From 661a894c85f451a4ef868abcc9871653914361bd Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Fri, 30 Aug 2019 18:22:13 -0500 Subject: [PATCH] Update R CRAN packages (#12019) * Update R CRAN packages This PR update R CRAN packages. It also ensures that spack built packages that correspond to R recommended packages are specified in the dependency list. This is needed for #12015. * Add more updates to packages * Updated dependencies of CRAN R packages Also, use cloud.r-project.org rather than cran.r-project.org to use automatic redirection to mirrors. This minimizes the load on the cran server. * Update to latest versions of CRAN R packages * Fix flake8 issues Some blank lines at the end of a coupple of package files crept in. * Adjust r-animation dependencies The r-magick package depends on image-magick, so r-animation should as well. Also, add in texlive for LaTeX support. * New package: r-magick * Adjust line spaces in r-magick * Add swftools dependenct to r-animation * New package: swftools This is needed bt r-animation * Add 'when' clause to some package dependencies - r-animation - r-coin - r-dt - r-openssl * New package: r-ellipsis * New package: r-vctrs * New package: r-zeallot * New package: r-generics * New package: r-cardata * Add r-progress dependency to r-readxl * New package: r-askpass * New package: r-openxlsx * New package: r-rio * New package: r-sys * New package: r-zip * Add more updated packages These are updates that have happened while working on this PR as well as catching the ones from the cran.rstudio.com URL that were missed before. * New package: r-gower * New package: r-recipes * New package: r-squarem * New package: r-libcoin * New package: r-rcmdcheck * New package: r-remotes * New package: r-sessioninfo * New package: r-xopen * New package: r-rgexf * New package: r-rook * New package: r-later * New package: r-promises * New package: r-xfun * New package: r-urca * New package: r-ggsignif * New package: r-polynom * New package: r-ucminf * New package: r-ordinal * New package: r-inum * New package: r-debugme * New package: r-fs * New package: r-shinyfiles * New package: r-gsa * New package: r-nmof * New package: r-dosnow * New package: r-rann * New package: r-reticulate * New package: r-future * New package: r-globals * New package: r-listenv * New package: r-future-apply * New package: r-rsvd * New package: r-sctransform * New package: r-mitools * Remove a stray FIXME line * Fix typo in dependency for r-rcmdcheck * Remove the dependency on r-splines The r-splines package never existed in spack, but it does not exist on CRAN either. There is an archive version from 1999 but it does not have the proper extension format for modern R packages. The latest version does not depend on r-splines, and apparently previous versions at least built without it. Also, bump the required R version. * Fix typo in r-rcpp dependency * Fix typos in dependencies - r-diagrammer - r-janitor - r-seurat Also, bump minimum R version for r-rngtools. * New package: r-clisymbols * New package: r-fitdistrplus * New package: r-gbrd * New package: r-gh * New package: r-ini * New package: r-metap * New package: r-npsurv * New package: r-rdpack * New package: r-snakecase * New package: r-tinytex * New package: r-usethis * Make recommended changes Made the changes that were recommended in the initial review. - change cran.rstudio.com to cloud.r-project.org - change R-project to r-project - for packages with no listed homepage use the canonical link to the package page - for packages with a dependency constraint on R itself, specify the dependency type - add `list_url` where missing from package * New package: r-hdf5r This is needed for some older versions of r-seurat. * Set R versions in packages If the R version is specified in the DESCRIPTION file then set it in the respective spack package.py file. * Update var/spack/repos/builtin/packages/r-aer/package.py Change dependency version of r-car. Co-Authored-By: Adam J. Stewart * Set constraint of mlbench dependency of r-adabag * Set constraint on r-rcpp dependency of r-ape * Removed "suggested" r-testthat from r-bibtex * Update var/spack/repos/builtin/packages/r-bindrcpp/package.py Fix dependency spec of r-bindr in r-bindrcpp. Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/r-blob/package.py Add r-vctrs version constraint. Co-Authored-By: Adam J. Stewart * Remove r-base64enc dependency from r-callr * Update var/spack/repos/builtin/packages/r-car/package.py Set constraint on r-cardata dependency. Co-Authored-By: Adam J. Stewart * Remove unneeded dependencies from r-clipr * Add gmake dependency to r-construct * Set the proper homepage for r-crayon * Add r-jsonlite as a dependency for r-crul The jsonlite package moved from "suggests" to "imports" with 0.8.4. * Remove accidental colon after package name * Add version constraint to r-fpc dependency in r-dendextend * Additional constraints for R version with r-digest * Add r-jsonlite dependency for latest verion of r-dt * Add r-htmltools dependency in r-dygraphs package * Removed unneeded dependencies from r-fnn * Remove unneeded dependencies from r-formatr * Add version constraint for r-mvtnorm dependency in r-fpc * Added gmake dependency to r-fs * Add r-globals dependency in r-future-apply * Add perl dependency to r-gdata * Add openssl dependency for r-ggally * Removed unneeded dependencies from r-globaloptions * Update r-haven - Add version constraint on r-forcats - Add gmake build dependency * Fixed gmake dependency Gmake is a build only dependency. * Apply suggestions from code review Apply a batch of suggestions from Adam Stewart. Co-Authored-By: Adam J. Stewart * Remove unneeded dependencies from r-hoardr * Fix r-htmlwidgets homepage * Add gmake build dependency to r-httpuv * Remove unneeded dependency from r-log4r * Remove unneeded dependency from r-maldiquant * Add gmake build dependency to r-minqa * Remove unneeded dependency from r-mlbench * Set constraint on R6 dependenvy of r-pbdzmq * Set constraints on r-callr dependency of r-pkgbuild * Remove unneeded dependency from r-nloptr * Remove unneeded dependencies from r-pkgmaker * Set R version constraint for r-raster * Set version constraint on rcpp for r-rcppprorgess * Added gmake build dependency * Remove unneeded dependencies from r-rematch * Remove unneeded dependency from r-plogr * Add gmake build dependency for r-rcurl * Apply suggestions from code review Bring in more suggestions from Adam Stewart. Co-Authored-By: Adam J. Stewart * Remove cnpy dependency from r-rcppcnpy The