confidence interval. These functions help you to obtain effect size from published work, and then to conduct a priori power analysis or meta-analysis, even if a researcher do not report effect size in a published work.""" diff --git a/var/spack/repos/builtin/packages/r-rrblup/package.py b/var/spack/repos/builtin/packages/r-rrblup/package.py index d79b680071..790863fed0 100644 --- a/var/spack/repos/builtin/packages/r-rrblup/package.py +++ b/var/spack/repos/builtin/packages/r-rrblup/package.py @@ -7,7 +7,7 @@ from spack import * class RRrblup(RPackage): - """Ridge Regression and Other Kernels for Genomic Selection + """Ridge Regression and Other Kernels for Genomic Selection. Software for genomic prediction with the RR-BLUP mixed model (Endelman 2011, <doi:10.3835/plantgenome2011.08.0024>). One application is to @@ -15,9 +15,7 @@ class RRrblup(RPackage): calculated based on an additive relationship matrix or a Gaussian kernel.""" - homepage = "https://potatobreeding.cals.wisc.edu/software" - url = "https://cloud.r-project.org/src/contrib/rrBLUP_4.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rrBLUP" + cran = "rrBLUP" version('4.6.1', sha256='e9230e74cc430a83ac5567071cb1c7f00b35c368f7d79bcc1cfde7225446c4db') version('4.6', sha256='28b475a1466fcdc1780caace75cf34155338fda496cebd5799315598a4bc84af') diff --git a/var/spack/repos/builtin/packages/r-rrcov/package.py b/var/spack/repos/builtin/packages/r-rrcov/package.py index e97ec63101..f9a8f69c48 100644 --- a/var/spack/repos/builtin/packages/r-rrcov/package.py +++ b/var/spack/repos/builtin/packages/r-rrcov/package.py @@ -7,7 +7,7 @@ from spack import * class RRrcov(RPackage): - """Scalable Robust Estimators with High Breakdown Point + """Scalable Robust Estimators with High Breakdown Point. Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point: principal component analysis (Filzmoser and @@ -19,10 +19,10 @@ class RRrcov(RPackage): Filzmoser (2010) <doi:10.18637/jss.v032.i03> and Boudt et al. (2019) <doi:10.1007/s11222-019-09869-x>.""" - homepage = "https://cloud.r-project.org/package=rrcov" - url = "https://cloud.r-project.org/src/contrib/rrcov_1.4-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rrcov" + cran = "rrcov" + version('1.6-1', sha256='9f3b500f2bdac375d0374cd1b120806c785b1981101d7d018fc1fcc73e305d90') + version('1.6-0', sha256='795f3a49b3e17c9c6e0fdd865e81a0402cefda970032c8299bcf2056ca7ec944') version('1.5-5', sha256='1f7f07558e347e7d1f1adff68631764670bc672777a7d990901c4fa94cc0e629') version('1.4-7', sha256='cbd08ccce8b583a2f88946a3267c8fc494ee2b44ba749b9296a6e3d818f6f293') @@ -31,4 +31,5 @@ class RRrcov(RPackage): depends_on('r-mvtnorm', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-pcapp', type=('build', 'run')) - depends_on('r-cluster', when='@:1.4-7', type=('build', 'run')) + + depends_on('r-cluster', type=('build', 'run'), when='@:1.4-7') diff --git a/var/spack/repos/builtin/packages/r-rrpp/package.py b/var/spack/repos/builtin/packages/r-rrpp/package.py index 2ee4990a58..273b13ccef 100644 --- a/var/spack/repos/builtin/packages/r-rrpp/package.py +++ b/var/spack/repos/builtin/packages/r-rrpp/package.py @@ -8,7 +8,8 @@ from spack import * class RRrpp(RPackage): - """Linear Model Evaluation with Randomized Residuals in a Permutation Procedure + """Linear Model Evaluation with Randomized Residuals in a Permutation + Procedure. Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are @@ -22,14 +23,15 @@ class RRrpp(RPackage): data, especially in ecology and evolutionary biology, but certainly other fields, as well.""" - homepage = "https://github.com/mlcollyer/RRPP" - url = "https://cloud.r-project.org/src/contrib/RRPP_0.3.0.tar.gz" - list_url = "https://cron.r-project.org/src/contrib/Archive/RRPP" + cran = "RRPP" + version('1.1.2', sha256='2b563f3db9e349abe481444f48a1a3e6bc1154de8259b7a7060ab588287e80c0') version('0.6.2', sha256='f8ffa318d806184c0e65929ea1b8b6a88bb9e45f77db2da5a83c6fe550b084dc') version('0.4.2', sha256='21a4ebb549d21f66ee9107adf762eee630e478bc740f232f384ba1a6b1cd3bf4') version('0.4.1', sha256='d7cd3b089240d7f7e13f65f0259487669a378ffae062aee33d4dc6ab0f86f899') version('0.3.0', sha256='34fea6ce7a78e4f38398d3b99585bab11a8171bc8b9a4e461b6d984ed1373739') - depends_on('r@3.5.0:', when='@0.6.2:', type=('build', 'run')) - depends_on('r-ape', when='@0.6.2:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.6.2:') + depends_on('r-ape', type=('build', 'run'), when='@0.6.2:') + depends_on('r-ggplot2', type=('build', 'run'), when='@1.1.2:') + depends_on('r-matrix', type=('build', 'run'), when='@1.1.2:') diff --git a/var/spack/repos/builtin/packages/r-rsconnect/package.py b/var/spack/repos/builtin/packages/r-rsconnect/package.py index 3a3bdb535a..71ba58ad45 100644 --- a/var/spack/repos/builtin/packages/r-rsconnect/package.py +++ b/var/spack/repos/builtin/packages/r-rsconnect/package.py @@ -7,14 +7,13 @@ from spack import * class RRsconnect(RPackage): - """Deployment Interface for R Markdown Documents and Shiny Applications: + """Deployment Interface for R Markdown Documents and Shiny Applications. Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'RStudio Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.""" - homepage = "https://github.com/rstudio/rsconnect" - cran = "rsconnect" + cran = "rsconnect" version('0.8.25', sha256='3c055277f745f2ca37a73e2f425249307cea4dc95ecc59fbe05ee8b6cf26d9cf') version('0.8.17', sha256='64767a4d626395b7871375956a9f0455c3d64ff6e779633b0e554921d85da231') @@ -24,7 +23,7 @@ class RRsconnect(RPackage): depends_on('r-digest', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-openssl', type=('build', 'run')) - depends_on('r-packrat@0.6:', when='@0.8.18:', type=('build', 'run')) + depends_on('r-packrat@0.6:', type=('build', 'run'), when='@0.8.18:') depends_on('r-packrat@0.5:', type=('build', 'run')) depends_on('r-rstudioapi@0.5:', type=('build', 'run')) depends_on('r-yaml@2.1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py index 41c5298225..235421cdc1 100644 --- a/var/spack/repos/builtin/packages/r-rsnns/package.py +++ b/var/spack/repos/builtin/packages/r-rsnns/package.py @@ -8,20 +8,19 @@ from spack import * class RRsnns(RPackage): - """Neural Networks using the Stuttgart Neural Network Simulator (SNNS) + """Neural Networks using the Stuttgart Neural Network Simulator (SNNS). - The Stuttgart Neural Network Simulator (SNNS) is a library containing - many standard implementations of neural networks. This package wraps the - SNNS functionality to make it available from within R. Using the RSNNS - low-level interface, all of the algorithmic functionality and flexibility - of SNNS can be accessed. Furthermore, the package contains a convenient - high-level interface, so that the most common neural network topologies - and learning algorithms integrate seamlessly into R.""" + The Stuttgart Neural Network Simulator (SNNS) is a library containing many + standard implementations of neural networks. This package wraps the SNNS + functionality to make it available from within R. Using the RSNNS low-level + interface, all of the algorithmic functionality and flexibility of SNNS can + be accessed. Furthermore, the package contains a convenient high-level + interface, so that the most common neural network topologies and learning + algorithms integrate seamlessly into R.""" - homepage = "https://sci2s.ugr.es/dicits/software/RSNNS" - url = "https://cloud.r-project.org/src/contrib/RSNNS_0.4-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RSNNS" + cran = "RSNNS" + version('0.4-14', sha256='7f6262cb2b49b5d5979ccce9ded9cbb2c0b348fd7c9eabc1ea1d31c51a102c20') version('0.4-12', sha256='b18dfeda71573bc92c6888af72da407651bff7571967965fd3008f0d331743b9') version('0.4-11', sha256='87943126e98ae47f366e3025d0f3dc2f5eb0aa2924508fd9ee9a0685d7cb477c') version('0.4-10.1', sha256='38bb3d172390bd01219332ec834744274b87b01f94d23b29a9d818c2bca04071') diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py index 4f9747056d..7ceef0cead 100644 --- a/var/spack/repos/builtin/packages/r-rsolnp/package.py +++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py @@ -7,12 +7,12 @@ from spack import * class RRsolnp(RPackage): - """General Non-linear Optimization Using Augmented Lagrange Multiplier + """General Non-Linear Optimization. + + General Non-linear Optimization Using Augmented Lagrange Multiplier Method.""" - homepage = "https://cloud.r-project.org/package=Rsolnp" - url = "https://cloud.r-project.org/src/contrib/Rsolnp_1.16.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Rsolnp" + cran = "Rsolnp" version('1.16', sha256='3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670') diff --git a/var/spack/repos/builtin/packages/r-rspectra/package.py b/var/spack/repos/builtin/packages/r-rspectra/package.py index dfee912101..26d4266612 100644 --- a/var/spack/repos/builtin/packages/r-rspectra/package.py +++ b/var/spack/repos/builtin/packages/r-rspectra/package.py @@ -7,7 +7,7 @@ from spack import * class RRspectra(RPackage): - """Solvers for Large-Scale Eigenvalue and SVD Problems + """Solvers for Large-Scale Eigenvalue and SVD Problems. R interface to the 'Spectra' library <https://spectralib.org/> for large-scale eigenvalue and SVD problems. It is typically used to compute a @@ -20,9 +20,7 @@ class RRspectra(RPackage): on can be dense, sparse, or in the form of an operator defined by the user.""" - homepage = "https://github.com/yixuan/RSpectra" - url = "https://cloud.r-project.org/src/contrib/RSpectra_0.15-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RSpectra" + cran = "RSpectra" version('0.16-0', sha256='aaf1cfc9ffe3a4c6684247899924e1c18306971dfef4bae1dc596a2fb42a64a9') version('0.15-0', sha256='1ad5698201007044a0420cb10b7c48e94312a8a1d22b9d946d5de1c6743969a9') diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index 34fee5b33d..ef8eeb30cd 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -7,16 +7,15 @@ from spack import * class RRsqlite(RPackage): - """'SQLite' Interface for R + """'SQLite' Interface for R. This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.""" - homepage = "https://cloud.r-project.org/package=RSQLite" - url = "https://cloud.r-project.org/src/contrib/RSQLite_2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RSQLite" + cran = "RSQLite" + version('2.2.9', sha256='4423f1fea179ecd1c09b0b52bfb684983a27de82d5807590b5fc723697d5bb1c') version('2.2.2', sha256='299ceafd4986f60dbca2d705112aa3c29ff68fcbc188d9caaa0493e63a57a873') version('2.1.2', sha256='66dad425d22b09651c510bf84b7fc36375ce537782f02585cf1c6856ae82d9c6') version('2.1.0', sha256='ad6081be2885be5921b1a44b1896e6a8568c8cff40789f43bfaac9f818767642') @@ -29,5 +28,7 @@ class RRsqlite(RPackage): depends_on('r-memoise', type=('build', 'run')) depends_on('r-pkgconfig', type=('build', 'run')) depends_on('r-rcpp@0.12.7:', type=('build', 'run')) - depends_on('r-bh', type=('build', 'run')) + depends_on('r-rcpp@1.0.7:', type=('build', 'run'), when='@2.2.9:') depends_on('r-plogr@0.2.0:', type=('build', 'run')) + + depends_on('r-bh', type=('build', 'run'), when='@:2.2.2') diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index eb3c001006..1844b5cf92 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -7,11 +7,11 @@ from spack import * class RRstan(RPackage): - """R Interface to Stan + """R Interface to Stan. - User-facing R functions are provided to parse, compile, test, estimate, - and analyze Stan models by accessing the header-only Stan library provided - by the 'StanHeaders' package. The Stan project develops a probabilistic + User-facing R functions are provided to parse, compile, test, estimate, and + analyze Stan models by accessing the header-only Stan library provided by + the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via @@ -19,10 +19,9 @@ class RRstan(RPackage): quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.""" - homepage = "https://mc-stan.org/users/interfaces/rstan" - url = "https://cloud.r-project.org/src/contrib/rstan_2.10.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rstan" + cran = "rstan" + version('2.21.3', sha256='76bcbf1cb246a202e5680ea6e91bb4142ce19156e8960a9850f6ea0e206f92b1') version('2.21.2', sha256='e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a') version('2.19.2', sha256='31e4ceb9c327cd62873225097ffa538c2ac4cb0547c52271e52e4c7652d508da') version('2.18.2', sha256='4d75dad95610d5a1d1c89a4ddbaf4326462e4ffe0ad28aed2129f2d9292e70ff') @@ -31,24 +30,25 @@ class RRstan(RPackage): depends_on('r+X', type=('build', 'run')) depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.4.0:', when='@2.18.1:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@2.18.1:') depends_on('r-stanheaders@2.18.1:', type=('build', 'run')) - depends_on('r-stanheaders@2.21.0:', when='@2.21.2:', type=('build', 'run')) + depends_on('r-stanheaders@2.21.0:', type=('build', 'run'), when='@2.21.2:') depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) - depends_on('r-ggplot2@3.0.0:', when='@2.21.2:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run'), when='@2.21.2:') depends_on('r-inline', type=('build', 'run')) depends_on('r-gridextra@2.0.0:', type=('build', 'run')) depends_on('r-rcpp@0.12.0:', type=('build', 'run')) - depends_on('r-rcppparallel@5.0.1:', when='@2.21.2:', type=('build', 'run')) - depends_on('r-loo@2.0.0:', when='@2.18:', type=('build', 'run')) - depends_on('r-loo@2.3.0:', when='@2.21.2:', type=('build', 'run')) - depends_on('r-pkgbuild', when='@2.18:', type=('build', 'run')) - depends_on('r-withr', when='@2.21.2:', type=('build', 'run')) - depends_on('r-v8', when='@2.21.2:', type=('build', 'run')) + depends_on('r-rcppparallel@5.0.1:', type=('build', 'run'), when='@2.21.2:') + depends_on('r-loo@2.0.0:', type=('build', 'run'), when='@2.18:') + depends_on('r-loo@2.3.0:', type=('build', 'run'), when='@2.21.2:') + depends_on('r-pkgbuild', type=('build', 'run'), when='@2.18:') depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run')) depends_on('r-bh@1.69.0:', type=('build', 'run')) - depends_on('r-bh@1.72.0-2:', when='@2.21.2:', type=('build', 'run')) + depends_on('r-bh@1.72.0-2:', type=('build', 'run'), when='@2.21.2:') depends_on('gmake', type='build') depends_on('pandoc', type='build') + depends_on('r-withr', type=('build', 'run'), when='@2.21.2') + depends_on('r-v8', type=('build', 'run'), when='@2.21.2') + conflicts('%gcc@:4.9', when='@2.18:') diff --git a/var/spack/repos/builtin/packages/r-rstantools/package.py b/var/spack/repos/builtin/packages/r-rstantools/package.py index f0deffe9b2..46c672947b 100644 --- a/var/spack/repos/builtin/packages/r-rstantools/package.py +++ b/var/spack/repos/builtin/packages/r-rstantools/package.py @@ -7,7 +7,7 @@ from spack import * class RRstantools(RPackage): - """Tools for Developing R Packages Interfacing with 'Stan' + """Tools for Developing R Packages Interfacing with 'Stan'. Provides various tools for developers of R packages interfacing with 'Stan' <https://mc-stan.org>, including functions to set up the required package @@ -15,15 +15,13 @@ class RRstantools(RPackage): 'Stan'-based R packages, and vignettes with recommendations for developers.""" - homepage = "https://discourse.mc-stan.org/" - url = "https://cloud.r-project.org/src/contrib/rstantools_1.5.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rstantools" + cran = "rstantools" version('2.1.1', sha256='c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d') version('1.5.1', sha256='5cab16c132c12e84bd08e18cd6ef25ba39d67a04ce61015fc4490659c7cfb485') depends_on('r+X', type=('build', 'run')) - depends_on('r-desc', when='@2.1.1:', type=('build', 'run')) - depends_on('r-rcpp@0.12.16:', when='@2.1.1:', type=('build', 'run')) - depends_on('r-rcppparallel@5.0.1:', when='@2.1.1:', type=('build', 'run')) + depends_on('r-desc', type=('build', 'run'), when='@2.1.1:') + depends_on('r-rcpp@0.12.16:', type=('build', 'run'), when='@2.1.1:') + depends_on('r-rcppparallel@5.0.1:', type=('build', 'run'), when='@2.1.1:') depends_on('pandoc', type='build') diff --git a/var/spack/repos/builtin/packages/r-rstatix/package.py b/var/spack/repos/builtin/packages/r-rstatix/package.py index e0c32d2d40..2e77674be8 100644 --- a/var/spack/repos/builtin/packages/r-rstatix/package.py +++ b/var/spack/repos/builtin/packages/r-rstatix/package.py @@ -7,7 +7,7 @@ from spack import * class RRstatix(RPackage): - """Pipe-Friendly Framework for Basic Statistical Tests + """Pipe-Friendly Framework for Basic Statistical Tests. Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy, for performing basic statistical tests, @@ -24,16 +24,16 @@ class RRstatix(RPackage): functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.""" - homepage = "https://rpkgs.datanovia.com/rstatix/" - url = "https://cloud.r-project.org/src/contrib/rstatix_0.6.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rstatix" + cran = "rstatix" + version('0.7.0', sha256='a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c') version('0.6.0', sha256='ebb28e20c7e28809194a2a027bc83303b17be1e3db32f49325727c9279df9c5b') depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-tidyr@1.0.0:', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) depends_on('r-broom@0.5.6:', type=('build', 'run')) + depends_on('r-broom@0.7.4:', type=('build', 'run'), when='@0.7.0:') depends_on('r-rlang@0.3.1:', type=('build', 'run')) depends_on('r-tibble@2.1.3:', type=('build', 'run')) depends_on('r-dplyr@0.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index eac0986a94..4edb04668c 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -7,14 +7,12 @@ from spack import * class RRstudioapi(RPackage): - """Safely Access the RStudio API + """Safely Access the RStudio API. Access the RStudio API (if available) and provide informative error messages when it's not.""" - homepage = "https://cloud.r-project.org/package=rstudioapi" - url = "https://cloud.r-project.org/src/contrib/rstudioapi_0.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rstudioapi" + cran = "rstudioapi" version('0.13', sha256='aac35bbdcb4a8e8caba943bc8a2b98120e8940b80cd1020224bb1a26ff776d8b') version('0.11', sha256='13e07fb7e2eba8cf1d885db2721901d676d219a1042d7ef5d166125e4905306b') diff --git a/var/spack/repos/builtin/packages/r-rsvd/package.py b/var/spack/repos/builtin/packages/r-rsvd/package.py index 9364ad37ee..12f6283d05 100644 --- a/var/spack/repos/builtin/packages/r-rsvd/package.py +++ b/var/spack/repos/builtin/packages/r-rsvd/package.py @@ -7,7 +7,7 @@ from spack import * class RRsvd(RPackage): - """Randomized Singular Value Decomposition + """Randomized Singular Value Decomposition. Low-rank matrix decompositions are fundamental tools and widely used for data analysis, dimension reduction, and data compression. Classically, @@ -24,12 +24,12 @@ class RRsvd(RPackage): The methods are discussed in detail by Erichson et al. (2016) <arXiv:1608.02148>.""" - homepage = "https://github.com/erichson/rSVD" - url = "https://cloud.r-project.org/src/contrib/rsvd_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rsvd" + cran = "rsvd" + version('1.0.5', sha256='e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e') version('1.0.3', sha256='13560e0fc3ae6927c4cc4d5ad816b1f640a2a445b712a5a612ab17ea0ce179bb') version('1.0.2', sha256='c8fe5c18bf7bcfe32604a897e3a7caae39b49e47e93edad9e4d07657fc392a3a') depends_on('r@3.2.2:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@1.0.5:') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rtsne/package.py b/var/spack/repos/builtin/packages/r-rtsne/package.py index aca2130021..58dc56b5c1 100644 --- a/var/spack/repos/builtin/packages/r-rtsne/package.py +++ b/var/spack/repos/builtin/packages/r-rtsne/package.py @@ -7,12 +7,13 @@ from spack import * class RRtsne(RPackage): - """An R wrapper around the fast T-distributed Stochastic Neighbor - Embedding implementation.""" + """T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut + Implementation. - homepage = "https://cloud.r-project.org/package=Rtsne" - url = "https://cloud.r-project.org/src/contrib/Rtsne_0.13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Rtsne" + An R wrapper around the fast T-distributed Stochastic Neighbor Embedding + implementation.""" + + cran = "Rtsne" version('0.15', sha256='56376e4f0a382fad3d3d40e2cb0562224be5265b827622bcd235e8fc63df276c') version('0.13', sha256='1c3bffe3bd11733ee4fe01749c293669daafda1af2ec74f9158f6080625b999d') diff --git a/var/spack/repos/builtin/packages/r-runit/package.py b/var/spack/repos/builtin/packages/r-runit/package.py index 9ceac70647..959902fc4b 100644 --- a/var/spack/repos/builtin/packages/r-runit/package.py +++ b/var/spack/repos/builtin/packages/r-runit/package.py @@ -7,11 +7,12 @@ from spack import * class RRunit(RPackage): - """RUnit: R Unit Test Framework""" + """R Unit Test Framework. - homepage = "https://cloud.r-project.org/package=RUnit" - url = "https://cloud.r-project.org/src/contrib/RUnit_0.4.32.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RUnit/" + R functions implementing a standard Unit Testing framework, with additional + code inspection and report generation tools. """ + + cran = "RUnit" version('0.4.32', sha256='23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1') diff --git a/var/spack/repos/builtin/packages/r-runjags/package.py b/var/spack/repos/builtin/packages/r-runjags/package.py index fe322a917f..a74c9f8e5a 100644 --- a/var/spack/repos/builtin/packages/r-runjags/package.py +++ b/var/spack/repos/builtin/packages/r-runjags/package.py @@ -8,7 +8,7 @@ from spack import * class RRunjags(RPackage): """Interface Utilities, Model Templates, Parallel Computing Methods and - Additional Distributions for MCMC Models in JAGS: + Additional Distributions for MCMC Models in JAGS. User-friendly interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) @@ -20,9 +20,9 @@ class RRunjags(RPackage): additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.""" - homepage = "https://github.com/ku-awdc/runjags" - cran = "runjags" + cran = "runjags" + version('2.2.0-3', sha256='1b1fc0b0cfecf9ecdecc3abcba804cdc114b3c5352d5cc801602deeca90db528') version('2.2.0-2', sha256='e5dfeb83d36faf19ebe64429f6db64aedecf3c9a040fd5bf9c0200914bf5039a') depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ruv/package.py b/var/spack/repos/builtin/packages/r-ruv/package.py index da1f6285b6..997addcd23 100644 --- a/var/spack/repos/builtin/packages/r-ruv/package.py +++ b/var/spack/repos/builtin/packages/r-ruv/package.py @@ -7,7 +7,7 @@ from spack import * class RRuv(RPackage): - """Detect and Remove Unwanted Variation using Negative Controls: + """Detect and Remove Unwanted Variation using Negative Controls. Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in @@ -22,8 +22,7 @@ class RRuv(RPackage): 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.""" - homepage = "http://www-personal.umich.edu/~johanngb/ruv/" - cran = "ruv" + cran = "ruv" version('0.9.7.1', sha256='a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8') diff --git a/var/spack/repos/builtin/packages/r-rvcheck/package.py b/var/spack/repos/builtin/packages/r-rvcheck/package.py index f011bf5854..201db39016 100644 --- a/var/spack/repos/builtin/packages/r-rvcheck/package.py +++ b/var/spack/repos/builtin/packages/r-rvcheck/package.py @@ -7,20 +7,21 @@ from spack import * class RRvcheck(RPackage): - """R/Package Version Check + """R/Package Version Check. Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').""" - homepage = "https://cloud.r-project.org/package=rvcheck" - url = "https://cloud.r-project.org/src/contrib/rvcheck_0.0.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rvcheck" + cran = "rvcheck" + version('0.2.1', sha256='2ad9efd2af8d103e88bff0a01692f0e32515805f269152f2694eadbfe9947026') version('0.1.8', sha256='4ca5aa48fbf543e6171696ca7e1bff81e3112d06c919e88769b5c38a115b4718') version('0.1.3', sha256='0b59986c1ccc5b89f8aca8fa7cf62d0b875719addb40e08dbda1791cfd334fc4') version('0.0.9', sha256='6e7be7b029d28181a1b57ebd4d25978f3459722ffdb45a3698157a7f943bea92') - depends_on('r@3.3.0:', when='@:0.1.1', type=('build', 'run')) - depends_on('r@3.4.0:', when='@0.1.3:', type=('build', 'run')) - depends_on('r-biocmanager', when='@0.1.8:', type=('build', 'run')) - depends_on('r-rlang', when='@0.1.1:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@0.1.3:') + depends_on('r-biocmanager', type=('build', 'run'), when='@0.1.8:') + depends_on('r-yulab-utils', type=('build', 'run'), when='@0.2.1:') + + depends_on('r-rlang', type=('build', 'run'), when='@0.1.1:0.1.8') diff --git a/var/spack/repos/builtin/packages/r-rversions/package.py b/var/spack/repos/builtin/packages/r-rversions/package.py index a774776f7e..255f8741e0 100644 --- a/var/spack/repos/builtin/packages/r-rversions/package.py +++ b/var/spack/repos/builtin/packages/r-rversions/package.py @@ -7,16 +7,15 @@ from spack import * class RRversions(RPackage): - """Query 'R' Versions, Including 'r-release' and 'r-oldrel' + """Query 'R' Versions, Including 'r-release' and 'r-oldrel'. Query the main 'R' 'SVN' repository to find the versions 'r-release' and 'r-oldrel' refer to, and also all previous 'R' versions and their release dates.""" - homepage = "https://cloud.r-project.org/package=rversions" - url = "https://cloud.r-project.org/src/contrib/rversions_2.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rversions" + cran = "rversions" + version('2.1.1', sha256='79aaacf5a1258d91ac0ddedf3c8c16a2d10d39010993dcc7b0a2638afee27cb1') version('2.0.2', sha256='3523f4b7393365341d429500b01ba3a224056e89d134635b81dfb4918ba2173e') version('2.0.1', sha256='51ec1f64e7d628e88d716a020d5d521eba71d472e3c9ae7b694428ef6dd786c5') version('2.0.0', sha256='b50c321d9e973284ae6b1d0c89bd46a40f5174de51fb28e3c77cd12ef34f6f56') diff --git a/var/spack/repos/builtin/packages/r-rvest/package.py b/var/spack/repos/builtin/packages/r-rvest/package.py index a1fdd837b4..2e51772980 100644 --- a/var/spack/repos/builtin/packages/r-rvest/package.py +++ b/var/spack/repos/builtin/packages/r-rvest/package.py @@ -7,12 +7,11 @@ from spack import * class RRvest(RPackage): - """Easily Harvest (Scrape) Web Pages + """Easily Harvest (Scrape) Web Pages. Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.""" - homepage = "https://github.com/hadley/rvest" cran = "rvest" version('1.0.2', sha256='89bb477e0944c80298a52ccf650db8f6377fd7ed3c1bc7034d000f695fdf05a4') @@ -21,14 +20,14 @@ class RRvest(RPackage): version('0.3.3', sha256='b10a87fa2d733f7c0fc567242ef0ab10a1a77d58d51796996cc0fd81381a556f') version('0.3.2', sha256='0d6e8837fb1df79b1c83e7b48d8f1e6245f34a10c4bb6952e7bec7867e4abb12') - depends_on('r@3.0.1:', when='@:0.3.2', type=('build', 'run')) - depends_on('r@3.1:', when='@0.3.3', type=('build', 'run')) - depends_on('r@3.2:', when='@0.3.4:', type=('build', 'run')) + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@0.3.3') + depends_on('r@3.2:', type=('build', 'run'), when='@0.3.4:') depends_on('r-httr@0.5:', type=('build', 'run')) - depends_on('r-lifecycle@1.0.0:', when='@1:', type=('build', 'run')) + depends_on('r-lifecycle@1.0.0:', type=('build', 'run'), when='@1:') depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-rlang@0.4.10:', when='@1:', type=('build', 'run')) + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@1:') depends_on('r-selectr', type=('build', 'run')) - depends_on('r-tibble', when='@1:', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run'), when='@1:') depends_on('r-xml2', type=('build', 'run')) - depends_on('r-xml2@1.3:', when='@1:', type=('build', 'run')) + depends_on('r-xml2@1.3:', type=('build', 'run'), when='@1:') diff --git a/var/spack/repos/builtin/packages/r-rviennacl/package.py b/var/spack/repos/builtin/packages/r-rviennacl/package.py index 79fba1bf44..251770efe6 100644 --- a/var/spack/repos/builtin/packages/r-rviennacl/package.py +++ b/var/spack/repos/builtin/packages/r-rviennacl/package.py @@ -7,10 +7,16 @@ from spack import * class RRviennacl(RPackage): - """RViennaCL: 'ViennaCL' C++ Header Files""" + """'ViennaCL' C++ Header Files. - homepage = "https://cloud.r-project.org/package=RViennaCL" - url = "https://cloud.r-project.org/src/contrib/RViennaCL_1.7.1.8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/RViennaCL" + 'ViennaCL' is a free open-source linear algebra library for computations on + many-core architectures (GPUs, MIC) and multi-core CPUs. The library is + written in C++ and supports 'CUDA', 'OpenCL', and 'OpenMP' (including + switches at runtime). I have placed these libraries in this package as a + more efficient distribution system for CRAN. The idea is that you can write + a package that depends on the 'ViennaCL' library and yet you do not need to + distribute a copy of this code with your package.""" + + cran = "RViennaCL" version('1.7.1.8', sha256='adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252') diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index 54c374fab4..c50c4c7c03 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -8,19 +8,18 @@ from spack import * class RRzmq(RPackage): - """R Bindings for 'ZeroMQ' + """R Bindings for 'ZeroMQ'. Interface to the 'ZeroMQ' lightweight messaging kernel (see <http://www.zeromq.org/> for more information).""" - homepage = "https://github.com/armstrtw/rzmq" - url = "https://cloud.r-project.org/src/contrib/rzmq_0.7.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/rzmq" + cran = "rzmq" + version('0.9.8', sha256='815a7eb502b1da3a84246b2dfb6594ca3f241a8675783e6bcdbbf9c952ec1c53') version('0.9.7', sha256='5f47b67b75fd4a230780406f7a55a3708ce8c014cff755a809a6bfa1a6925a45') version('0.9.6', sha256='80a3fc6eb6f7851224c4cd5e219ca4db0286551ad429359d4df853ccb9234316') version('0.9.4', sha256='03fbda756d823c11fba359b94a6213c3440e61973331668eaac35779717f73ad') version('0.7.7', sha256='bdbaf77a0e04c5b6d6ce79ab2747848a5044355eed2e2c4d39c4ba16f97dc83d') - depends_on('r@3.1.0:', when='@0.9.0:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@0.9.0:') depends_on('libzmq@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-s2/package.py b/var/spack/repos/builtin/packages/r-s2/package.py index deb46f91c2..893af8437a 100644 --- a/var/spack/repos/builtin/packages/r-s2/package.py +++ b/var/spack/repos/builtin/packages/r-s2/package.py @@ -7,7 +7,7 @@ from spack import * class RS2(RPackage): - """Spherical Geometry Operators Using the S2 Geometry Library + """Spherical Geometry Operators Using the S2 Geometry Library. Provides R bindings for Google's s2 library for geometric calculations on the sphere. High-performance constructors and exporters provide high @@ -16,11 +16,13 @@ class RS2(RPackage): geometries based on spatial relationships, and accessors extract information about geometries.""" - homepage = "https://r-spatial.github.io/s2/" - cran = "s2" + cran = "s2" + version('1.0.7', sha256='2010c1c6ae29938ec9cd153a8b2c06a333ea4d647932369b2fc7d0c68d6d9e3f') version('1.0.4', sha256='3c274ebae33aa5473f94afb3066c6f388aced17ff3b5f6add9edcc9af22b985e') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-wk', type=('build', 'run')) + depends_on('r-wk@0.5.0:', type=('build', 'run'), when='@1.0.7:') + depends_on('openssl@1.0.1:', when='@1.0.7:') diff --git a/var/spack/repos/builtin/packages/r-samr/package.py b/var/spack/repos/builtin/packages/r-samr/package.py index 9013f672f3..f62c57c78b 100644 --- a/var/spack/repos/builtin/packages/r-samr/package.py +++ b/var/spack/repos/builtin/packages/r-samr/package.py @@ -7,17 +7,19 @@ from spack import * class RSamr(RPackage): - """Significance Analysis of Microarrays.""" + """SAM: Significance Analysis of Microarrays. + + Significance Analysis of Microarrays for differential expression analysis, + RNAseq data and related problems.""" + + cran = "samr" - homepage = "https://cloud.r-project.org/package=samr" - url = "https://cloud.r-project.org/src/contrib/samr_2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/samr" version('3.0', sha256='25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506') version('2.0', sha256='090b5becd91d60f4bb8269df5c9bc19a03c09917d327b28e75b0ee7b80624e67') depends_on('r-impute', type=('build', 'run')) depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r-shiny', when='@3.0:', type=('build', 'run')) - depends_on('r-shinyfiles', when='@3.0:', type=('build', 'run')) - depends_on('r-openxlsx', when='@3.0:', type=('build', 'run')) - depends_on('r-gsa', when='@3.0:', type=('build', 'run')) + depends_on('r-shiny', type=('build', 'run'), when='@3.0:') + depends_on('r-shinyfiles', type=('build', 'run'), when='@3.0:') + depends_on('r-openxlsx', type=('build', 'run'), when='@3.0:') + depends_on('r-gsa', type=('build', 'run'), when='@3.0:') diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index 667f9dcf50..7dc5437fe3 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -7,7 +7,7 @@ from spack import * class RSandwich(RPackage): - """Robust Covariance Matrix Estimators + """Robust Covariance Matrix Estimators. Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance @@ -23,15 +23,14 @@ class RSandwich(RPackage): <doi:10.18637/jss.v095.i01>, Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.""" - homepage = "https://cloud.r-project.org/package=sandwich" - url = "https://cloud.r-project.org/src/contrib/sandwich_2.3-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sandwich" + cran = "sandwich" + version('3.0-1', sha256='f6584b7084f3223bbc0c4722f53280496be73849747819b0cb4e8f3910284a89') version('3.0-0', sha256='828fe53b5e09db5015efd529b2db4dcd40251bce110fea7b0b219fa9ac36d529') version('2.5-1', sha256='dbef6f4d12b83e166f9a2508b7c732b04493641685d6758d29f3609e564166d6') version('2.5-0', sha256='6cc144af20739eb23e5539010d3833d7c7fc53cbca2addb583ab933167c11399') version('2.3-4', sha256='2052f7e3d19a05c372f422c5480f1058a4107e420cd038a9bd7240c4f0746d4d') depends_on('r@2.10.0:', type=('build', 'run')) - depends_on('r@3.0.0:', when='@3.0-0:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run'), when='@3.0-0:') depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sass/package.py b/var/spack/repos/builtin/packages/r-sass/package.py new file mode 100644 index 0000000000..86d6139171 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sass/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 RSass(RPackage): + """Syntactically Awesome Style Sheets ('Sass'). + + An 'SCSS' compiler, powered by the 'LibSass' library. With this, R + developers can use variables, inheritance, and functions to generate + dynamic style sheets. The package uses the 'Sass CSS' extension language, + which is stable, powerful, and CSS compatible.""" + + cran = "sass" + + version('0.4.0', sha256='7d06ca15239142a49e88bb3be494515abdd8c75f00f3f1b0ee7bccb55019bc2b') + + depends_on('r-fs', type=('build', 'run')) + depends_on('r-rlang@0.4.10:', type=('build', 'run')) + depends_on('r-htmltools@0.5.1:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rappdirs', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-satellite/package.py b/var/spack/repos/builtin/packages/r-satellite/package.py index 24fd26e258..86345fa6e1 100644 --- a/var/spack/repos/builtin/packages/r-satellite/package.py +++ b/var/spack/repos/builtin/packages/r-satellite/package.py @@ -7,7 +7,7 @@ from spack import * class RSatellite(RPackage): - """Handling and Manipulating Remote Sensing Data + """Handling and Manipulating Remote Sensing Data. Herein, we provide a broad variety of functions which are useful for handling, manipulating, and visualizing satellite-based remote sensing @@ -21,11 +21,13 @@ class RSatellite(RPackage): (OLI/TIRS Combined), and additional compatibility is ensured for the Landsat Global Land Survey data set.""" - cran = "satellite" + cran = "satellite" + version('1.0.4', sha256='99e79577a70489930c32da46ac26453af53e21c2d3a99f51fbf1f55f2d80dc7c') version('1.0.2', sha256='6447476bd31216e5abe504221e465677954d07419b4174ab4f4e4f7a197969c5') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-raster', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) depends_on('r-rcpp@0.10.3:', type=('build', 'run')) + depends_on('r-terra', type=('build', 'run'), when='@1.0.4:') diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index b09aa92b96..b91b880051 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -7,14 +7,12 @@ from spack import * class RScales(RPackage): - """Scale Functions for Visualization + """Scale Functions for Visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.""" - homepage = "https://github.com/hadley/scales" - url = "https://cloud.r-project.org/src/contrib/scales_0.5.