r-rcppcnpy package has its own modified copy of the cnpy source and will build from that internal source. The cnpy dependency is therefore unnecessary. * Add comment to reconcile dependencies The CRAN site lists Perl, Getopt::Long as a dependency. The Spack Perl will have the Getopt::Long package installed so just depend on Perl. * Add dependency on udunits2 with newer versions of r-units * Set additional proj constraint for r-sf Support for PROJ6 was added in r-sf-0.7-4. * New package: pandoc This package installs the pandoc and pandoc-citeproc binaries in order to satisfy dependencies on pandoc until the Haskell framework is in Spack. * Add pandoc dependency to r-bookdown * Add comment about MPI in r-ergm * Add pandoc dependency for r-reprex * Add proj constraints to r-rgdal dependencies Support for PROJ6 was added in version 1.4-2. * Modifications to r-rgl - Rearranged the dependencies to be more consistent with other packages - put the type last on the depends_on lines to be consistent with other packages - Added version constraints for some dependencies - Added pandoc build dependency * Be more accurate with rjsonio constraint for r-rgooglemaps * Remove unneeded dependencies from r-rhmmer * Tweak constraints for r-rjava - Set java version constraint - add gmake build dependency * Add pandoc dependency to r-markdown * Remove unneeded dependencies from r-rrcov * Tweak r-rstan package - remove duplicate specifications - remove unneeded when conditions - add version constraints - arrange to follow order on CRAN page more closely - add gmake build dependency - add pandoc build dependency * Add pandoc build dependency for r-rstantools * Remove unneeded dependency from r-runit * Remove unneeded dependencies from r-selectr * Remove example R code from description The example would module loading to break, at least in the case of Lmod using TCL module files. It could be during the TCL to Lua conversion but the module fails due to interpreting ipart of the example as a command. * Update r-seurat New version of r-seurat with new dependencies. * New package: r-dqrng * New package: r-leiden * New package: r-rcppannoy * New package: r-rcppparallel * New package: r-rspectra * New package: r-sitmo * New package: r-uwot * Remove unneeded dependency from r-snow * Remove unneeded dependency from r-sourcetools * Added pandoc build dependency for r-stanheaders * Remove unneeded dependencies from r-taxizedb * Remove unneeded dependencies from r-tclust * Add dependency constraints for r-threejs The following are needed for version 0.2.2: - r-matrix - r-jsonlite * Remove unneeded dependencies from r-vfs * Remove unneeded dependencies from r-vgam * Remove unneeded dependency from r-xlconnectjars * Remove unneeded dependency from r-xlsxjars * Remove unneeded dependency from r-xnomial * Remove ~mpi from fftw dependency of swftools * Apply suggestions from code review Add latest round of suggestions from Adam Stewart. Co-Authored-By: Adam J. Stewart * Fix rjsonio spec for r-rgooglemaps The r-rjsonio spec is a when conditional. * Rename 3 R.* packages - r-utils --> r-r-utils (R.utils) - r-oo --> r-r-oo (R.oo) - r-methodss3 --> r-r-methodss3 (R.methodsS3) Also, renamed dependencies in packages that depend on these three. * Loosen version constraint on mariadb for r-rmysql Make the mariadb constraint on mariadb-5.5 rather than the more specific, and limiting, mariadb-5.5.56. This will allow an external mariadb, such as mariadb-5.5.60 on CentOS-7.5 to be used. 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var/spack/repos/builtin/packages/r-nmof/package.py create mode 100644 var/spack/repos/builtin/packages/r-npsurv/package.py create mode 100644 var/spack/repos/builtin/packages/r-openxlsx/package.py create mode 100644 var/spack/repos/builtin/packages/r-ordinal/package.py create mode 100644 var/spack/repos/builtin/packages/r-polynom/package.py create mode 100644 var/spack/repos/builtin/packages/r-promises/package.py rename var/spack/repos/builtin/packages/{r-methodss3 => r-r-methodss3}/package.py (73%) rename var/spack/repos/builtin/packages/{r-oo => r-r-oo}/package.py (67%) create mode 100644 var/spack/repos/builtin/packages/r-r-utils/package.py create mode 100644 var/spack/repos/builtin/packages/r-rann/package.py create mode 100644 var/spack/repos/builtin/packages/r-rcmdcheck/package.py create mode 100644 var/spack/repos/builtin/packages/r-rcppannoy/package.py create mode 100644 var/spack/repos/builtin/packages/r-rcppparallel/package.py create mode 100644 var/spack/repos/builtin/packages/r-rdpack/package.py create mode 100644 var/spack/repos/builtin/packages/r-recipes/package.py create mode 100644 var/spack/repos/builtin/packages/r-remotes/package.py create mode 100644 var/spack/repos/builtin/packages/r-reticulate/package.py create mode 100644 var/spack/repos/builtin/packages/r-rgexf/package.py create mode 100644 var/spack/repos/builtin/packages/r-rio/package.py create mode 100644 var/spack/repos/builtin/packages/r-rook/package.py create mode 100644 var/spack/repos/builtin/packages/r-rspectra/package.py create mode 100644 var/spack/repos/builtin/packages/r-rsvd/package.py create mode 100644 var/spack/repos/builtin/packages/r-sctransform/package.py create mode 100644 var/spack/repos/builtin/packages/r-sessioninfo/package.py create mode 100644 var/spack/repos/builtin/packages/r-shinyfiles/package.py create mode 100644 var/spack/repos/builtin/packages/r-sitmo/package.py create mode 100644 var/spack/repos/builtin/packages/r-snakecase/package.py create mode 100644 var/spack/repos/builtin/packages/r-squarem/package.py create mode 100644 var/spack/repos/builtin/packages/r-sys/package.py create mode 100644 var/spack/repos/builtin/packages/r-tinytex/package.py create mode 100644 var/spack/repos/builtin/packages/r-ucminf/package.py create mode 100644 var/spack/repos/builtin/packages/r-urca/package.py create mode 100644 var/spack/repos/builtin/packages/r-usethis/package.py delete mode 100644 var/spack/repos/builtin/packages/r-utils/package.py create mode 100644 var/spack/repos/builtin/packages/r-uwot/package.py create mode 100644 var/spack/repos/builtin/packages/r-vctrs/package.py create mode 100644 var/spack/repos/builtin/packages/r-xfun/package.py create mode 100644 var/spack/repos/builtin/packages/r-xopen/package.py create mode 100644 var/spack/repos/builtin/packages/r-zeallot/package.py create mode 100644 var/spack/repos/builtin/packages/r-zip/package.py create mode 100644 var/spack/repos/builtin/packages/swftools/configure.patch create mode 100644 var/spack/repos/builtin/packages/swftools/package.py create mode 100644 var/spack/repos/builtin/packages/swftools/swfs_Makefile.in.patch diff --git a/var/spack/repos/builtin/packages/pandoc/package.py b/var/spack/repos/builtin/packages/pandoc/package.py new file mode 100644 index 00000000000..c0efc2cb8c1 --- /dev/null +++ b/var/spack/repos/builtin/packages/pandoc/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 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 * +import platform + + +class Pandoc(Package): + """If you need to convert files from one markup format into another, pandoc + is your swiss-army knife.""" + + homepage = "https://pandoc.org" + + # The following installs the binaries for pandoc and pandoc-cireproc. The + # reason for installing binaries is that pandoc is a Haskell package and + # the Haskell framework is not yet in Spack. See #1408 for a discussion of + # the challenges with Haskell. Until the Haskell framework is in Spack this + # package will meet the needs of packages that have a dependency on pandoc. + + if platform.system() == "Linux": + url = "https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-linux.tar.gz" + version('2.7.3', sha256='eb775fd42ec50329004d00f0c9b13076e707cdd44745517c8ce2581fb8abdb75') + elif platform.system() == "Darwin": + url = "https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-macOS.zip" + version('2.7.3', sha256='fb93800c90f3fab05dbd418ee6180d086b619c9179b822ddfecb608874554ff0') + + depends_on('texlive') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index 62f948a4e28..0174733ccf1 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -12,8 +12,11 @@ class RAbind(RPackage): higher-dimensional arrays. Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.""" - homepage = "https://cran.r-project.org/" - url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/abind" + 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" + version('1.4-5', sha256='3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c') version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') + + depends_on('r@1.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acepack/package.py b/var/spack/repos/builtin/packages/r-acepack/package.py index 01eb083a7f3..f10d79caba8 100644 --- a/var/spack/repos/builtin/packages/r-acepack/package.py +++ b/var/spack/repos/builtin/packages/r-acepack/package.py @@ -9,8 +9,8 @@ class RAcepack(RPackage): """ACE and AVAS for Selecting Multiple Regression Transformations.""" - homepage = "https://CRAN.R-project.org/package=acepack" - url = "https://cran.rstudio.com/src/contrib/acepack_1.4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/acepack" + 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" version('1.4.1', 'a35354655e5260afa0e1860fcc68d871') diff --git a/var/spack/repos/builtin/packages/r-ada/package.py b/var/spack/repos/builtin/packages/r-ada/package.py index 83d4ec8d945..ef015df04e6 100644 --- a/var/spack/repos/builtin/packages/r-ada/package.py +++ b/var/spack/repos/builtin/packages/r-ada/package.py @@ -10,10 +10,11 @@ class RAda(RPackage): """Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.""" - homepage = "https://cran.r-project.org/web/packages/ada/index.html" - url = "https://cran.r-project.org/src/contrib/ada_2.0-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ada" + 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" version('2.0-5', '25ac0dc2650fba9e19f3d15c7c6721c1') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rpart', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py index a0c3f8583be..ce7a675430b 100644 --- a/var/spack/repos/builtin/packages/r-adabag/package.py +++ b/var/spack/repos/builtin/packages/r-adabag/package.py @@ -9,12 +9,15 @@ class RAdabag(RPackage): """Applies Multiclass AdaBoost.M1, SAMME and Bagging.""" - homepage = "https://cran.r-project.org/package=adabag" - url = "https://cran.r-project.org/src/contrib/adabag_4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/adabag" + 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" + version('4.2', sha256='47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81') version('4.1', '2e019f053d49f62ebb3b1697bbb50afa') depends_on('r-rpart', type=('build', 'run')) - depends_on('r-mlbench', 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')) diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py index 86ef54bbe16..ef6ff1a84ca 100644 --- a/var/spack/repos/builtin/packages/r-ade4/package.py +++ b/var/spack/repos/builtin/packages/r-ade4/package.py @@ -11,9 +11,12 @@ class RAde4(RPackage): Environmental Sciences""" homepage = "http://pbil.univ-lyon1.fr/ADE-4" - url = "https://cran.r-project.org/src/contrib/ade4_1.7-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ade4" + url = "https://cloud.r-project.org/src/contrib/ade4_1.7-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ade4" + version('1.7-13', sha256='f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b') + version('1.7-11', sha256='4ccd799ae99bd625840b866a697c4a48adb751660470bf0d6cf9207b1927a572') version('1.7-6', '63401ca369677538c96c3d7b75b3f4a1') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py index a3f9d73df98..563ed378a6d 100644 --- a/var/spack/repos/builtin/packages/r-adegenet/package.py +++ b/var/spack/repos/builtin/packages/r-adegenet/package.py @@ -18,13 +18,16 @@ class RAdegenet(RPackage): to illustrate various methods.""" homepage = "https://github.com/thibautjombart/adegenet/wiki" - url = "https://cran.r-project.org/src/contrib/adegenet_2.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/adegenet" + url = "https://cloud.r-project.org/src/contrib/adegenet_2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/adegenet" + version('2.1.1', sha256='3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a') + version('2.1.0', sha256='7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a') version('2.0.1', 'ecb1220ce7c9affaba2987bc7f38adda') - depends_on('r@2.14:') + depends_on('r@2.14:', type=('build', 'run')) depends_on('r-ade4', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) depends_on('r-shiny', type=('build', 'run')) @@ -34,3 +37,4 @@ class RAdegenet(RPackage): 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-boot', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aer/package.py b/var/spack/repos/builtin/packages/r-aer/package.py index 3a8749dfa95..c31dc05fcc1 100644 --- a/var/spack/repos/builtin/packages/r-aer/package.py +++ b/var/spack/repos/builtin/packages/r-aer/package.py @@ -12,16 +12,18 @@ class RAer(RPackage): Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.""" - homepage = "https://cran.r-project.org/web/packages/AER/index.html" - url = "https://cran.r-project.org/src/contrib/AER_1.2-5.