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/scales" + cran = "scales" version('1.1.1', sha256='40b2b66522f1f314a20fd09426011b0cdc9d16b23ee2e765fe1930292dd03705') version('1.0.0', sha256='0c1f4a14edd336a404da34a3cc71a6a9d0ca2040ba19360c41a79f36e06ca30c') @@ -23,15 +21,16 @@ class RScales(RPackage): version('0.4.0', sha256='851ef6136339b361b3f843fb73ea89f9112279b9cc126bdb38acde8d24c1c6a7') depends_on('r@2.13:', type=('build', 'run')) - depends_on('r@3.1:', when='@1.0.0:', type=('build', 'run')) - depends_on('r@3.2:', when='@1.1.1:', type=('build', 'run')) - depends_on('r-farver@2.0.3:', when='@1.1.1:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@1.0.0:') + depends_on('r@3.2:', type=('build', 'run'), when='@1.1.1:') + depends_on('r-farver@2.0.3:', type=('build', 'run'), when='@1.1.1:') depends_on('r-labeling', type=('build', 'run')) - depends_on('r-lifecycle', when='@1.1.1:', type=('build', 'run')) + depends_on('r-lifecycle', type=('build', 'run'), when='@1.1.1:') depends_on('r-munsell@0.5:', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-viridislite', type=('build', 'run')) - depends_on('r-dichromat', when='@:0.5.0', type=('build', 'run')) - depends_on('r-plyr', when='@:0.5.0', type=('build', 'run')) - depends_on('r-rcpp', when='@:1.0.0', type=('build', 'run')) + + depends_on('r-dichromat', type=('build', 'run'), when='@:0.5.0') + depends_on('r-plyr', type=('build', 'run'), when='@:0.5.0') + depends_on('r-rcpp', type=('build', 'run'), when='@:1.0.0') diff --git a/var/spack/repos/builtin/packages/r-scattermore/package.py b/var/spack/repos/builtin/packages/r-scattermore/package.py index 4c0f67adb4..7b7b5078a6 100644 --- a/var/spack/repos/builtin/packages/r-scattermore/package.py +++ b/var/spack/repos/builtin/packages/r-scattermore/package.py @@ -7,14 +7,12 @@ from spack import * class RScattermore(RPackage): - """Scatterplots with More Points + """Scatterplots with More Points. C-based conversion of large scatterplot data to rasters. Speeds up plotting of data with millions of points.""" - homepage = "https://github.com/exaexa/scattermore" - url = "https://cloud.r-project.org/src/contrib/scattermore_0.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/scattermore" + cran = "scattermore" version('0.7', sha256='f36280197b8476314d6ce81a51c4ae737180b180204043d2937bc25bf3a5dfa2') diff --git a/var/spack/repos/builtin/packages/r-scatterpie/package.py b/var/spack/repos/builtin/packages/r-scatterpie/package.py index 84bf09eb9d..3a7a8e6e28 100644 --- a/var/spack/repos/builtin/packages/r-scatterpie/package.py +++ b/var/spack/repos/builtin/packages/r-scatterpie/package.py @@ -7,19 +7,20 @@ from spack import * class RScatterpie(RPackage): - """Scatter Pie Plot + """Scatter Pie Plot. Creates scatterpie plots, especially useful for plotting pies on a map.""" - homepage = "https://cloud.r-project.org/package=scatterpie" - url = "https://cloud.r-project.org/src/contrib/scatterpie_0.1.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/scatterpie" + cran = "scatterpie" + version('0.1.7', sha256='3f7807519cfe135066ca79c8d8a09b59da9aa6d8aaee5e9aff40cca3d0bebade') version('0.1.5', sha256='e13237b7effc302acafc1c9b520b4904e55875f4a3b804f653eed2940ca08840') depends_on('r@3.4.0:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-ggforce', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) - depends_on('r-rvcheck', type=('build', 'run')) + depends_on('r-ggfun', type=('build', 'run'), when='@0.1.7:') depends_on('r-tidyr', type=('build', 'run')) + + depends_on('r-rvcheck', type=('build', 'run'), when='@:0.1.5') diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py index 55d8691259..dea4ac6261 100644 --- a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py +++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py @@ -7,11 +7,11 @@ from spack import * class RScatterplot3d(RPackage): - """scatterplot3d: 3D Scatter Plot""" + """3D Scatter Plot. - homepage = "https://cloud.r-project.org/package=scatterplot3d" - url = "https://cloud.r-project.org/src/contrib/scatterplot3d_0.3-40.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/scatterplot3d" + Plots a three dimensional (3D) point cloud.""" + + cran = "scatterplot3d" version('0.3-41', sha256='4c8326b70a3b2d37126ca806771d71e5e9fe1201cfbe5b0d5a0a83c3d2c75d94') version('0.3-40', sha256='8249118aa29199017a6686d8245fed5343dabcf049b1588141a7cf83245b6a29') diff --git a/var/spack/repos/builtin/packages/r-scrime/package.py b/var/spack/repos/builtin/packages/r-scrime/package.py index 17c4bf0758..1afaff714b 100644 --- a/var/spack/repos/builtin/packages/r-scrime/package.py +++ b/var/spack/repos/builtin/packages/r-scrime/package.py @@ -7,11 +7,13 @@ from spack import * class RScrime(RPackage): - """scrime: Analysis of High-Dimensional Categorical Data Such as SNP - Data""" + """Analysis of High-Dimensional Categorical Data Such as SNP Data. - homepage = "https://cloud.r-project.org/package=scrime" - url = "https://cloud.r-project.org/src/contrib/scrime_1.3.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/scrime" + Tools for the analysis of high-dimensional data developed/implemented at + the group "Statistical Complexity Reduction In Molecular Epidemiology" + (SCRIME). Main focus is on SNP data. But most of the functions can also be + applied to other types of categorical data.""" + + cran = "scrime" version('1.3.5', sha256='5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578') diff --git a/var/spack/repos/builtin/packages/r-sctransform/package.py b/var/spack/repos/builtin/packages/r-sctransform/package.py index d612d75e2f..184eacf740 100644 --- a/var/spack/repos/builtin/packages/r-sctransform/package.py +++ b/var/spack/repos/builtin/packages/r-sctransform/package.py @@ -7,7 +7,7 @@ from spack import * class RSctransform(RPackage): - """Variance Stabilizing Transformations for Single Cell UMI Data + """Variance Stabilizing Transformations for Single Cell UMI Data. A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative @@ -16,23 +16,27 @@ class RSctransform(RPackage): correction, and data correction. See Hafemeister and Satija 2019 <doi:10.1101/576827> for more details.""" - homepage = "https://github.com/ChristophH/sctransform" - url = "https://cloud.r-project.org/src/contrib/sctransform_0.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sctransform" + cran = "sctransform" + version('0.3.3', sha256='83af125c40f211e1ddae5098f88766aea1453c02ae98486081f3efadb3620b2b') version('0.3.2', sha256='5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc') version('0.2.0', sha256='d7f4c7958693823454f1426b23b0e1e9c207ad61a7a228602a1885a1318eb3e4') depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.1.0:', when='@0.3.2:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@0.3.2:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.3.3:') + depends_on('r-dplyr', type=('build', 'run'), when='@0.3.3:') + depends_on('r-magrittr', type=('build', 'run'), when='@0.3.3:') depends_on('r-mass', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-future-apply', type=('build', 'run')) depends_on('r-future', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@0.3.3:') depends_on('r-gridextra', type=('build', 'run')) - depends_on('r-matrixstats', when='@0.3.2:', type=('build', 'run')) - depends_on('r-rcpparmadillo', when='@0.3.2:', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run'), when='@0.3.2:') + depends_on('r-rcpparmadillo', type=('build', 'run'), when='@0.3.2:') depends_on('r-rcpp@0.11.0:', type=('build', 'run')) - depends_on('r-rcppeigen', when='@:0.2.0', type=('build', 'run')) + + depends_on('r-rcppeigen', type=('build', 'run'), when='@:0.2.0') diff --git a/var/spack/repos/builtin/packages/r-sdmtools/package.py b/var/spack/repos/builtin/packages/r-sdmtools/package.py index 9be23f06ba..a61f467c3c 100644 --- a/var/spack/repos/builtin/packages/r-sdmtools/package.py +++ b/var/spack/repos/builtin/packages/r-sdmtools/package.py @@ -8,7 +8,7 @@ from spack import * class RSdmtools(RPackage): """Species Distribution Modelling Tools: Tools for processing data - associated with species distribution modelling exercises + associated with species distribution modelling exercises. This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for @@ -19,9 +19,7 @@ class RSdmtools(RPackage): Australian Research Council & ARC Research Network for Earth System Science.""" - homepage = "https://cloud.r-project.org/package=SDMTools" - url = "https://cloud.r-project.org/src/contrib/SDMTools_1.1-221.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SDMTools" + cran = "SDMTools" # This package was removed from CRAN on 2020-01-12 # The spack recipe contains the latest version available from the archives diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py index 037100b7eb..bb62bae35e 100644 --- a/var/spack/repos/builtin/packages/r-segmented/package.py +++ b/var/spack/repos/builtin/packages/r-segmented/package.py @@ -7,7 +7,7 @@ from spack import * class RSegmented(RPackage): - """Regression Models with Break-Points / Change-Points Estimation + """Regression Models with Break-Points / Change-Points Estimation. Given a regression model, segmented 'updates' it by adding one or more segmented (i.e., piece-wise linear) relationships. Several variables with @@ -18,12 +18,14 @@ class RSegmented(RPackage): <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).""" - homepage = "https://cloud.r-project.org/package=segmented" - url = "https://cloud.r-project.org/src/contrib/segmented_0.5-1.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/segmented" + cran = "segmented" + version('1.4-0', sha256='306940d3fe38588d5f52a52a217b560620b9ec9f338b32f604dfd78ffd43c276') + version('1.3-4', sha256='8276bfbb3e5c1d7a9a61098f72ac9b2b0f52c89ae9f9b715f76b22303cc3902d') version('1.3-1', sha256='b9b6e82bf72f108c69cb8fa01bd02fb99946c73ca3c8c2f8ae0abb1f460c143d') version('1.0-0', sha256='eeadc89b4bb4744bbd1e4e6c3b6536ff96fc7ee09016228dfdc0a8ebdc74fac5') version('0.5-4.0', sha256='7ff63a19915cbd1e190d3a4875892b4c7bd97890b0dc2909126348a19aec4071') version('0.5-2.2', sha256='3aa7136370dd77911ba8e061b5215560d120bc71f355eeadc0856389dfecb2f1') version('0.5-1.4', sha256='b1dc5f79ccc076c2943b15fe4f339368afa241797b7e80c91b62132cfa66809c') + + depends_on('r-mass', type=('build', 'run'), when='@1.4-0:') diff --git a/var/spack/repos/builtin/packages/r-selectr/package.py b/var/spack/repos/builtin/packages/r-selectr/package.py index 873f2c45af..aab2f9311c 100644 --- a/var/spack/repos/builtin/packages/r-selectr/package.py +++ b/var/spack/repos/builtin/packages/r-selectr/package.py @@ -7,7 +7,7 @@ from spack import * class RSelectr(RPackage): - """Translate CSS Selectors to XPath Expressions + """Translate CSS Selectors to XPath Expressions. Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only @@ -15,9 +15,7 @@ class RSelectr(RPackage): for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' (<https://cssselect.readthedocs.io/>).""" - homepage = "https://sjp.co.nz/projects/selectr" - url = "https://cloud.r-project.org/src/contrib/selectr_0.3-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/selectr" + cran = "selectr" version('0.4-2', sha256='5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127') version('0.4-1', sha256='8bd42f167629344e485e586f9b05fed342746132489079084d82133d7b3ee2ca') @@ -26,4 +24,4 @@ class RSelectr(RPackage): depends_on('r@3.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-r6', when='@0.4-0:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run'), when='@0.4-0:') diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py index 8fbf6488e8..45588c34b1 100644 --- a/var/spack/repos/builtin/packages/r-seqinr/package.py +++ b/var/spack/repos/builtin/packages/r-seqinr/package.py @@ -7,17 +7,16 @@ from spack import * class RSeqinr(RPackage): - """Biological Sequences Retrieval and Analysis + """Biological Sequences Retrieval and Analysis. Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 <doi:10.1093/nar/12.1Part1.121>.""" - homepage = "https://seqinr.r-forge.r-project.org" - url = "https://cloud.r-project.org/src/contrib/seqinr_3.3-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/seqinr" + cran = "seqinr" + version('4.2-8', sha256='584b34e9dec0320cef02096eb356a0f6115bbd24356cf62e67356963e9d5e9f7') version('4.2-5', sha256='de9860759c23af2ec2f2ef03b5dd1cea72c804438eadd369b7d9269bdf8d32fc') version('3.4-5', sha256='162a347495fd52cbb62e8187a4692e7c50b9fa62123c5ef98f2744c98a05fb9f') version('3.3-6', sha256='42a3ae01331db744d67cc9c5432ce9ae389bed465af826687b9c10216ac7a08d') diff --git a/var/spack/repos/builtin/packages/r-servr/package.py b/var/spack/repos/builtin/packages/r-servr/package.py index cd1b73ce28..b6b088dde3 100644 --- a/var/spack/repos/builtin/packages/r-servr/package.py +++ b/var/spack/repos/builtin/packages/r-servr/package.py @@ -7,16 +7,15 @@ from spack import * class RServr(RPackage): - """A Simple HTTP Server to Serve Static Files or Dynamic Documents + """A Simple HTTP Server to Serve Static Files or Dynamic Documents. Start an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.""" - homepage = "https://github.com/yihui/servr" - url = "https://cloud.r-project.org/src/contrib/servr_0.21.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/servr" + cran = "servr" + version('0.24', sha256='d94e1d31802ce6bbab7a5838ff94cbca8cd998237d834ff25fedf7514f41a087') version('0.21', sha256='3fc0da063dd04b796a49ce62bf8e69d5854679520da90cc92ee3fc0a0b2ad389') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sessioninfo/package.py b/var/spack/repos/builtin/packages/r-sessioninfo/package.py index aa6fa53b3b..9b599679b9 100644 --- a/var/spack/repos/builtin/packages/r-sessioninfo/package.py +++ b/var/spack/repos/builtin/packages/r-sessioninfo/package.py @@ -7,15 +7,19 @@ from spack import * class RSessioninfo(RPackage): - """Query and print information about the current R session. It is similar - to 'utils::sessionInfo()', but includes more information about packages, - and where they were installed from.""" + """R Session Information. - homepage = "https://github.com/r-lib/sessioninfo#readme" - url = "https://cloud.r-project.org/src/contrib/sessioninfo_1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sessioninfo" + Query and print information about the current R session. It is similar to + 'utils::sessionInfo()', but includes more information about packages, and + where they were installed from.""" + cran = "sessioninfo" + + version('1.2.2', sha256='f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb') version('1.1.1', sha256='166b04678448a7decd50f24afabe5e2ad613e3c55b180ef6e8dd7a870a1dae48') + depends_on('r@2.10:', type=('build', 'run'), when='@1.2.2:') depends_on('r-cli', type=('build', 'run')) - depends_on('r-withr', type=('build', 'run')) + depends_on('r-cli@3.1.0:', type=('build', 'run'), when='@1.2.2:') + + depends_on('r-withr', type=('build', 'run'), when='@:1.1.1') diff --git a/var/spack/repos/builtin/packages/r-seurat/package.py b/var/spack/repos/builtin/packages/r-seurat/package.py index f0d9be1a8a..fc54baab6a 100644 --- a/var/spack/repos/builtin/packages/r-seurat/package.py +++ b/var/spack/repos/builtin/packages/r-seurat/package.py @@ -7,7 +7,7 @@ from spack import * class RSeurat(RPackage): - """Tools for Single Cell Genomics + """Tools for Single Cell Genomics. A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret @@ -17,10 +17,9 @@ class RSeurat(RPackage): R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.""" - homepage = "https://satijalab.org/seurat/" - url = "https://cloud.r-project.org/src/contrib/Seurat_2.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/Seurat" + cran = "Seurat" + version('4.1.0', sha256='2505829a2763e449684dd1b107ee6982e019ee9fecb093adca7b283cad1b315d') version('3.2.3', sha256='83aa48f75c3756bee23e108a8b01028366e24f237fe990cb441f3525e0613f87') version('3.1.0', sha256='d8d3fad2950a8f791376e3d20c72ea07c68bf8d82d800661cab5ce696db39d45') version('3.0.2', sha256='16df5dec6b41d49320c5bf5ce30eb3b7dedeea69b054b55b77528f2f2b7bce04') @@ -28,83 +27,91 @@ class RSeurat(RPackage): version('2.1.0', sha256='7d20d231b979a4aa63cd7dae7e725405212e8975889f12b8d779c6c896c10ac3') version('2.0.1', sha256='6aa33aa3afb29a8be364ab083c7071cfbc56ad042a019bcf6f939e0c8c7744f0') - depends_on('r@3.2.0:', when='@:2.3.0', type=('build', 'run')) - depends_on('r@3.4.0:', when='@2.3.1:', type=('build', 'run')) - depends_on('r@3.6.0:', when='@3.2.3:', type=('build', 'run')) - depends_on('r-cluster', when='@2.3.0:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@2.3.1:') + depends_on('r@3.6.0:', type=('build', 'run'), when='@3.2.3:') + depends_on('r@4.0.0:', type=('build', 'run'), when='@4.1.0:') + depends_on('r-cluster', type=('build', 'run'), when='@2.3.0:') depends_on('r-cowplot', type=('build', 'run')) - depends_on('r-fitdistrplus', when='@2.3.0:', type=('build', 'run')) - depends_on('r-future', when='@3.0.0:', type=('build', 'run')) - depends_on('r-future-apply', when='@3.0.0:', type=('build', 'run')) + depends_on('r-fitdistrplus', type=('build', 'run'), when='@2.3.0:') + depends_on('r-future', type=('build', 'run'), when='@3.0.0:') + depends_on('r-future-apply', type=('build', 'run'), when='@3.0.0:') depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) - depends_on('r-ggplot2@3.3.0:', when='@3.2.3:', type=('build', 'run')) - depends_on('r-ggrepel', when='@3.0.0:', type=('build', 'run')) - depends_on('r-ggridges', when='@2.2.0:', type=('build', 'run')) - depends_on('r-httr', when='@2.3.4:', type=('build', 'run')) + depends_on('r-ggplot2@3.3.0:', type=('build', 'run'), when='@3.2.3:') + depends_on('r-ggrepel', type=('build', 'run'), when='@3.0.0:') + depends_on('r-ggridges', type=('build', 'run'), when='@2.2.0:') + depends_on('r-httr', type=('build', 'run'), when='@2.3.4:') depends_on('r-ica', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) depends_on('r-irlba', type=('build', 'run')) - depends_on('r-jsonlite', when='@3.2.3:', type=('build', 'run')) - depends_on('r-kernsmooth', when='@3.0.0:', type=('build', 'run')) - depends_on('r-leiden@0.3.1:', when='@3.1.0:', type=('build', 'run')) - depends_on('r-lmtest', when='@2.3.0:', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run'), when='@3.2.3:') + depends_on('r-kernsmooth', type=('build', 'run'), when='@3.0.0:') + depends_on('r-leiden@0.3.1:', type=('build', 'run'), when='@3.1.0:') + depends_on('r-lmtest', type=('build', 'run'), when='@2.3.0:') depends_on('r-mass', type=('build', 'run')) - depends_on('r-matrix@1.2.14:', type=('build', 'run')) - depends_on('r-matrixstats', when='@3.2.3:', type=('build', 'run')) - depends_on('r-miniui', when='@3.2.3:', type=('build', 'run')) - depends_on('r-patchwork', when='@3.2.3:', type=('build', 'run')) + depends_on('r-matrix@1.2-14:', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run'), when='@3.2.3:') + depends_on('r-miniui', type=('build', 'run'), when='@3.2.3:') + depends_on('r-patchwork', type=('build', 'run'), when='@3.2.3:') depends_on('r-pbapply', type=('build', 'run')) depends_on('r-plotly', type=('build', 'run')) - depends_on('r-plotly@4.9.0:', when='@3.2.3:', type=('build', 'run')) - depends_on('r-png', when='@2.3.0:', type=('build', 'run')) - depends_on('r-rann', when='@2.3.0:', type=('build', 'run')) + depends_on('r-plotly@4.9.0:', type=('build', 'run'), when='@3.2.3:') + depends_on('r-png', type=('build', 'run'), when='@2.3.0:') + depends_on('r-rann', type=('build', 'run'), when='@2.3.0:') depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) - depends_on('r-rcppannoy', when='@3.1.0:', type=('build', 'run')) - depends_on('r-reticulate', when='@2.3.1:', type=('build', 'run')) - depends_on('r-rlang', when='@3.0.0:', type=('build', 'run')) + depends_on('r-rcpp@1.0.7:', type=('build', 'run'), when='@4.1.0:') + depends_on('r-rcppannoy', type=('build', 'run'), when='@3.1.0:') + depends_on('r-rcppannoy@0.0.18:', type=('build', 'run'), when='@4.1.0:') + depends_on('r-reticulate', type=('build', 'run'), when='@2.3.1:') + depends_on('r-rlang', type=('build', 'run'), when='@3.0.0:') depends_on('r-rocr', type=('build', 'run')) - depends_on('r-rsvd', when='@3.0.0:', type=('build', 'run')) depends_on('r-rtsne', type=('build', 'run')) - depends_on('r-scales', when='@3.0.0:', type=('build', 'run')) - depends_on('r-scattermore@0.7:', when='@3.2.3:', type=('build', 'run')) - depends_on('r-sctransform@0.2.0:', when='@3.0.0:', type=('build', 'run')) - depends_on('r-sctransform@0.3.1:', when='@3.2.3:', type=('build', 'run')) - depends_on('r-shiny', when='@3.2.3:', type=('build', 'run')) - depends_on('r-spatstat', when='@3.2.3:', type=('build', 'run')) - depends_on('r-tibble', when='@3.2.3:', type=('build', 'run')) - depends_on('r-uwot', when='@3.1.0:', type=('build', 'run')) - depends_on('r-uwot@0.1.9:', when='@3.2.3:', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run'), when='@3.0.0:') + depends_on('r-scattermore@0.7:', type=('build', 'run'), when='@3.2.3:') + depends_on('r-sctransform@0.2.0:', type=('build', 'run'), when='@3.0.0:') + depends_on('r-sctransform@0.3.1:', type=('build', 'run'), when='@3.2.3:') + depends_on('r-sctransform@0.3.3:', type=('build', 'run'), when='@4.1.0:') + depends_on('r-seuratobject@4.0.4:', type=('build', 'run'), when='@4.1.0:') + depends_on('r-shiny', type=('build', 'run'), when='@3.2.3:') + depends_on('r-spatstat-core', type=('build', 'run'), when='@4.1.0:') + depends_on('r-spatstat-geom', type=('build', 'run'), when='@4.1.0:') + depends_on('r-tibble', type=('build', 'run'), when='@3.2.3:') + depends_on('r-uwot', type=('build', 'run'), when='@3.1.0:') + depends_on('r-uwot@0.1.9:', type=('build', 'run'), when='@3.2.3:') depends_on('r-rcppeigen', type=('build', 'run')) depends_on('r-rcppprogress', type=('build', 'run')) - depends_on('r-gplots', when='@:2.3.4', type=('build', 'run')) - depends_on('r-reshape2', when='@:2.3.4', type=('build', 'run')) - depends_on('r-ape', when='@:3.1.0', type=('build', 'run')) - depends_on('r-tidyr', when='@:2.3.4', type=('build', 'run')) - depends_on('r-caret', when='@:2.3.2', type=('build', 'run')) - depends_on('r-gdata', when='@:2.3.2', type=('build', 'run')) - depends_on('r-gridextra', when='@:2.3.0', type=('build', 'run')) - depends_on('r-hmisc', when='@:2.3.4', type=('build', 'run')) - depends_on('r-nmf', when='@:2.2.0', type=('build', 'run')) - depends_on('r-fpc', when='@:2.3.4', type=('build', 'run')) - depends_on('r-lars', when='@:2.3.4', type=('build', 'run')) - depends_on('r-dtw', when='@:2.3.4', type=('build', 'run')) - depends_on('r-mixtools', when='@:2.3.4', type=('build', 'run')) - depends_on('r-diffusionmap', when='@:2.3.3', type=('build', 'run')) - depends_on('r-tsne', when='@:3.1.0', type=('build', 'run')) - depends_on('r-ranger', when='@:2.3.2', type=('build', 'run')) - depends_on('r-ggjoy', when='@:2.1.0', type=('build', 'run')) - depends_on('r-sdmtools', when='@:3.1.0', type=('build', 'run')) - depends_on('r-tclust', when='@:2.3.2', type=('build', 'run')) - depends_on('r-fnn', when='@:2.3.2', type=('build', 'run')) - depends_on('r-vgam', when='@:2.3.2', type=('build', 'run')) - depends_on('r-e1071', when='@:2.0.1', type=('build', 'run')) - depends_on('r-compositions', when='@:2.0.1', type=('build', 'run')) - depends_on('r-nmof', when='@:2.0.1', type=('build', 'run')) - depends_on('r-metap', when='@2.2.1:3.1.0', type=('build', 'run')) - depends_on('r-stringr', when='@:2.3.2', type=('build', 'run')) - depends_on('r-dplyr', when='@:2.3.4', type=('build', 'run')) - depends_on('r-dosnow', when='@2.3.0:2.3.4', type=('build', 'run')) - depends_on('r-foreach', when='@2.3.0:2.3.4', type=('build', 'run')) - depends_on('r-hdf5r', when='@2.3.2:2.3.4', type=('build', 'run')) + + depends_on('r-gplots', type=('build', 'run'), when='@:2.3.4') + depends_on('r-reshape2', type=('build', 'run'), when='@:2.3.4') + depends_on('r-ape', type=('build', 'run'), when='@:3.1.0') + depends_on('r-tidyr', type=('build', 'run'), when='@:2.3.4') + depends_on('r-caret', type=('build', 'run'), when='@:2.3.2') + depends_on('r-gdata', type=('build', 'run'), when='@:2.3.2') + depends_on('r-gridextra', type=('build', 'run'), when='@:2.3.0') + depends_on('r-hmisc', type=('build', 'run'), when='@:2.3.4') + depends_on('r-nmf', type=('build', 'run'), when='@:2.2.0') + depends_on('r-fpc', type=('build', 'run'), when='@:2.3.4') + depends_on('r-lars', type=('build', 'run'), when='@:2.3.4') + depends_on('r-dtw', type=('build', 'run'), when='@:2.3.4') + depends_on('r-mixtools', type=('build', 'run'), when='@:2.3.4') + depends_on('r-diffusionmap', type=('build', 'run'), when='@:2.3.3') + depends_on('r-tsne', type=('build', 'run'), when='@:3.1.0') + depends_on('r-ranger', type=('build', 'run'), when='@:2.3.2') + depends_on('r-ggjoy', type=('build', 'run'), when='@:2.1.0') + depends_on('r-sdmtools', type=('build', 'run'), when='@:3.1.0') + depends_on('r-tclust', type=('build', 'run'), when='@:2.3.2') + depends_on('r-fnn', type=('build', 'run'), when='@:2.3.2') + depends_on('r-vgam', type=('build', 'run'), when='@:2.3.2') + depends_on('r-e1071', type=('build', 'run'), when='@:2.0.1') + depends_on('r-compositions', type=('build', 'run'), when='@:2.0.1') + depends_on('r-nmof', type=('build', 'run'), when='@:2.0.1') + depends_on('r-metap', type=('build', 'run'), when='@2.2.1:3.1.0') + depends_on('r-stringr', type=('build', 'run'), when='@:2.3.2') + depends_on('r-dplyr', type=('build', 'run'), when='@:2.3.4') + depends_on('r-dosnow', type=('build', 'run'), when='@2.3.0:2.3.4') + depends_on('r-foreach', type=('build', 'run'), when='@2.3.0:2.3.4') + depends_on('r-hdf5r', type=('build', 'run'), when='@2.3.2:2.3.4') + depends_on('r-rsvd', type=('build', 'run'), when='@3.0.0:3.2.3') + depends_on('r-spatstat@:1.64-1', type=('build', 'run'), when='@3.2.3') depends_on('java', when='@:2.3.0') diff --git a/var/spack/repos/builtin/packages/r-seuratobject/package.py b/var/spack/repos/builtin/packages/r-seuratobject/package.py new file mode 100644 index 0000000000..f03c67fbf8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-seuratobject/package.py @@ -0,0 +1,29 @@ +# 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 RSeuratobject(RPackage): + """Data Structures for Single Cell Data. + + Defines S4 classes for single-cell genomic data and associated information, + such as dimensionality reduction embeddings, nearest-neighbor graphs, and + spatially-resolved coordinates. Provides data access methods and R-native + hooks to ensure the Seurat object is familiar to other R users. See Satija + R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, + Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart + T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more + details.""" + + cran = "SeuratObject" + + version('4.0.4', sha256='585261b7d2045193accf817a29e2e3356e731f57c554bed37d232fa49784088c') + + depends_on('r@4.0.0:', type=('build', 'run')) + depends_on('r-matrix@1.3-3:', type=('build', 'run')) + depends_on('r-rcpp@1.0.5:', type=('build', 'run')) + depends_on('r-rlang@0.4.7:', type=('build', 'run')) + depends_on('r-rcppeigen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sf/package.py b/var/spack/repos/builtin/packages/r-sf/package.py index a535321017..8dae661ffe 100644 --- a/var/spack/repos/builtin/packages/r-sf/package.py +++ b/var/spack/repos/builtin/packages/r-sf/package.py @@ -7,7 +7,7 @@ from spack import * class RSf(RPackage): - """Simple Features for R + """Simple Features for R. Support for simple features, a standardized way to encode spatial vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for @@ -15,10 +15,9 @@ class RSf(RPackage): transformations. Optionally uses the 's2' package for spherical geometry operations on geographic coordinates.""" - homepage = "https://github.com/r-spatial/sf/" - url = "https://cloud.r-project.org/src/contrib/sf_0.5-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sf" + cran = "sf" + version('1.0-5', sha256='290c28fa5ea777d555e70962c59079c134f02f7bdf60259a72eea79a064a1ac4') version('0.9-7', sha256='4acac2f78badf9d252da5bf377975f984927c14a56a72d9f83d285c0adadae9c') version('0.7-7', sha256='d1780cb46a285b30c7cc41cae30af523fbc883733344e53f7291e2d045e150a4') version('0.7-5', sha256='53ed0567f502216a116c4848f5a9262ca232810f82642df7b98e0541a2524868') @@ -26,13 +25,17 @@ class RSf(RPackage): depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-classint@0.2-1:', type=('build', 'run')) - depends_on('r-classint@0.4-1:', when='@0.9-7:', type=('build', 'run')) + depends_on('r-classint@0.4-1:', type=('build', 'run'), when='@0.9-7:') depends_on('r-dbi@0.8:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-units@0.6-0:', type=('build', 'run')) depends_on('r-rcpp@0.12.18:', type=('build', 'run')) + depends_on('r-s2@1.0.7:', type=('build', 'run'), when='@1.0-5:') + depends_on('r-units@0.6-0:', type=('build', 'run'), when='@1.0-5:') depends_on('gdal@2.0.1:') depends_on('geos@3.4.0:') depends_on('proj@4.8.0:5', when='@:0.7-3') - depends_on('proj@4.8.0:6', when='@0.7-4:') + depends_on('proj@4.8.0:6', when='@0.7-4:0.7-7') + depends_on('proj@4.8.0:') depends_on('sqlite', when='@0.9-7') + + depends_on('r-units@0.6-0:', type=('build', 'run'), when='@:9.9-7') diff --git a/var/spack/repos/builtin/packages/r-sfheaders/package.py b/var/spack/repos/builtin/packages/r-sfheaders/package.py new file mode 100644 index 0000000000..9092e191df --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sfheaders/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 RSfheaders(RPackage): + """Converts Between R Objects and Simple Feature Objects. + + Converts between R and Simple Feature 'sf' objects, without depending on + the Simple Feature library. Conversion functions are available at both the + R level, and through 'Rcpp'.""" + + cran = "sfheaders" + + version('0.4.0', sha256='86bcd61018a0491fc8a1e7fb0422c918296287b82be299a79ccee8fcb515e045') + + depends_on('r-geometries@0.2.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sfsmisc/package.py b/var/spack/repos/builtin/packages/r-sfsmisc/package.py index 4846054002..d88e9de019 100644 --- a/var/spack/repos/builtin/packages/r-sfsmisc/package.py +++ b/var/spack/repos/builtin/packages/r-sfsmisc/package.py @@ -7,7 +7,7 @@ from spack import * class RSfsmisc(RPackage): - """Utilities from 'Seminar fuer Statistik' ETH Zurich + """Utilities from 'Seminar fuer Statistik' ETH Zurich. Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, some of which were ported from S-plus in the 1990s.; For graphics, have pretty @@ -19,14 +19,14 @@ class RSfsmisc(RPackage): efficient prime numbers, integer codes, Duplicated(), toLatex.numeric() and is.whole().""" - homepage = "https://cloud.r-project.org/package=sfsmisc" - url = "https://cloud.r-project.org/src/contrib/sfsmisc_1.1-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sfsmisc" + cran = "sfsmisc" + version('1.1-12', sha256='9b12184a28fff87cacd0c3602d0cf63acb4d0f3049ad3a6ff16177f6df350782') version('1.1-8', sha256='b6556af5f807f0769489657a676422cb0734f3d6c918543d2989ef17febc1fa5') version('1.1-4', sha256='44b6a9c859922e86b7182e54eb781d3264f3819f310343518ebc66f54f305c7d') version('1.1-3', sha256='58eff7d4a9c79212321858efe98d2a6153630e263ff0218a31d5e104b8b545f8') version('1.1-0', sha256='7f430cf3ebb95bac806fbf093fb1e2112deba47416a93be8d5d1064b76bc0015') - depends_on('r@3.0.1:', when='@:1.1-1', type=('build', 'run')) - depends_on('r@3.2.0:', when='@1.1-2:', type=('build', 'run')) + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@1.1-2:') + depends_on('r@3.3.0:', type=('build', 'run'), when='@1.1-12:') diff --git a/var/spack/repos/builtin/packages/r-shadowtext/package.py b/var/spack/repos/builtin/packages/r-shadowtext/package.py index 6e6c4f67c8..5bd0438474 100644 --- a/var/spack/repos/builtin/packages/r-shadowtext/package.py +++ b/var/spack/repos/builtin/packages/r-shadowtext/package.py @@ -7,15 +7,14 @@ from spack import * class RShadowtext(RPackage): - """Shadow Text Grob and Layer + """Shadow Text Grob and Layer. Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'. These functions create/draw text grob with background shadow.""" - homepage = "https://github.com/GuangchuangYu/shadowtext/" - url = "https://cloud.r-project.org/src/contrib/shadowtext_0.0.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/shadowtext" + cran = "shadowtext" + version('0.1.1', sha256='eb06581d7ed06c963eee47548932688fd48eba70b3ebd2a7b41a6501d6e00006') version('0.0.7', sha256='6e32b1dfd3d4816803848b876666185258b888286ec3d3e8500499ec3eba31e8') depends_on('r@3.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shape/package.py b/var/spack/repos/builtin/packages/r-shape/package.py index eb57d4d6fc..02ba974545 100644 --- a/var/spack/repos/builtin/packages/r-shape/package.py +++ b/var/spack/repos/builtin/packages/r-shape/package.py @@ -7,15 +7,14 @@ from spack import * class RShape(RPackage): - """Functions for Plotting Graphical Shapes, Colors + """Functions for Plotting Graphical Shapes, Colors. Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...""" - homepage = "https://cloud.r-project.org/package=shape" - url = "https://cloud.r-project.org/src/contrib/shape_1.4.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/shape" + cran = "shape" + version('1.4.6', sha256='b9103e5ed05c223c8147dbe3b87a0d73184697343634a353a2ae722f7ace0b7b') version('1.4.5', sha256='094a79b8f42226189227fd7af71868e42106caa25a4d7f80a26977e8bc84189f') version('1.4.4', sha256='f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41') version('1.4.3', sha256='720f6ca9c70a39a3900af9d074bff864b18ac58013b21d48b779047481b93ded') diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index f8c86b3ce3..b43c68713b 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -7,17 +7,16 @@ from spack import * class RShiny(RPackage): - """Web Application Framework for R + """Web Application Framework for R. Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.""" - homepage = "https://shiny.rstudio.com/" - url = "https://cloud.r-project.org/src/contrib/shiny_1.0.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/shiny" + cran = "shiny" + version('1.7.1', sha256='c03b2056fb41430352c7c0e812bcc8632e6ec4caef077d2f7633512d91721d00') version('1.5.0', sha256='23cb8bfa448389c256efdab75e7e8d3ff90e5de66264c4ab02df322fb4298e9e') version('1.3.2', sha256='28b851ae6c196ca845f6e815c1379247595ac123a4faa10a16533d1a9ce0c24f') version('1.0.5', sha256='20e25f3f72f3608a2151663f7836f2e0c6da32683a555d7541063ae7a935fa42') @@ -25,23 +24,32 @@ class RShiny(RPackage): depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-httpuv@1.5.0:', type=('build', 'run')) - depends_on('r-httpuv@1.5.2:', when='@1.5.0:', type=('build', 'run')) + depends_on('r-httpuv@1.5.2:', type=('build', 'run'), when='@1.5.0:') depends_on('r-mime@0.3:', type=('build', 'run')) depends_on('r-jsonlite@0.9.16:', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) - depends_on('r-digest', type=('build', 'run')) + depends_on('r-fontawesome@0.2.1:', type=('build', 'run'), when='@1.7.1:') depends_on('r-htmltools@0.3.6:', type=('build', 'run')) - depends_on('r-htmltools@0.4.0.9003:', when='@1.5.0:', type=('build', 'run')) + depends_on('r-htmltools@0.4.0.9003:', type=('build', 'run'), when='@1.5.0:') + depends_on('r-htmltools@0.5.2:', type=('build', 'run'), when='@1.7.1:') depends_on('r-r6@2.0:', type=('build', 'run')) depends_on('r-sourcetools', type=('build', 'run')) - depends_on('r-later@0.7.2:', when='@1.1.0:', type=('build', 'run')) - depends_on('r-later@1.0.0:', when='@1.5.0:', type=('build', 'run')) - depends_on('r-promises@1.0.1:', when='@1.1.0:', type=('build', 'run')) - depends_on('r-promises@1.1.0:', when='@1.5.0:', type=('build', 'run')) - depends_on('r-crayon', when='@1.1.0:', type=('build', 'run')) - depends_on('r-rlang', when='@1.1.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.0:', when='@1.5.0:', type=('build', 'run')) - depends_on('r-fastmap@1.0.0:', when='@1.5.0:', type=('build', 'run')) - depends_on('r-withr', when='@1.5.0:', type=('build', 'run')) - depends_on('r-commonmark@1.7:', when='@1.5.0:', type=('build', 'run')) - depends_on('r-glue@1.3.2:', when='@1.5.0:', type=('build', 'run')) + depends_on('r-later@0.7.2:', type=('build', 'run'), when='@1.1.0:') + depends_on('r-later@1.0.0:', type=('build', 'run'), when='@1.5.0:') + depends_on('r-promises@1.0.1:', type=('build', 'run'), when='@1.1.0:') + depends_on('r-promises@1.1.0:', type=('build', 'run'), when='@1.5.0:') + depends_on('r-crayon', type=('build', 'run'), when='@1.1.0:') + depends_on('r-rlang', type=('build', 'run'), when='@1.1.0:') + depends_on('r-rlang@0.4.0:', type=('build', 'run'), when='@1.5.0:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@1.7.1:') + depends_on('r-fastmap@1.0.0:', type=('build', 'run'), when='@1.5.0:') + depends_on('r-fastmap@1.1.0:', type=('build', 'run'), when='@1.7.1:') + depends_on('r-withr', type=('build', 'run'), when='@1.5.0:') + depends_on('r-commonmark@1.7:', type=('build', 'run'), when='@1.5.0:') + depends_on('r-glue@1.3.2:', type=('build', 'run'), when='@1.5.0:') + depends_on('r-bslib@0.3.0:', type=('build', 'run'), when='@1.7.1:') + depends_on('r-cachem', type=('build', 'run'), when='@1.7.1:') + depends_on('r-ellipsis', type=('build', 'run'), when='@1.7.1:') + depends_on('r-lifecycle@0.2.0:', type=('build', 'run'), when='@1.7.1:') + + depends_on('r-digest', type=('build', 'run'), when='@:1.5.0') diff --git a/var/spack/repos/builtin/packages/r-shinydashboard/package.py b/var/spack/repos/builtin/packages/r-shinydashboard/package.py index 217cbf6468..2ef0b14044 100644 --- a/var/spack/repos/builtin/packages/r-shinydashboard/package.py +++ b/var/spack/repos/builtin/packages/r-shinydashboard/package.py @@ -7,17 +7,19 @@ from spack import * class RShinydashboard(RPackage): - """Create Dashboards with 'Shiny'""" + """Create Dashboards with 'Shiny'. - homepage = "https://cloud.r-project.org/package=shinydashboard" - url = "https://cloud.r-project.org/src/contrib/shinydashboard_0.7.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/shinydashboard" + Create dashboards with 'Shiny'. This package provides a theme on top of + 'Shiny', making it easy to create attractive dashboards.""" + cran = "shinydashboard" + + version('0.7.2', sha256='a56ee48572649830cd8d82f1caa2099411461e19e19223cbad36a375299f3843') version('0.7.1', sha256='51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e') version('0.7.0', sha256='0b7b102e9e5bea78ddc4da628d072a358270f2db9b63a6ebe4d8bdce3066d883') version('0.6.1', sha256='1ee38f257433d24455426bc9d85c36f588735a54fbf6143935fed9cccb3bf193') depends_on('r@3.0:', type=('build', 'run')) - depends_on('r-htmltools@0.2.6:', type=('build', 'run')) depends_on('r-shiny@1.0.0:', type=('build', 'run')) - depends_on('r-promises', when='@0.7.1:', type=('build', 'run')) + depends_on('r-htmltools@0.2.6:', type=('build', 'run')) + depends_on('r-promises', type=('build', 'run'), when='@0.7.1:') diff --git a/var/spack/repos/builtin/packages/r-shinyfiles/package.py b/var/spack/repos/builtin/packages/r-shinyfiles/package.py index bd6c0863ca..5fc37bbbbb 100644 --- a/var/spack/repos/builtin/packages/r-shinyfiles/package.py +++ b/var/spack/repos/builtin/packages/r-shinyfiles/package.py @@ -7,18 +7,17 @@ from spack import * class RShinyfiles(RPackage): - """A Server-Side File System Viewer for Shiny + """A Server-Side File System Viewer for Shiny. - Provides functionality for client-side navigation of the server side - file system in shiny apps. In case the app is running locally this gives - the user direct access to the file system without the need to "download" - files to a temporary location. Both file and folder selection as well as - file saving is available.""" + Provides functionality for client-side navigation of the server side file + system in shiny apps. In case the app is running locally this gives the + user direct access to the file system without the need to "download" files + to a temporary location. Both file and folder selection as well as file + saving is available.""" - homepage = "https://github.com/thomasp85/shinyFiles" - url = "https://cloud.r-project.org/src/contrib/shinyFiles_0.7.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/shinyFiles" + cran = "shinyFiles" + version('0.9.1', sha256='05694630ed5ae6ac15307ffcb211c83097fee0f38ca59340a7e68cac62730d39') version('0.9.0', sha256='51ad2aad61bcae22fb2c48a79d02bf6f86e36ffc49a3b64e26a76d133a955167') version('0.7.3', sha256='710c8a6191aaf336379bc748daff1160d0d2858e2aee0d98e2ad48e7121d5a05') diff --git a/var/spack/repos/builtin/packages/r-shinyjs/package.py b/var/spack/repos/builtin/packages/r-shinyjs/package.py index 6fb01c0730..e9bd0fb05d 100644 --- a/var/spack/repos/builtin/packages/r-shinyjs/package.py +++ b/var/spack/repos/builtin/packages/r-shinyjs/package.py @@ -7,7 +7,7 @@ from spack import * class RShinyjs(RPackage): - """Easily Improve the User Experience of Your Shiny Apps in Seconds + """Easily Improve the User Experience of Your Shiny Apps in Seconds. Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. Examples include: @@ -16,14 +16,15 @@ class RShinyjs(RPackage): useful functions for both the end user and the developer. 'shinyjs' can also be used to easily call your own custom JavaScript functions from R.""" - homepage = "https://deanattali.com/shinyjs/" - cran = "shinyjs" + cran = "shinyjs" + version('2.1.0', sha256='7ec20cbf1b1fd7a32d85a56dfc0df8b5f67c828d241da400a21d893cb37ea9c5') version('2.0.0', sha256='c2cdd9fab41f6b46bb41b288cd9b3fb3a7fe9627b664e3a58a0cb5dd4c19f8ff') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-digest@0.6.8:', type=('build', 'run')) - depends_on('r-htmltools@0.2.9:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-shiny@1.0.0:', type=('build', 'run')) - depends_on('pandoc', type='build') + + depends_on('r-htmltools@0.2.9:', type=('build', 'run'), when='@:2.0.0') + depends_on('pandoc', type='build', when='@:2.0.0') diff --git a/var/spack/repos/builtin/packages/r-shinystan/package.py b/var/spack/repos/builtin/packages/r-shinystan/package.py index b8b72b1d9e..d7acec1f06 100644 --- a/var/spack/repos/builtin/packages/r-shinystan/package.py +++ b/var/spack/repos/builtin/packages/r-shinystan/package.py @@ -8,7 +8,7 @@ from spack import * class RShinystan(RPackage): """Interactive Visual and Numerical Diagnostics and Posterior Analysis for - Bayesian Models: + Bayesian Models. A graphical user interface for interactive Markov chain Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. @@ -17,8 +17,7 @@ class RShinystan(RPackage): programming language (and has extended functionality for 'Stan' models fit using the 'rstan' and 'rstanarm' packages).""" - homepage = "https://mc-stan.org/" - cran = "shinystan" + cran = "shinystan" version('2.5.0', sha256='45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1') diff --git a/var/spack/repos/builtin/packages/r-shinythemes/package.py b/var/spack/repos/builtin/packages/r-shinythemes/package.py index c1f7ee173e..bc3b7bb3ad 100644 --- a/var/spack/repos/builtin/packages/r-shinythemes/package.py +++ b/var/spack/repos/builtin/packages/r-shinythemes/package.py @@ -7,14 +7,13 @@ from spack import * class RShinythemes(RPackage): - """Themes for Shiny: + """Themes for Shiny. Themes for use with Shiny. Includes several Bootstrap themes from <https://bootswatch.com/>, which are packaged for use with Shiny applications.""" - homepage = "https://rstudio.github.io/shinythemes/" - cran = "shinythemes" + cran = "shinythemes" version('1.2.0', sha256='37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963') diff --git a/var/spack/repos/builtin/packages/r-sitmo/package.py b/var/spack/repos/builtin/packages/r-sitmo/package.py index e9f211e0ff..79be0fa870 100644 --- a/var/spack/repos/builtin/packages/r-sitmo/package.py +++ b/var/spack/repos/builtin/packages/r-sitmo/package.py @@ -7,8 +7,10 @@ from spack import * class RSitmo(RPackage): - """Provided within are two high quality and fast PPRNGs that may be used in - an 'OpenMP' parallel environment. In addition, there is a generator for one + """Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files. + + Provided within are two high quality and fast PPRNGs that may be used in an + 'OpenMP' parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence. The objective of this library to consolidate the distribution of the 'sitmo' (C++98 & C++11), 'threefry' and 'vandercorput' (C++11-only) engines on CRAN by enabling others to link to @@ -17,10 +19,9 @@ class RSitmo(RPackage): example implementations using the 'sitmo' package and three accompanying vignette that provide additional information.""" - homepage = "https://github.com/coatless/sitmo" - url = "https://cloud.r-project.org/src/contrib/sitmo_2.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sitmo" + cran = "sitmo" + version('2.0.2', sha256='448ef8d56e36783354011845daf33f1efb83ea3b9685eea75eaf5134e24fa8c2') version('2.0.1', sha256='0c90d357af334d5c99c8956739dc12623ddd87dda5efa59f4a43f7393c87ed2a') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sm/package.py b/var/spack/repos/builtin/packages/r-sm/package.py index 4045dc75fb..cbb01fac8a 100644 --- a/var/spack/repos/builtin/packages/r-sm/package.py +++ b/var/spack/repos/builtin/packages/r-sm/package.py @@ -7,14 +7,15 @@ from spack import * class RSm(RPackage): - """This is software linked to the book 'Applied Smoothing Techniques for - Data Analysis - The Kernel Approach with S-Plus Illustrations' - Oxford University Press.""" + """Smoothing Methods for Nonparametric Regression and Density Estimation. - homepage = "http://www.stats.gla.ac.uk/~adrian/sm" - url = "https://cloud.r-project.org/src/contrib/sm_2.2-5.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sm" + This is software linked to the book 'Applied Smoothing Techniques for Data + Analysis - The Kernel Approach with S-Plus Illustrations' Oxford University + Press.""" + cran = "sm" + + version('2.2-5.7', sha256='2607a2cafc68d7e99005daf99e36f4a66eaf569ebb6b7500e962642cf58be80f') version('2.2-5.6', sha256='b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30') version('2.2-5.5', sha256='43e212a14c364b98b10018b56fe0a619ccffe4bde1294e6c45b3eafe7caf82e7') diff --git a/var/spack/repos/builtin/packages/r-smoof/package.py b/var/spack/repos/builtin/packages/r-smoof/package.py index dbbb357c80..5657c7860e 100644 --- a/var/spack/repos/builtin/packages/r-smoof/package.py +++ b/var/spack/repos/builtin/packages/r-smoof/package.py @@ -7,7 +7,7 @@ from spack import * class RSmoof(RPackage): - """Single and Multi-Objective Optimization Test Functions + """Single and Multi-Objective Optimization Test Functions. Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of @@ -15,9 +15,7 @@ class RSmoof(RPackage): convenient functions to generate, plot and work with objective functions.""" - homepage = "https://github.com/jakobbossek/smoof" - url = "https://cloud.r-project.org/src/contrib/smoof_1.5.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/smoof" + cran = "smoof" version('1.6.0.2', sha256='d82dba9702eade00afb84c2c12167de6cec790be7d23ac227f8fe705bdcefc93') version('1.5.1', sha256='cfb6f6460e9593351428656b225b5ba3867a216d35a05f2babdb20db6ba35306') diff --git a/var/spack/repos/builtin/packages/r-sn/package.py b/var/spack/repos/builtin/packages/r-sn/package.py index c6b9e19070..7b0a6b8372 100644 --- a/var/spack/repos/builtin/packages/r-sn/package.py +++ b/var/spack/repos/builtin/packages/r-sn/package.py @@ -7,17 +7,16 @@ from spack import * class RSn(RPackage): - """The Skew-Normal and Related Distributions Such as the Skew-t + """The Skew-Normal and Related Distributions Such as the Skew-t. - Build and manipulate probability distributions of the skew-normal - family and some related ones, notably the skew-t family, and provide - related statistical methods for data fitting and diagnostics, in the - univariate and the multivariate case.""" + Build and manipulate probability distributions of the skew-normal family + and some related ones, notably the skew-t family, and provide related + statistical methods for data fitting and diagnostics, in the univariate and + the multivariate case.""" - homepage = "https://cloud.r-project.org/package=sn" - url = "https://cloud.r-project.org/src/contrib/sn_1.5-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sn" + cran = "sn" + version('2.0.1', sha256='86b3890087657a80fca7a0a756b07410612c34a44d7a1fd7a8f24584379fa8fc') version('1.6-2', sha256='2fd4730c315efc48958b47990ddb0cbc6ce075f7a27255944a292fb4fc593d9d') version('1.5-4', sha256='46677ebc109263a68f62b5cf53ec59916cda490e5bc5bbb08276757a677f8674') version('1.5-3', sha256='cc21b97ddd674c9b1296260f2a72ffb085cdcb877c8332f0bfa96ff028517183') @@ -28,6 +27,8 @@ class RSn(RPackage): version('1.2-3', sha256='1af8ced9ed33680d731ab5132be4674d170d76c64a3059ff56c33159d8396154') depends_on('r@2.15.3:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run'), when='@2.0.1:') depends_on('r-mnormt@1.5-4:', type=('build', 'run')) + depends_on('r-mnormt@2.0.0:', type=('build', 'run'), when='@2.0.1:') depends_on('r-numderiv', type=('build', 'run')) - depends_on('r-quantreg', when='@1.6-2:', type=('build', 'run')) + depends_on('r-quantreg', type=('build', 'run'), when='@1.6-2:') diff --git a/var/spack/repos/builtin/packages/r-snakecase/package.py b/var/spack/repos/builtin/packages/r-snakecase/package.py index 6f404c2a6f..a7c59f1178 100644 --- a/var/spack/repos/builtin/packages/r-snakecase/package.py +++ b/var/spack/repos/builtin/packages/r-snakecase/package.py @@ -7,12 +7,12 @@ from spack import * class RSnakecase(RPackage): - """A consistent, flexible and easy to use tool to parse and convert strings + """Convert Strings into any Case. + + A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.""" - homepage = "https://github.com/Tazinho/snakecase" - url = "https://cloud.r-project.org/src/contrib/snakecase_0.11.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/snakecase" + cran = "snakecase" version('0.11.0', sha256='998420a58391ac85785e60bcdf6fd6927c82758ad2859a9a73a0e57299e8c1cf') diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py index 17a02046f6..00f52108f0 100644 --- a/var/spack/repos/builtin/packages/r-snow/package.py +++ b/var/spack/repos/builtin/packages/r-snow/package.py @@ -7,12 +7,13 @@ from spack import * class RSnow(RPackage): - """Support for simple parallel computing in R.""" + """Simple Network of Workstations. - homepage = "https://cloud.r-project.org/package=snow" - url = "https://cloud.r-project.org/src/contrib/snow_0.4-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/snow" + Support for simple parallel computing in R.""" + cran = "snow" + + version('0.4-4', sha256='84587f46f222a96f3e2fde10ad6ec6ddbd878f4e917cd926d632f61a87db13c9') version('0.4-3', sha256='8512537daf334ea2b8074dbb80cf5e959a403a78d68bc1e97664e8a4f64576d8') version('0.4-2', sha256='ee070187aea3607c9ca6235399b3db3e181348692405d038e962e06aefccabd7') diff --git a/var/spack/repos/builtin/packages/r-snowfall/package.py b/var/spack/repos/builtin/packages/r-snowfall/package.py index ebc4a6331d..4255cb2b75 100644 --- a/var/spack/repos/builtin/packages/r-snowfall/package.py +++ b/var/spack/repos/builtin/packages/r-snowfall/package.py @@ -7,15 +7,15 @@ from spack import * class RSnowfall(RPackage): - """Usability wrapper around snow for easier development of parallel R - programs. This package offers e.g. extended error checks, and additional - functions. All functions work in sequential mode, too, if no cluster is - present or wished. Package is also designed as connector to the cluster - management tool sfCluster, but can also used without it.""" + """Easier cluster computing (based on snow). - homepage = "https://cloud.r-project.org/package=snowfall" - url = "https://cloud.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/snowfall" + Usability wrapper around snow for easier development of parallel R + programs. This package offers e.g. extended error checks, and additional + functions. All functions work in sequential mode, too, if no cluster is + present or wished. Package is also designed as connector to the cluster + management tool sfCluster, but can also used without it.""" + + cran = "snowfall" version('1.84-6.1', sha256='5c446df3a931e522a8b138cf1fb7ca5815cc82fcf486dbac964dcbc0690e248d') diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py index 7ff1e58232..2b50810821 100644 --- a/var/spack/repos/builtin/packages/r-som/package.py +++ b/var/spack/repos/builtin/packages/r-som/package.py @@ -7,11 +7,11 @@ from spack import * class RSom(RPackage): - """Self-Organizing Map (with application in gene clustering).""" + """Self-Organizing Map. - homepage = "https://cloud.r-project.org/package=som" - url = "https://cloud.r-project.org/src/contrib/som_0.3-5.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/som" + Self-Organizing Map (with application in gene clustering).""" + + cran = "som" version('0.3-5.1', sha256='a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9') version('0.3-5', sha256='f7672afaaffcf41a8b2dd50e4c76b3a640ea2ad099f18b5dfcf00389abf6ba07') diff --git a/var/spack/repos/builtin/packages/r-sourcetools/package.py b/var/spack/repos/builtin/packages/r-sourcetools/package.py index 33584b9195..e2e4086c21 100644 --- a/var/spack/repos/builtin/packages/r-sourcetools/package.py +++ b/var/spack/repos/builtin/packages/r-sourcetools/package.py @@ -7,11 +7,13 @@ from spack import * class RSourcetools(RPackage): - """Tools for Reading, Tokenizing and Parsing R Code.""" + """Tools for Reading, Tokenizing and Parsing R Code. - homepage = "https://cloud.r-project.org/package=sourcetools" - url = "https://cloud.r-project.org/src/contrib/sourcetools_0.1.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sourcetools" + Tools for the reading and tokenization of R code. The 'sourcetools' package + provides both an R and C++ interface for the tokenization of R code, and + helpers for interacting with the tokenized representation of R code.""" + + cran = "sourcetools" version('0.1.7', sha256='47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca') version('0.1.6', sha256='c9f48d2f0b7f7ed0e7fecdf8e730b0b80c4d567f0e1e880d118b0944b1330c51') diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py index 7496bd5064..404121017f 100644 --- a/var/spack/repos/builtin/packages/r-sp/package.py +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -7,17 +7,16 @@ from spack import * class RSp(RPackage): - """Classes and Methods for Spatial Data + """Classes and Methods for Spatial Data. Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.""" - homepage = "https://github.com/edzer/sp/" - url = "https://cloud.r-project.org/src/contrib/sp_1.2-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sp" + cran = "sp" + version('1.4-6', sha256='9aebb3ef2140e8984a67eb93d72f686b8707d48d82445db0c54ae895576ba226') version('1.4-5', sha256='6beeb216d540475cdead5f2c72d6c7ee400fe2423c1882d72cf57f6df58f09da') version('1.3-1', sha256='57988b53ba8acc35f3912d62feba4b929a0f757c6b54080c623c5d805e0cb59f') version('1.2-7', sha256='6d60e03e1abd30a7d4afe547d157ce3dd7a8c166fc5e407fd6d62ae99ff30460') diff --git a/var/spack/repos/builtin/packages/r-spacetime/package.py b/var/spack/repos/builtin/packages/r-spacetime/package.py index 247bdecb75..d3b9f269c4 100644 --- a/var/spack/repos/builtin/packages/r-spacetime/package.py +++ b/var/spack/repos/builtin/packages/r-spacetime/package.py @@ -7,7 +7,7 @@ from spack import * class RSpacetime(RPackage): - """Classes and Methods for Spatio-Temporal Data + """Classes and Methods for Spatio-Temporal Data. Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility @@ -16,10 +16,10 @@ class RSpacetime(RPackage): subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.""" - homepage = "https://github.com/edzer/spacetime" - url = "https://cloud.r-project.org/src/contrib/spacetime_1.2-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spacetime" + cran = "spacetime" + version('1.2-6', sha256='8fd46606ed9589ffce19368d40004890f96e8fe77f13b546e6a2f8b9ced0dd81') + version('1.2-5', sha256='8f2acc3886780a902fb0476d6ab271e6640be1a1af4c7f9a21d8a2882fb72746') version('1.2-3', sha256='ca7c0b962d5da0741f6dd85b271d693598756e0eeeb364ada828dbb6d1b9b25b') version('1.2-2', sha256='1e9d3f92e5c4614a69c82a58bf0b5c829b4ed262bf1250bef943ae286056ea2d') diff --git a/var/spack/repos/builtin/packages/r-spades-addins/package.py b/var/spack/repos/builtin/packages/r-spades-addins/package.py index 668cc4e32e..3a1bb8b03f 100644 --- a/var/spack/repos/builtin/packages/r-spades-addins/package.py +++ b/var/spack/repos/builtin/packages/r-spades-addins/package.py @@ -7,20 +7,20 @@ from spack import * class RSpadesAddins(RPackage): - """Development Tools for 'SpaDES' and 'SpaDES' Modules + """Development Tools for 'SpaDES' and 'SpaDES' Modules. Provides 'RStudio' addins for 'SpaDES' packages and 'SpaDES' module development. See '?SpaDES.addins' for an overview of the tools provided.""" - homepage = "https://spades-addins.predictiveecology.org/" - url = "https://cloud.r-project.org/src/contrib/SpaDES.addins_0.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SpaDES.addins" + cran = "SpaDES.addins" maintainers = ['dorton21'] + version('0.1.3', sha256='b77aef21d1c725f855fe6f03456187d3c8b8070d56d80b7e6733979b644e162e') version('0.1.2', sha256='0a16bd9423797a4b4ed66a5e669cdd7f6984a3f30aa1aadc078678ee2622367c') depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@3.6:', type=('build', 'run'), when='@0.1.3:') depends_on('r-devtools', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-miniui@0.1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spades-core/package.py b/var/spack/repos/builtin/packages/r-spades-core/package.py index 08b37dd3c6..037c38f54a 100644 --- a/var/spack/repos/builtin/packages/r-spades-core/package.py +++ b/var/spack/repos/builtin/packages/r-spades-core/package.py @@ -7,30 +7,34 @@ from spack import * class RSpadesCore(RPackage): - """Utilities for Developing and Running Spatially Explicit Discrete Event Models + """Utilities for Developing and Running Spatially Explicit Discrete Event + Models. Provides the core framework for a discrete event system (DES) to implement acomplete data-to-decisions, reproducible workflow. The core DES components facilitate modularity, and easily enable the user to include additional - functionality by running user-built modules. Includes conditional scheduling, - restart after interruption, packaging of reusable modules, tools for - developing arbitrary automated workflows, automated interweaving of modules - of different temporal resolution, and tools for visualizing and understanding - the DES project.""" + functionality by running user-built modules. Includes conditional + scheduling, restart after interruption, packaging of reusable modules, + tools for developing arbitrary automated workflows, automated interweaving + of modules of different temporal resolution, and tools for visualizing and + understanding the DES project.""" - homepage = "https://spades-core.predictiveecology.org/" - url = "https://cloud.r-project.org/src/contrib/SpaDES.core_1.0.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SpaDES.core" + cran = "SpaDES.core" maintainers = ['dorton21'] + version('1.0.10', sha256='05e20f7d9aeef9ba68e50e993ef3027b8c85afc5e3f83f5ecaee9d1a7873e379') + version('1.0.9', sha256='1176a41a1af334388c1b16ff4ed9a6f30007bb5ed1fa14d798c59461042537dd') version('1.0.5', sha256='c8b18cb5f932ea57f3cb3c7f2a302cbe7e06c875da7cd3928300d6003602f0a6') depends_on('r@3.6:', type=('build', 'run')) + depends_on('r@4.0:', type=('build', 'run'), when='@1.0.10:') depends_on('r-quickplot@0.1.4:', type=('build', 'run')) depends_on('r-reproducible@1.2.1.9007:', type=('build', 'run')) + depends_on('r-reproducible@1.2.7:', type=('build', 'run'), when='@1.0.9:') depends_on('r-crayon', type=('build', 'run')) depends_on('r-data-table@1.10.4:', type=('build', 'run')) + depends_on('r-data-table@1.11.0:', type=('build', 'run'), when='@1.0.9:') depends_on('r-fastdigest', type=('build', 'run')) depends_on('r-igraph@1.0.1:', type=('build', 'run')) depends_on('r-qs@0.21.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spades-tools/package.py b/var/spack/repos/builtin/packages/r-spades-tools/package.py index b34cf46146..3b6066be59 100644 --- a/var/spack/repos/builtin/packages/r-spades-tools/package.py +++ b/var/spack/repos/builtin/packages/r-spades-tools/package.py @@ -7,23 +7,23 @@ from spack import * class RSpadesTools(RPackage): - """Tools for Spatially Explicit Discrete Event Simulation (SpaDES) Models + """Tools for Spatially Explicit Discrete Event Simulation (SpaDES) Models. - Provides GIS and map utilities, plus additional modeling tools for developing - cellular automata, dynamic raster models, and agent based models in 'SpaDES'. - Included are various methods for spatial spreading, spatial agents, GIS - operations, random map generation, and others. See '?SpaDES.tools' for an - categorized overview of these additional tools.""" + Provides GIS and map utilities, plus additional modeling tools for + developing cellular automata, dynamic raster models, and agent based models + in 'SpaDES'. Included are various methods for spatial spreading, spatial + agents, GIS operations, random map generation, and others. See + '?SpaDES.tools' for an categorized overview of these additional tools.""" - homepage = "https://spades-tools.predictiveecology.org/" - url = "https://cloud.r-project.org/src/contrib/SpaDES.tools_0.3.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SpaDES.tools" + cran = "SpaDES.tools" maintainers = ['dorton21'] + version('0.3.9', sha256='84dc47f55ded58746dcb943fde97fa4a4b852e1d2f45949ab1914cf8454e00f3') version('0.3.6', sha256='661f8ee792874e7447be78103775b63f18ec69e773a7b275dd977adb406dd3e5') depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r@3.6:', type=('build', 'run'), when='@0.3.9:') depends_on('r-backports', type=('build', 'run')) depends_on('r-checkmate@1.8.2:', type=('build', 'run')) depends_on('r-circstats@0.2-4:', type=('build', 'run')) @@ -35,5 +35,6 @@ class RSpadesTools(RPackage): depends_on('r-raster@2.5-8:', type=('build', 'run')) depends_on('r-rcpp@0.12.12:', type=('build', 'run')) depends_on('r-reproducible@0.2.0:', type=('build', 'run')) + depends_on('r-reproducible@1.2.7:', type=('build', 'run'), when='@0.3.9:') depends_on('r-rgeos', type=('build', 'run')) depends_on('r-sp@1.2-4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spades/package.py b/var/spack/repos/builtin/packages/r-spades/package.py index 1ac55dfd28..2d67db5d68 100644 --- a/var/spack/repos/builtin/packages/r-spades/package.py +++ b/var/spack/repos/builtin/packages/r-spades/package.py @@ -7,23 +7,32 @@ from spack import * class RSpades(RPackage): - """Develop and Run Spatially Explicit Discrete Event Simulation Models - - Metapackage for implementing a variety of event-based models, with a - focus on spatially explicit models. These include raster-based, - event-based, and agent-based models.""" - - homepage = "https://spades.predictiveecology.org/" - url = "https://cloud.r-project.org/src/contrib/SpaDES_2.0.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SpaDES" + """Develop and Run Spatially Explicit Discrete Event Simulation Models. + + Metapackage for implementing a variety of event-based models, with a focus + on spatially explicit models. These include raster-based, event-based, and + agent-based models. The core simulation components (provided by + 'SpaDES.core') are built upon a discrete event simulation (DES; see Matloff + (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>) framework that + facilitates modularity, and easily enables the user to include additional + functionality by running user-built simulation modules (see also + 'SpaDES.tools'). Included are numerous tools to visualize rasters and other + maps (via 'quickPlot'), and caching methods for reproducible simulations + (via 'reproducible'). Tools for running simulation experiments are provided + by 'SpaDES.experiment'. Additional functionality is provided by the + 'SpaDES.addins' and 'SpaDES.shiny' packages.""" + + cran = "SpaDES" maintainers = ['dorton21'] + version('2.0.7', sha256='5b62e9d701aa178be57f22369a5d043c9793a1bd3dcd4acac18c5a6b906ed8a0') version('2.0.6', sha256='0fa59d1737c67abeb04eae894939bc4700f92d6c2cc2ec3489b4650720ede5a3') depends_on('r@3.6:', type=('build', 'run')) depends_on('r-quickplot', type=('build', 'run')) depends_on('r-reproducible@1.2.1.9007:', type=('build', 'run')) - depends_on('r-spades-addins', type=('build', 'run')) depends_on('r-spades-core@1.0.4:', type=('build', 'run')) depends_on('r-spades-tools', type=('build', 'run')) + + depends_on('r-spades-addins', type=('build', 'run'), when='@:2.0.6') diff --git a/var/spack/repos/builtin/packages/r-spam/package.py b/var/spack/repos/builtin/packages/r-spam/package.py index fe5f113f32..1bad55a1e3 100644 --- a/var/spack/repos/builtin/packages/r-spam/package.py +++ b/var/spack/repos/builtin/packages/r-spam/package.py @@ -7,7 +7,7 @@ from spack import * class RSpam(RPackage): - """SPArse Matrix + """SPArse Matrix. Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix @@ -17,10 +17,9 @@ class RSpam(RPackage): vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.""" - homepage = "https://www.math.uzh.ch/pages/spam/" - url = "https://cloud.r-project.org/src/contrib/spam_2.3-0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spam" + cran = "spam" + version('2.8-0', sha256='d98177435b028d1c706d0197ea8132bfaffae6052c3ce6064a7f64178512d6aa') version('2.6-0', sha256='638fdd658e94f7544b46f6b6568b20a9f390bcd703aff572a3a5249fef66be5c') version('2.3-0.2', sha256='848fa95c0a71ac82af6344539af7b1c33563c687f06ead42851a68b621fff533') diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index 3fbec2c583..b9c7010be4 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -7,16 +7,15 @@ from spack import * class RSparsem(RPackage): - """Sparse Linear Algebra + """Sparse Linear Algebra. Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.""" - homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html" - url = "https://cloud.r-project.org/src/contrib/SparseM_1.74.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SparseM" + cran = "SparseM" + version('1.81', sha256='bd838f381ace680fa38508ff70b3d83cb9ffa28ac1ab568509249bca53c34b33') version('1.78', sha256='d6b79ec881a10c91cb03dc23e6e783080ded9db4f2cb723755aa0d7d29a8b432') version('1.77', sha256='a9329fef14ae4fc646df1f4f6e57efb0211811599d015f7bc04c04285495d45c') version('1.76', sha256='c2c8e44376936a5fe6f09a37f3668016e66cbc687519cc952aa346a658a2b69b') diff --git a/var/spack/repos/builtin/packages/r-spatial/package.py b/var/spack/repos/builtin/packages/r-spatial/package.py index d104a3f526..8d60671413 100644 --- a/var/spack/repos/builtin/packages/r-spatial/package.py +++ b/var/spack/repos/builtin/packages/r-spatial/package.py @@ -7,16 +7,16 @@ from spack import * class RSpatial(RPackage): - """Functions for Kriging and Point Pattern Analysis + """Functions for Kriging and Point Pattern Analysis. Functions for kriging and point pattern analysis.""" - homepage = "https://cloud.r-project.org/package=spatial" - url = "https://cloud.r-project.org/src/contrib/spatial_7.3-11.