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/AER" + 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" + version('1.2-7', sha256='3aee5c606313710c2dca6c1e9b2c20a145aa33f2a3ecc5cfcec66c8e91838a93') + version('1.2-6', sha256='653c3a2d253819e0ce8c2cf12cff2ab222bf3d19dbf382b7c4b4c3d762469474') version('1.2-5', '419df9dc8ee6e5edd79678fee06719ae') - depends_on('r@2.13.0:', type=('build', 'run')) - depends_on('r-car@2.10-19:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-car@2.0-19:', type=('build', 'run')) depends_on('r-lmtest', type=('build', 'run')) - depends_on('r-sandwich', type=('build', 'run')) + depends_on('r-sandwich@2.4-0:', type=('build', 'run')) depends_on('r-survival@2.37-5:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) - depends_on('r-formula', type=('build', 'run')) + depends_on('r-formula@0.2-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-als/package.py b/var/spack/repos/builtin/packages/r-als/package.py index 6314a095640..685fbf5f628 100644 --- a/var/spack/repos/builtin/packages/r-als/package.py +++ b/var/spack/repos/builtin/packages/r-als/package.py @@ -15,11 +15,12 @@ class RAls(RPackage): decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.""" - homepage = "https://cran.r-project.org/package=ALS" - url = "https://cran.rstudio.com/src/contrib/ALS_0.0.6.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/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" version('0.0.6', 'b72d97911e8ab7e4f8aed1a710b3d62d') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-iso', type=('build', 'run')) - depends_on('r-nnls', type=('build', 'run')) + depends_on('r-nnls@1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-amap/package.py b/var/spack/repos/builtin/packages/r-amap/package.py index b22d6ff6fb9..36cdc693f35 100644 --- a/var/spack/repos/builtin/packages/r-amap/package.py +++ b/var/spack/repos/builtin/packages/r-amap/package.py @@ -11,9 +11,11 @@ class RAmap(RPackage): (With robust methods, and parallelized functions).""" homepage = "http://mulcyber.toulouse.inra.fr/projects/amap/" - url = "https://cran.rstudio.com/src/contrib/amap_0.8-16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/amap/" + url = "https://cloud.r-project.org/src/contrib/amap_0.8-16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/amap/" + version('0.8-17', sha256='6b8473d1d35a9cbc611661882c8f681162e8f913f911ccd51629200ae72289c6') version('0.8-16', sha256='d3775ad7f660581f7d2f070e426be95ae0d6743622943e6f5491988e5217d4e2') - depends_on('r@2.10.0:', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py index dc39191fffc..69426a1cd7f 100644 --- a/var/spack/repos/builtin/packages/r-animation/package.py +++ b/var/spack/repos/builtin/packages/r-animation/package.py @@ -13,11 +13,16 @@ class RAnimation(RPackage): computational statistics, data mining and machine learning. These functions maybe helpful in teaching statistics and data analysis.""" - homepage = "https://cran.r-project.org/package=animation" - url = "https://cran.r-project.org/src/contrib/animation_2.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/animation" + 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" + version('2.6', sha256='90293638920ac436e7e4de76ebfd92e1643ccdb0259b62128f16dd0b13245b0a') version('2.5', sha256='b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f') - extends('r') - depends_on('r', type=('build', 'run')) + depends_on('r@2.14:', type=('build', 'run')) + depends_on('r-magick', when='@2.6:', type=('build', 'run')) + depends_on('image-magick') + depends_on('ffmpeg') + depends_on('swftools') + depends_on('texlive') diff --git a/var/spack/repos/builtin/packages/r-ape/package.py b/var/spack/repos/builtin/packages/r-ape/package.py index 1d5aaabddbe..c028e568426 100644 --- a/var/spack/repos/builtin/packages/r-ape/package.py +++ b/var/spack/repos/builtin/packages/r-ape/package.py @@ -24,9 +24,10 @@ class RApe(RPackage): whose results are returned into R.""" homepage = "http://ape-package.ird.fr/" - url = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ape" + url = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ape" + version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23') version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415') version('5.1', sha256='b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e') version('5.0', sha256='c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960') @@ -35,4 +36,4 @@ class RApe(RPackage): depends_on('r@3.2:', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-argparse/package.py b/var/spack/repos/builtin/packages/r-argparse/package.py index 902a17aa4dd..25c05ebcf8c 100644 --- a/var/spack/repos/builtin/packages/r-argparse/package.py +++ b/var/spack/repos/builtin/packages/r-argparse/package.py @@ -12,12 +12,14 @@ class RArgparse(RPackage): arguments and automatically generate usage.""" homepage = "https://github.com/trevorld/argparse" - url = "https://cran.r-project.org/src/contrib/argparse_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/argparse" + url = "https://cloud.r-project.org/src/contrib/argparse_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/argparse" + version('2.0.1', sha256='949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab') version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b') - depends_on('r-proto@1:', type=('build', 'run')) + 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-findpython', type=('build', 'run')) - depends_on('r-getopt', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-askpass/package.py b/var/spack/repos/builtin/packages/r-askpass/package.py new file mode 100644 index 00000000000..ea3bcd0572e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-askpass/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 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 RAskpass(RPackage): + """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 + from R via the askpass() function, or indirectly as password-entry back-end + for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS + 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" + + version('1.1', sha256='db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f') + + depends_on('r-sys@2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py index 1bef74953c1..2e88e9525ed 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -12,8 +12,10 @@ class RAssertthat(RPackage): producing friendly error