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spatial" + cran = "spatial" + version('7.3-15', sha256='e5613be94d6f5c1f54813dadc96e4a86b3417dea28106cc90cb24dfd6c3c8cef') version('7.3-12', sha256='7639039ee7407bd088e1b253376b2cb4fcdf4cc9124d6b48e4119d5cda872d63') version('7.3-11', sha256='624448d2ac22e1798097d09fc5dc4605908a33f490b8ec971fc6ea318a445c11') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r-mass', when='@:7.3-11', type=('build', 'run')) + + depends_on('r-mass', type=('build', 'run'), when='@:7.3-11') diff --git a/var/spack/repos/builtin/packages/r-spatialeco/package.py b/var/spack/repos/builtin/packages/r-spatialeco/package.py index 849bf5e792..89dd67eb61 100644 --- a/var/spack/repos/builtin/packages/r-spatialeco/package.py +++ b/var/spack/repos/builtin/packages/r-spatialeco/package.py @@ -7,7 +7,7 @@ from spack import * class RSpatialeco(RPackage): - """Spatial Analysis and Modelling Utilities + """Spatial Analysis and Modelling Utilities. Utilities to support spatial data manipulation, query, sampling and modelling. Functions include models for species population density, @@ -17,32 +17,35 @@ class RSpatialeco(RPackage): landscape metrics, auto-logistic model, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.""" - homepage = "https://cloud.r-project.org/package=spatialEco" - url = "https://cloud.r-project.org/src/contrib/spatialEco_1.3-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spatialEco" + cran = "spatialEco" + version('1.3-7', sha256='38688466d9a2a56675e2fe45cf69833a163133ad3afb6f95e9ac2e8eab221b7a') version('1.3-5', sha256='d4fb211124edf828333841c44a5af01165c53d89af460144214d81e3c13983c7') version('1.3-2', sha256='9dfa427ee8b112446b582f6739a1c40a6e3ad3d050f522082a28ce47c675e57a') version('1.3-1', sha256='ff12e26cc1bbf7934fbf712c99765d96ce6817e8055faa15a26d9ebade4bbf1c') version('1.3-0', sha256='cfa09673cb3bbed30b243082fc2d63ac09f48b9f072a18d32b95c2c29979d1d0') depends_on('r@3.6:', type=('build', 'run')) + depends_on('r@4.0:', type=('build', 'run'), when='@1.3-7:') depends_on('r-sp', type=('build', 'run')) depends_on('r-sf', type=('build', 'run')) depends_on('r-raster', type=('build', 'run')) - depends_on('r-spatstat', type=('build', 'run')) + depends_on('r-spatstat-geom', type=('build', 'run'), when='@1.3-7:') + depends_on('r-spatstat-core', type=('build', 'run'), when='@1.3-7:') depends_on('r-spdep', type=('build', 'run')) depends_on('r-rgeos', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r-dplyr', when='@:1.3-2', type=('build', 'run')) - depends_on('r-exactextractr', when='@:1.3-2', type=('build', 'run')) - depends_on('r-rcurl', when='@:1.3-2', type=('build', 'run')) - depends_on('r-rms', when='@:1.3-2', type=('build', 'run')) - depends_on('r-yaimpute', when='@:1.3-2', type=('build', 'run')) - depends_on('r-spatialpack@0.3:', when='@:1.3-2', type=('build', 'run')) - depends_on('r-mgcv', when='@:1.3-2', type=('build', 'run')) - depends_on('r-envstats', when='@:1.3-2', type=('build', 'run')) - depends_on('r-cluster', when='@:1.3-2', type=('build', 'run')) - depends_on('r-readr', when='@:1.3-2', type=('build', 'run')) - depends_on('r-rann', when='@:1.3-2', type=('build', 'run')) - depends_on('r-maptools', when='@:1.3-2', type=('build', 'run')) + + depends_on('r-dplyr', type=('build', 'run'), when='@:1.3-2') + depends_on('r-exactextractr', type=('build', 'run'), when='@:1.3-2') + depends_on('r-rcurl', type=('build', 'run'), when='@:1.3-2') + depends_on('r-rms', type=('build', 'run'), when='@:1.3-2') + depends_on('r-yaimpute', type=('build', 'run'), when='@:1.3-2') + depends_on('r-spatialpack@0.3:', type=('build', 'run'), when='@:1.3-2') + depends_on('r-mgcv', type=('build', 'run'), when='@:1.3-2') + depends_on('r-envstats', type=('build', 'run'), when='@:1.3-2') + depends_on('r-cluster', type=('build', 'run'), when='@:1.3-2') + depends_on('r-readr', type=('build', 'run'), when='@:1.3-2') + depends_on('r-rann', type=('build', 'run'), when='@:1.3-2') + depends_on('r-maptools', type=('build', 'run'), when='@:1.3-2') + depends_on('r-spatstat', type=('build', 'run'), when='@:1.3-5') diff --git a/var/spack/repos/builtin/packages/r-spatialpack/package.py b/var/spack/repos/builtin/packages/r-spatialpack/package.py index a6ff0d9247..1007dcbfa9 100644 --- a/var/spack/repos/builtin/packages/r-spatialpack/package.py +++ b/var/spack/repos/builtin/packages/r-spatialpack/package.py @@ -7,7 +7,7 @@ from spack import * class RSpatialpack(RPackage): - """Tools to assess the association between two spatial processes + """Tools to assess the association between two spatial processes. Tools to assess the association between two spatial processes. Currently, several methodologies are implemented: A modified t-test to perform @@ -17,14 +17,12 @@ class RSpatialpack(RPackage): and several others. Functions for image processing and computing the spatial association between images are also provided.""" - homepage = "https://cloud.r-project.org/package=SpatialPack" - url = "https://cloud.r-project.org/src/contrib/SpatialPack_0.3-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SpatialPack" + cran = "SpatialPack" version('0.3-8196', sha256='9027e1656db97b721a12f5eda46532c6a99b4a079299b8d12fb57d445b237b4d') version('0.3-8', sha256='a0e54b5dee3cd30a634e2d30380fe163942b672073fd909be888803332ed5151') version('0.3', sha256='4c80fc1c77bc97fc678e6e201ecf7f0f89dcf3417b3b497a28a3639e9b30bd8a') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@0.3-8196:', type=('build', 'run')) - depends_on('r-fastmatrix', when='@0.3-8196:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@0.3-8196:') + depends_on('r-fastmatrix', type=('build', 'run'), when='@0.3-8196:') diff --git a/var/spack/repos/builtin/packages/r-spatialreg/package.py b/var/spack/repos/builtin/packages/r-spatialreg/package.py index 2f926a99cf..c4c3009386 100644 --- a/var/spack/repos/builtin/packages/r-spatialreg/package.py +++ b/var/spack/repos/builtin/packages/r-spatialreg/package.py @@ -7,7 +7,7 @@ from spack import * class RSpatialreg(RPackage): - """Spatial Regression Analysis + """Spatial Regression Analysis. A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up @@ -31,16 +31,16 @@ class RSpatialreg(RPackage): through to 'spatialreg', but will mask those in 'spatialreg'. From versions 1.2-*, the functions will be made defunct in 'spdep'.""" - homepage = "https://cloud.r-project.org/package=spatialreg" - url = "https://cloud.r-project.org/src/contrib/spatialreg_1.1-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spatialreg" + cran = "spatialreg" + version('1.2-1', sha256='4c40b6b331aa8818254633cfb80d4b9a03b2b6fac2c0104b3b99201d447ba081') version('1.1-5', sha256='ddbf0773bad2e99b306116ae99a57bf29eecf723d1735820935a6fb7f331b27d') version('1.1-3', sha256='7609cdfcdfe427d2643a0db6b5360be3f6d60ede8229436ab52092d1c9cf0480') depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-spdata', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) + depends_on('r-sf', type=('build', 'run'), when='@1.2-1:') depends_on('r-spdep', type=('build', 'run')) depends_on('r-expm', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatstat-core/package.py b/var/spack/repos/builtin/packages/r-spatstat-core/package.py new file mode 100644 index 0000000000..e699eab73c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spatstat-core/package.py @@ -0,0 +1,57 @@ +# 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 RSpatstatCore(RPackage): + """Core Functionality of the 'spatstat' Family. + + Functionality for data analysis and modelling of spatial data, mainly + spatial point patterns, in the 'spatstat' family of packages. (Excludes + analysis of spatial data on a linear network, which is covered by the + separate package 'spatstat.linnet'.) Exploratory methods include quadrat + counts, K-functions and their simulation envelopes, nearest neighbour + distance and empty space statistics, Fry plots, pair correlation function, + kernel smoothed intensity, relative risk estimation with cross-validated + bandwidth selection, mark correlation functions, segregation indices, mark + dependence diagnostics, and kernel estimates of covariate effects. Formal + hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte + Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and + tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, + ANOVA) are also supported. Parametric models can be fitted to point pattern + data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). + Types of models include Poisson, Gibbs and Cox point processes, + Neyman-Scott cluster processes, and determinantal point processes. Models + may involve dependence on covariates, inter-point interaction, cluster + formation and dependence on marks. Models are fitted by maximum likelihood, + logistic regression, minimum contrast, and composite likelihood methods. A + model can be fitted to a list of point patterns (replicated point pattern + data) using the function mppm(). The model can include random effects and + fixed effects depending on the experimental design, in addition to all the + features listed above. Fitted point process models can be simulated, + automatically. Formal hypothesis tests of a fitted model are supported + (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with + basic tools for model selection (stepwise(), AIC()) and variable selection + (sdr). Tools for validating the fitted model include simulation envelopes, + residuals, residual plots and Q-Q plots, leverage and influence + diagnostics, partial residuals, and added variable plots.""" + + cran = "spatstat.core" + + version('2.3-2', sha256='7f4d6d997f9187eda71097a53917e7cbe03f8dcfb4e758d86a90fbe42c92f63c') + + depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r-spatstat-data@2.1-0:', type=('build', 'run')) + depends_on('r-spatstat-geom@2.3-0:', type=('build', 'run')) + depends_on('r-nlme', type=('build', 'run')) + depends_on('r-rpart', type=('build', 'run')) + depends_on('r-spatstat-utils@2.2-0:', type=('build', 'run')) + depends_on('r-spatstat-sparse@2.0-0:', type=('build', 'run')) + depends_on('r-mgcv', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-abind', type=('build', 'run')) + depends_on('r-tensor', type=('build', 'run')) + depends_on('r-goftest@1.2-2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatstat-data/package.py b/var/spack/repos/builtin/packages/r-spatstat-data/package.py index 44ba88d213..b9ab00c448 100644 --- a/var/spack/repos/builtin/packages/r-spatstat-data/package.py +++ b/var/spack/repos/builtin/packages/r-spatstat-data/package.py @@ -7,19 +7,19 @@ from spack import * class RSpatstatData(RPackage): - """Datasets for 'spatstat' + """Datasets for 'spatstat' Family. - Contains all the datasets for the 'spatstat' package.""" + Contains all the datasets for the 'spatstat' family of packages.""" - homepage = "https://cloud.r-project.org/package=spatstat.data" - url = "https://cloud.r-project.org/src/contrib/spatstat.data_1.4-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spatstat.data" + cran = "spatstat.data" + version('2.1-2', sha256='bbd118a8e6cd2c41abc764b9f2e798514070862f11e3f2080c27f72268271ae5') version('1.7-0', sha256='bbc192d43f2b37b308566694cb48ecdbbc4f20ef44b6fc7636564a717a03c12f') version('1.4-3', sha256='8955b6ac40cc7d0d89e02334bb46f4c223ff0755e5818f132fee753e77918ea2') version('1.4-0', sha256='121e5bb92beb7ccac920f921e760f429fd71bcfe11cb9b07a7e7326c7a72ec8c') depends_on('r@3.3:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.7-0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.7-0:') depends_on('r-spatstat-utils', type=('build', 'run')) + depends_on('r-spatstat-utils@2.1-0:', type=('build', 'run'), when='@2.1-2:') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatstat-geom/package.py b/var/spack/repos/builtin/packages/r-spatstat-geom/package.py new file mode 100644 index 0000000000..5b540b6a16 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spatstat-geom/package.py @@ -0,0 +1,35 @@ +# 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 RSpatstatGeom(RPackage): + """Geometrical Functionality of the 'spatstat' Family. + + Defines spatial data types and supports geometrical operations on them. + Data types include point patterns, windows (domains), pixel images, line + segment patterns, tessellations and hyperframes. Capabilities include + creation and manipulation of data (using command line or graphical + interaction), plotting, geometrical operations (rotation, shift, rescale, + affine transformation), convex hull, discretisation and pixellation, + Dirichlet tessellation, Delaunay triangulation, pairwise distances, + nearest-neighbour distances, distance transform, morphological operations + (erosion, dilation, closing, opening), quadrat counting, geometrical + measurement, geometrical covariance, colour maps, calculus on spatial + domains, Gaussian blur, level sets of images, transects of images, + intersections between objects, minimum distance matching. (Excludes spatial + data on a network, which are supported by the package + 'spatstat.linnet'.)""" + + cran = "spatstat.geom" + + version('2.3-1', sha256='f23e58d05a6d6bfab1345951fa528a9865f2a744e162fe4456161e1b0b5172c0') + + depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r-spatstat-data@2.0-0:', type=('build', 'run')) + depends_on('r-spatstat-utils@2.2-0:', type=('build', 'run')) + depends_on('r-deldir@1.0-2:', type=('build', 'run')) + depends_on('r-polyclip@1.10-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatstat-linnet/package.py b/var/spack/repos/builtin/packages/r-spatstat-linnet/package.py new file mode 100644 index 0000000000..4a76a1e408 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spatstat-linnet/package.py @@ -0,0 +1,50 @@ +# 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 RSpatstatLinnet(RPackage): + """Linear Networks Functionality of the 'spatstat' Family. + + Defines types of spatial data on a linear network and provides + functionality for geometrical operations, data analysis and modelling of + data on a linear network, in the 'spatstat' family of packages. Contains + definitions and support for linear networks, including creation of + networks, geometrical measurements, topological connectivity, geometrical + operations such as inserting and deleting vertices, intersecting a network + with another object, and interactive editing of networks. Data types + defined on a network include point patterns, pixel images, functions, and + tessellations. Exploratory methods include kernel estimation of intensity + on a network, K-functions and pair correlation functions on a network, + simulation envelopes, nearest neighbour distance and empty space distance, + relative risk estimation with cross-validated bandwidth selection. Formal + hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte + Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and + tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, + ANOVA) are also supported. Parametric models can be fitted to point pattern + data using the function lppm() similar to glm(). Only Poisson models are + implemented so far. Models may involve dependence on covariates and + dependence on marks. Models are fitted by maximum likelihood. Fitted point + process models can be simulated, automatically. Formal hypothesis tests of + a fitted model are supported (likelihood ratio test, analysis of deviance, + Monte Carlo tests) along with basic tools for model selection (stepwise(), + AIC()) and variable selection (sdr). Tools for validating the fitted model + include simulation envelopes, residuals, residual plots and Q-Q plots, + leverage and influence diagnostics, partial residuals, and added variable + plots. Random point patterns on a network can be generated using a variety + of models.""" + + cran = "spatstat.linnet" + + version('2.3-1', sha256='119ba6e3da651aa9594f70a7a35349209534215aa640c2653aeddc6aa25038c3') + + depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r-spatstat-data@2.1-0:', type=('build', 'run')) + depends_on('r-spatstat-geom@2.3-0:', type=('build', 'run')) + depends_on('r-spatstat-core@2.3-0:', type=('build', 'run')) + depends_on('r-spatstat-utils@2.2-0:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-spatstat-sparse@2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatstat-sparse/package.py b/var/spack/repos/builtin/packages/r-spatstat-sparse/package.py new file mode 100644 index 0000000000..1fd525ef3a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spatstat-sparse/package.py @@ -0,0 +1,24 @@ +# 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 RSpatstatSparse(RPackage): + """Sparse Three-Dimensional Arrays and Linear Algebra Utilities. + + Defines sparse three-dimensional arrays and supports standard operations on + them. The package also includes utility functions for matrix calculations + that are common in statistics, such as quadratic forms.""" + + cran = "spatstat.sparse" + + version('2.1-0', sha256='0019214418668cba9f01ee5901ed7f4dba9cfee5ff62d5c7e1c914adfbea0e91') + + depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-abind', type=('build', 'run')) + depends_on('r-tensor', type=('build', 'run')) + depends_on('r-spatstat-utils@2.1-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatstat-utils/package.py b/var/spack/repos/builtin/packages/r-spatstat-utils/package.py index c8042473c3..3e0ed0e1c7 100644 --- a/var/spack/repos/builtin/packages/r-spatstat-utils/package.py +++ b/var/spack/repos/builtin/packages/r-spatstat-utils/package.py @@ -7,15 +7,14 @@ from spack import * class RSpatstatUtils(RPackage): - """Utility Functions for 'spatstat' + """Utility Functions for 'spatstat'. Contains utility functions for the 'spatstat' package which may also be useful for other purposes.""" - homepage = "https://cloud.r-project.org/package=spatstat.utils" - url = "https://cloud.r-project.org/src/contrib/spatstat.utils_1.17-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spatstat.utils" + cran = "spatstat.utils" + version('2.3-0', sha256='5f096ce5a201482d61e6d6859be7d40a55705ba5c6ebadd4875367ef9cb0db1a') version('1.20-2', sha256='62c2413f989965a9fa6395742a605004b736a27c24304e6ffaebf2134019ce18') version('1.17-0', sha256='39cd683ed7f41d8adc9e28af073d91b244aa1cf5ad966dfbb396ee3ee79f0922') version('1.15-0', sha256='90e07d730b6939f47f93c939afae10874b2c82bd402960ede4133de67dca2a0c') diff --git a/var/spack/repos/builtin/packages/r-spatstat/package.py b/var/spack/repos/builtin/packages/r-spatstat/package.py index a636985163..eeb31eebf8 100644 --- a/var/spack/repos/builtin/packages/r-spatstat/package.py +++ b/var/spack/repos/builtin/packages/r-spatstat/package.py @@ -7,26 +7,67 @@ from spack import * class RSpatstat(RPackage): - """Comprehensive open-source toolbox for - analysing Spatial Point Patterns. - """ + """Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests. - homepage = "https://cloud.r-project.org/package=spatstat" - url = "https://cloud.r-project.org/src/contrib/spatstat_1.64-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spatstat" + Comprehensive open-source toolbox for analysing Spatial Point Patterns. + Focused mainly on two-dimensional point patterns, including + multitype/marked points, in any spatial region. Also supports + three-dimensional point patterns, space-time point patterns in any number + of dimensions, point patterns on a linear network, and patterns of other + geometrical objects. Supports spatial covariate data such as pixel images. + Contains over 2000 functions for plotting spatial data, exploratory data + analysis, model-fitting, simulation, spatial sampling, model diagnostics, + and formal inference. Data types include point patterns, line segment + patterns, spatial windows, pixel images, tessellations, and linear + networks. Exploratory methods include quadrat counts, K-functions and their + simulation envelopes, nearest neighbour distance and empty space + statistics, Fry plots, pair correlation function, kernel smoothed + intensity, relative risk estimation with cross-validated bandwidth + selection, mark correlation functions, segregation indices, mark dependence + diagnostics, and kernel estimates of covariate effects. Formal hypothesis + tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, + Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests + for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) + are also supported. Parametric models can be fitted to point pattern data + using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types + of models include Poisson, Gibbs and Cox point processes, Neyman-Scott + cluster processes, and determinantal point processes. Models may involve + dependence on covariates, inter-point interaction, cluster formation and + dependence on marks. Models are fitted by maximum likelihood, logistic + regression, minimum contrast, and composite likelihood methods. A model can + be fitted to a list of point patterns (replicated point pattern data) using + the function mppm(). The model can include random effects and fixed effects + depending on the experimental design, in addition to all the features + listed above. Fitted point process models can be simulated, automatically. + Formal hypothesis tests of a fitted model are supported (likelihood ratio + test, analysis of deviance, Monte Carlo tests) along with basic tools for + model selection (stepwise(), AIC()) and variable selection (sdr). Tools for + validating the fitted model include simulation envelopes, residuals, + residual plots and Q-Q plots, leverage and influence diagnostics, partial + residuals, and added variable plots.""" + cran = "spatstat" + + version('2.3-0', sha256='da02443722f2c7ef9d59a2799b7b8002c94cecf73f2b0d2b29280d39f49c4c06') version('1.64-1', sha256='ca3fc7d0d6b7a83fd045a7502bf03c6871fa1ab2cf411647c438fd99b4eb551a') version('1.63-3', sha256='07b4a1a1b37c91944f31779dd789598f4a5ad047a3de3e9ec2ca99b9e9565528') depends_on('r@3.3:', type=('build', 'run')) - depends_on('r-rpart', type=('build', 'run')) - depends_on('r-nlme', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@2.3-0:') depends_on('r-spatstat-data@1.4-2:', type=('build', 'run')) + depends_on('r-spatstat-data@2.1-0:', type=('build', 'run'), when='@2.3-0:') + depends_on('r-spatstat-geom@2.3-0:', type=('build', 'run'), when='@2.3-0:') + depends_on('r-spatstat-core@2.3-0:', type=('build', 'run'), when='@2.3-0:') + depends_on('r-spatstat-linnet@2.3-0:', type=('build', 'run'), when='@2.3-0:') depends_on('r-spatstat-utils@1.17:', type=('build', 'run')) - depends_on('r-mgcv', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-deldir@0.0-21:', type=('build', 'run')) - depends_on('r-abind', type=('build', 'run')) - depends_on('r-tensor', type=('build', 'run')) - depends_on('r-polyclip@1.10:', type=('build', 'run')) - depends_on('r-goftest@1.2-2:', type=('build', 'run')) + depends_on('r-spatstat-utils@2.2-0:', type=('build', 'run'), when='@2.3-0:') + + depends_on('r-rpart', type=('build', 'run'), when='@:1.64-1') + depends_on('r-nlme', type=('build', 'run'), when='@:1.64-1') + depends_on('r-mgcv', type=('build', 'run'), when='@:1.64-1') + depends_on('r-matrix', type=('build', 'run'), when='@:1.64-1') + depends_on('r-deldir@0.0-21:', type=('build', 'run'), when='@:1.64-1') + depends_on('r-abind', type=('build', 'run'), when='@:1.64-1') + depends_on('r-tensor', type=('build', 'run'), when='@:1.64-1') + depends_on('r-polyclip@1.10:', type=('build', 'run'), when='@:1.64-1') + depends_on('r-goftest@1.2-2:', type=('build', 'run'), when='@:1.64-1') diff --git a/var/spack/repos/builtin/packages/r-spdata/package.py b/var/spack/repos/builtin/packages/r-spdata/package.py index 179a28b1dd..cb12570d1e 100644 --- a/var/spack/repos/builtin/packages/r-spdata/package.py +++ b/var/spack/repos/builtin/packages/r-spdata/package.py @@ -7,7 +7,7 @@ from spack import * class RSpdata(RPackage): - """Datasets for Spatial Analysis + """Datasets for Spatial Analysis. Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class sf (defined by the @@ -18,13 +18,12 @@ class RSpdata(RPackage): analysis techniques. cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.""" - homepage = "https://github.com/Nowosad/spData" - url = "https://cloud.r-project.org/src/contrib/spData_0.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spData" + cran = "spData" + version('2.0.1', sha256='c635a3e2e5123b4cdb2e6877b9b09e3d50169e1512a53b2ba2db7fbe63b990fc') version('0.3.8', sha256='7a61268db4fdbfb004b77d36e953cbb3fdfdac7e8bb6c500628ec6c592c79ad6') version('0.3.0', sha256='de24ea659541a6c795cd26a1f6a213e15061af9c97a24cba1c24ce30c6c24c98') depends_on('r@3.3.0:', type=('build', 'run')) - depends_on('r-sp', when='@0.3.8:', type=('build', 'run')) - depends_on('r-raster', when='@0.3.8:', type=('build', 'run')) + depends_on('r-sp', type=('build', 'run'), when='@0.3.8:') + depends_on('r-raster', type=('build', 'run'), when='@0.3.8:') diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py index 14e1373776..576e31422d 100644 --- a/var/spack/repos/builtin/packages/r-spdep/package.py +++ b/var/spack/repos/builtin/packages/r-spdep/package.py @@ -7,7 +7,7 @@ from spack import * class RSpdep(RPackage): - """Spatial Dependence: Weighting Schemes, Statistics + """Spatial Dependence: Weighting Schemes, Statistics. A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, @@ -19,26 +19,30 @@ class RSpdep(RPackage): statistic, Empirical Bayes estimates and 'Assuncao/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO""" - homepage = "https://r-forge.r-project.org/projects/spdep" - url = "https://cloud.r-project.org/src/contrib/spdep_0.6-13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/spdep" + cran = "spdep" + version('1.2-2', sha256='94f46f98be3bedde1655f8768b7ef2a977c399b5ca8977c68007e9e3b7515e23') + version('1.2-1', sha256='e8cc788d4e6fbb962f4e1fb45dff166cd9dd0935a9fd502699f9a95fdf4a43f9') version('1.1-5', sha256='47cb46cf5cf1f4386eb1b5e4d8541d577d7f2939e74addbdb884ecf2323f6d5d') version('1.1-2', sha256='ba0ca3a0ad6b9cc1dc46cadd9e79259949ad38c88f738e98e482d6c06640b31a') version('1.0-2', sha256='6f9efa4347d5c13b49922b75481ac403431c3c76a65a109af29954aa7bb138b2') version('0.6-13', sha256='ed345f4c7ea7ba064b187eb6b25f0ac46f17616f3b56ab89978935cdc67df1c4') - depends_on('r@3.0.0:', when='@:0.7-7', type=('build', 'run')) - depends_on('r@3.3.0:', when='@0.7-8:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.7-8:') depends_on('r-sp@1.0:', type=('build', 'run')) - depends_on('r-spdata@0.2.6.0:', when='@1.0-2:', type=('build', 'run')) - depends_on('r-sf', when='@1.0-2:', type=('build', 'run')) + depends_on('r-spdata@0.2.6.0:', type=('build', 'run'), when='@1.0-2:') + depends_on('r-sf', type=('build', 'run'), when='@1.0-2:') depends_on('r-deldir', type=('build', 'run')) depends_on('r-boot@1.3-1:', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-learnbayes', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) - depends_on('r-coda', type=('build', 'run')) - depends_on('r-expm', type=('build', 'run')) - depends_on('r-gmodels', type=('build', 'run')) - depends_on('r-nlme', type=('build', 'run')) + depends_on('r-units', type=('build', 'run'), when='@1.2-1:') + depends_on('r-s2', type=('build', 'run'), when='@1.2-1:') + depends_on('r-e1071', type=('build', 'run'), when='@1.2-1:') + + depends_on('r-matrix', type=('build', 'run'), when='@:1.1-5') + depends_on('r-learnbayes', type=('build', 'run'), when='@:1.1-5') + depends_on('r-mass', type=('build', 'run'), when='@:1.1-5') + depends_on('r-coda', type=('build', 'run'), when='@:1.1-5') + depends_on('r-expm', type=('build', 'run'), when='@:1.1-5') + depends_on('r-gmodels', type=('build', 'run'), when='@:1.1-5') + depends_on('r-nlme', type=('build', 'run'), when='@:1.1-5') diff --git a/var/spack/repos/builtin/packages/r-speedglm/package.py b/var/spack/repos/builtin/packages/r-speedglm/package.py index c4fe5ecb37..bc34f898b3 100644 --- a/var/spack/repos/builtin/packages/r-speedglm/package.py +++ b/var/spack/repos/builtin/packages/r-speedglm/package.py @@ -7,14 +7,12 @@ from spack import * class RSpeedglm(RPackage): - """Fitting Linear and Generalized Linear Models to Large Data Sets + """Fitting Linear and Generalized Linear Models to Large Data Sets. - Fitting linear models and generalized linear models to - large data sets by updating algorithms.""" + Fitting linear models and generalized linear models to large data sets by + updating algorithms.""" - homepage = "https://cloud.r-project.org/package=speedglm" - url = "https://cloud.r-project.org/src/contrib/speedglm_0.3-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/speedglm" + cran = "speedglm" version('0.3-3', sha256='d065d0ee42fb772760fca8d97ad2aa56cd76b1d9ecb4e97478ec362429e16738') version('0.3-2', sha256='5fcaf18324dc754152f528a44894944063303f780d33e58569ea7c306bfc45ac') diff --git a/var/spack/repos/builtin/packages/r-splancs/package.py b/var/spack/repos/builtin/packages/r-splancs/package.py index fe451b9bc6..f82da03d8f 100644 --- a/var/spack/repos/builtin/packages/r-splancs/package.py +++ b/var/spack/repos/builtin/packages/r-splancs/package.py @@ -7,12 +7,15 @@ from spack import * class RSplancs(RPackage): - """Spatial and Space-Time Point Pattern Analysis""" + """Spatial and Space-Time Point Pattern Analysis. - homepage = "https://cloud.r-project.org/package=splancs" - url = "https://cloud.r-project.org/src/contrib/splancs_2.01-40.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/splancs" + The Splancs package was written as an enhancement to S-Plus for display and + analysis of spatial point pattern data; it has been ported to R and is in + "maintenance mode".""" + cran = "splancs" + + version('2.01-42', sha256='8c0af4764521e20b629dba6afd5c284e7be48786f378c37668eacfa26d2ef0aa') version('2.01-40', sha256='79744381ebc4a361740a36dca3c9fca9ae015cfe0bd585b7856a664a3da74363') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-splitstackshape/package.py b/var/spack/repos/builtin/packages/r-splitstackshape/package.py index c6a344d96c..c2870d283e 100644 --- a/var/spack/repos/builtin/packages/r-splitstackshape/package.py +++ b/var/spack/repos/builtin/packages/r-splitstackshape/package.py @@ -11,16 +11,13 @@ class RSplitstackshape(RPackage): Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The - concat.split (cSplit) family of functions splits such data into - separate cells. The package also includes functions to stack groups - of columns and to reshape wide data, even when the data are - "unbalanced" something which reshape (from base R) does not handle, - and which melt and dcast from reshape2 do not easily handle. - """ + concat.split (cSplit) family of functions splits such data into separate + cells. The package also includes functions to stack groups of columns and + to reshape wide data, even when the data are "unbalanced" something which + reshape (from base R) does not handle, and which melt and dcast from + reshape2 do not easily handle.""" - homepage = "https://github.com/mrdwab/splitstackshape" - url = "https://cloud.r-project.org/src/contrib/splitstackshape_1.4.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/splitstackshape" + cran = "splitstackshape" version('1.4.8', sha256='656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56') version('1.4.6', sha256='b9888f9508babdb8e09f57674facaa8b158a06255ef1e61c8df813f58881860f') diff --git a/var/spack/repos/builtin/packages/r-sqldf/package.py b/var/spack/repos/builtin/packages/r-sqldf/package.py index b9f2535448..ba15a96c86 100644 --- a/var/spack/repos/builtin/packages/r-sqldf/package.py +++ b/var/spack/repos/builtin/packages/r-sqldf/package.py @@ -7,20 +7,19 @@ from spack import * class RSqldf(RPackage): - """The sqldf() function is typically passed a single argument - which is an SQL select statement where the table names are - ordinary R data frame names. sqldf() transparently sets up a - database, imports the data frames into that database, performs the - SQL select or other statement and returns the result using a - heuristic to determine which class to assign to each column of the - returned data frame. The sqldf() or read.csv.sql() functions can - also be used to read filtered files into R even if the original - files are larger than R itself can handle. 'RSQLite', 'RH2', - 'RMySQL' and 'RPostgreSQL' backends are supported.""" + """Manipulate R Data Frames Using SQL. - homepage = "https://cloud.r-project.org/package=sqldf" - url = "https://cloud.r-project.org/src/contrib/sqldf_0.4-11.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sqldf" + The sqldf() function is typically passed a single argument which is an SQL + select statement where the table names are ordinary R data frame names. + sqldf() transparently sets up a database, imports the data frames into that + database, performs the SQL select or other statement and returns the result + using a heuristic to determine which class to assign to each column of the + returned data frame. The sqldf() or read.csv.sql() functions can also be + used to read filtered files into R even if the original files are larger + than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' + backends are supported.""" + + cran = "sqldf" version('0.4-11', sha256='cee979d4e8c67b4924655365d925a8d67104e62adf71741f645cdc5196de2260') diff --git a/var/spack/repos/builtin/packages/r-squarem/package.py b/var/spack/repos/builtin/packages/r-squarem/package.py index 5213d0e0a7..fac73c2342 100644 --- a/var/spack/repos/builtin/packages/r-squarem/package.py +++ b/var/spack/repos/builtin/packages/r-squarem/package.py @@ -7,7 +7,8 @@ from spack import * class RSquarem(RPackage): - """Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms + """Squared Extrapolation Methods for Accelerating EM-Like Monotone + Algorithms. Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used @@ -17,9 +18,7 @@ class RSquarem(RPackage): vignette("SQUAREM"). Refer to the J Stat Software article: <doi:10.18637/jss.v092.i07>.""" - homepage = "https://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html" - url = "https://cloud.r-project.org/src/contrib/SQUAREM_2017.10-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SQUAREM" + cran = "SQUAREM" version('2021.1', sha256='66e5e18ca29903e4950750bbd810f0f9df85811ee4195ce0a86d939ba8183a58') version('2017.10-1', sha256='9b89905b436f1cf3faa9e3dabc585a76299e729e85ca659bfddb4b7cba11b283') diff --git a/var/spack/repos/builtin/packages/r-squash/package.py b/var/spack/repos/builtin/packages/r-squash/package.py index eba0ad5f09..311ae25cdf 100644 --- a/var/spack/repos/builtin/packages/r-squash/package.py +++ b/var/spack/repos/builtin/packages/r-squash/package.py @@ -7,7 +7,7 @@ from spack import * class RSquash(RPackage): - """Color-Based Plots for Multivariate Visualization + """Color-Based Plots for Multivariate Visualization. Functions for color-based visualization of multivariate data, i.e. colorgrams or heatmaps. Lower-level functions map numeric values to colors, @@ -15,9 +15,7 @@ class RSquash(RPackage): plotting functions generate a bivariate histogram, a dendrogram aligned with a color-coded matrix, a triangular distance matrix, and more.""" - homepage = "https://cloud.r-project.org/package=squash" - url = "https://cloud.r-project.org/src/contrib/squash_1.0.8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/squash" + cran = "squash" version('1.0.9', sha256='ff381c85071e3407574e3db28d789657f64e7d3f9d74ac123539de22ab8ac6f4') version('1.0.8', sha256='e6932c0a461d5c85f7180a31d18a3eb4f28afd6769efe251075a4de12de039f4') diff --git a/var/spack/repos/builtin/packages/r-stabledist/package.py b/var/spack/repos/builtin/packages/r-stabledist/package.py index c7a5e1c004..07b03af3e7 100644 --- a/var/spack/repos/builtin/packages/r-stabledist/package.py +++ b/var/spack/repos/builtin/packages/r-stabledist/package.py @@ -7,13 +7,12 @@ from spack import * class RStabledist(RPackage): - """Density, Probability and Quantile functions, and random number - generation for (skew) stable distributions, using the parametrizations of - Nolan.""" + """Stable Distribution Functions. - homepage = "https://www.rmetrics.org/" - url = "https://cloud.r-project.org/src/contrib/stabledist_0.7-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/stabledist" + Density, Probability and Quantile functions, and random number generation + for (skew) stable distributions, using the parametrizations of Nolan.""" + + cran = "stabledist" version('0.7-1', sha256='06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69') diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py index 4632832ad9..9e0f09531b 100644 --- a/var/spack/repos/builtin/packages/r-stanheaders/package.py +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -7,10 +7,10 @@ from spack import * class RStanheaders(RPackage): - """C++ Header Files for Stan + """C++ Header Files for Stan. - The C++ header files of the Stan project are provided by this package, - but it contains no R code, vignettes, or function documentation. There is a + The C++ header files of the Stan project are provided by this package, but + it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to @@ -25,9 +25,7 @@ class RStanheaders(RPackage): 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.""" - homepage = "https://mc-stan.org/" - url = "https://cloud.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/StanHeaders" + cran = "StanHeaders" version('2.21.0-7', sha256='27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b') version('2.21.0-6', sha256='a0282a054d0e6ab310ec7edcffa953b77c7e4a858d9ac7028aab1b4fb4ce8cf3') @@ -37,7 +35,7 @@ class RStanheaders(RPackage): version('2.10.0-2', sha256='ce4e335172bc65da874699302f6ba5466cdbcf69458c11954c0f131fc78b59b7') depends_on('r+X', type=('build', 'run')) - depends_on('r@3.4.0:', when='@2.18.0:', type=('build', 'run')) - depends_on('r-rcppparallel@5.0.1:', when='@2.21.0:', type=('build', 'run')) - depends_on('r-rcppeigen', when='@2.21.0:', type=('build', 'run')) + depends_on('r@3.4.0:', type=('build', 'run'), when='@2.18.0:') + depends_on('r-rcppparallel@5.0.1:', type=('build', 'run'), when='@2.21.0:') + depends_on('r-rcppeigen', type=('build', 'run'), when='@2.21.0:') depends_on('pandoc', type='build') diff --git a/var/spack/repos/builtin/packages/r-stargazer/package.py b/var/spack/repos/builtin/packages/r-stargazer/package.py index 15e1ae1c53..9806d460e2 100644 --- a/var/spack/repos/builtin/packages/r-stargazer/package.py +++ b/var/spack/repos/builtin/packages/r-stargazer/package.py @@ -7,10 +7,12 @@ from spack import * class RStargazer(RPackage): - """stargazer: Well-Formatted Regression and Summary Statistics Tables""" + """Well-Formatted Regression and Summary Statistics Tables. - homepage = "https://cloud.r-project.org/package=stargazer" - url = "https://cloud.r-project.org/src/contrib/stargazer_5.2.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/stargazer" + Produces LaTeX code, HTML/CSS code and ASCII text for well-formatted tables + that hold regression analysis results from several models side-by-side, as + well as summary statistics.""" + + cran = "stargazer" version('5.2.2', sha256='70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de') diff --git a/var/spack/repos/builtin/packages/r-statmod/package.py b/var/spack/repos/builtin/packages/r-statmod/package.py index d6f1e6711e..6f8bbd85c7 100644 --- a/var/spack/repos/builtin/packages/r-statmod/package.py +++ b/var/spack/repos/builtin/packages/r-statmod/package.py @@ -7,7 +7,7 @@ from spack import * class RStatmod(RPackage): - """Statistical Modeling + """Statistical Modeling. A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, @@ -17,10 +17,9 @@ class RStatmod(RPackage): model functions including Tweedie and Digamma distributional families and a secure convergence algorithm.""" - homepage = "https://cloud.r-project.org/package=statmod" - url = "https://cloud.r-project.org/src/contrib/statmod_1.4.30.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/statmod" + cran = "statmod" + version('1.4.36', sha256='14e897c83d426caca4d920d3d5bead7ae9a679276b3cb2e227f299ad189d7bc2') version('1.4.35', sha256='de5e428f81c306849af47b9ae583362855e166b1da62893734f1154cb5b3f8fe') version('1.4.32', sha256='2f67a1cfa66126e6345f8a40564a3077d08f1748f17cb8c8fb05c94ed0f57e20') version('1.4.30', sha256='9d2c1722a85f53623a9ee9f73d835119ae22ae2b8ec7b50d675401e314ea641f') diff --git a/var/spack/repos/builtin/packages/r-statnet-common/package.py b/var/spack/repos/builtin/packages/r-statnet-common/package.py index f77a79c26a..108a571c11 100644 --- a/var/spack/repos/builtin/packages/r-statnet-common/package.py +++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py @@ -7,20 +7,20 @@ from spack import * class RStatnetCommon(RPackage): - """Common R Scripts and Utilities Used by the Statnet Project Software + """Common R Scripts and Utilities Used by the Statnet Project Software. Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.""" - homepage = "https://www.statnet.org" - url = "https://cloud.r-project.org/src/contrib/statnet.common_3.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/statnet.common" + cran = "statnet.common" + version('4.5.0', sha256='3cdb23db86f3080462f15e29bcf3e941590bc17ea719993b301199b22d6f882f') version('4.4.1', sha256='4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd') version('4.3.0', sha256='834a3359eac967df0420eee416ae4983e3b502a3de56bb24f494a7ca4104e959') version('4.2.0', sha256='1176c3303436ebe858d02979cf0a0c33e4e2d1f3637516b4761d573ccd132461') version('3.3.0', sha256='d714c4e7b0cbf71b7a628af443f5be530e74ad1e21f6b04f1b1087f6d7e40fa4') - depends_on('r@3.5:', when='@4.2.0:', type=('build', 'run')) - depends_on('r-coda', when='@4.1.2:', type=('build', 'run')) - depends_on('r-rle', when='@4.4.1:', type=('build', 'run')) + depends_on('r@3.5:', type=('build', 'run'), when='@4.2.0:') + depends_on('r-coda', type=('build', 'run'), when='@4.1.2:') + + depends_on('r-rle', type=('build', 'run'), when='@4.4.1') diff --git a/var/spack/repos/builtin/packages/r-stringfish/package.py b/var/spack/repos/builtin/packages/r-stringfish/package.py index 4b9f4dc41c..df8f03e61a 100644 --- a/var/spack/repos/builtin/packages/r-stringfish/package.py +++ b/var/spack/repos/builtin/packages/r-stringfish/package.py @@ -7,20 +7,20 @@ from spack import * class RStringfish(RPackage): - """Alt String Implementation + """Alt String Implementation. Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.""" - homepage = "https://github.com/traversc/stringfish" - url = "https://cloud.r-project.org/src/contrib/stringfish_0.14.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/stringfish" + cran = "stringfish" maintainers = ['dorton21'] + version('0.15.5', sha256='9df21146a7710e5a9ab4bb53ebc231a580c798b7e541b8d78df53207283f8129') version('0.14.2', sha256='9373cfc715cda1527fd20179435977b8e59e19d8c5ef82a31e519f93fb624ced') - depends_on('gmake', type='build') depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run'), when='@0.15.5:') depends_on('r-rcpp@0.12.18.3:', type=('build', 'run')) depends_on('r-rcppparallel', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index 9435431aae..f8de74aa61 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -7,7 +7,7 @@ from spack import * class RStringi(RPackage): - """Character String Processing Facilities + """Character String Processing Facilities. A multitude of character string/text/natural language processing tools: pattern searching (e.g., with 'Java'-like regular expressions or the @@ -18,9 +18,9 @@ class RStringi(RPackage): (International Components for Unicode) library - portable across all locales and platforms.""" - homepage = "https://stringi.gagolewski.com/" - cran = "stringi" + cran = "stringi" + version('1.7.6', sha256='0ea3d5afec5701977ff53de9afbaceb53b00aa34f5fb641cadc1eeb7759119ec') version('1.6.2', sha256='3a151dd9b982696370ac8df3920afe462f8abbd4e41b479ff8b66cfd7b602dae') version('1.5.3', sha256='224f1e8dedc962a676bc2e1f53016f6a129a0a38aa0f35daf6dece62ff714010') version('1.4.3', sha256='13cecb396b700f81af38746e97b550a1d9fda377ca70c78f6cdfc770d33379ed') @@ -30,8 +30,8 @@ class RStringi(RPackage): version('1.1.2', sha256='e50b7162ceb7ebae403475f6f8a76a39532a2abc82112db88661f48aa4b9218e') version('1.1.1', sha256='243178a138fe68c86384feb85ead8eb605e8230113d638da5650bca01e24e165') - depends_on('r@2.14:', when='@:1.5.3', type=('build', 'run')) - depends_on('r@3.1:', when='@1.6.1:', type=('build', 'run')) + depends_on('r@2.14:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run'), when='@1.6.1:') depends_on('icu4c@52:') depends_on('icu4c@55:', when='@1.5.3:') # since version 1.6.1 there is also a SystemRequirement on C++11 diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index de692e153a..84c116b4f1 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -7,15 +7,15 @@ from spack import * class RStringr(RPackage): - """A consistent, simple and easy to use set of wrappers around the - fantastic 'stringi' package. All function and argument names (and - positions) are consistent, all functions deal with "NA"'s and zero length - vectors in the same way, and the output from one function is easy to feed - into the input of another.""" + """Simple, Consistent Wrappers for Common String Operations. - homepage = "https://cloud.r-project.org/package=stringr" - url = "https://cloud.r-project.org/src/contrib/stringr_1.1.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/stringr" + A consistent, simple and easy to use set of wrappers around the fantastic + 'stringi' package. All function and argument names (and positions) are + consistent, all functions deal with "NA"'s and zero length vectors in the + same way, and the output from one function is easy to feed into the input + of another.""" + + cran = "stringr" version('1.4.0', sha256='87604d2d3a9ad8fd68444ce0865b59e2ffbdb548a38d6634796bbd83eeb931dd') version('1.3.1', sha256='7a8b8ea038e45978bd797419b16793f44f10c5355ad4c64b74d15276fef20343') @@ -26,4 +26,4 @@ class RStringr(RPackage): depends_on('r@3.1:', type=('build', 'run')) depends_on('r-stringi@1.1.7:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-glue@1.2.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-glue@1.2.0:', type=('build', 'run'), when='@1.3.0:') diff --git a/var/spack/repos/builtin/packages/r-strucchange/package.py b/var/spack/repos/builtin/packages/r-strucchange/package.py index cac957af57..cb3962901c 100644 --- a/var/spack/repos/builtin/packages/r-strucchange/package.py +++ b/var/spack/repos/builtin/packages/r-strucchange/package.py @@ -7,7 +7,7 @@ from spack import * class RStrucchange(RPackage): - """Testing, Monitoring, and Dating Structural Changes + """Testing, Monitoring, and Dating Structural Changes. Testing, monitoring and dating structural changes in (linear) regression models. strucchange features tests/methods from the generalized fluctuation @@ -19,9 +19,7 @@ class RStrucchange(RPackage): be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.""" - homepage = "https://cloud.r-project.org/package=strucchange" - url = "https://cloud.r-project.org/src/contrib/strucchange_1.5-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/strucchange" + cran = "strucchange" version('1.5-2', sha256='7d247c5ae6f5a63c80e478799d009c57fb8803943aa4286d05f71235cc1002f8') version('1.5-1', sha256='740e2e20477b9fceeef767ae1002adc5ec397cb0f7daba5289a2c23b0dddaf31') diff --git a/var/spack/repos/builtin/packages/r-strucchangercpp/package.py b/var/spack/repos/builtin/packages/r-strucchangercpp/package.py new file mode 100644 index 0000000000..b66777a8c0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-strucchangercpp/package.py @@ -0,0 +1,31 @@ +# 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 RStrucchangercpp(RPackage): + """Testing, Monitoring, and Dating Structural Changes: C++ Version. + + A fast implementation with additional experimental features for testing, + monitoring and dating structural changes in (linear) regression models. + 'strucchangeRcpp' features tests/methods from the generalized fluctuation test + framework as well as from the F test (Chow test) framework. This includes + methods to fit, plot and test fluctuation processes (e.g. cumulative/moving + sum, recursive/moving estimates) and F statistics, respectively. These methods + are described in Zeileis et al. (2002) <doi:10.18637/jss.v007.i02>. Finally, + the breakpoints in regression models with structural changes can be estimated + together with confidence intervals, and their magnitude as well as the model + fit can be evaluated using a variety of statistical measures.""" + + cran = "strucchangeRcpp" + + version('1.5-3-1.0.4', sha256='f506fcb593ce4bacf1892de25154257d0fe02260ef956a75438c6330195cd86d') + + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-zoo', type=('build', 'run')) + depends_on('r-sandwich', type=('build', 'run')) + depends_on('r-rcpp@0.12.7:', type=('build', 'run')) + depends_on('r-rcpparmadillo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-styler/package.py b/var/spack/repos/builtin/packages/r-styler/package.py index 30db161bb1..60f6bf58c1 100644 --- a/var/spack/repos/builtin/packages/r-styler/package.py +++ b/var/spack/repos/builtin/packages/r-styler/package.py @@ -7,19 +7,23 @@ from spack import * class RStyler(RPackage): - """styler: Non-Invasive Pretty Printing of R Code""" + """Non-Invasive Pretty Printing of R Code. - homepage = "https://cloud.r-project.org/package=styler" - url = "https://cloud.r-project.org/src/contrib/styler_1.3.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/styler" + Pretty-prints R code without changing the user's formatting intent.""" + cran = "styler" + + version('1.6.2', sha256='a62fcc76aac851069f33874f9eaabdd580973b619cfc625d6ec910476015f75c') version('1.3.2', sha256='3fcf574382c607c2147479bad4f9fa8b823f54fb1462d19ec4a330e135a44ff1') depends_on('r-backports@1.1.0:', type=('build', 'run')) depends_on('r-cli@1.1.0:', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run'), when='@1.6.2:') depends_on('r-magrittr@1.0.1:', type=('build', 'run')) + depends_on('r-magrittr@2.0.0:', type=('build', 'run'), when='@1.6.2:') depends_on('r-purrr@0.2.3:', type=('build', 'run')) depends_on('r-r-cache@0.14.0:', type=('build', 'run')) + depends_on('r-r-cache@0.15.0:', type=('build', 'run'), when='@1.6.2:') depends_on('r-rematch2@2.0.1:', type=('build', 'run')) depends_on('r-rlang@0.1.1:', type=('build', 'run')) depends_on('r-rprojroot@1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-subplex/package.py b/var/spack/repos/builtin/packages/r-subplex/package.py index 7733c71587..5954badca0 100644 --- a/var/spack/repos/builtin/packages/r-subplex/package.py +++ b/var/spack/repos/builtin/packages/r-subplex/package.py @@ -7,15 +7,14 @@ from spack import * class RSubplex(RPackage): - """Unconstrained Optimization using the Subplex Algorithm + """Unconstrained Optimization using the Subplex Algorithm. The subplex algorithm for unconstrained optimization, developed by Tom Rowan <https://www.netlib.org/opt/subplex.tgz>.""" - homepage = "https://cloud.r-project.org/package=subplex" - url = "https://cloud.r-project.org/src/contrib/subplex_1.4-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/subplex" + cran = "subplex" + version('1.7', sha256='d5ecf4a484936d71cb294f08c3968ef5a8dcbdc861bfc0e97e3b1ab99afff887') version('1.6', sha256='0d05da1622fffcd20a01cc929fc6c2b7df40a8246e7018f7f1f3c175b774cbf9') version('1.5-4', sha256='ff94cf6b1560f78c31712c05bc2bc1b703339e09c7fc777ee94abf15fa7a8b81') version('1.5-2', sha256='6f8c3ccadf1ccd7f11f3eae28cec16eed3695f14e351b864d807dbaba6cd3ded') diff --git a/var/spack/repos/builtin/packages/r-suppdists/package.py b/var/spack/repos/builtin/packages/r-suppdists/package.py index 1ff3dd4bd4..7812fb7f2a 100644 --- a/var/spack/repos/builtin/packages/r-suppdists/package.py +++ b/var/spack/repos/builtin/packages/r-suppdists/package.py @@ -7,16 +7,17 @@ from spack import * class RSuppdists(RPackage): - """Ten distributions supplementing those built into R. Inverse Gauss, + """Supplementary Distributions. + + Ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions.""" - homepage = "https://cloud.r-project.org/package=SuppDists" - url = "https://cloud.r-project.org/src/contrib/SuppDists_1.1-9.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/SuppDists" + cran = "SuppDists" + version('1.1-9.7', sha256='6b5527e2635c0ff762eb7af8154704c85e66d7f79a9524089a5c98dfa94dab08') version('1.1-9.5', sha256='680b67145c07d44e200275e08e48602fe19cd99fb106c05422b3f4a244c071c4') depends_on('r@3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py index 810ddb96f0..12ddda333e 100644 --- a/var/spack/repos/builtin/packages/r-survey/package.py +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -7,7 +7,7 @@ from spack import * class RSurvey(RPackage): - """Analysis of Complex Survey Samples + """Analysis of Complex Survey Samples. Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general @@ -17,21 +17,21 @@ class RSurvey(RPackage): calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.""" - homepage = "https://r-survey.r-forge.r-project.org/survey/" - url = "https://cloud.r-project.org/src/contrib/survey_3.30-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/survey" + cran = "survey" + version('4.1-1', sha256='05e89a1678a39e32bfb41af8a31d643b04fc4d2660a96e701825e6bffcd75a52') version('4.0', sha256='b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1') version('3.36', sha256='90f32e9d2b52eacf881e6717a4b5edfc5a3beb5da516f8372293549589d79475') version('3.35-1', sha256='11e5ddde9c8c21dfaed0b1247036e068ad32782c76ff71f7937eb7585dd364db') version('3.30-3', sha256='be45d00b22d857e66905789031f2db1037505f80ce15d4b0ea84dabb03bc9e6d') depends_on('r@2.14.0:', type=('build', 'run')) - depends_on('r@2.16.0:', when='@3.32:3.34', type=('build', 'run')) - depends_on('r@3.1.0:', when='@3.35:', type=('build', 'run')) - depends_on('r-matrix', when='@3.31:', type=('build', 'run')) - depends_on('r-survival', when='@3.31:', type=('build', 'run')) - depends_on('r-lattice', when='@3.31:', type=('build', 'run')) - depends_on('r-minqa', when='@3.34:', type=('build', 'run')) - depends_on('r-numderiv', when='@3.34:', type=('build', 'run')) - depends_on('r-mitools@2.4:', when='@3.36:', type=('build', 'run')) + depends_on('r@2.16.0:', type=('build', 'run'), when='@3.32:') + depends_on('r@3.1.0:', type=('build', 'run'), when='@3.35:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@4.1-1:') + depends_on('r-matrix', type=('build', 'run'), when='@3.31:') + depends_on('r-survival', type=('build', 'run'), when='@3.31:') + depends_on('r-lattice', type=('build', 'run'), when='@3.31:') + depends_on('r-minqa', type=('build', 'run'), when='@3.34:') + depends_on('r-numderiv', type=('build', 'run'), when='@3.34:') + depends_on('r-mitools@2.4:', type=('build', 'run'), when='@3.36:') diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py index 7d82a5b22c..1f567e1281 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -7,16 +7,15 @@ from spack import * class RSurvival(RPackage): - """Survival Analysis + """Survival Analysis. - Contains the core survival analysis routines, including definition of - Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox - models, and parametric accelerated failure time models.""" + Contains the core survival analysis routines, including definition of Surv + objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, + and parametric accelerated failure time models.""" - homepage = "https://cloud.r-project.org/package=survival" - url = "https://cloud.r-project.org/src/contrib/survival_2.41-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/survival" + cran = "survival" + version('3.2-13', sha256='3fab9c0ba2c4e2b6a475207e2629a7f06a104c70093dfb768f50a7caac9a317f') version('3.2-7', sha256='5356cd73da7ecfda4042e8a8ae00d3531b106f7b39ca31a1843eadf288418a46') version('3.1-12', sha256='b62ed66eb646f3df13f7e9bf6571e3bfecae128c66491e174c8833cbef1bf21f') version('2.44-1.1', sha256='55b151e15fcd24ccb3acf60331c9a7ad82bc10f3841ab3be9bc2a37e9ee751b9') @@ -26,5 +25,6 @@ class RSurvival(RPackage): version('2.39-5', sha256='607170ebe36080d102e884cf13c3b29df01d6bb3b593258afffa67fee2a0ada7') depends_on('r@2.13.0:', type=('build', 'run')) - depends_on('r@3.4:', when='@3.1-12:', type=('build', 'run')) + depends_on('r@3.4:', type=('build', 'run'), when='@3.1-12:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@3.2-13:') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-svglite/package.py b/var/spack/repos/builtin/packages/r-svglite/package.py index 262ab0b37a..62bfbd74b6 100644 --- a/var/spack/repos/builtin/packages/r-svglite/package.py +++ b/var/spack/repos/builtin/packages/r-svglite/package.py @@ -7,13 +7,12 @@ from spack import * class RSvglite(RPackage): - """An 'SVG' Graphics Device + """An 'SVG' Graphics Device. A graphics device for R that produces 'Scalable Vector Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.""" - homepage = "https://svglite.r-lib.org/" - cran = "svglite" + cran = "svglite" version('2.0.0', sha256='76e625fe172a5b7ce99a67b6d631b037b3f7f0021cfe15f2e15e8851b89defa5') diff --git a/var/spack/repos/builtin/packages/r-sys/package.py b/var/spack/repos/builtin/packages/r-sys/package.py index 4348819ff4..7cf5487453 100644 --- a/var/spack/repos/builtin/packages/r-sys/package.py +++ b/var/spack/repos/builtin/packages/r-sys/package.py @@ -7,17 +7,15 @@ from spack import * class RSys(RPackage): - """Powerful and Reliable Tools for Running System Commands in R + """Powerful and Reliable Tools for Running System Commands in R. - Drop-in replacements for the base system2() function with fine control - and consistent behavior across platforms. Supports clean interruption, - timeout, background tasks, and streaming STDIN / STDOUT / STDERR over - binary or text connections. Arguments on Windows automatically get encoded - and quoted to work on different locales.""" + Drop-in replacements for the base system2() function with fine control and + consistent behavior across platforms. Supports clean interruption, timeout, + background tasks, and streaming STDIN / STDOUT / STDERR over binary or text + connections. Arguments on Windows automatically get encoded and quoted to + work on different locales.""" - homepage = "https://github.com/jeroen/sys#readme" - url = "https://cloud.r-project.org/src/contrib/sys_3.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/sys" + cran = "sys" version('3.4', sha256='17f88fbaf222f1f8fd07919461093dac0e7175ae3c3b3264b88470617afd0487') version('3.2', sha256='2819498461fe2ce83d319d1a47844e86bcea6d01d10861818dba289e7099bbcc') diff --git a/var/spack/repos/builtin/packages/r-systemfonts/package.py b/var/spack/repos/builtin/packages/r-systemfonts/package.py index 3fc84c1fef..fe28f554a5 100644 --- a/var/spack/repos/builtin/packages/r-systemfonts/package.py +++ b/var/spack/repos/builtin/packages/r-systemfonts/package.py @@ -7,7 +7,7 @@ from spack import * class RSystemfonts(RPackage): - """System Native Font Finding + """System Native Font Finding. Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts @@ -17,9 +17,9 @@ class RSystemfonts(RPackage): use is intended to be from compiled code but 'systemfonts' also provides access from R.""" - homepage = "https://github.com/r-lib/systemfonts" - cran = "systemfonts" + cran = "systemfonts" + version('1.0.3', sha256='647c99d5ea6f90a49768ea7b10b39816af6be85168475273369fd973a20dbbba') version('1.0.1', sha256='401db4d9e78e3a5e00b7a0b4fbad7fbb1c584734469b65fe5b7ebe1851c7a797') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py index 607db87f16..b00219845b 100644 --- a/var/spack/repos/builtin/packages/r-tarifx/package.py +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -7,13 +7,11 @@ from spack import * class RTarifx(RPackage): - """Collection of Utility and Convenience Functions + """Collection of Utility and Convenience Functions. A collection of various utility and convenience functions.""" - homepage = "https://cloud.r-project.org/package=taRifx" - url = "https://cloud.r-project.org/src/contrib/taRifx_1.0.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/taRifx" + cran = "taRifx" version('1.0.6.2', sha256='89d031db00a94ae57c7ace0d9aa39ba2f960f96fd48d2d1e4c7ebb62a2969b15') version('1.0.6.1', sha256='d4c832b26d476a395ddf8349c42613270023c8bbf52a274d280be6284c11d7e2') diff --git a/var/spack/repos/builtin/packages/r-taxizedb/package.py b/var/spack/repos/builtin/packages/r-taxizedb/package.py index 984793a6e5..ca40cd557d 100644 --- a/var/spack/repos/builtin/packages/r-taxizedb/package.py +++ b/var/spack/repos/builtin/packages/r-taxizedb/package.py @@ -7,16 +7,14 @@ from spack import * class RTaxizedb(RPackage): - """Tools for Working with 'Taxonomic' Databases + """Tools for Working with 'Taxonomic' Databases. Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.""" - homepage = "https://cloud.r-project.org/package=taxizedb" - url = "https://cloud.r-project.org/src/contrib/taxizedb_0.1.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/taxizedb/" + cran = "taxizedb" version('0.3.0', sha256='5f28338a233f0021097147e74c5f83107e5847de3413eceb308208e39af9fcb4') version('0.1.4', sha256='5a40569a2b5abe56201f112a10220150353412df39b7e8d21ea8698f424cf295') @@ -25,11 +23,12 @@ class RTaxizedb(RPackage): depends_on('r-dbi@0.6-1:', type=('build', 'run')) depends_on('r-rsqlite@1.1.2:', type=('build', 'run')) depends_on('r-dplyr@0.7.0:', type=('build', 'run')) - depends_on('r-tibble', when='@0.3.0:', type=('build', 'run')) - depends_on('r-rlang', when='@0.3.0:', type=('build', 'run')) - depends_on('r-readr@1.1.1:', when='@0.3.0:', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run'), when='@0.3.0:') + depends_on('r-rlang', type=('build', 'run'), when='@0.3.0:') + depends_on('r-readr@1.1.1:', type=('build', 'run'), when='@0.3.0:') depends_on('r-dbplyr@1.0.0:', type=('build', 'run')) depends_on('r-magrittr@1.5:', type=('build', 'run')) depends_on('r-hoardr@0.1.0:', type=('build', 'run')) - depends_on('r-rpostgresql@0.4.1:', when='@:0.1.4', type=('build', 'run')) - depends_on('r-rmysql@0.10.11:', when='@:0.1.4', type=('build', 'run')) + + depends_on('r-rpostgresql@0.4.1:', type=('build', 'run'), when='@:0.1.4') + depends_on('r-rmysql@0.10.11:', type=('build', 'run'), when='@:0.1.4') diff --git a/var/spack/repos/builtin/packages/r-tclust/package.py b/var/spack/repos/builtin/packages/r-tclust/package.py index 1e864a9a18..ec7828d2ea 100644 --- a/var/spack/repos/builtin/packages/r-tclust/package.py +++ b/var/spack/repos/builtin/packages/r-tclust/package.py @@ -7,16 +7,14 @@ from spack import * class RTclust(RPackage): - """Robust Trimmed Clustering + """Robust Trimmed Clustering. Provides functions for robust trimmed clustering. The methods are described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>, Fritz et al. (2012) <doi:10.18637/jss.v047.i12>, Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.""" - homepage = "https://cloud.r-project.org/package=tclust" - url = "https://cloud.r-project.org/src/contrib/tclust_1.3-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tclust" + cran = "tclust" version('1.4-2', sha256='95dcd07dbd16383f07f5cea8561e7f3bf314e4a7483879841103b149fc8c65d9') version('1.4-1', sha256='4b0be612c8ecd7b4eb19a44ab6ac8f5d40515600ae1144c55989b6b41335ad9e') diff --git a/var/spack/repos/builtin/packages/r-teachingdemos/package.py b/var/spack/repos/builtin/packages/r-teachingdemos/package.py index 3782db8e6c..8a79786df9 100644 --- a/var/spack/repos/builtin/packages/r-teachingdemos/package.py +++ b/var/spack/repos/builtin/packages/r-teachingdemos/package.py @@ -13,9 +13,7 @@ class RTeachingdemos(RPackage): statistical concepts, or on your own to better understand the concepts or the programming.""" - homepage = "https://cloud.r-project.org/package=TeachingDemos" - url = "https://cloud.r-project.org/src/contrib/TeachingDemos_2.10.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/TeachingDemos" + cran = "TeachingDemos" version('2.12', sha256='3e75405ce1affa406d6df85e06f96381412bc7a2810b25d8c81bfe64c4698644') version('2.10', sha256='2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704') diff --git a/var/spack/repos/builtin/packages/r-tensor/package.py b/var/spack/repos/builtin/packages/r-tensor/package.py index eaa465151d..5523077dce 100644 --- a/var/spack/repos/builtin/packages/r-tensor/package.py +++ b/var/spack/repos/builtin/packages/r-tensor/package.py @@ -7,14 +7,13 @@ from spack import * class RTensor(RPackage): - """The tensor product of two arrays is notionally an outer product of - the arrays collapsed in specific extents by summing along the - appropriate diagonals. - """ + """Tensor product of arrays. - homepage = "https://cloud.r-project.org/package=tensor" - url = "https://cloud.r-project.org/src/contrib/tensor_1.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tensor" + The tensor product of two arrays is notionally an outer product of the + arrays collapsed in specific extents by summing along the appropriate + diagonals.""" + + cran = "tensor" version('1.5', sha256='e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6') version('1.4', sha256='6f1643da018d58a0aaa27260df6fdf687fc36f4cd1964931b3180b7df8c0e642') diff --git a/var/spack/repos/builtin/packages/r-tensora/package.py b/var/spack/repos/builtin/packages/r-tensora/package.py index 46a0788642..1fee14b0ce 100644 --- a/var/spack/repos/builtin/packages/r-tensora/package.py +++ b/var/spack/repos/builtin/packages/r-tensora/package.py @@ -7,16 +7,14 @@ from spack import * class RTensora(RPackage): - """Advanced Tensor Arithmetic with Named Indices + """Advanced Tensor Arithmetic with Named Indices. Provides convenience functions for advanced linear algebra with tensors and computation with data sets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, parallel computations on sequences of tensors.""" - homepage = "https://cloud.r-project.org/package=tensorA" - url = "https://cloud.r-project.org/src/contrib/tensorA_0.36.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tensorA" + cran = "tensorA" version('0.36.2', sha256='8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7') version('0.36.1', sha256='c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c') diff --git a/var/spack/repos/builtin/packages/r-terra/package.py b/var/spack/repos/builtin/packages/r-terra/package.py new file mode 100644 index 0000000000..a7db76eb16 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-terra/package.py @@ -0,0 +1,33 @@ +# 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 RTerra(RPackage): + """Spatial Data Analysis. + + Methods for spatial data analysis with raster and vector data. Raster + methods allow for low-level data manipulation as well as high-level global, + local, zonal, and focal computation. The predict and interpolate methods + facilitate the use of regression type (interpolation, machine learning) + models for spatial prediction, including with satellite remote sensing + data. Processing of very large files is supported. See the manual and + tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very + similar to the 'raster' package; but 'terra' can do more, is easier to use, + and it is faster.""" + + cran = "terra" + + version('1.5-17', sha256='e7ac57d1712d280616a4b5a85cd915b2b3e24fe08ee044b740588d884e6be6e7') + version('1.5-12', sha256='865cc14ee8c3239037c08170df4011eed27cf638ac1d05f0b7cd704abf97cc19') + version('1.4-22', sha256='b8eccfa36764577248d7b390e24af6db65fb8824c07f9b782bd6b83c4d2b3976') + + depends_on('r@3.5.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('gdal@2.2.3:') + depends_on('geos@3.4.0:') + depends_on('proj@4.9.3:') + depends_on('sqlite') diff --git a/var/spack/repos/builtin/packages/r-tester/package.py b/var/spack/repos/builtin/packages/r-tester/package.py index 7971044c6e..3522bf212f 100644 --- a/var/spack/repos/builtin/packages/r-tester/package.py +++ b/var/spack/repos/builtin/packages/r-tester/package.py @@ -7,11 +7,11 @@ from spack import * class RTester(RPackage): - """tester allows you to test characteristics of common R objects.""" + """Tests and checks characteristics of R objects. - homepage = "https://github.com/gastonstat/tester" - url = "https://cloud.r-project.org/src/contrib/tester_0.1.7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tester" + tester allows you to test characteristics of common R objects.""" + + cran = "tester" version('0.1.7', sha256='b9c645119c21c69450f3d366c911ed92ac7c14ef61652fd676a38fb9d420b5f4') diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py index 1ab1b97410..8f623a6acf 100644 --- a/var/spack/repos/builtin/packages/r-testit/package.py +++ b/var/spack/repos/builtin/packages/r-testit/package.py @@ -8,15 +8,14 @@ from spack import * class RTestit(RPackage): - """A Simple Package for Testing R Packages + """A Simple Package for Testing R Packages. Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.""" - homepage = "https://cloud.r-project.org/package=testit" - url = "https://cloud.r-project.org/src/contrib/testit_0.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/testit" + cran = "testit" + version('0.13', sha256='90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80') version('0.12', sha256='9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89') version('0.9', sha256='9cf6b3df9b2c700e4e7dcbd5b8cb64fabefe674e1f40346ccaf39fe7feda5e55') version('0.8', sha256='08a9c19c962eae60f4ab58885a23e0bc239efc39da682290be436c066f8d97f7') diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py index 47325edceb..2f43aabf21 100644 --- a/var/spack/repos/builtin/packages/r-testthat/package.py +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -7,16 +7,16 @@ from spack import * class RTestthat(RPackage): - """Unit Testing for R + """Unit Testing for R. Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.""" - homepage = "https://github.com/hadley/testthat" - url = "https://cloud.r-project.org/src/contrib/testthat_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/testthat" + cran = "testthat" + version('3.1.2', sha256='ed41a6168ca22869b6aebe1e5865bb2f5338a7c35ca0a13cf69ac2f5c6aeb659') + version('3.1.1', sha256='e6755fb4f5388751af952edfd555533bb55d6252606f6fcef07bdb6268c8cf80') version('3.0.1', sha256='297fc45c719684f11ddf9dc9088f5528fdf9b44625165543384eaf579f243ad0') version('2.3.2', sha256='1a268d8df07f7cd8d282d03bb96ac2d96a24a95c9aa52f4cca5138a09dd8e06c') version('2.2.1', sha256='67ee0512bb312695c81fd74338bb8ce9e2e58763681ddbcdfdf35f52dfdb0b78') @@ -24,27 +24,29 @@ class RTestthat(RPackage): version('1.0.2', sha256='0ef7df0ace1fddf821d329f9d9a5d42296085350ae0d94af62c45bd203c8415e') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r-brio', when='@3.0.1:', type=('build', 'run')) - depends_on('r-callr@3.5.1:', when='@3.0.1:', type=('build', 'run')) - depends_on('r-cli', when='@2.0.0:', type=('build', 'run')) - depends_on('r-cli@2.2.0:', when='@3.0.1:', type=('build', 'run')) + depends_on('r-brio', type=('build', 'run'), when='@3.0.1:') + depends_on('r-callr@3.5.1:', type=('build', 'run'), when='@3.0.1:') + depends_on('r-cli', type=('build', 'run'), when='@2.0.0:') + depends_on('r-cli@2.2.0:', type=('build', 'run'), when='@3.0.1:') depends_on('r-crayon@1.3.4:', type=('build', 'run')) - depends_on('r-desc', when='@3.0.1:', type=('build', 'run')) + depends_on('r-desc', type=('build', 'run'), when='@3.0.1:') depends_on('r-digest', type=('build', 'run')) - depends_on('r-ellipsis', when='@2.3.2:', type=('build', 'run')) - depends_on('r-ellipsis@0.2.0:', when='@3.0.1:', type=('build', 'run')) - depends_on('r-evaluate', when='@2.2.0:', type=('build', 'run')) - depends_on('r-jsonlite', when='@3.0.1:', type=('build', 'run')) - depends_on('r-lifecycle', when='@3.0.1:', type=('build', 'run')) + depends_on('r-ellipsis', type=('build', 'run'), when='@2.3.2:') + depends_on('r-ellipsis@0.2.0:', type=('build', 'run'), when='@3.0.1:') + depends_on('r-evaluate', type=('build', 'run'), when='@2.2.0:') + depends_on('r-jsonlite', type=('build', 'run'), when='@3.0.1:') + depends_on('r-lifecycle', type=('build', 'run'), when='@3.0.1:') depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-pkgload', when='@2.3.2:', type=('build', 'run')) + depends_on('r-pkgload', type=('build', 'run'), when='@2.3.2:') depends_on('r-praise', type=('build', 'run')) - depends_on('r-processx', when='@3.0.1:', type=('build', 'run')) - depends_on('r-ps@1.3.4:', when='@3.0.1:', type=('build', 'run')) + depends_on('r-processx', type=('build', 'run'), when='@3.0.1:') + depends_on('r-ps@1.3.4:', type=('build', 'run'), when='@3.0.1:') depends_on('r-r6@2.2.0:', type=('build', 'run')) - depends_on('r-rlang@0.3.0:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.1:', when='@2.3.2:', type=('build', 'run')) - depends_on('r-rlang@0.4.9:', when='@3.0.1:', type=('build', 'run')) - depends_on('r-waldo@0.2.1:', when='@3.0.1:', type=('build', 'run')) - depends_on('r-withr@2.0.0:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-withr@2.3.0:', when='@3.0.1:', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-rlang@0.4.1:', type=('build', 'run'), when='@2.3.2:') + depends_on('r-rlang@0.4.9:', type=('build', 'run'), when='@3.0.1:') + depends_on('r-waldo@0.2.1:', type=('build', 'run'), when='@3.0.1:') + depends_on('r-waldo@0.2.4:', type=('build', 'run'), when='@3.1.1:') + depends_on('r-withr@2.0.0:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-withr@2.3.0:', type=('build', 'run'), when='@3.0.1:') + depends_on('r-withr@2.4.3:', type=('build', 'run'), when='@3.1.2:') diff --git a/var/spack/repos/builtin/packages/r-tfisher/package.py b/var/spack/repos/builtin/packages/r-tfisher/package.py index dbffb8dbb7..5d9211725c 100644 --- a/var/spack/repos/builtin/packages/r-tfisher/package.py +++ b/var/spack/repos/builtin/packages/r-tfisher/package.py @@ -7,7 +7,7 @@ from spack import * class RTfisher(RPackage): - """Optimal Thresholding Fisher's P-Value Combination Method + """Optimal Thresholding Fisher's P-Value Combination Method. We provide the cumulative distribution function (CDF), quantile, and statistical power calculator for a collection of thresholding Fisher's @@ -19,9 +19,7 @@ class RTfisher(RPackage): Wu. "TFisher Tests: Optimal and Adaptive Thresholding for Combining p-Values", submitted.""" - homepage = "https://cloud.r-project.org/package=TFisher" - url = "https://cloud.r-project.org/src/contrib/TFisher_0.2.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/TFisher" + cran = "TFisher" version('0.2.0', sha256='bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f') diff --git a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py index e9ff9e92d0..53b9021c06 100644 --- a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py +++ b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py @@ -7,17 +7,16 @@ from spack import * class RTfmpvalue(RPackage): - """In putative Transcription Factor Binding Sites (TFBSs) identification - from sequence/alignments, we are interested in the significance of - certain match score. TFMPvalue provides the accurate calculation of - P-value with score threshold for Position Weight Matrices, or the score - with given P-value. This package is an interface to code originally - made available by Helene Touzet and Jean-Stephane Varre, 2007, - Algorithms Mol Biol:2, 15.""" + """Efficient and Accurate P-Value Computation for Position Weight Matrices. - homepage = "https://github.com/ge11232002/TFMPvalue" - url = "https://cloud.r-project.org/src/contrib/TFMPvalue_0.0.6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/TFMPvalue" + In putative Transcription Factor Binding Sites (TFBSs) identification from + sequence/alignments, we are interested in the significance of certain match + score. TFMPvalue provides the accurate calculation of P-value with score + threshold for Position Weight Matrices, or the score with given P-value. + This package is an interface to code originally made available by Helene + Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.""" + + cran = "TFMPvalue" version('0.0.8', sha256='6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841') version('0.0.6', sha256='cee3aa2d4e22856865d820f695e29a5f23486e5e08cd42cb95a0728f5f9522a1') diff --git a/var/spack/repos/builtin/packages/r-th-data/package.py b/var/spack/repos/builtin/packages/r-th-data/package.py index 5ee8c71753..c42ef33359 100644 --- a/var/spack/repos/builtin/packages/r-th-data/package.py +++ b/var/spack/repos/builtin/packages/r-th-data/package.py @@ -7,17 +7,19 @@ from spack import * class RThData(RPackage): - """Contains data sets used in other packages Torsten Hothorn maintains.""" + """TH's Data Archive. - homepage = "https://cloud.r-project.org/package=TH.data" - url = "https://cloud.r-project.org/src/contrib/TH.data_1.0-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/TH.data" + Contains data sets used in other packages Torsten Hothorn maintains.""" + cran = "TH.data" + + version('1.1-0', sha256='21b37e251da5635ae91668f64b4c6f6a7ccedbe1f01af769d30fb532af83113e') version('1.0-10', sha256='618a1c67a30536d54b1e48ba3af46a6edcd6c2abef17935b5d4ba526a43aff55') version('1.0-9', sha256='d8318a172ce2b9f7f284dc297c8a8d5093de8eccbb566c8e7580e70938dfae0f') version('1.0-8', sha256='478f109fcc1226500ead8e3bd6e047cecde2294fde4df8ec216d38313db79a9d') version('1.0-7', sha256='29e126344daccbebc7df68924730ae4159a0faad77f86302070920684ba6070e') depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.1-0:') depends_on('r-survival', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py index 444e447e74..1bcaaf3d4e 100644 --- a/var/spack/repos/builtin/packages/r-threejs/package.py +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -7,23 +7,22 @@ from spack import * class RThreejs(RPackage): - """Interactive 3D Scatter Plots, Networks and Globes + """Interactive 3D Scatter Plots, Networks and Globes. Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library ("https://threejs.org/").""" - homepage = "https://bwlewis.github.io/rthreejs" - url = "https://cloud.r-project.org/src/contrib/threejs_0.2.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/threejs" + cran = "threejs" version('0.3.3', sha256='76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c') version('0.3.1', sha256='71750b741672a435ecf749b69c72f0681aa8bb795e317f4e3056d5e33f6d79e8') version('0.2.2', sha256='41fe949490fbe0f71e39b0a144791da427bd7361d027579cb4a002ed53520cc5') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r-igraph@1.0.0:', when='@0.3.1:', type=('build', 'run')) + depends_on('r-igraph@1.0.0:', type=('build', 'run'), when='@0.3.1:') depends_on('r-htmlwidgets@0.3.2:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-crosstalk', when='@0.3.1:', type=('build', 'run')) - depends_on('r-matrix', when='@0.2.2', type=('build', 'run')) - depends_on('r-jsonlite', when='@0.2.2', type=('build', 'run')) + depends_on('r-crosstalk', type=('build', 'run'), when='@0.3.1:') + + depends_on('r-matrix', type=('build', 'run'), when='@0.2.2') + depends_on('r-jsonlite', type=('build', 'run'), when='@0.2.2') diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 475af937b1..1bc847cf83 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -7,14 +7,14 @@ from spack import * class RTibble(RPackage): - """Simple Data Frames + """Simple Data Frames. Provides a 'tbl_df' class (the 'tibble') that provides stricter checking and better formatting than the traditional data frame.""" - homepage = "https://github.com/tidyverse/tibble" cran = "tibble" + version('3.1.6', sha256='5b33d909f146ebad38e262f6a57cb91ab70bfe240c2af01004beec11b3898292') version('3.1.5', sha256='da6387ba683a67cd7fc2a111f6b62468e480a8078bc1867d433a40c5460edbe7') version('3.0.5', sha256='1cc92d7bf5ecf8291718682fb7fcb96f6f87751f1ed101a7441cad5120195190') version('2.1.3', sha256='9a8cea9e6b5d24a7e9bf5f67ab38c40b2b6489eddb0d0edb8a48a21ba3574e1a') @@ -26,26 +26,26 @@ class RTibble(RPackage): version('1.2', sha256='ed8a8bd0591223f742be80fd1cd8c4a9618d0f04011ec95c272b61ea45193104') version('1.1', sha256='10ea18890e5514faa4c2c05fa231a6e2bbb7689f3800850cead214306414c88e') - depends_on('r@3.1.2:', when='@:1.2', type=('build', 'run')) - depends_on('r@3.1.0:', when='@1.3.0:', type=('build', 'run')) - depends_on('r-ellipsis@0.2.0:', when='@3.0.5:', type=('build', 'run')) - depends_on('r-ellipsis@0.3.2:', when='@3.1.2:', type=('build', 'run')) - depends_on('r-fansi@0.4.0:', when='@2.0.0:', type=('build', 'run')) - depends_on('r-lifecycle@0.2.0:', when='@3.0.5:', type=('build', 'run')) - depends_on('r-lifecycle@1.0.0:', when='@3.1.5:', type=('build', 'run')) - depends_on('r-magrittr', when='@3.0.5:', type=('build', 'run')) - depends_on('r-pillar@1.3.1:', when='@1.4.1:', type=('build', 'run')) - depends_on('r-pillar@1.4.3:', when='@3.0.5:', type=('build', 'run')) - depends_on('r-pillar@1.6.0:', when='@3.1:', type=('build', 'run')) - depends_on('r-pillar@1.6.2:', when='@3.1.4:', type=('build', 'run')) - depends_on('r-pkgconfig', when='@2.0.0:', type=('build', 'run')) - depends_on('r-rlang@0.3.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-rlang@0.4.3:', when='@3.0.5:', type=('build', 'run')) - depends_on('r-vctrs@0.3.2:', when='@3.0.5:', type=('build', 'run')) - depends_on('r-vctrs@0.3.8:', when='@3.1.2:', type=('build', 'run')) - - depends_on('r-cli', when='@1.4.2:3.0', type=('build', 'run')) - depends_on('r-crayon@1.3.4:', when='@1.4.1:3.0', type=('build', 'run')) - depends_on('r-assertthat', when='@:1.3.1', type=('build', 'run')) - depends_on('r-lazyeval@0.1.10:', when='@:1.3.0', type=('build', 'run')) - depends_on('r-rcpp@0.12.3:', when='@:1.3.4', type=('build', 'run')) + depends_on('r@3.1.2:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-ellipsis@0.2.0:', type=('build', 'run'), when='@3.0.5:') + depends_on('r-ellipsis@0.3.2:', type=('build', 'run'), when='@3.1.2:') + depends_on('r-fansi@0.4.0:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-lifecycle@0.2.0:', type=('build', 'run'), when='@3.0.5:') + depends_on('r-lifecycle@1.0.0:', type=('build', 'run'), when='@3.1.5:') + depends_on('r-magrittr', type=('build', 'run'), when='@3.0.5:') + depends_on('r-pillar@1.3.1:', type=('build', 'run'), when='@1.4.1:') + depends_on('r-pillar@1.4.3:', type=('build', 'run'), when='@3.0.5:') + depends_on('r-pillar@1.6.0:', type=('build', 'run'), when='@3.1.0:') + depends_on('r-pillar@1.6.2:', type=('build', 'run'), when='@3.1.4:') + depends_on('r-pkgconfig', type=('build', 'run'), when='@2.0.0:') + depends_on('r-rlang@0.3.0:', type=('build', 'run'), when='@1.3.1:') + depends_on('r-rlang@0.4.3:', type=('build', 'run'), when='@3.0.5:') + depends_on('r-vctrs@0.3.2:', type=('build', 'run'), when='@3.0.5:') + depends_on('r-vctrs@0.3.8:', type=('build', 'run'), when='@3.1.2:') + + depends_on('r-cli', type=('build', 'run'), when='@1.4.2:3.0') + depends_on('r-crayon@1.3.4:', type=('build', 'run'), when='@1.4.1:3.0') + depends_on('r-assertthat', type=('build', 'run'), when='@:1.3.1') + depends_on('r-lazyeval@0.1.10:', type=('build', 'run'), when='@:1.3.0') + depends_on('r-rcpp@0.12.3:', type=('build', 'run'), when='@:1.3.4') diff --git a/var/spack/repos/builtin/packages/r-tictoc/package.py b/var/spack/repos/builtin/packages/r-tictoc/package.py index 3b5bca13fd..0b34c25f31 100644 --- a/var/spack/repos/builtin/packages/r-tictoc/package.py +++ b/var/spack/repos/builtin/packages/r-tictoc/package.py @@ -10,16 +10,14 @@ class RTictoc(RPackage): """Functions for timing R scripts, as well as implementations of Stack and List structures. - This package provides the timing functions 'tic' and 'toc' - that can be nested. One can record all timings while a - complex script is running, and examine the values later. It - is also possible to instrument the timing calls with custom - callbacks. In addition, this package provides class - 'Stack', implemented as a vector, and class 'List', - implemented as a list, both of which support operations - 'push', 'pop', 'first', 'last' and 'clear'.""" + This package provides the timing functions 'tic' and 'toc' that can be + nested. One can record all timings while a complex script is running, and + examine the values later. It is also possible to instrument the timing + calls with custom callbacks. In addition, this package provides class + 'Stack', implemented as a vector, and class 'List', implemented as a list, + both of which support operations 'push', 'pop', 'first', 'last' and + 'clear'.""" - homepage = "https://collectivemedia.github.io/tictoc/" cran = "tictoc" version('1.0.1', sha256='a09a1535c417ddf6637bbbda5fca6edab6c7f7b252a64e57e99d4d0748712705') diff --git a/var/spack/repos/builtin/packages/r-tidycensus/package.py b/var/spack/repos/builtin/packages/r-tidycensus/package.py index 0276e63d72..216a50d811 100644 --- a/var/spack/repos/builtin/packages/r-tidycensus/package.py +++ b/var/spack/repos/builtin/packages/r-tidycensus/package.py @@ -7,18 +7,18 @@ from spack import * class RTidycensus(RPackage): - """Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames + """Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready + Data Frames. An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for all Census - geographies. """ + geographies.""" - homepage = "https://cloud.r-project.org/package=tidycensus" - url = "https://cloud.r-project.org/src/contrib/tidycensus_0.3.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tidycensus" + cran = "tidycensus" + version('1.1', sha256='8914fdec64a86896f1faa3a92272d1cd008a194af4cd86eba2d69df5707062c0') version('0.11', sha256='da2fba4cd987615dedd22f64d9f38804f4e2161af31bacf1f3b5a013d71fdd43') version('0.9.2', sha256='2454525301caff9eaaf6ebe14f58706ece1fbace6187ce8bf3fff04c842b9536') version('0.3.1', sha256='d03cbee7abbf87bb4ce2e649726bdd143d47b549f30b5a11aaaa6c4aff78e778') @@ -27,16 +27,18 @@ class RTidycensus(RPackage): depends_on('r-httr', type=('build', 'run')) depends_on('r-sf', type=('build', 'run')) depends_on('r-dplyr@0.7.0:', type=('build', 'run')) - depends_on('r-dplyr@0.8.0:', when='@0.11:', type=('build', 'run')) + depends_on('r-dplyr@0.8.0:', type=('build', 'run'), when='@0.11:') + depends_on('r-dplyr@1.0.0:', type=('build', 'run'), when='@1.1:') depends_on('r-tigris', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-jsonlite@1.5.0:', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) depends_on('r-rvest', type=('build', 'run')) depends_on('r-tidyr@0.7.0:', type=('build', 'run')) - depends_on('r-tidyr@1.0.0:', when='@0.11:', type=('build', 'run')) + depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@0.11:') depends_on('r-rappdirs', type=('build', 'run')) depends_on('r-readr', type=('build', 'run')) depends_on('r-xml2', type=('build', 'run')) depends_on('r-units', type=('build', 'run')) - depends_on('r-rlang', when='@0.11:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run'), when='@0.11:') + depends_on('r-crayon', type=('build', 'run'), when='@1.1:') diff --git a/var/spack/repos/builtin/packages/r-tidygraph/package.py b/var/spack/repos/builtin/packages/r-tidygraph/package.py index 894cb81bc1..2d96e015cc 100644 --- a/var/spack/repos/builtin/packages/r-tidygraph/package.py +++ b/var/spack/repos/builtin/packages/r-tidygraph/package.py @@ -15,16 +15,14 @@ class RTidygraph(RPackage): in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.""" - homepage = "https://github.com/thomasp85/tidygraph" - url = "https://cloud.r-project.org/src/contrib/tidygraph_1.1.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tidygraph" + cran = "tidygraph" version('1.2.0', sha256='057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f') version('1.1.2', sha256='5642001d4cccb122d66481b7c61a06c724c02007cbd356ee61cb29726a56fafe') depends_on('r-tibble', type=('build', 'run')) depends_on('r-dplyr@0.8:', type=('build', 'run')) - depends_on('r-dplyr@0.8.5:', when='@1.2.0:', type=('build', 'run')) + depends_on('r-dplyr@0.8.5:', type=('build', 'run'), when='@1.2.0:') depends_on('r-igraph', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index 2a101d1402..361059eb2e 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -7,7 +7,7 @@ from spack import * class RTidyr(RPackage): - """Tidy Messy Data + """Tidy Messy Data. Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' @@ -17,7 +17,6 @@ class RTidyr(RPackage): It also includes tools for working with missing values (both implicit and explicit).""" - homepage = "https://github.com/hadley/tidyr" cran = "tidyr" version('1.1.4', sha256='0b0c98be98a433e15a2550f60330b31a58529a9c58bc2abd7bff6462ab761241') @@ -29,21 +28,21 @@ class RTidyr(RPackage): depends_on('r@3.1:', type=('build', 'run')) depends_on('r-dplyr@0.7.0:', type=('build', 'run')) - depends_on('r-dplyr@0.8.2:', when='@1.1.2:', type=('build', 'run')) - depends_on('r-ellipsis@0.1.0:', when='@1.1.2:', type=('build', 'run')) + depends_on('r-dplyr@0.8.2:', type=('build', 'run'), when='@1.1.2:') + depends_on('r-ellipsis@0.1.0:', type=('build', 'run'), when='@1.1.2:') depends_on('r-glue', type=('build', 'run')) - depends_on('r-lifecycle', when='@1.1.2:', type=('build', 'run')) + depends_on('r-lifecycle', type=('build', 'run'), when='@1.1.2:') depends_on('r-magrittr', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) - depends_on('r-tibble@2.1.1:', when='@1.1.2:', type=('build', 'run')) + depends_on('r-tibble@2.1.1:', type=('build', 'run'), when='@1.1.2:') depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) - depends_on('r-tidyselect@1.1.0:', when='@1.1.2:', type=('build', 'run')) - depends_on('r-vctrs@0.3.0:', when='@1.1.2:', type=('build', 'run')) - depends_on('r-vctrs@0.3.6:', when='@1.1.3:', type=('build', 'run')) - depends_on('r-cpp11@0.2.1:', when='@1.1.2:', type=('build', 'run')) - depends_on('r-cpp11@0.2.6:', when='@1.1.3:', type=('build', 'run')) - - depends_on('r-stringi', when='@:0.8.3', type=('build', 'run')) - depends_on('r-rcpp', when='@:0.8.3', type=('build', 'run')) + depends_on('r-tidyselect@1.1.0:', type=('build', 'run'), when='@1.1.2:') + depends_on('r-vctrs@0.3.0:', type=('build', 'run'), when='@1.1.2:') + depends_on('r-vctrs@0.3.6:', type=('build', 'run'), when='@1.1.3:') + depends_on('r-cpp11@0.2.1:', type=('build', 'run'), when='@1.1.2:') + depends_on('r-cpp11@0.2.6:', type=('build', 'run'), when='@1.1.3:') + + depends_on('r-stringi', type=('build', 'run'), when='@:0.8.3') + depends_on('r-rcpp', type=('build', 'run'), when='@:0.8.3') diff --git a/var/spack/repos/builtin/packages/r-tidyselect/package.py b/var/spack/repos/builtin/packages/r-tidyselect/package.py index 1da9bb9d76..c5ad825fc9 100644 --- a/var/spack/repos/builtin/packages/r-tidyselect/package.py +++ b/var/spack/repos/builtin/packages/r-tidyselect/package.py @@ -7,13 +7,12 @@ from spack import * class RTidyselect(RPackage): - """Select from a Set of Strings + """Select from a Set of Strings. A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.""" - homepage = "https://cloud.r-project.org/package=tidyselect" cran = "tidyselect" version('1.1.1', sha256='18eb6a6746196a81ce19ee6cbf1db0c33f494177b97e2419312ef25a00ae486b') @@ -23,14 +22,14 @@ class RTidyselect(RPackage): version('0.2.3', sha256='0c193abc8251a60e1d2a32a99c77651c336bc185e3c2a72e5f8781813d181c2c') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r@3.2:', when='@1.1.0:', type=('build', 'run')) - depends_on('r-ellipsis', when='@1.1.0:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@1.1.0:') + depends_on('r-ellipsis', type=('build', 'run'), when='@1.1.0:') depends_on('r-glue@1.3.0:', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-purrr@0.3.2:', when='@1.1.0:', type=('build', 'run')) + depends_on('r-purrr@0.3.2:', type=('build', 'run'), when='@1.1.0:') depends_on('r-rlang@0.2.2:', type=('build', 'run')) - depends_on('r-rlang@0.4.6:', when='@1.1.0:', type=('build', 'run')) - depends_on('r-vctrs@0.2.2:', when='@1.1.0:', type=('build', 'run')) - depends_on('r-vctrs@0.3.0:', when='@1.1.1:', type=('build', 'run')) + depends_on('r-rlang@0.4.6:', type=('build', 'run'), when='@1.1.0:') + depends_on('r-vctrs@0.2.2:', type=('build', 'run'), when='@1.1.0:') + depends_on('r-vctrs@0.3.0:', type=('build', 'run'), when='@1.1.1:') - depends_on('r-rcpp@0.12.0:', when='@:0.2.5', type=('build', 'run')) + depends_on('r-rcpp@0.12.0:', type=('build', 'run'), when='@:0.2.5') diff --git a/var/spack/repos/builtin/packages/r-tidyverse/package.py b/var/spack/repos/builtin/packages/r-tidyverse/package.py index 4408e10186..5313a91890 100644 --- a/var/spack/repos/builtin/packages/r-tidyverse/package.py +++ b/var/spack/repos/builtin/packages/r-tidyverse/package.py @@ -7,7 +7,7 @@ from spack import * class RTidyverse(RPackage): - """Easily Install and Load the 'Tidyverse' + """Easily Install and Load the 'Tidyverse'. The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is @@ -15,90 +15,88 @@ class RTidyverse(RPackage): in a single step. Learn more about the 'tidyverse' at <https://tidyverse.org>.""" - homepage = "https://tidyverse.tidyverse.org/" cran = "tidyverse" version('1.3.1', sha256='83cf95109d4606236274f5a8ec2693855bf75d3a1b3bc1ab4426dcc275ed6632') version('1.3.0', sha256='6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09') version('1.2.1', sha256='ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b') - depends_on('r@3.3:', when='@1.3.1:', type=('build', 'run')) - depends_on('r@3.2:', when='@1.3.0:', type=('build', 'run')) depends_on('r+X', type=('build', 'run')) - - depends_on('r-broom@0.7.6:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-broom@0.5.2:', when='@1.3.0:', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run'), when='@1.3.0:') + depends_on('r@3.3:', type=('build', 'run'), when='@1.3.1:') depends_on('r-broom@0.4.2:', type=('build', 'run')) - depends_on('r-cli@2.4.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-cli@1.1.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-broom@0.5.2:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-broom@0.7.6:', type=('build', 'run'), when='@1.3.1:') depends_on('r-cli@1.0.0:', type=('build', 'run')) - depends_on('r-crayon@1.4.1:', when='@1.3.1:', type=('build', 'run')) + depends_on('r-cli@1.1.0:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-cli@2.4.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-crayon@1.3.4:', type=('build', 'run')) - depends_on('r-dbplyr@2.1.1:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-dbplyr@1.4.2:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-crayon@1.4.1:', type=('build', 'run'), when='@1.3.1:') depends_on('r-dbplyr@1.1.0:', type=('build', 'run')) - depends_on('r-dplyr@1.0.5:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-dplyr@0.8.3:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-dbplyr@1.4.2:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-dbplyr@2.1.1:', type=('build', 'run'), when='@1.3.1:') depends_on('r-dplyr@0.7.4:', type=('build', 'run')) - depends_on('r-dtplyr@1.1.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-forcats@0.5.1:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-forcats@0.4.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-dplyr@0.8.3:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-dplyr@1.0.5:', type=('build', 'run'), when='@1.3.1:') + depends_on('r-dtplyr@1.1.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-forcats@0.2.0:', type=('build', 'run')) - depends_on('r-googledrive@1.0.1:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-googlesheets4@0.3.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-ggplot2@3.3.3:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-ggplot2@3.2.1:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-forcats@0.4.0:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-forcats@0.5.1:', type=('build', 'run'), when='@1.3.1:') + depends_on('r-googledrive@1.0.1:', type=('build', 'run'), when='@1.3.1:') + depends_on('r-googlesheets4@0.3.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-ggplot2@2.2.1:', type=('build', 'run')) - depends_on('r-haven@2.3.1:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-haven@2.2.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-ggplot2@3.2.1:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-ggplot2@3.3.3:', type=('build', 'run'), when='@1.3.1:') depends_on('r-haven@1.1.0:', type=('build', 'run')) - depends_on('r-hms@1.0.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-hms@0.5.2:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-haven@2.2.0:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-haven@2.3.1:', type=('build', 'run'), when='@1.3.1:') depends_on('r-hms@0.3:', type=('build', 'run')) - depends_on('r-httr@1.4.2:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-httr@1.4.1:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-hms@0.5.2:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-hms@1.0.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-httr@1.3.1:', type=('build', 'run')) - depends_on('r-jsonlite@1.7.2:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-jsonlite@1.6:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-httr@1.4.1:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-httr@1.4.2:', type=('build', 'run'), when='@1.3.1:') depends_on('r-jsonlite@1.5:', type=('build', 'run')) - depends_on('r-lubridate@1.7.10:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-lubridate@1.7.4:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-jsonlite@1.6:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-jsonlite@1.7.2:', type=('build', 'run'), when='@1.3.1:') depends_on('r-lubridate@1.7.1:', type=('build', 'run')) - depends_on('r-magrittr@2.0.1:', when='@1.3.1:', type=('build', 'run')) + depends_on('r-lubridate@1.7.4:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-lubridate@1.7.10:', type=('build', 'run'), when='@1.3.1:') depends_on('r-magrittr@1.5:', type=('build', 'run')) - depends_on('r-modelr@0.1.8:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-modelr@0.1.5:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-magrittr@2.0.1:', type=('build', 'run'), when='@1.3.1:') depends_on('r-modelr@0.1.1:', type=('build', 'run')) - depends_on('r-pillar@1.6.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-pillar@1.4.2:', when='@1.3.0:', type=('build', 'run')) - depends_on('r-purrr@0.3.4:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-purrr@0.3.3:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-modelr@0.1.5:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-modelr@0.1.8:', type=('build', 'run'), when='@1.3.1:') + depends_on('r-pillar@1.4.2:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-pillar@1.6.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-purrr@0.2.4:', type=('build', 'run')) - depends_on('r-readr@1.4.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-readr@1.3.1:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-purrr@0.3.3:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-purrr@0.3.4:', type=('build', 'run'), when='@1.3.1:') depends_on('r-readr@1.1.1:', type=('build', 'run')) - depends_on('r-readxl@1.3.1:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-readr@1.3.1:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-readr@1.4.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-readxl@1.0.0:', type=('build', 'run')) - depends_on('r-reprex@2.0.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-reprex@0.3.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-readxl@1.3.1:', type=('build', 'run'), when='@1.3.0:') depends_on('r-reprex@0.1.1:', type=('build', 'run')) - depends_on('r-rlang@0.4.10:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-rlang@0.4.1:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-reprex@0.3.0:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-reprex@2.0.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-rlang@0.1.4:', type=('build', 'run')) - depends_on('r-rstudioapi@0.13:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-rstudioapi@0.10:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-rlang@0.4.1:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@1.3.1:') depends_on('r-rstudioapi@0.7:', type=('build', 'run')) - depends_on('r-rvest@1.0.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-rvest@0.3.5:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-rstudioapi@0.10:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-rstudioapi@0.13:', type=('build', 'run'), when='@1.3.1:') depends_on('r-rvest@0.3.2:', type=('build', 'run')) - depends_on('r-stringr@1.4.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-rvest@0.3.5:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-rvest@1.0.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-stringr@1.2.0:', type=('build', 'run')) - depends_on('r-tibble@3.1.0:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-tibble@2.1.3:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-stringr@1.4.0:', type=('build', 'run'), when='@1.3.0:') depends_on('r-tibble@1.3.4:', type=('build', 'run')) - depends_on('r-tidyr@1.1.3:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-tidyr@1.0.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-tibble@2.1.3:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-tibble@3.1.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-tidyr@0.7.2:', type=('build', 'run')) - depends_on('r-xml2@1.3.2:', when='@1.3.1:', type=('build', 'run')) - depends_on('r-xml2@1.2.2:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-tidyr@1.1.3:', type=('build', 'run'), when='@1.3.1:') depends_on('r-xml2@1.1.1:', type=('build', 'run')) + depends_on('r-xml2@1.2.2:', type=('build', 'run'), when='@1.3.0:') + depends_on('r-xml2@1.3.2:', type=('build', 'run'), when='@1.3.1:') diff --git a/var/spack/repos/builtin/packages/r-tiff/package.py b/var/spack/repos/builtin/packages/r-tiff/package.py index 9645ea7f5b..6cf31a9783 100644 --- a/var/spack/repos/builtin/packages/r-tiff/package.py +++ b/var/spack/repos/builtin/packages/r-tiff/package.py @@ -7,16 +7,16 @@ from spack import * class RTiff(RPackage): - """Read and write TIFF images + """Read and write TIFF images. This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.""" - homepage = "https://www.rforge.net/tiff/" - url = "https://cloud.r-project.org/src/contrib/tiff_0.1-5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tiff" + cran = "tiff" + version('0.1-11', sha256='b8c3ea15114d972f8140541c7b01f5ce2e5322af1f63c1a083aaf766fd3eec75') + version('0.1-10', sha256='535154e89e85e14fe697469d2c59826a44c7937e7eca2eaca1aee6b0fe320afe') version('0.1-6', sha256='623bd9c16a426df7e6056738c5d91da86ea9b49df375eea6b5127e4e458dc4fb') version('0.1-5', sha256='9514e6a9926fcddc29ce1dd12b1072ad8265900373f738de687ef4a1f9124e2b') diff --git a/var/spack/repos/builtin/packages/r-tigris/package.py b/var/spack/repos/builtin/packages/r-tigris/package.py index f5a93aa591..c1c17027d7 100644 --- a/var/spack/repos/builtin/packages/r-tigris/package.py +++ b/var/spack/repos/builtin/packages/r-tigris/package.py @@ -7,21 +7,20 @@ from spack import * class RTigris(RPackage): - """Load Census TIGER/Line Shapefiles + """Load Census TIGER/Line Shapefiles. - Download TIGER/Line shapefiles from the United States Census Bureau - and load into R as 'SpatialDataFrame' or 'sf' objects.""" + Download TIGER/Line shapefiles from the United States Census Bureau and + load into R as 'SpatialDataFrame' or 'sf' objects.""" - homepage = "https://cloud.r-project.org/package=tigris" - url = "https://cloud.r-project.org/src/contrib/tigris_0.5.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tigris" + cran = "tigris" + version('1.5', sha256='5ef71ca83817ad6b97ee86d1e560e8e86ee21bdcb1807ce40c945b3213c04472') version('1.0', sha256='97c76568c7cf0615abcbf923a0b4387f6b8c1915b9eb42d0c34cb0f707654403') version('0.8.2', sha256='ed8d6ab25332c2cc800858d58324bd8264772d8a916a3f0a8d489250a7e7140e') version('0.5.3', sha256='6ecf76f82216798465cd9704acb432caea47469ffc4953f1aaefa4d642a28445') - depends_on('r@3.0.0:', when='@:0.5.3', type=('build', 'run')) - depends_on('r@3.3.0:', when='@0.6.1:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.6.1:') depends_on('r-stringr', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-rgdal', type=('build', 'run')) @@ -32,4 +31,5 @@ class RTigris(RPackage): depends_on('r-uuid', type=('build', 'run')) depends_on('r-sf', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-rgeos', when='@:0.5.3', type=('build', 'run')) + + depends_on('r-rgeos', type=('build', 'run'), when='@:0.5.3') diff --git a/var/spack/repos/builtin/packages/r-timedate/package.py b/var/spack/repos/builtin/packages/r-timedate/package.py index 719c1afbd6..4054af3feb 100644 --- a/var/spack/repos/builtin/packages/r-timedate/package.py +++ b/var/spack/repos/builtin/packages/r-timedate/package.py @@ -7,12 +7,19 @@ from spack import * class RTimedate(RPackage): - """Environment for teaching "Financial Engineering and Computational - Finance". Managing chronological and calendar objects.""" + """Rmetrics - Chronological and Calendar Objects. - homepage = "https://cloud.r-project.org/package=timeDate" - url = "https://cloud.r-project.org/src/contrib/timeDate_3012.100.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/timeDate" + The 'timeDate' class fulfils the conventions of the ISO 8601 standard as + well as of the ANSI C and POSIX standards. Beyond these standards it + provides the "Financial Center" concept which allows to handle data records + collected in different time zones and mix them up to have always the proper + time stamps with respect to your personal financial center, or + alternatively to the GMT reference time. It can thus also handle time + stamps from historical data records from the same time zone, even if the + financial centers changed day light saving times at different calendar + dates.""" + + cran = "timeDate" version('3043.102', sha256='377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473') version('3042.101', sha256='6c8d4c7689b31c6a43555d9c7258516556ba03b132e5643691e3e317b89a8c6d') diff --git a/var/spack/repos/builtin/packages/r-tinytex/package.py b/var/spack/repos/builtin/packages/r-tinytex/package.py index 7ae85a0394..7a2d45f5bf 100644 --- a/var/spack/repos/builtin/packages/r-tinytex/package.py +++ b/var/spack/repos/builtin/packages/r-tinytex/package.py @@ -7,7 +7,8 @@ from spack import * class RTinytex(RPackage): - """Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents + """Helper Functions to Install and Maintain TeX Live, and Compile LaTeX + Documents. Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform, @@ -15,13 +16,14 @@ class RTinytex(RPackage): contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.""" - homepage = "https://github.com/yihui/tinytex" - cran = "tinytex" + cran = "tinytex" + version('0.36', sha256='65e6c1b981686573dd406e97b9639224cc2640d55a59d6381360449f10763b78') version('0.32', sha256='70fa28195ae6c8b8d43790205b49745c5a062aab78e64cec39bfbe5ed604c29f') version('0.28', sha256='76a0650aeab04eb252dc9cfa9ba855d88b09dfc2207c4a8ea2ea04fa0e0eea86') version('0.15', sha256='5d0988d3b7f763dfa65c722f177452a21344e428415a4b31aeb51478f0abad90') depends_on('r-xfun@0.5:', type=('build', 'run')) - depends_on('r-xfun@0.19:', when='@0.28:', type=('build', 'run')) - depends_on('r-xfun@0.23:', when='@0.32:', type=('build', 'run')) + depends_on('r-xfun@0.19:', type=('build', 'run'), when='@0.28:') + depends_on('r-xfun@0.23:', type=('build', 'run'), when='@0.32:') + depends_on('r-xfun@0.29:', type=('build', 'run'), when='@0.36:') diff --git a/var/spack/repos/builtin/packages/r-tmvnsim/package.py b/var/spack/repos/builtin/packages/r-tmvnsim/package.py index b1030ee805..7dc28e50ff 100644 --- a/var/spack/repos/builtin/packages/r-tmvnsim/package.py +++ b/var/spack/repos/builtin/packages/r-tmvnsim/package.py @@ -7,7 +7,7 @@ from spack import * class RTmvnsim(RPackage): - """Truncated Multivariate Normal Simulation + """Truncated Multivariate Normal Simulation. Importance sampling from the truncated multivariate normal using the GHK (Geweke-Hajivassiliou-Keane) simulator. Unlike Gibbs sampling which can get @@ -19,8 +19,6 @@ class RTmvnsim(RPackage): returned along with sampling weights, based on which, one can calculate integrals over truncated regions for multivariate normals.""" - homepage = "https://cloud.r-project.org/package=tmvnsim" - url = "https://cloud.r-project.org/src/contrib/tmvnsim_1.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tmvnsim" + cran = "tmvnsim" version('1.0-2', sha256='97f63d0bab3b240cc7bdbe6e6e74e90ad25a4382a345ee51a26fe3959edeba0f') diff --git a/var/spack/repos/builtin/packages/r-triebeard/package.py b/var/spack/repos/builtin/packages/r-triebeard/package.py index 71f8c569df..9d60082a39 100644 --- a/var/spack/repos/builtin/packages/r-triebeard/package.py +++ b/var/spack/repos/builtin/packages/r-triebeard/package.py @@ -7,11 +7,14 @@ from spack import * class RTriebeard(RPackage): - """triebeard: 'Radix' Trees in 'Rcpp'""" + """'Radix' Trees in 'Rcpp'. - homepage = "https://github.com/Ironholds/triebeard/" - url = "https://cloud.r-project.org/src/contrib/triebeard_0.3.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/triebeard" + 'Radix trees', or 'tries', are key-value data structures optimised for + efficient lookups, similar in purpose to hash tables. 'triebeard' provides + an implementation of 'radix trees' for use in R programming and in + developing packages with 'Rcpp'.""" + + cran = "triebeard" version('0.3.0', sha256='bf1dd6209cea1aab24e21a85375ca473ad11c2eff400d65c6202c0fb4ef91ec3') diff --git a/var/spack/repos/builtin/packages/r-trimcluster/package.py b/var/spack/repos/builtin/packages/r-trimcluster/package.py index 67fd5a5306..87bf0a4373 100644 --- a/var/spack/repos/builtin/packages/r-trimcluster/package.py +++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py @@ -7,14 +7,12 @@ from spack import * class RTrimcluster(RPackage): - """Cluster analysis with trimming + """Cluster analysis with trimming. Trimmed k-means clustering. The method is described in Cuesta-Albertos et al. (1997) <doi:10.1214/aos/1031833664>.""" - homepage = "https://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cloud.r-project.org/src/contrib/trimcluster_0.1-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/trimcluster" + cran = "trimcluster" version('0.1-5', sha256='9239f20e4a06ac2fa89e5d5d89b23a45c8c534a7264d89bede8a35d43dda518b') version('0.1-2.1', sha256='b64a872a6c2ad677dfeecc776c9fe5aff3e8bab6bc6a8c86957b5683fd5d2300') diff --git a/var/spack/repos/builtin/packages/r-truncdist/package.py b/var/spack/repos/builtin/packages/r-truncdist/package.py index 1745566c88..09db765886 100644 --- a/var/spack/repos/builtin/packages/r-truncdist/package.py +++ b/var/spack/repos/builtin/packages/r-truncdist/package.py @@ -7,11 +7,17 @@ from spack import * class RTruncdist(RPackage): - """truncdist: Truncated Random Variables""" + """Truncated Random Variables. - homepage = "https://cloud.r-project.org/package=truncdist" - url = "https://cloud.r-project.org/src/contrib/truncdist_1.0-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/truncdist" + A collection of tools to evaluate probability density functions, cumulative + distribution functions, quantile functions and random numbers for truncated + random variables. These functions are provided to also compute the expected + value and variance. Nadarajah and Kotz (2006) developed most of the + functions. QQ plots can be produced. All the probability functions in the + stats, stats4 and evd packages are automatically available for + truncation.""" + + cran = "truncdist" version('1.0-2', sha256='b848b68bdd983bd496fa7327632ffa8add8d2231229b8af5c8bc29d823e1300a') diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py index 0d541c4181..e4010cf532 100644 --- a/var/spack/repos/builtin/packages/r-truncnorm/package.py +++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py @@ -7,12 +7,12 @@ from spack import * class RTruncnorm(RPackage): - """Density, probability, quantile and random number generation functions - for the truncated normal distribution.""" + """Truncated Normal Distribution. - homepage = "https://cloud.r-project.org/package=truncnorm" - url = "https://cloud.r-project.org/src/contrib/truncnorm_1.0-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/truncnorm" + Density, probability, quantile and random number generation functions for + the truncated normal distribution.""" + + cran = "truncnorm" version('1.0-8', sha256='49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e') diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py index f8689e065f..8a4e72faed 100644 --- a/var/spack/repos/builtin/packages/r-trust/package.py +++ b/var/spack/repos/builtin/packages/r-trust/package.py @@ -7,14 +7,12 @@ from spack import * class RTrust(RPackage): - """Trust Region Optimization + """Trust Region Optimization. Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.""" - homepage = "https://www.stat.umn.edu/geyer/trust" - url = "https://cloud.r-project.org/src/contrib/trust_0.1-7.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/trust" + cran = "trust" version('0.1-8', sha256='952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac') version('0.1-7', sha256='e3d15aa84a71becd2824253d4a8156bdf1ab9ac3b72ced0cd53f3bb370ac6f04') diff --git a/var/spack/repos/builtin/packages/r-tseries/package.py b/var/spack/repos/builtin/packages/r-tseries/package.py index 8ae8ffe6b4..4ff59ca012 100644 --- a/var/spack/repos/builtin/packages/r-tseries/package.py +++ b/var/spack/repos/builtin/packages/r-tseries/package.py @@ -7,14 +7,11 @@ from spack import * class RTseries(RPackage): - """Time series analysis and computational finance + """Time series analysis and computational finance.""" - Time series analysis and computational finance.""" - - homepage = "https://cloud.r-project.org/package=tseries" - url = "https://cloud.r-project.org/src/contrib/tseries_0.10-42.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tseries" + cran = "tseries" + version('0.10-49', sha256='45bf26d8f41f12a72954bbe5fb6f4da6cc4ef29ee075c49fe7cc8456926c14ba') version('0.10-48', sha256='53bd22708c936205c5f839a10f2e302524d2cc54dc309e7d885ebd081ccb4471') version('0.10-47', sha256='202377df56806fe611c2e12c4d9732c71b71220726e2defa7e568d2b5b62fb7b') version('0.10-46', sha256='12940afd1d466401160e46f993ed4baf28a42cef98d3757b66ee15e916e07222') diff --git a/var/spack/repos/builtin/packages/r-tsne/package.py b/var/spack/repos/builtin/packages/r-tsne/package.py index 826f19b95a..bb65555bf5 100644 --- a/var/spack/repos/builtin/packages/r-tsne/package.py +++ b/var/spack/repos/builtin/packages/r-tsne/package.py @@ -7,11 +7,11 @@ from spack import * class RTsne(RPackage): - """A "pure R" implementation of the t-SNE algorithm.""" + """T-Distributed Stochastic Neighbor Embedding for R (t-SNE). - homepage = "https://cloud.r-project.org/package=tsne" - url = "https://cloud.r-project.org/src/contrib/tsne_0.1-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tnse" + A "pure R" implementation of the t-SNE algorithm.""" + + cran = "tsne" version('0.1-3', sha256='66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69') version('0.1-2', sha256='c6c3455e0f0f5dcac14299b3dfeb1a5f1bfe5623cdaf602afc892491d3d1058b') diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py index 28aa3a1f2d..60271d22ce 100644 --- a/var/spack/repos/builtin/packages/r-ttr/package.py +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -7,16 +7,15 @@ from spack import * class RTtr(RPackage): - """Technical Trading Rules + """Technical Trading Rules. A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.""" - homepage = "https://github.com/joshuaulrich/TTR" - url = "https://cloud.r-project.org/src/contrib/TTR_0.23-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/TTR" + cran = "TTR" + version('0.24.3', sha256='4d9aef32647664be5cf965b05f21ed62cde9425fa87c21530852e05ef7aaba87') version('0.24.2', sha256='2587b988d9199474a19470b9b999b99133d0d8aa45410813e05c5f0ed763711b') version('0.23-4', sha256='eb17604da986213b3b924f0af65c3d089502a658a253ee34f6b8f6caccf6bfa2') version('0.23-3', sha256='2136032c7a2cd2a82518a4412fc655ecb16597b123dbdebe5684caef9f15261f') @@ -24,4 +23,4 @@ class RTtr(RPackage): depends_on('r-xts@0.10-0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) - depends_on('r-curl', when='@0.23-4:', type=('build', 'run')) + depends_on('r-curl', type=('build', 'run'), when='@0.23-4:') diff --git a/var/spack/repos/builtin/packages/r-tweenr/package.py b/var/spack/repos/builtin/packages/r-tweenr/package.py index a1315a83c4..04ceec1cb0 100644 --- a/var/spack/repos/builtin/packages/r-tweenr/package.py +++ b/var/spack/repos/builtin/packages/r-tweenr/package.py @@ -7,16 +7,21 @@ from spack import * class RTweenr(RPackage): - """tweenr: Interpolate Data for Smooth Animations""" + """Interpolate Data for Smooth Animations. - homepage = "https://github.com/thomasp85/tweenr" - url = "https://cloud.r-project.org/src/contrib/tweenr_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/tweenr" + In order to create smooth animation between states of data, tweening is + necessary. This package provides a range of functions for creating tweened + data that can be used as basis for animation. Furthermore it adds a number + of vectorized interpolaters for common R data types such as numeric, date + and colour.""" + cran = "tweenr" + + version('1.0.2', sha256='1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f') version('1.0.1', sha256='efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b') depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.3:', type=('build', 'run')) depends_on('r-farver', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-rcpp@0.12.3:', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tzdb/package.py b/var/spack/repos/builtin/packages/r-tzdb/package.py index 17168f2179..ea2b2509cc 100644 --- a/var/spack/repos/builtin/packages/r-tzdb/package.py +++ b/var/spack/repos/builtin/packages/r-tzdb/package.py @@ -19,8 +19,7 @@ class RTzdb(RPackage): are provided for calendar specific calculations, along with a limited interface for time zone manipulations.""" - homepage = "https://github.com/r-lib/tzdb" - cran = "tzdb" + cran = "tzdb" version('0.2.0', sha256='c335905d452b400af7ed54b916b5246cb3f47ede0602911a2bcb25a1cf56d5a9') diff --git a/var/spack/repos/builtin/packages/r-ucminf/package.py b/var/spack/repos/builtin/packages/r-ucminf/package.py index 65c214cf81..e3e7764934 100644 --- a/var/spack/repos/builtin/packages/r-ucminf/package.py +++ b/var/spack/repos/builtin/packages/r-ucminf/package.py @@ -7,14 +7,14 @@ from spack import * class RUcminf(RPackage): - """An algorithm for general-purpose unconstrained non-linear optimization. + """General-Purpose Unconstrained Non-Linear Optimization. + + An algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of 'ucminf' is designed for easy interchange with 'optim'.""" - homepage = "https://cloud.r-project.org/package=ucminf" - url = "https://cloud.r-project.org/src/contrib/ucminf_1.1-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/ucminf" + cran = "ucminf" version('1.1-4', sha256='a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07') diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py index 904d9ef6ef..448dc9acb7 100644 --- a/var/spack/repos/builtin/packages/r-udunits2/package.py +++ b/var/spack/repos/builtin/packages/r-udunits2/package.py @@ -7,12 +7,13 @@ from spack import * class RUdunits2(RPackage): - """Provides simple bindings to Unidata's udunits library.""" + """Udunits-2 Bindings for R. - homepage = "https://github.com/pacificclimate/Rudunits2" - url = "https://cloud.r-project.org/src/contrib/udunits2_0.13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/udunits2" + Provides simple bindings to Unidata's udunits library.""" + cran = "udunits2" + + version('0.13.2', sha256='ee00898801b3282717cba40a9ef930515506386aa82a050356d1a9c80a9f5969') version('0.13', sha256='d155d3c07f6202b65dec4075ffd1e1c3f4f35f5fdece8cfb319d39256a3e5b79') depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py index 54e778bdbc..b812e276fd 100644 --- a/var/spack/repos/builtin/packages/r-units/package.py +++ b/var/spack/repos/builtin/packages/r-units/package.py @@ -7,7 +7,7 @@ from spack import * class RUnits(RPackage): - """Measurement Units for R Vectors + """Measurement Units for R Vectors. Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising @@ -18,10 +18,9 @@ class RUnits(RPackage): <doi:10.32614/RJ-2016-061>), included in this package as a vignette; see 'citation("units")' for details.""" - homepage = "https://github.com/edzer/units/" - url = "https://cloud.r-project.org/src/contrib/units_0.4-6.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/units" + cran = "units" + version('0.7-2', sha256='b90be023431100632b3081747af9e743e615452b4ad38810991f7b024b7040eb') version('0.6-7', sha256='3f73a62bafdbe0f93bbf00ac4b1adb8f919dd04649ff8f1d007f2986e35cb7e5') version('0.6-3', sha256='03de88d9dcfe80d22dd3813413f33657c576aed24a8091dbfc7f68602020a64f') version('0.6-2', sha256='5e286775d0712c8e15b6ae3a533d4c4349b0f6410c2d9d897ca519c3d0e5f170') @@ -29,5 +28,6 @@ class RUnits(RPackage): depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-rcpp@0.12.10:', type=('build', 'run')) - depends_on('r-udunits2@0.13:', when='@:0.5-1', type=('build', 'run')) depends_on('udunits', when='@0.6-0:') + + depends_on('r-udunits2@0.13:', type=('build', 'run'), when='@:0.5-1') diff --git a/var/spack/repos/builtin/packages/r-upsetr/package.py b/var/spack/repos/builtin/packages/r-upsetr/package.py index 244e0894b1..eccbdcb0c2 100644 --- a/var/spack/repos/builtin/packages/r-upsetr/package.py +++ b/var/spack/repos/builtin/packages/r-upsetr/package.py @@ -7,12 +7,14 @@ from spack import * class RUpsetr(RPackage): - """UpSetR: A More Scalable Alternative to Venn and Euler Diagrams - forVisualizing Intersecting Sets""" + """A More Scalable Alternative to Venn and Euler Diagrams for Visualizing + Intersecting Sets. - homepage = "https://github.com/hms-dbmi/UpSetR" - url = "https://cloud.r-project.org/src/contrib/UpSetR_1.4.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/UpSetR" + Creates visualizations of intersecting sets using a novel matrix design, + along with visualizations of several common set, element and attribute + related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.""" + + cran = "UpSetR" version('1.4.0', sha256='351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100') diff --git a/var/spack/repos/builtin/packages/r-urca/package.py b/var/spack/repos/builtin/packages/r-urca/package.py index 0a024f1aae..5f773d8b7e 100644 --- a/var/spack/repos/builtin/packages/r-urca/package.py +++ b/var/spack/repos/builtin/packages/r-urca/package.py @@ -7,12 +7,12 @@ from spack import * class RUrca(RPackage): - """Unit root and cointegration tests encountered in applied econometric + """Unit Root and Cointegration Tests for Time Series Data. + + Unit root and cointegration tests encountered in applied econometric analysis are implemented.""" - homepage = "https://cloud.r-project.org/package=urca" - url = "https://cloud.r-project.org/src/contrib/urca_1.3-0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/urca" + cran = "urca" version('1.3-0', sha256='621cc82398e25b58b4a16edf000ed0a1484d9a0bc458f734e97b6f371cc76aaa') diff --git a/var/spack/repos/builtin/packages/r-urltools/package.py b/var/spack/repos/builtin/packages/r-urltools/package.py index f1098c3916..eb6355eb98 100644 --- a/var/spack/repos/builtin/packages/r-urltools/package.py +++ b/var/spack/repos/builtin/packages/r-urltools/package.py @@ -7,11 +7,16 @@ from spack import * class RUrltools(RPackage): - """urltools: Vectorised Tools for URL Handling and Parsing""" + """Vectorised Tools for URL Handling and Parsing. - homepage = "https://github.com/Ironholds/urltools/" - url = "https://cloud.r-project.org/src/contrib/urltools_1.7.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/urltools" + A toolkit for all URL-handling needs, including encoding and decoding, + parsing, parameter extraction and modification. All functions are designed + to be both fast and entirely vectorised. It is intended to be useful for + people dealing with web-related datasets, such as server-side logs, + although may be useful for other situations involving large sets of + URLs.""" + + cran = "urltools" version('1.7.3', sha256='6020355c1b16a9e3956674e5dea9ac5c035c8eb3eb6bbdd841a2b5528cafa313') diff --git a/var/spack/repos/builtin/packages/r-usethis/package.py b/var/spack/repos/builtin/packages/r-usethis/package.py index 48229a97e1..cda4f1c143 100644 --- a/var/spack/repos/builtin/packages/r-usethis/package.py +++ b/var/spack/repos/builtin/packages/r-usethis/package.py @@ -7,45 +7,52 @@ from spack import * class RUsethis(RPackage): - """Automate Package and Project Setup + """Automate Package and Project Setup. Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.""" - homepage = "https://usethis.r-lib.org/" - url = "https://cloud.r-project.org/src/contrib/usethis_1.5.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/usethis" + cran = "usethis" + version('2.1.5', sha256='7d539e16ecdc1cd45ba1a215d42d8b9c16bc38280ddd27048003dbb37b16f052') version('2.0.0', sha256='22aa2b59f36a8701a4648554c7b0e010253bf917a0f431f06efac7d8a6b59854') version('1.6.1', sha256='60339059a97ed07dea7f8908b828b5bb42e0fd0b471165c061bc9660b0d59d6f') version('1.5.1', sha256='9e3920a04b0df82adf59eef2c1b2b4d835c4a757a51b3c163b8fc619172f561d') depends_on('r@3.2:', type=('build', 'run')) - depends_on('r-cli', when='@1.6.1:', type=('build', 'run')) + depends_on('r@3.4:', type=('build', 'run'), when='@2.1.5:') + depends_on('r-cli', type=('build', 'run'), when='@1.6.1:') + depends_on('r-cli@3.0.1:', type=('build', 'run'), when='@2.1.5:') depends_on('r-clipr@0.3.0:', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) depends_on('r-curl@2.7:', type=('build', 'run')) depends_on('r-desc', type=('build', 'run')) + depends_on('r-desc@1.4.0:', type=('build', 'run'), when='@2.1.5:') depends_on('r-fs@1.3.0:', type=('build', 'run')) - depends_on('r-gert@1.0.2:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-gert@1.0.2:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-gert@1.4.1:', type=('build', 'run'), when='@2.1.5:') depends_on('r-gh', type=('build', 'run')) - depends_on('r-gh@1.1.0:', when='@1.6.1:', type=('build', 'run')) - depends_on('r-gh@1.2.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-gh@1.1.0:', type=('build', 'run'), when='@1.6.1:') + depends_on('r-gh@1.2.0:', type=('build', 'run'), when='@2.0.0:') + depends_on('r-gh@1.2.1:', type=('build', 'run'), when='@2.1.5:') depends_on('r-glue@1.3.0:', type=('build', 'run')) - depends_on('r-jsonlite', when='@2.0.0:', type=('build', 'run')) - depends_on('r-lifecycle', when='@2.0.0:', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run'), when='@2.0.0:') + depends_on('r-lifecycle', type=('build', 'run'), when='@2.0.0:') + depends_on('r-lifecycle@1.0.0:', type=('build', 'run'), when='@2.1.5:') depends_on('r-purrr', type=('build', 'run')) - depends_on('r-rappdirs', when='@2.0.0:', type=('build', 'run')) + depends_on('r-rappdirs', type=('build', 'run'), when='@2.0.0:') depends_on('r-rlang', type=('build', 'run')) - depends_on('r-rlang@0.4.3:', when='@1.6.1:', type=('build', 'run')) + depends_on('r-rlang@0.4.3:', type=('build', 'run'), when='@1.6.1:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@2.1.5:') depends_on('r-rprojroot@1.2:', type=('build', 'run')) depends_on('r-rstudioapi', type=('build', 'run')) depends_on('r-whisker', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) - depends_on('r-withr@2.3.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-withr@2.3.0:', type=('build', 'run'), when='@2.0.0:') depends_on('r-yaml', type=('build', 'run')) - depends_on('r-clisymbols', when='@:1.5', type=('build', 'run')) - depends_on('r-git2r@0.23:', when='@:1.6.1', type=('build', 'run')) - depends_on('r-rematch2', when='@1.6.1', type=('build', 'run')) + + depends_on('r-clisymbols', type=('build', 'run'), when='@:1.5') + depends_on('r-git2r@0.23:', type=('build', 'run'), when='@:1.6.1') + depends_on('r-rematch2', type=('build', 'run'), when='@1.6.1') diff --git a/var/spack/repos/builtin/packages/r-utf8/package.py b/var/spack/repos/builtin/packages/r-utf8/package.py index 383a7b8d5b..8441eaaeeb 100644 --- a/var/spack/repos/builtin/packages/r-utf8/package.py +++ b/var/spack/repos/builtin/packages/r-utf8/package.py @@ -7,13 +7,14 @@ from spack import * class RUtf8(RPackage): - """Process and print 'UTF-8' encoded international text - (Unicode). Input, validate, normalize, encode, format, and display.""" + """Unicode Text Processing. - homepage = "https://cloud.r-project.org/package=utf8" - url = "https://cloud.r-project.org/src/contrib/utf8_1.1.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/utf8" + Process and print 'UTF-8' encoded international text (Unicode). Input, + validate, normalize, encode, format, and display.""" + cran = "utf8" + + version('1.2.2', sha256='a71aee87d43a9bcf29249c7a5a2e9ca1d2a836e8d5ee3a264d3062f25378d8f4') version('1.1.4', sha256='f6da9cadfc683057d45f54b43312a359cf96ec2731c0dda18a8eae31d1e31e54') version('1.1.3', sha256='43b394c3274ba0f66719d28dc4a7babeb87187e766de8d8ca716e0548091440f') version('1.1.2', sha256='148517aadb75d82aba61f63afe2a30d254abebbdc7e32dd0830e12ff443915b9') diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py index 3bb287e947..875f199d32 100644 --- a/var/spack/repos/builtin/packages/r-uuid/package.py +++ b/var/spack/repos/builtin/packages/r-uuid/package.py @@ -8,15 +8,14 @@ from spack import * class RUuid(RPackage): - """Tools for Generating and Handling of UUIDs + """Tools for Generating and Handling of UUIDs. Tools for generating and handling of UUIDs (Universally Unique Identifiers).""" - homepage = "https://www.rforge.net/uuid" - url = "https://cloud.r-project.org/src/contrib/uuid_0.1-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/uuid" + cran = "uuid" + version('1.0-3', sha256='456e4633659f20242fd7cd585ad005a3e07265f1d1db383fca6794c8ac2c8346') version('0.1-4', sha256='98e0249dda17434bfa209c2058e9911e576963d4599be9f7ea946e664f8ca93e') version('0.1-2', sha256='dd71704dc336b0857981b92a75ed9877d4ca47780b1682def28839304cd3b1be') diff --git a/var/spack/repos/builtin/packages/r-uwot/package.py b/var/spack/repos/builtin/packages/r-uwot/package.py index 32a0288a4c..e7bb652c07 100644 --- a/var/spack/repos/builtin/packages/r-uwot/package.py +++ b/var/spack/repos/builtin/packages/r-uwot/package.py @@ -7,7 +7,8 @@ from spack import * class RUwot(RPackage): - """The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction + """The Uniform Manifold Approximation and Projection (UMAP) Method for + Dimensionality Reduction. An implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018) <arXiv:1802.03426>. It @@ -19,10 +20,9 @@ class RUwot(RPackage): (<https://github.com/jlmelville/uwot>) for more documentation and examples.""" - homepage = "https://github.com/jlmelville/uwot" - url = "https://cloud.r-project.org/src/contrib/uwot_0.1.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/uwot" + cran = "uwot" + version('0.1.11', sha256='4fcf90f1369a2a1f01db9e05a2365b155b2ada8e51e1f7f3ba5122d86affd41b') version('0.1.10', sha256='6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23') version('0.1.3', sha256='4936e6922444cae8a71735e945b6bb0828a1012232eb94568054f78451c406d7') @@ -31,9 +31,10 @@ class RUwot(RPackage): depends_on('r-fnn', type=('build', 'run')) depends_on('r-rspectra', type=('build', 'run')) depends_on('r-rcppannoy@0.0.11:', type=('build', 'run')) - depends_on('r-rcppannoy@0.0.17:', when='@0.1.10:', type=('build', 'run')) + depends_on('r-rcppannoy@0.0.17:', type=('build', 'run'), when='@0.1.10:') depends_on('r-irlba', type=('build', 'run')) depends_on('r-rcppprogress', type=('build', 'run')) depends_on('r-dqrng', type=('build', 'run')) - depends_on('r-rcppparallel', when='@:0.1.3', type=('build', 'run')) - depends_on('gmake', when='@:0.1.3', type='build') + + depends_on('r-rcppparallel', type=('build', 'run'), when='@:0.1.3') + depends_on('gmake', type='build', when='@:0.1.3') diff --git a/var/spack/repos/builtin/packages/r-v8/package.py b/var/spack/repos/builtin/packages/r-v8/package.py index 1609e9b9bb..a054b9a04c 100644 --- a/var/spack/repos/builtin/packages/r-v8/package.py +++ b/var/spack/repos/builtin/packages/r-v8/package.py @@ -7,11 +7,15 @@ from spack import * class RV8(RPackage): - """V8: Embedded JavaScript and WebAssembly Engine for R""" + """Embedded JavaScript and WebAssembly Engine for R. + + An R interface to V8: Google's open source JavaScript and WebAssembly + engine. This package can be compiled either with V8 version 6 and up or + NodeJS when built as a shared library.""" - homepage = "https://github.com/jeroen/v8" cran = "V8" + version('4.0.0', sha256='146a4cb671264f865ac2f2e35bfdfb37e2df70e4f6784354fb6e8a80a19dbbc8') version('3.6.0', sha256='a3969898bf4a7c13d3130fae0d385cd048d46372ff4a412917b914b159261377') version('3.4.0', sha256='f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd', deprecated=True) diff --git a/var/spack/repos/builtin/packages/r-varselrf/package.py b/var/spack/repos/builtin/packages/r-varselrf/package.py index 8365d3b3fd..030ec89edf 100644 --- a/var/spack/repos/builtin/packages/r-varselrf/package.py +++ b/var/spack/repos/builtin/packages/r-varselrf/package.py @@ -7,16 +7,16 @@ from spack import * class RVarselrf(RPackage): - """Variable selection from random forests using both backwards variable + """Variable Selection using Random Forests. + + Variable selection from random forests using both backwards variable elimination (for the selection of small sets of non-redundant variables) and selection based on the importance spectrum (somewhat similar to scree - plots; for the selection of large, potentially highly-correlated variables) - . Main applications in high-dimensional data (e.g., microarray data, - and other genomics and proteomics applications).""" + plots; for the selection of large, potentially highly-correlated + variables). Main applications in high-dimensional data (e.g., microarray + data, and other genomics and proteomics applications).""" - homepage = "https://ligarto.org/rdiaz/Software/Software.html" - url = "https://cloud.r-project.org/src/contrib/varSelRF_0.7-8.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/varSelRF" + cran = "varSelRF" version('0.7-8', sha256='719487fb560cb4733816bafe4cbc958a132674825e3b9d4f82ce8f2003cd8940') diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py index 0cf94b091c..aa2d4d3104 100644 --- a/var/spack/repos/builtin/packages/r-vcd/package.py +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -7,19 +7,18 @@ from spack import * class RVcd(RPackage): - """Visualizing Categorical Data + """Visualizing Categorical Data. - Visualization techniques, data sets, summary and inference procedures - aimed particularly at categorical data. Special emphasis is given to highly + Visualization techniques, data sets, summary and inference procedures aimed + particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).""" - homepage = "https://cloud.r-project.org/package=vcd" - url = "https://cloud.r-project.org/src/contrib/vcd_1.4-1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/vcd" + cran = "vcd" + version('1.4-9', sha256='a5b420ad5ff1a27fa92f98099a8b43f2dded7e5f60297b3e4d947ad6f039568f') version('1.4-8', sha256='236fcb183152f6e9d131eeb3931d5a064a5ff79be91e4533df9148fd2ff41e0c') version('1.4-4', sha256='a561adf120b5ce41b66e0c0c321542fcddc772eb12b3d7020d86e9cd014ce9d2') version('1.4-3', sha256='17ce89927421d9cd01285b6093eeaaecb1e7252388007f66d3b9222e58cc5f15') diff --git a/var/spack/repos/builtin/packages/r-vcfr/package.py b/var/spack/repos/builtin/packages/r-vcfr/package.py index 412e982a4b..3622914b1d 100644 --- a/var/spack/repos/builtin/packages/r-vcfr/package.py +++ b/var/spack/repos/builtin/packages/r-vcfr/package.py @@ -7,7 +7,7 @@ from spack import * class RVcfr(RPackage): - """Manipulate and Visualize VCF Data + """Manipulate and Visualize VCF Data. Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is @@ -18,8 +18,7 @@ class RVcfr(RPackage): converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.""" - homepage = "https://github.com/knausb/vcfR" - cran = "vcfR" + cran = "vcfR" maintainers = ['dorton21'] diff --git a/var/spack/repos/builtin/packages/r-vctrs/package.py b/var/spack/repos/builtin/packages/r-vctrs/package.py index 4bcbdbe515..2a65475e9b 100644 --- a/var/spack/repos/builtin/packages/r-vctrs/package.py +++ b/var/spack/repos/builtin/packages/r-vctrs/package.py @@ -7,14 +7,13 @@ from spack import * class RVctrs(RPackage): - """Vector Helpers + """Vector Helpers. Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analyzing function interfaces.""" - homepage = "https://github.com/r-lib/vctrs" cran = "vctrs" version('0.3.8', sha256='7f4e8b75eda115e69dddf714f0643eb889ad61017cdc13af24389aab2a2d1bb1') @@ -23,11 +22,12 @@ class RVctrs(RPackage): version('0.2.0', sha256='5bce8f228182ecaa51230d00ad8a018de9cf2579703e82244e0931fe31f20016') depends_on('r@3.2:', type=('build', 'run')) - depends_on('r@3.3:', when='@0.3.5:', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run'), when='@0.3.5:') depends_on('r-ellipsis@0.2.0:', type=('build', 'run')) depends_on('r-glue', type=('build', 'run')) depends_on('r-rlang@0.4.0:', type=('build', 'run')) - depends_on('r-rlang@0.4.7:', when='@0.3.5:', type=('build', 'run')) - depends_on('r-rlang@0.4.10:', when='@0.3.7:', type=('build', 'run')) - depends_on('r-digest', when='@:0.3.6', type=('build', 'run')) - depends_on('r-zeallot', when='@:0.2.0', type=('build', 'run')) + depends_on('r-rlang@0.4.7:', type=('build', 'run'), when='@0.3.5:') + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@0.3.7:') + + depends_on('r-digest', type=('build', 'run'), when='@:0.3.6') + depends_on('r-zeallot', type=('build', 'run'), when='@:0.2.0') diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py index a2fa09668a..688db4af04 100644 --- a/var/spack/repos/builtin/packages/r-vegan/package.py +++ b/var/spack/repos/builtin/packages/r-vegan/package.py @@ -7,14 +7,12 @@ from spack import * class RVegan(RPackage): - """Community Ecology Package + """Community Ecology Package. - Ordination methods, diversity analysis and other functions for - community and vegetation ecologists.""" + Ordination methods, diversity analysis and other functions for community + and vegetation ecologists.""" - homepage = "https://github.com/vegandevs/vegan" - url = "https://cloud.r-project.org/src/contrib/vegan_2.4-3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/vegan" + cran = "vegan" version('2.5-7', sha256='e63b586951ea7d8b0118811f329c700212892ec1db3b93951603ce1d68aa462a') version('2.5-5', sha256='876b5266f29f3034fed881020d16f476e62d145a00cb450a1a213e019e056971') @@ -22,9 +20,9 @@ class RVegan(RPackage): version('2.4-3', sha256='2556b1281a62e53f32bb57539bc600c00a599d0699867912220535d1a3ebec97') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.1.0:', when='@2.5-1', type=('build', 'run')) - depends_on('r@3.2.0:', when='@2.5-2:2.5-4', type=('build', 'run')) - depends_on('r@3.4.0:', when='@2.5-5:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@2.5-1') + depends_on('r@3.2.0:', type=('build', 'run'), when='@2.5-2:') + depends_on('r@3.4.0:', type=('build', 'run'), when='@2.5-5:') depends_on('r-permute@0.9-0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vfs/package.py b/var/spack/repos/builtin/packages/r-vfs/package.py index fbcfc609ec..ef72634d0a 100644 --- a/var/spack/repos/builtin/packages/r-vfs/package.py +++ b/var/spack/repos/builtin/packages/r-vfs/package.py @@ -7,11 +7,16 @@ from spack import * class RVfs(RPackage): - """VFS: Vegetated Filter Strip and Erosion Model""" + """Vegetated Filter Strip and Erosion Model. - homepage = "https://cloud.r-project.org/package=VFS" - url = "https://cloud.r-project.org/src/contrib/VFS_1.0.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/VFS" + Empirical models for runoff, erosion, and phosphorus loss across a + vegetated filter strip, given slope, soils, climate, and vegetation (Gall + et al., 2018) <doi:10.1007/s00477-017-1505-x>. It also includes functions + for deriving climate parameters from measured daily weather data, and for + simulating rainfall. Models implemented include MUSLE (Williams, 1975) and + APLE (Vadas et al., 2009 <doi:10.2134/jeq2008.0337>).""" + + cran = "VFS" version('1.0.2', sha256='8ff7e7e13919ff21f10c7c693ef596a2c7b57c7ca37d79278e443ed122a21aad') diff --git a/var/spack/repos/builtin/packages/r-vgam/package.py b/var/spack/repos/builtin/packages/r-vgam/package.py index 9c01f66037..26644803a6 100644 --- a/var/spack/repos/builtin/packages/r-vgam/package.py +++ b/var/spack/repos/builtin/packages/r-vgam/package.py @@ -7,7 +7,7 @@ from spack import * class RVgam(RPackage): - """Vector Generalized Linear and Additive Models + """Vector Generalized Linear and Additive Models. An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted @@ -26,9 +26,7 @@ class RVgam(RPackage): effect detection is implemented. Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.""" - homepage = "https://cloud.r-project.org/package=VGAM" - url = "https://cloud.r-project.org/src/contrib/VGAM_1.0-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/VGAM" + cran = "VGAM" version('1.1-5', sha256='30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb') version('1.1-1', sha256='de192bd65a7e8818728008de8e60e6dd3b61a13616c887a43e0ccc8147c7da52') @@ -40,6 +38,6 @@ class RVgam(RPackage): version('1.0-0', sha256='6acdd7db49c0987c565870afe593160ceba72a6ca4a84e6da3cf6f74d1fa02e1') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r@3.1.0:', when='@1.0-2:1.0-3', type=('build', 'run')) - depends_on('r@3.4.0:', when='@1.0-4:', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.1-5:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@1.0-2:') + depends_on('r@3.4.0:', type=('build', 'run'), when='@1.0-4:') + depends_on('r@3.5.0:', type=('build', 'run'), when='@1.1-5:') diff --git a/var/spack/repos/builtin/packages/r-vioplot/package.py b/var/spack/repos/builtin/packages/r-vioplot/package.py index ae32159601..bf5a43851a 100644 --- a/var/spack/repos/builtin/packages/r-vioplot/package.py +++ b/var/spack/repos/builtin/packages/r-vioplot/package.py @@ -7,15 +7,14 @@ from spack import * class RVioplot(RPackage): - """Violin Plot + """Violin Plot. A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots. """ - homepage = "https://cloud.r-project.org/package=vioplot" - url = "https://cloud.r-project.org/src/contrib/vioplot_0.3.2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/vioplot" + cran = "vioplot" + version('0.3.7', sha256='06475d9a47644245ec91598e9aaef7db1c393802d9fc314420ac5139ae56adb6') version('0.3.5', sha256='1b64833c1bd6851036cf1c400c7d0036a047e71def94a399c897263b4b303e2a') version('0.3.2', sha256='7b51d0876903a3c315744cb051ac61920eeaa1f0694814959edfae43ce956e8e') diff --git a/var/spack/repos/builtin/packages/r-vipor/package.py b/var/spack/repos/builtin/packages/r-vipor/package.py index 293e5603b8..401ae6adde 100644 --- a/var/spack/repos/builtin/packages/r-vipor/package.py +++ b/var/spack/repos/builtin/packages/r-vipor/package.py @@ -7,11 +7,13 @@ from spack import * class RVipor(RPackage): - """Plot Categorical Data Using Quasirandom Noise and Density Estimates""" + """Plot Categorical Data Using Quasirandom Noise and Density Estimates. - homepage = "https://cloud.r-project.org/package=vipor" - url = "https://cloud.r-project.org/src/contrib/vipor_0.4.5.