messages so that your users know what they've done wrong.""" - homepage = "https://cran.r-project.org/package=assertthat" - url = "https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/assertthat" + 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" + + version('0.2.1', sha256='85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f') version('0.2.0', '8134f0072c6a84fd738d3bfc5e7f68ef') version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') diff --git a/var/spack/repos/builtin/packages/r-backports/package.py b/var/spack/repos/builtin/packages/r-backports/package.py index 045ae660228..6aef4037501 100644 --- a/var/spack/repos/builtin/packages/r-backports/package.py +++ b/var/spack/repos/builtin/packages/r-backports/package.py @@ -15,9 +15,13 @@ class RBackports(RPackage): can make use of the new functions without worrying about the minimum required R version.""" - homepage = "https://cran.r-project.org/package=backports" - url = "https://cran.r-project.org/src/contrib/backports_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/backports" + homepage = "https://cloud.r-project.org/package=backports" + url = "https://cloud.r-project.org/src/contrib/backports_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/backports" + version('1.1.4', sha256='ee4b5efef22fa7ef27d7983ffcd31db52f81e1fbb7189c6e89ee09b69349ff03') + version('1.1.3', sha256='e41bd146824ec921994f1b176d0e4cca0b36dd3db32ca7a954d872a5ba214cc1') version('1.1.1', '969543a0af32dc23bba9bb37ec82008c') version('1.1.0', 'b97a71b026fd7ede0e449be93d160c17') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-base64/package.py b/var/spack/repos/builtin/packages/r-base64/package.py index 69d69f8c14d..9aa2ae08647 100644 --- a/var/spack/repos/builtin/packages/r-base64/package.py +++ b/var/spack/repos/builtin/packages/r-base64/package.py @@ -11,9 +11,9 @@ class RBase64(RPackage): Francois. New applications should use the 'openssl' or 'base64enc' package instead.""" - homepage = "https://cran.r-project.org/package=base64" - url = "https://cran.rstudio.com/src/contrib/base64_2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/base64" + 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" version('2.0', 'f5a653842f75ad717ef6a00969868ae5') diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py index 081dba47454..5c1fcc99799 100644 --- a/var/spack/repos/builtin/packages/r-base64enc/package.py +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -11,7 +11,9 @@ class RBase64enc(RPackage): flexible than the orphaned base64 package.""" homepage = "http://www.rforge.net/base64enc" - url = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc" + url = "https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/base64enc" version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') + + depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bayesm/package.py b/var/spack/repos/builtin/packages/r-bayesm/package.py index cc30692af21..10dc0cc7f1c 100644 --- a/var/spack/repos/builtin/packages/r-bayesm/package.py +++ b/var/spack/repos/builtin/packages/r-bayesm/package.py @@ -9,10 +9,13 @@ class RBayesm(RPackage): """Bayesian Inference for Marketing/Micro-Econometrics""" - homepage = "https://cran.r-project.org/web/packages/bayesm/index.html" - url = "https://cran.r-project.org/src/contrib/bayesm_3.1-0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bayesm" + 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" + version('3.1-3', sha256='51e4827eca8cd4cf3626f3c2282543df7c392b3ffb843f4bfb386fe104642a10') + version('3.1-2', sha256='a332f16e998ab10b17a2b1b9838d61660c36e914fe4d2e388a59f031d52ad736') + version('3.1-1', sha256='4854517dec30ab7c994de862aae1998c2d0c5e71265fd9eb7ed36891d4676078') version('3.1-0.1', '34998382cafd3e7972d8a03245eac768') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bbmisc/package.py b/var/spack/repos/builtin/packages/r-bbmisc/package.py index 8bc2144b941..400b7c8972e 100644 --- a/var/spack/repos/builtin/packages/r-bbmisc/package.py +++ b/var/spack/repos/builtin/packages/r-bbmisc/package.py @@ -11,8 +11,8 @@ class RBbmisc(RPackage): guys, mainly for package development.""" homepage = "https://github.com/berndbischl/BBmisc" - url = "https://cran.r-project.org/src/contrib/BBmisc_1.11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.11', '681642628037406beb6088d5f773473d') diff --git a/var/spack/repos/builtin/packages/r-beanplot/package.py b/var/spack/repos/builtin/packages/r-beanplot/package.py index e23094434f8..db560b5772a 100644 --- a/var/spack/repos/builtin/packages/r-beanplot/package.py +++ b/var/spack/repos/builtin/packages/r-beanplot/package.py @@ -10,8 +10,8 @@ class RBeanplot(RPackage): """Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.""" - homepage = "https://cran.r-project.org/web/packages/beanplot/index.html" - url = "https://cran.rstudio.com/src/contrib/beanplot_1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/beanplot" + 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" version('1.2', 'b24943208a4e61ee9ee0dc152634d5da') diff --git a/var/spack/repos/builtin/packages/r-bfast/package.py b/var/spack/repos/builtin/packages/r-bfast/package.py index 49a92cb9721..54b07e9e611 100644 --- a/var/spack/repos/builtin/packages/r-bfast/package.py +++ b/var/spack/repos/builtin/packages/r-bfast/package.py @@ -9,9 +9,9 @@ class RBfast(RPackage): """bfast: Breaks For Additive Season and Trend (BFAST)""" - homepage = "https://cran.r-project.org/package=bfast" - url = "https://cran.r-project.org/src/contrib/bfast_1.5.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bfast" + 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" version('1.5.7', sha256='01585fe8944d05ebdb13795214077bc1365f0c0372e2a1f7edb914356dace558') diff --git a/var/spack/repos/builtin/packages/r-bglr/package.py b/var/spack/repos/builtin/packages/r-bglr/package.py index f25c167b715..68f87952ed7 100644 --- a/var/spack/repos/builtin/packages/r-bglr/package.py +++ b/var/spack/repos/builtin/packages/r-bglr/package.py @@ -9,9 +9,9 @@ class RBglr(RPackage): """BGLR: Bayesian Generalized Linear Regression""" - homepage = "https://cran.r-project.org/package=BGLR" - url = "https://cran.r-project.org/src/contrib/BGLR_1.0.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/BGLR" + 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" version('1.0.8', sha256='5e969590d80b2f272c02a43b487ab1ffa13af386e0342993e6ac484fc82c9b95') diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py index 1ee6eb483e6..23d2909ddd1 100644 --- a/var/spack/repos/builtin/packages/r-bh/package.py +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -22,9 +22,9 @@ class RBh(RPackage): 'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit' 'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'.""" - homepage = "https://cran.r-project.org/web/packages/BH/index.html" - url = "https://cran.r-project.org/src/contrib/BH_1.65.0-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/BH" + homepage = "https://cloud.r-project.org/package=BH" + url = "https://cloud.r-project.org/src/contrib/BH_1.65.0-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/BH" version('1.69.0-1', sha256='a0fd4364b7e368f09c56dec030823f52c16da0787580af7e4615eddeb99baca2') version('1.65.0-1', '7d0402188e4af59f4103f36616d6ee55') diff --git a/var/spack/repos/builtin/packages/r-biasedurn/package.py b/var/spack/repos/builtin/packages/r-biasedurn/package.py index 35224e36796..429ed842a9e 100644 --- a/var/spack/repos/builtin/packages/r-biasedurn/package.py +++ b/var/spack/repos/builtin/packages/r-biasedurn/package.py @@ -15,7 +15,7 @@ class RBiasedurn(RPackage): explanation of these distributions.""" homepage = "http://www.agner.org/random/" - url = "https://cran.rstudio.com/src/contrib/BiasedUrn_1.07.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/BiasedUrn/" + url = "https://cloud.r-project.org/src/contrib/BiasedUrn_1.07.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/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 8f91f3b9451..8fd9a0154e7 100644 --- a/var/spack/repos/builtin/packages/r-bibtex/package.py +++ b/var/spack/repos/builtin/packages/r-bibtex/package.py @@ -11,12 +11,11 @@ class RBibtex(RPackage): Utility to parse a bibtex file.""" - homepage = "https://cran.r-project.org/package=bibtex" - url = "https://cran.r-project.org/src/contrib/bibtex_0.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bibtex/" + 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/" version('0.4.2', sha256='1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bindr/package.py b/var/spack/repos/builtin/packages/r-bindr/package.py index 68183e8ddd7..a3556e3b88c 100644 --- a/var/spack/repos/builtin/packages/r-bindr/package.py +++ b/var/spack/repos/builtin/packages/r-bindr/package.py @@ -11,8 +11,8 @@ class RBindr(RPackage): bound function accepts additional arguments.""" homepage = "https://github.com/krlmlr/bindr" - url = "https://cran.r-project.org/src/contrib/bindr_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.1.1', 'cfa02c563196a79bf8bb4db2e66585fd') version('0.1', 'f3897a70cbad2d2981272772fa30bb59') diff --git a/var/spack/repos/builtin/packages/r-bindrcpp/package.py b/var/spack/repos/builtin/packages/r-bindrcpp/package.py index fc2e541f184..f20e62f7293 100644 --- a/var/spack/repos/builtin/packages/r-bindrcpp/package.py +++ b/var/spack/repos/builtin/packages/r-bindrcpp/package.py @@ -11,12 +11,12 @@ class RBindrcpp(RPackage): call a C++ function.""" homepage = "https://github.com/krlmlr/bindrcpp" - url = "https://cran.r-project.org/src/contrib/bindrcpp_0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.2.2', '48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467') version('0.2', '2ed7f19fd9a12587f882d90060e7a343') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-bindr', type=('build', 'run')) + depends_on('r-rcpp@0.12.16:', type=('build', 'run')) + depends_on('r-bindr@0.1.1:', type=('build', 'run')) depends_on('r-plogr', type=('build', 'run')) 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 e20580db69e..7377db73a1c 100644 --- a/var/spack/repos/builtin/packages/r-biom-utils/package.py +++ b/var/spack/repos/builtin/packages/r-biom-utils/package.py @@ -12,8 +12,8 @@ class RBiomUtils(RPackage): """ homepage = "https://github.com/braithwaite/BIOM.utils/" - url = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/biom/" + 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/" version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375') diff --git a/var/spack/repos/builtin/packages/r-bit/package.py b/var/spack/repos/builtin/packages/r-bit/package.py index 8a618951acf..ceb1975d7da 100644 --- a/var/spack/repos/builtin/packages/r-bit/package.py +++ b/var/spack/repos/builtin/packages/r-bit/package.py @@ -9,7 +9,11 @@ class RBit(RPackage): """ A class for vectors of 1-bit booleans.""" - homepage = "https://cran.rstudio.com/web/packages/bit/index.html" - url = "https://cran.rstudio.com/src/contrib/bit_1.1-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bit" + 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" + + version('1.1-14', sha256='5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254') version('1.1-12', 'c4473017beb93f151a8e672e4d5747af') + + depends_on('r@2.9.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bit64/package.py b/var/spack/repos/builtin/packages/r-bit64/package.py index 141f3be1c8c..5155c6a196d 100644 --- a/var/spack/repos/builtin/packages/r-bit64/package.py +++ b/var/spack/repos/builtin/packages/r-bit64/package.py @@ -20,9 +20,11 @@ class RBit64(RPackage): inter- active data exploration and manipulation and optionally leverage caching.""" - homepage = "https://cran.rstudio.com/web/packages/bit64/index.html" - url = "https://cran.rstudio.com/src/contrib/bit64_0.9-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bit64" + 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" + version('0.9-7', 'ac4bc39827338c552d329d3d4d2339c2') - depends_on('r-bit', type=('build', 'run')) + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r-bit@1.1-12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py index 25dce86116a..1d1cde59fdf 100644 --- a/var/spack/repos/builtin/packages/r-bitops/package.py +++ b/var/spack/repos/builtin/packages/r-bitops/package.py @@ -10,8 +10,8 @@ class RBitops(RPackage): """Functions for bitwise operations on integer vectors.""" - homepage = "https://cran.r-project.org/package=bitops" - url = "https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bitops" + 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" version('1.0-6', 'fba16485a51b1ccd354abde5816b6bdd') diff --git a/var/spack/repos/builtin/packages/r-blob/package.py b/var/spack/repos/builtin/packages/r-blob/package.py index 89b1ccc2252..3a979ba3842 100644 --- a/var/spack/repos/builtin/packages/r-blob/package.py +++ b/var/spack/repos/builtin/packages/r-blob/package.py @@ -12,9 +12,14 @@ class RBlob(RPackage): package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.""" - homepage = "https://cran.rstudio.com/web/packages/blob/index.html" - url = "https://cran.rstudio.com/src/contrib/blob_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/blob" + homepage = "https://cloud.r-project.org/package=blob" + url = "https://cloud.r-project.org/src/contrib/blob_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/blob" + + version('1.2.0', sha256='1af1cfa28607bc0e2f1f01598a00a7d5d1385ef160a9e79e568f30f56538e023') version('1.1.0', '1c729aca36fd5193d81b1cd5ed9d8a00') - depends_on('r-tibble', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-blockmodeling/package.py b/var/spack/repos/builtin/packages/r-blockmodeling/package.py index fcc0eedc2a8..f1333ba7c00 100644 --- a/var/spack/repos/builtin/packages/r-blockmodeling/package.py +++ b/var/spack/repos/builtin/packages/r-blockmodeling/package.py @@ -10,10 +10,11 @@ class RBlockmodeling(RPackage): """blockmodeling: Generalized and Classical Blockmodeling of Valued Networks""" - homepage = "https://cran.r-project.org/package=blockmodeling" - url = "https://cran.rstudio.com/src/contrib/blockmodeling_0.3.