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/vipor" + Generate a violin point plot, a combination of a violin/histogram plot and + a scatter plot by offsetting points within a category based on their + density using quasirandom noise.""" + + cran = "vipor" version('0.4.5', sha256='7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84') version('0.4.4', sha256='5abfd7869dae42ae2e4f52206c23433a43b485b1220685e445877ee5864a3f5c') diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py index 02ed68cbdb..36bf29e579 100644 --- a/var/spack/repos/builtin/packages/r-viridis/package.py +++ b/var/spack/repos/builtin/packages/r-viridis/package.py @@ -7,17 +7,25 @@ from spack import * class RViridis(RPackage): - """viridis: Default Color Maps from 'matplotlib'""" + """Colorblind-Friendly Color Maps for R. - homepage = "https://github.com/sjmgarnier/viridis" - url = "https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/viridis" + Color maps designed to improve graph readability for readers with common + forms of color blindness and/or color vision deficiency. The color maps are + also perceptually-uniform, both in regular form and also when converted to + black-and-white for printing. This package also contains 'ggplot2' bindings + for discrete and continuous color and fill scales. A lean version of the + package called 'viridisLite' that does not include the 'ggplot2' bindings + can be found at <https://cran.r-project.org/package=viridisLite>.""" + cran = "viridis" + + version('0.6.2', sha256='69b58cd1d992710a08b0b227fd0a9590430eea3ed4858099412f910617e41311') version('0.5.1', sha256='ddf267515838c6eb092938133035cee62ab6a78760413bfc28b8256165701918') version('0.5.0', sha256='fea477172c1e11be40554545260b36d6ddff3fe6bc3bbed87813ffb77c5546cd') version('0.4.0', sha256='93d2ded68ed7cec5633c260dbc47051416147aae074f29ebe135cc329250b00e') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-viridislite@0.3.0:', type=('build', 'run')) + depends_on('r-viridislite@0.4.0:', type=('build', 'run'), when='@0.6.2:') depends_on('r-ggplot2@1.0.1:', type=('build', 'run')) depends_on('r-gridextra', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-viridislite/package.py b/var/spack/repos/builtin/packages/r-viridislite/package.py index dfbb0737da..50eda98d39 100644 --- a/var/spack/repos/builtin/packages/r-viridislite/package.py +++ b/var/spack/repos/builtin/packages/r-viridislite/package.py @@ -7,9 +7,16 @@ from spack import * class RViridislite(RPackage): - """viridisLite: Default Color Maps from 'matplotlib' (Lite Version)""" + """Colorblind-Friendly Color Maps (Lite Version). + + Color maps designed to improve graph readability for readers with common + forms of color blindness and/or color vision deficiency. The color maps are + also perceptually-uniform, both in regular form and also when converted to + black-and-white for printing. This is the 'lite' version of the 'viridis' + package that also contains 'ggplot2' bindings for discrete and continuous + color and fill scales and can be found at + <https://cran.r-project.org/package=viridis>.""" - homepage = "https://github.com/sjmgarnier/viridisLite" cran = "viridisLite" version('0.4.0', sha256='849955dc8ad9bc52bdc50ed4867fd92a510696fc8294e6971efa018437c83c6a') diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py index d0606e4c76..12c8264a2f 100644 --- a/var/spack/repos/builtin/packages/r-visnetwork/package.py +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -7,15 +7,14 @@ from spack import * class RVisnetwork(RPackage): - """Network Visualization using 'vis.js' Library + """Network Visualization using 'vis.js' Library. Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.""" - homepage = "https://github.com/datastorm-open/visNetwork" - url = "https://cloud.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/visNetwork" + cran = "visNetwork" + version('2.1.0', sha256='a2b91e7fbbd9d08a9929a5b2c891d9c0bca5977ad772fa37510d96656af1152f') version('2.0.9', sha256='5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420') version('2.0.7', sha256='15ad01636a3a19e1901be6743052805a5b6a9ac1240fb3dab765252b1e865128') version('2.0.6', sha256='ec2478e6a2af446569ef2d5210a2bc6b2600bcb7fd9908cef8f8c80b01e9c8aa') diff --git a/var/spack/repos/builtin/packages/r-vroom/package.py b/var/spack/repos/builtin/packages/r-vroom/package.py index b9535cdc77..2697380da2 100644 --- a/var/spack/repos/builtin/packages/r-vroom/package.py +++ b/var/spack/repos/builtin/packages/r-vroom/package.py @@ -15,8 +15,7 @@ class RVroom(RPackage): read. The writer formats the data in parallel and writes to disk asynchronously from formatting.""" - homepage = "https://github.com/r-lib/vroom" - cran = "vroom" + cran = "vroom" version('1.5.7', sha256='d087cb148f71c222fc89199d03df2502689149873414a6d89c2f006d3a109fde') version('1.5.5', sha256='1d45688c08f162a3300eda532d9e87d144f4bc686769a521bf9a12e3d3b465fe') diff --git a/var/spack/repos/builtin/packages/r-waldo/package.py b/var/spack/repos/builtin/packages/r-waldo/package.py index d41a3957ea..9c99dfb46d 100644 --- a/var/spack/repos/builtin/packages/r-waldo/package.py +++ b/var/spack/repos/builtin/packages/r-waldo/package.py @@ -7,22 +7,23 @@ from spack import * class RWaldo(RPackage): - """Find Differences Between R Objects + """Find Differences Between R Objects. Compare complex R objects and reveal the key differences. Designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures much easier.""" - homepage = "https://github.com/r-lib/waldo" - url = "https://cloud.r-project.org/src/contrib/waldo_0.2.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/waldo" + cran = "waldo" + version('0.3.1', sha256='ec2c8c1afbc413f8db8b6b0c6970194a875f616ad18e1e72a004bc4497ec019b') version('0.2.3', sha256='1fbab22fe9be6ca8caa3df7306c763d7025d81ab6f17b85daaf8bdc8c9455c53') depends_on('r-cli', type=('build', 'run')) depends_on('r-diffobj', type=('build', 'run')) + depends_on('r-diffobj@0.3.4:', type=('build', 'run'), when='@0.3.1:') depends_on('r-fansi', type=('build', 'run')) depends_on('r-glue', type=('build', 'run')) depends_on('r-rematch2', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) + depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@0.3.1:') depends_on('r-tibble', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-webshot/package.py b/var/spack/repos/builtin/packages/r-webshot/package.py index 6138fba7eb..f9d7793409 100644 --- a/var/spack/repos/builtin/packages/r-webshot/package.py +++ b/var/spack/repos/builtin/packages/r-webshot/package.py @@ -7,14 +7,12 @@ from spack import * class RWebshot(RPackage): - """Take Screenshots of Web Pages + """Take Screenshots of Web Pages. Takes screenshots of web pages, including Shiny applications and R Markdown documents.""" - homepage = "https://github.com/wch/webshot/" - url = "https://cloud.r-project.org/src/contrib/webshot_0.5.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/webshot/" + cran = "webshot" version('0.5.2', sha256='f183dc970157075b51ac543550a7a48fa3428b9c6838abb72fe987c21982043f') version('0.5.1', sha256='b9750d206c6fa0f1f16cc212b0a34f4f4bfa916962d2c877f0ee9a33620f4b23') diff --git a/var/spack/repos/builtin/packages/r-wgcna/package.py b/var/spack/repos/builtin/packages/r-wgcna/package.py index 92fdd797b1..e7fad2b3c9 100644 --- a/var/spack/repos/builtin/packages/r-wgcna/package.py +++ b/var/spack/repos/builtin/packages/r-wgcna/package.py @@ -7,7 +7,7 @@ from spack import * class RWgcna(RPackage): - """Weighted Correlation Network Analysis + """Weighted Correlation Network Analysis. Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) @@ -18,10 +18,9 @@ class RWgcna(RPackage): includes a number of utility functions for data manipulation and visualization.""" - homepage = "https://cloud.r-project.org/package=WGCNA" - url = "https://cloud.r-project.org/src/contrib/WGCNA_1.68.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/WGCNA/" + cran = "WGCNA" + version('1.70-3', sha256='b9843b839728183af6b746f239e9519d438b294613362b556002acdb8522cbd4') version('1.69', sha256='2ea152d45b2d4f0e40b4b9f7b5ea8a96e230f7744ece8be27bdba96cf39d5008') version('1.68', sha256='0a04f15a20817f9260ae1896eda3be83a7f4855a27a348df85c7f4d376f1efe8') version('1.67', sha256='c9cc9989763b2c80835489eabd38d9ee35b204305044d115ca7c775a103f6824') @@ -40,4 +39,5 @@ class RWgcna(RPackage): depends_on('r-go-db', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) - depends_on('r-robust', when='@:1.68', type=('build', 'run')) + + depends_on('r-robust', type=('build', 'run'), when='@:1.68') diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py index 088a9a5db9..7cc5fee459 100644 --- a/var/spack/repos/builtin/packages/r-whisker/package.py +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -7,13 +7,11 @@ from spack import * class RWhisker(RPackage): - """{{mustache}} for R, Logicless Templating + """{{mustache}} for R, Logicless Templating. Implements 'Mustache' logicless templating.""" - homepage = "https://github.com/edwindj/whisker" - url = "https://cloud.r-project.org/src/contrib/whisker_0.3-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/whisker" + cran = "whisker" version('0.4', sha256='7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8') version('0.3-2', sha256='484836510fcf123a66ddd13cdc8f32eb98e814cad82ed30c0294f55742b08c7c') diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index c5fdc0f39b..63ea6b745b 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -7,16 +7,16 @@ from spack import * class RWithr(RPackage): - """Run Code 'With' Temporarily Modified Global State + """Run Code 'With' Temporarily Modified Global State. A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.""" - homepage = "https://github.com/jimhester/withr" cran = "withr" + version('2.4.3', sha256='9bdac7459ccc6c2d599ecfd132a7f0aa68d958942d9fe7dbb0442c9eda129d4c') version('2.4.2', sha256='48f96a4cb780cf6fd5fbbea1f1eb04ea3102d7a4a644cae1ed1e91139dcbbac8') version('2.4.0', sha256='ede4cdc7e4d17e0ad24afc9fb940cba46fac4421d3a39281e9918377d73714f8') version('2.2.0', sha256='4c21e51cf48f8c281ddd5f5ec358ac446df3c982104fd00bfe62d9259d73b582') @@ -25,4 +25,4 @@ class RWithr(RPackage): version('1.0.1', sha256='7e245fdd17d290ff9e7c237159804dd06e1c6a3efe7855ed641eb0765a1e727d') depends_on('r@3.0.2:', type=('build', 'run')) - depends_on('r@3.2:', when='@2.2:', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run'), when='@2.2:') diff --git a/var/spack/repos/builtin/packages/r-wk/package.py b/var/spack/repos/builtin/packages/r-wk/package.py index fc105fdd62..92e38c61d9 100644 --- a/var/spack/repos/builtin/packages/r-wk/package.py +++ b/var/spack/repos/builtin/packages/r-wk/package.py @@ -7,7 +7,7 @@ from spack import * class RWk(RPackage): - """Lightweight Well-Known Geometry Parsing + """Lightweight Well-Known Geometry Parsing. Provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. @@ -16,9 +16,9 @@ class RWk(RPackage): useful in R if the information they contain can be accessed in R, for which high-performance functions are provided here.""" - homepage = "https://paleolimbot.github.io/wk/" - cran = "wk" + cran = "wk" + version('0.6.0', sha256='af2c2837056a6dcc9f64d5ace29601d6d668c95769f855ca0329648d7326eaf5') version('0.4.1', sha256='daa7351af0bd657740972016906c686f335b8fa922ba10250e5000ddc2bb8950') depends_on('r-cpp11', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xfun/package.py b/var/spack/repos/builtin/packages/r-xfun/package.py index 1f7a34fe6c..b43e0c8f1b 100644 --- a/var/spack/repos/builtin/packages/r-xfun/package.py +++ b/var/spack/repos/builtin/packages/r-xfun/package.py @@ -7,12 +7,14 @@ from spack import * class RXfun(RPackage): - """Miscellaneous functions commonly used in other packages maintained by + """Supporting Functions for Packages Maintained by 'Yihui Xie'. + + Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.""" - homepage = "https://github.com/yihui/xfun" - cran = "xfun" + cran = "xfun" + version('0.29', sha256='bf85bb7b4653d03e0730682ffe1d6d3544ac0b36989f9196b2054d356c224ef4') version('0.24', sha256='e3e39a95202f6db4f6de3a8b9a344074a4944a3a8a522d44971390c905e2b583') version('0.20', sha256='284239d12a3d5ea7d1ef8b1382fb0a7a4661af54c85510501279681871da7c10') version('0.8', sha256='c2f8ecf8b57ddec02f9be7f417d9e22fc1ae2c7db8d70aa703fc62bf4a5c5416') diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py index 74bdbbdb99..44c7849c10 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -8,21 +8,20 @@ from spack import * class RXgboost(RPackage): - """Extreme Gradient Boosting + """Extreme Gradient Boosting. - Extreme Gradient Boosting, which is an efficient implementation of - gradient boosting framework. This package is its R interface. The package - includes efficient linear model solver and tree learning algorithms. The - package can automatically do parallel computation on a single machine which - could be more than 10 times faster than existing gradient boosting - packages. It supports various objective functions, including regression, - classification and ranking. The package is made to be extensible, so that - users are also allowed to define their own objectives easily.""" + Extreme Gradient Boosting, which is an efficient implementation of gradient + boosting framework. This package is its R interface. The package includes + efficient linear model solver and tree learning algorithms. The package can + automatically do parallel computation on a single machine which could be + more than 10 times faster than existing gradient boosting packages. It + supports various objective functions, including regression, classification + and ranking. The package is made to be extensible, so that users are also + allowed to define their own objectives easily.""" - homepage = "https://github.com/dmlc/xgboost" - url = "https://cloud.r-project.org/src/contrib/xgboost_0.6-4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/xgboost" + cran = "xgboost" + version('1.5.0.2', sha256='4750b9a289d8cb685291939eed7c493bb42c5cc154ef98e13100abb1727eab13') version('1.3.2.1', sha256='2ff462b81ad51a4810bd7860cb014b9b88831a8b1d45774249a808547147f884') version('0.90.0.2', sha256='240584c1b4d54a95b4fef9074480752fae9a5b096e8f84747457d641decfc9bf') version('0.81.0.1', sha256='3e7ada32e66881ea5c90aeafdab948927014c76cfff60a8e3d7f9e1f8a9ed7ce') @@ -30,14 +29,16 @@ class RXgboost(RPackage): version('0.4-4', sha256='b955fc3352fcdc4894178c82fd62fbaf5e099c9d794f1e9daa2dd7b3494b61ff') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r@2.15.1:', when='@0.6-0:0.6-2', type=('build', 'run')) - depends_on('r@3.3.0:', when='@0.6-3:', type=('build', 'run')) + depends_on('r@2.15.1:', type=('build', 'run'), when='@0.6-0:') + depends_on('r@3.3.0:', type=('build', 'run'), when='@0.6-3:') depends_on('r-matrix@1.1-0:', type=('build', 'run')) depends_on('r-data-table@1.9.6:', type=('build', 'run')) - depends_on('r-magrittr@1.5:', type=('build', 'run')) - depends_on('r-stringi@0.5.2:', when='@:0.90.0.2', type=('build', 'run')) + depends_on('r-jsonlite@1.0:', type=('build', 'run'), when='@1.5.0.2:') depends_on('gmake', type='build') # This is not listed as required, but installation fails without it # ERROR: dependency 'stringr' is not available for package 'xgboost' depends_on('r-stringr', type=('build', 'run')) + + depends_on('r-stringi@0.5.2:', type=('build', 'run'), when='@:0.90.0.2') + depends_on('r-magrittr@1.5:', type=('build', 'run'), when='@:1.3.2.1') diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 57c4facd76..87fe53a430 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -7,15 +7,14 @@ from spack import * class RXlconnect(RPackage): - """Excel Connector for R + """Excel Connector for R. Provides comprehensive functionality to read, write and format Excel data.""" - homepage = "https://miraisolutions.wordpress.com/" - url = "https://cloud.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/XLConnect" + cran = "XLConnect" + version('1.0.5', sha256='975c2ef57f28ccfac79ae5d285b7e82e60791fb121052616c10bc52e2bca16ad') version('1.0.1', sha256='927aa34a3c81c12bf156e55edca9e2f5186c31435cce23feda4b906d049d6e39') version('0.2-15', sha256='26e1d8db65974719adbc25f1327c584003eb562dc1bb2121bffc2550cf3178b3') version('0.2-14', sha256='d1013ed26947572bad97d62a3d66346f74993cf96c6408d21d5b6ee567468819') @@ -24,9 +23,11 @@ class RXlconnect(RPackage): depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-rjava', type=('build', 'run')) - depends_on('r-xlconnectjars@0.2-9', when='@0.2-11', type=('build', 'run')) - depends_on('r-xlconnectjars@0.2-12', when='@0.2-12', type=('build', 'run')) - depends_on('r-xlconnectjars@0.2-14', when='@0.2-14', type=('build', 'run')) - depends_on('r-xlconnectjars@0.2-15', when='@0.2-15', type=('build', 'run')) depends_on('java@6:') depends_on('java@8:11', when='@1.0.1:') + depends_on('java@8:17', when='@1.0.5:') + + depends_on('r-xlconnectjars@0.2-9', type=('build', 'run'), when='@0.2-11') + depends_on('r-xlconnectjars@0.2-12', type=('build', 'run'), when='@0.2-12') + depends_on('r-xlconnectjars@0.2-14', type=('build', 'run'), when='@0.2-14') + depends_on('r-xlconnectjars@0.2-15', type=('build', 'run'), when='@0.2-15') diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index 753ca02aeb..30c7205b7f 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -7,11 +7,11 @@ from spack import * class RXlconnectjars(RPackage): - """Provides external JAR dependencies for the XLConnect package.""" + """JAR Dependencies for the XLConnect Package. - homepage = "https://miraisolutions.wordpress.com/" - url = "https://cloud.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/XLConnectJars" + Provides external JAR dependencies for the XLConnect package.""" + + cran = "XLConnectJars" version('0.2-15', sha256='bd6f48a72c3a02b7a5e9373bcfc671614bc793f41d7bb8f4f34115a89ff4f8c6') version('0.2-14', sha256='c675f0ccff0c3e56b2b1cc00d4d28bf8fdfa508266ac0ffab5c0641151dd7332') diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index 5490dc5a1a..7ae42cc9fe 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -7,14 +7,12 @@ from spack import * class RXlsx(RPackage): - """Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files + """Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files. Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.""" - homepage = "https://github.com/colearendt/xlsx" - url = "https://cloud.r-project.org/src/contrib/xlsx_0.6.1.tar.gz" - listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" + cran = "xlsx" version('0.6.5', sha256='378c5ed475a3d7631ea1ea13e0a69d619c1a52260922abda42818752dbb32107') version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index eac4277b27..a685f257ad 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -7,12 +7,12 @@ from spack import * class RXlsxjars(RPackage): - """The xlsxjars package collects all the external jars required for the - xlxs package. This release corresponds to POI 3.10.1.""" + """Package required POI jars for the xlsx package. - homepage = "https://cloud.r-project.org/package=xlsxjars" - url = "https://cloud.r-project.org/src/contrib/xlsxjars_0.6.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/xlsxjars" + The xlsxjars package collects all the external jars required for the xlxs + package. This release corresponds to POI 3.10.1.""" + + cran = "xlsxjars" version('0.6.1', sha256='37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6') diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py index c9825987dc..5fd7c108f9 100644 --- a/var/spack/repos/builtin/packages/r-xml/package.py +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -7,16 +7,15 @@ from spack import * class RXml(RPackage): - """Tools for Parsing and Generating XML Within R and S-Plus + """Tools for Parsing and Generating XML Within R and S-Plus. Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".""" - homepage = "https://cloud.r-project.org/package=XML" - url = "https://cloud.r-project.org/src/contrib/XML_3.98-1.9.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/XML" + cran = "XML" + version('3.99-0.8', sha256='081f691c2ee8ad39c7c95281e7d9153ec04cee79ca2d41f5d82c2ec2f1d36b50') version('3.99-0.5', sha256='60529b7360f162eba07da455eeb9b94a732b2dd623c49e0f04328a2e97bd53a6') version('3.98-1.20', sha256='46af86376ea9a0fb1b440cf0acdf9b89178686a05c4b77728fcff1f023aa4858') version('3.98-1.19', sha256='81b1c4a2df24c5747fa8b8ec2d76b4e9c3649b56ca94f6c93fbd106c8a72beab') @@ -25,5 +24,5 @@ class RXml(RPackage): version('3.98-1.4', sha256='9c0abc75312f66aac564266b6b79222259c678aedee9fc347462978354f11126') depends_on('r@2.13.0:', type=('build', 'run')) - depends_on('r@4.0.0:', when='@3.99-0.5:', type=('build', 'run')) + depends_on('r@4.0.0:', type=('build', 'run'), when='@3.99-0.5:') depends_on('libxml2@2.6.3:') diff --git a/var/spack/repos/builtin/packages/r-xml2/package.py b/var/spack/repos/builtin/packages/r-xml2/package.py index 32880f4af7..4db0d342ea 100644 --- a/var/spack/repos/builtin/packages/r-xml2/package.py +++ b/var/spack/repos/builtin/packages/r-xml2/package.py @@ -7,19 +7,21 @@ from spack import * class RXml2(RPackage): - """Work with XML files using a simple, consistent interface. Built on top - of the 'libxml2' C library.""" + """Package required POI jars for the xlsx package. - homepage = "https://cloud.r-project.org/package=xml2" - url = "https://cloud.r-project.org/src/contrib/xml2_1.1.1.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/xml2" + Work with XML files using a simple, consistent interface. Built on top of + the 'libxml2' C library.""" + cran = "xml2" + + version('1.3.3', sha256='cb4e9c0d31618ed67d2bfa4c7b5e52680e11612ed356a8164b541d44163c1c8d') version('1.3.2', sha256='df22f9e7e3189d8c9b8804eaf0105324fdac983cffe743552f6d76613600a4cf') version('1.2.2', sha256='3050f147c4335be2925a576557bbda36bd52a5bba3110d47b740a2dd811a78f4') version('1.2.1', sha256='5615bbc94607efc3bc192551992b349091df802ae34b855cfa817733f2690605') version('1.1.1', sha256='00f3e3b66b76760c19da5f6dddc98e6f30de36a96b211e59e1a3f4ff58763116') depends_on('r@3.1.0:', type=('build', 'run')) - depends_on('r-rcpp@0.12.12:', when='@:1.2', type=('build', 'run')) - depends_on('r-bh', when='@:1.1.1', type=('build', 'run')) depends_on('libxml2') + + depends_on('r-rcpp@0.12.12:', type=('build', 'run'), when='@:1.2') + depends_on('r-bh', type=('build', 'run'), when='@:1.1.1') diff --git a/var/spack/repos/builtin/packages/r-xnomial/package.py b/var/spack/repos/builtin/packages/r-xnomial/package.py index cdc26cbfd6..fa5fbc75c5 100644 --- a/var/spack/repos/builtin/packages/r-xnomial/package.py +++ b/var/spack/repos/builtin/packages/r-xnomial/package.py @@ -8,12 +8,21 @@ from spack import * class RXnomial(RPackage): - """XNomial: Exact Goodness-of-Fit Test for Multinomial Data with Fixed - Probabilities""" + """Exact Goodness-of-Fit Test for Multinomial Data with Fixed + Probabilities. - homepage = "https://cloud.r-project.org/package=XNomial" - url = "https://cloud.r-project.org/src/contrib/XNomial_1.0.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/XNomial/" + Tests whether a set of counts fit a given expected ratio. For example, a + genetic cross might be expected to produce four types in the relative + frequencies of 9:3:3:1. To see whether a set of observed counts fits this + expectation, one can examine all possible outcomes with xmulti() or a + random sample of them with xmonte() and find the probability of an + observation deviating from the expectation by at least as much as the + observed. As a measure of deviation from the expected, one can use the + log-likelihood ratio, the multinomial probability, or the classic + chi-square statistic. A histogram of the test statistic can also be plotted + and compared with the asymptotic curve.""" + + cran = "XNomial" version('1.0.4', sha256='e6237f79d96f02bb30af1cf055ae9f70541abba34ce045a9d4359b5304189dd7') diff --git a/var/spack/repos/builtin/packages/r-xopen/package.py b/var/spack/repos/builtin/packages/r-xopen/package.py index 667be1d0de..59ca045407 100644 --- a/var/spack/repos/builtin/packages/r-xopen/package.py +++ b/var/spack/repos/builtin/packages/r-xopen/package.py @@ -7,12 +7,12 @@ from spack import * class RXopen(RPackage): - """Cross platform solution to open files, directories or 'URLs' with their + """Open System Files, 'URLs', Anything. + + Cross platform solution to open files, directories or 'URLs' with their associated programs.""" - homepage = "https://github.com/r-lib/xopen#readme" - url = "https://cloud.r-project.org/src/contrib/xopen_1.0.0.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/xopen" + cran = "xopen" version('1.0.0', sha256='e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef') diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py index 33bf45795e..6ab845bbf6 100644 --- a/var/spack/repos/builtin/packages/r-xtable/package.py +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -7,11 +7,11 @@ from spack import * class RXtable(RPackage): - """Coerce data to LaTeX and HTML tables.""" + """Export Tables to LaTeX or HTML. - homepage = "https://xtable.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/xtable_1.8-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/xtable" + Coerce data to LaTeX and HTML tables.""" + + cran = "xtable" version('1.8-4', sha256='5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c') version('1.8-3', sha256='53b2b0fff8d7a8bba434063c2a01b867f510a4389ded2691fbedbc845f08c325') diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py index 22b560dd2f..b600bce1ce 100644 --- a/var/spack/repos/builtin/packages/r-xts/package.py +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -7,16 +7,14 @@ from spack import * class RXts(RPackage): - """eXtensible Time Series + """eXtensible Time Series. Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.""" - homepage = "https://r-forge.r-project.org/projects/xts/" - url = "https://cloud.r-project.org/src/contrib/xts_0.11-2.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/xts" + cran = "xts" version('0.12.1', sha256='d680584af946fc30be0b2046e838cff7b3a65e00df1eadba325ca5e96f3dca2c') version('0.11-2', sha256='12772f6a66aab5b84b0665c470f11a3d8d8a992955c027261cfe8e6077ee13b8') diff --git a/var/spack/repos/builtin/packages/r-yaimpute/package.py b/var/spack/repos/builtin/packages/r-yaimpute/package.py index d223ead2fd..d5dd494e4d 100644 --- a/var/spack/repos/builtin/packages/r-yaimpute/package.py +++ b/var/spack/repos/builtin/packages/r-yaimpute/package.py @@ -7,13 +7,20 @@ from spack import * class RYaimpute(RPackage): - """Performs nearest neighbor-based imputation using one or more - alternative approaches to processing multivariate data - """ + """Nearest Neighbor Observation Imputation and Evaluation Tools. - homepage = "https://cloud.r-project.org/package=yaImpute" - url = "https://cloud.r-project.org/src/contrib/yaImpute_1.0-32.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/yaImpute" + Performs nearest neighbor-based imputation using one or more alternative + approaches to processing multivariate data. These include methods based on + canonical correlation analysis, canonical correspondence analysis, and a + multivariate adaptation of the random forest classification and regression + techniques of Leo Breiman and Adele Cutler. Additional methods are also + offered. The package includes functions for comparing the results from + running alternative techniques, detecting imputation targets that are + notably distant from reference observations, detecting and correcting for + bias, bootstrapping and building ensemble imputations, and mapping + results.""" + + cran = "yaImpute" version('1.0-32', sha256='08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff') diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py index f66c4d2bd5..20030321d5 100644 --- a/var/spack/repos/builtin/packages/r-yaml/package.py +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -7,15 +7,14 @@ from spack import * class RYaml(RPackage): - """Methods to Convert R Data to YAML and Back + """Methods to Convert R Data to YAML and Back. Implements the 'libyaml' 'YAML' 1.1 parser and emitter (<https://pyyaml.org/wiki/LibYAML>) for R.""" - homepage = "https://cloud.r-project.org/package=yaml" - url = "https://cloud.r-project.org/src/contrib/yaml_2.1.13.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/yaml" + cran = "yaml" + version('2.2.2', sha256='a5dc6aba2719eb4422bdd7d3a7b2223bbb00e4470fa234d8c5b3a6835d99f730') version('2.2.1', sha256='1115b7bc2a397fa724956eec916df5160c600c99a3be186d21558dd38d782783') version('2.2.0', sha256='55bcac87eca360ab5904914fcff473a6981a1f5e6d2215d2634344d0ac30c546') version('2.1.19', sha256='e5db035693ac765e4b5fe1fc2e9711f8ca73e398e3f2bf27cc60def59ccd7f11') diff --git a/var/spack/repos/builtin/packages/r-yulab-utils/package.py b/var/spack/repos/builtin/packages/r-yulab-utils/package.py new file mode 100644 index 0000000000..27b5cff90a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-yulab-utils/package.py @@ -0,0 +1,16 @@ +# 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 RYulabUtils(RPackage): + """Supporting Functions for Packages Maintained by 'YuLab-SMU'. + + Miscellaneous functions commonly used by 'YuLab-SMU'.""" + + cran = "yulab.utils" + + version('0.0.4', sha256='38850663de53a9166b8e85deb85be1ccf1a5b310bbe4355f3b8bc823ed1b49ae') diff --git a/var/spack/repos/builtin/packages/r-zcompositions/package.py b/var/spack/repos/builtin/packages/r-zcompositions/package.py index a422d01f9f..de6929d0d6 100644 --- a/var/spack/repos/builtin/packages/r-zcompositions/package.py +++ b/var/spack/repos/builtin/packages/r-zcompositions/package.py @@ -8,16 +8,15 @@ from spack import * class RZcompositions(RPackage): """Treatment of Zeros, Left-Censored and Missing Values in Compositional - Data Sets + Data Sets. Principled methods for the imputation of zeros, left-censored and missing data in compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).""" - homepage = "https://cloud.r-project.org/package=zCompositions" - url = "https://cloud.r-project.org/src/contrib/zCompositions_1.3.4.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/zCompositions" + cran = "zCompositions" + version('1.4.0', sha256='a00d7d0ba861988b1836e947fd521d58137a4def04a5d7aa73a099314b7e530c') version('1.3.4', sha256='ae22c86fe92368a26265933f42eecc518b9b69e7d9b698bc31bfaabfc3c48e95') depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-zeallot/package.py b/var/spack/repos/builtin/packages/r-zeallot/package.py index e4e8ec9d58..48108c08d7 100644 --- a/var/spack/repos/builtin/packages/r-zeallot/package.py +++ b/var/spack/repos/builtin/packages/r-zeallot/package.py @@ -7,13 +7,13 @@ from spack import * class RZeallot(RPackage): - """Provides a %<-% operator to perform multiple, unpacking, and - destructuring assignment in R. The operator unpacks the right-hand side of - an assignment into multiple values and assigns these values to variables on - the left-hand side of the assignment.""" + """Multiple, Unpacking, and Destructuring Assignment. - homepage = "https://github.com/nteetor/zeallot" - url = "https://cloud.r-project.org/src/contrib/zeallot_0.1.0.tar.gz" - listurl = "https://cloud.r-project.org/src/contrib/Archive/zeallot" + Provides a %<-% operator to perform multiple, unpacking, and destructuring + assignment in R. The operator unpacks the right-hand side of an assignment + into multiple values and assigns these values to variables on the left-hand + side of the assignment.""" + + cran = "zeallot" version('0.1.0', sha256='439f1213c97c8ddef9a1e1499bdf81c2940859f78b76bc86ba476cebd88ba1e9') diff --git a/var/spack/repos/builtin/packages/r-zip/package.py b/var/spack/repos/builtin/packages/r-zip/package.py index e877b5d07c..7f4074f6a9 100644 --- a/var/spack/repos/builtin/packages/r-zip/package.py +++ b/var/spack/repos/builtin/packages/r-zip/package.py @@ -7,15 +7,14 @@ from spack import * class RZip(RPackage): - """Cross-Platform 'zip' Compression + """Cross-Platform 'zip' Compression. Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.""" - homepage = "https://github.com/r-lib/zip#readme" - url = "https://cloud.r-project.org/src/contrib/zip_2.0.3.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/zip" + cran = "zip" + version('2.2.0', sha256='9f95987c964039834f770ecda2d5f7e3d3a9de553c89db2a5926c4219bf4b9d8') version('2.1.1', sha256='11dd417932296d3a25c53aa8d3b908973c4945a496cc473dd321825dfaaa7c2c') version('2.0.3', sha256='4a8cb8e41eb630bbf448a0fd56bcaeb752b8484fef98c6419334edf46401317e') diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index 71cf383b35..2b14511cf0 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -7,7 +7,8 @@ from spack import * class RZoo(RPackage): - """S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations) + """S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered + Observations). An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and @@ -15,10 +16,9 @@ class RZoo(RPackage): index/date/time class and consistency with ts and base R by providing methods to extend standard generics.""" - homepage = "https://zoo.r-forge.r-project.org/" - url = "https://cloud.r-project.org/src/contrib/zoo_1.7-14.tar.gz" - list_url = "https://cloud.r-project.org/src/contrib/Archive/zoo" + cran = "zoo" + version('1.8-9', sha256='b7be259067a8b9d4a8f5d387e0946a5ba1eb43474baa67ccf4f8bf4b15f772a3') version('1.8-8', sha256='4e8cc4065047ba12e103b9664f3b607c770673096e9c2b694fad2b2ec3203ce7') version('1.8-6', sha256='2217a4f362f2201443b5fdbfd9a77d9a6caeecb05f02d703ee8b3b9bf2af37cc') version('1.8-5', sha256='8773969973d28d7d1a48f74b73be1dbd97acb3b22a4668a102e8bb585a7de826') @@ -26,5 +26,5 @@ class RZoo(RPackage): version('1.7-13', sha256='0ca5264d6077c785963705e462aec3e57e0d0651379f9bf4ee32e4f3b25dc754') depends_on('r@2.10.0:', type=('build', 'run')) - depends_on('r@3.1.0:', when='@1.8-2:', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run'), when='@1.8-2:') depends_on('r-lattice@0.20-27:', type=('build', 'run')) |