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/blockmodeling/" + 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/" + version('0.3.4', sha256='a269c83669dd5294cff0adddab36bc023db6a276a06b74b1fa94b7e407486987') version('0.3.1', sha256='39e8360400cec6baa920d5589d4e779568bdf2954f7331be0e3cadf22a217d31') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bookdown/package.py b/var/spack/repos/builtin/packages/r-bookdown/package.py index 6757a11babb..1cbe28a1206 100644 --- a/var/spack/repos/builtin/packages/r-bookdown/package.py +++ b/var/spack/repos/builtin/packages/r-bookdown/package.py @@ -10,13 +10,17 @@ class RBookdown(RPackage): """Output formats and utilities for authoring books and technical documents with R Markdown.""" - homepage = "https://cran.r-project.org/package=bookdown" - url = "https://cran.rstudio.com/src/contrib/bookdown_0.5.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/bookdown" + 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" + version('0.12', sha256='38eb4c5b877ccd85b16cfe74a48c3bc53de2f276da98e5515f37e7a06e065bb0') version('0.5', '7bad360948e2b22d28397870b9319f17') - depends_on('r-yaml@2.1.14:', type=('build', 'run')) - depends_on('r-rmarkdown@1.5:', type=('build', 'run')) - depends_on('r-knitr@1.16:', type=('build', 'run')) + depends_on('r-yaml@2.1.14:', when='@:0.10', type=('build', 'run')) + depends_on('r-rmarkdown@1.12:', type=('build', 'run')) + depends_on('r-knitr@1.22:', type=('build', 'run')) depends_on('r-htmltools@0.3.6:', type=('build', 'run')) + depends_on('r-xfun@0.6:', when='@0.12:', type=('build', 'run')) + depends_on('r-tinytex@0.12:', when='@0.12:', type=('build', 'run')) + 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 a2fc84c4c96..3f7632f13d4 100644 --- a/var/spack/repos/builtin/packages/r-boot/package.py +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -11,9 +11,13 @@ class RBoot(RPackage): Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.""" - homepage = "https://cran.r-project.org/package=boot" - url = "https://cran.r-project.org/src/contrib/boot_1.3-18.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/boot" + 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" + version('1.3-23', sha256='30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f') + version('1.3-22', sha256='cf1f0cb1e0a7a36dcb6ae038f5d0211a0e7a009c149bc9d21acb9c58c38b4dfc') version('1.3-20', 'bb879fb4204a4f94ab82c98dd1ad5eca') version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py index e2d4271bd81..c6e882e825a 100644 --- a/var/spack/repos/builtin/packages/r-brew/package.py +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -11,8 +11,8 @@ class RBrew(RPackage): report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.""" - homepage = "https://cran.r-project.org/package=brew" - url = "https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/brew" + 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" version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806') diff --git a/var/spack/repos/builtin/packages/r-broom/package.py b/var/spack/repos/builtin/packages/r-broom/package.py index 3ec5b427797..51305071093 100644 --- a/var/spack/repos/builtin/packages/r-broom/package.py +++ b/var/spack/repos/builtin/packages/r-broom/package.py @@ -17,14 +17,22 @@ class RBroom(RPackage): model-level statistics.""" homepage = "http://github.com/tidyverse/broom" - url = "https://cran.r-project.org/src/contrib/broom_0.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/broom" + url = "https://cloud.r-project.org/src/contrib/broom_0.4.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/broom" + + version('0.5.2', sha256='16af7b446b24bc14461efbda9bea1521cf738c778c5e48fcc7bad45660a4ac62') + version('0.5.1', sha256='da9e6bf7cb8f960b83309cf107743976cc32b54524675f6471982abe3d1aae2e') version('0.4.2', '6eabab1f2eaec10f93cf9aa56d6a61de') - depends_on('r-plyr', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-plyr', when='@:0.4.2', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-psych', type=('build', 'run')) + depends_on('r-psych', when='@:0.4.2', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) + depends_on('r-backports', when='@0.5.0:', type=('build', 'run')) + depends_on('r-generics@0.0.2:', when='@0.5.1:', type=('build', 'run')) + depends_on('r-purrr', when='@0.5.0:', type=('build', 'run')) + depends_on('r-tibble', when='@0.5.0:', 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 c81646f77e2..0ca78a69be3 100644 --- a/var/spack/repos/builtin/packages/r-c50/package.py +++ b/var/spack/repos/builtin/packages/r-c50/package.py @@ -10,10 +10,14 @@ class RC50(RPackage): """C5.0 decision trees and rule-based models for pattern recognition.""" - homepage = "https://cran.r-project.org/package=C50" - url = "https://cran.r-project.org/src/contrib/C50_0.1.0-24.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/C50" + 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" + version('0.1.2', sha256='8f459856e0309274bee24462b7145db4eba1d71031c236db39000a5375bdfaba') + version('0.1.1', sha256='03bc1fc2f64bcd5c680568a24902deafab1965074a66f8802bc4cd0335bd01df') version('0.1.0-24', '42631e65c5c579532cc6edf5ea175949') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-partykit', type=('build', 'run')) + depends_on('r-cubist@0.2.1:', 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 0240b9d1591..e0004484e44 100644 --- a/var/spack/repos/builtin/packages/r-cairo/package.py +++ b/var/spack/repos/builtin/packages/r-cairo/package.py @@ -11,10 +11,12 @@ class RCairo(RPackage): bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output""" - homepage = "https://cran.r-project.org/web/packages/Cairo/index.html" - url = "https://cran.r-project.org/src/contrib/Cairo_1.5-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Cairo" + 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" + version('1.5-10', sha256='7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5') version('1.5-9', '2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4') + depends_on('r@2.4.0:', type=('build', 'run')) depends_on('cairo@1.2:') diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py index 21ce4194d0d..1cce1052596 100644 --- a/var/spack/repos/builtin/packages/r-callr/package.py +++ b/var/spack/repos/builtin/packages/r-callr/package.py @@ -12,13 +12,13 @@ class RCallr(RPackage): does exactly that.""" homepage = "https://github.com/MangoTheCat/callr" - url = "https://cran.r-project.org/src/contrib/callr_1.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/callr/" + url = "https://cloud.r-project.org/src/contrib/callr_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/callr/" + version('3.3.1', sha256='bf60da47357d3336aa395b0c9643235a621763c80d28bc9bb2257767d0a37967') + version('3.2.0', sha256='4bb47b1018e8eb5c683a86c05d0d9b8b25848db1f1b30e92cfebedc0ce14b0e8') version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7') version('1.0.0', 'd9af99bb95696310fa1e5d1cb7166c91') - depends_on('r-base64enc', type=('build', 'run'), when='@3.0.0:') - depends_on('r-processx@3.2.0:', type=('build', 'run'), when='@3.0.0') - depends_on('r-r6', type=('build', 'run'), when='@2.0.0') - depends_on('r-utils', type=('build', 'run'), when='@2.0.0') + depends_on('r-processx@3.4.0:', type=('build', 'run'), when='@3.0.0:') + 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 b44421ea2dc..fbd5266bfee 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -11,14 +11,24 @@ class RCar(RPackage): Companion to Applied Regression, Second Edition, Sage, 2011.""" homepage = "https://r-forge.r-project.org/projects/car/" - url = "https://cran.r-project.org/src/contrib/car_2.1-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/car" + url = "https://cloud.r-project.org/src/contrib/car_2.1-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/car" + version('3.0-3', sha256='fa807cb12f6e7fb38ec534cac4eef54747945c2119a7d51155a2492ad778c36f') + version('3.0-2', sha256='df59a9ba8fed67eef5ddb8f92f2b41745df715d5695c71d562d7031513f37c50') version('2.1-4', 'a66c307e8ccf0c336ed197c0f1799565') version('2.1-2', '0f78ad74ef7130126d319acec23951a0') + 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-mass', type=('build', 'run')) depends_on('r-mgcv', type=('build', 'run')) depends_on('r-nnet', type=('build', 'run')) - depends_on('r-pbkrtest', 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:', type=('build', 'run')) + depends_on('r-lme4', when='@3.0:', type=('build', 'run')) + depends_on('r-nlme', when='@3.0:', 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 new file mode 100644 index 00000000000..6e9c430d7fb --- /dev/null +++ b/var/spack/repos/builtin/packages/r-cardata/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 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 RCardata(RPackage): + """Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied + Regression, Third Edition, Sage (forthcoming).""" + + 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" + + version('3.0-2', sha256='3b5c4eff1cc1e456a5331084774503eaa06cf61fb7acf6b9e8a6bfabd5735494') + + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py index f37b5099ae8..fcbf54004bb 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -11,19 +11,23 @@ class RCaret(RPackage): models.""" homepage = "https://github.com/topepo/caret/" - url = "https://cran.r-project.org/src/contrib/caret_6.0-73.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/caret" + url = "https://cloud.r-project.org/src/contrib/caret_6.0-73.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/caret" + version('6.0-84', sha256='a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d') + version('6.0-83', sha256='9bde5e4da1f0b690bfe06c2439c0136504e851a8d360bf56b644f171fe20dcef') version('6.0-73', 'ca869e3357b5358f028fb926eb62eb70') version('6.0-70', '202d7abb6a679af716ea69fb2573f108') - depends_on('r@2.10:') - + depends_on('r@2.10:', when='@:6.0-81', type=('build', 'run')) + depends_on('r@3.2.0:', when='@6.0-82:', type=('build', 'run')) depends_on('r-lattice@0.20:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-car', type=('build', 'run')) + depends_on('r-car', when='@:6.0-73', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) depends_on('r-modelmetrics@1.1.0:', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-recipes@0.1.4:', when='@6.0-83:', type=('build', 'run')) + depends_on('r-withr@2.0.0:', when='@6.0-83:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-caroline/package.py b/var/spack/repos/builtin/packages/r-caroline/package.py index 152edc7cfca..a72a4977db5 100644 --- a/var/spack/repos/builtin/packages/r-caroline/package.py +++ b/var/spack/repos/builtin/packages/r-caroline/package.py @@ -10,9 +10,9 @@ class RCaroline(RPackage): """caroline: A Collection of Database, Data Structure, Visualization, andUtility Functions for R""" - homepage = "https://cran.r-project.org/package=caroline" - url = "https://cran.r-project.org/src/contrib/caroline_0.7.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/caroline" + 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" 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 5cbdcea39b5..9898ab68b35 100644 --- a/var/spack/repos/builtin/packages/r-catools/package.py +++ b/var/spack/repos/builtin/packages/r-catools/package.py @@ -13,10 +13,13 @@ class RCatools(RPackage): files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.""" - homepage = "https://cran.r-project.org/package=caTools" - url = "https://cran.r-project.org/src/contrib/caTools_1.17.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/caTools" + 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" + version('1.17.1.2', sha256='69cc542fab5677462b1a768709d0c4a0a0790f5db53e1fe9ae7123787c18726b') + version('1.17.1.1', sha256='d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06') version('1.17.1', '5c872bbc78b177b306f36709deb44498') + depends_on('r@2.2.0:', type=('build', 'run')) depends_on('r-bitops', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cdcfluview/package.py b/var/spack/repos/builtin/packages/r-cdcfluview/package.py index e1a2e4770c1..fa99d27ca99 100644 --- a/var/spack/repos/builtin/packages/r-cdcfluview/package.py +++ b/var/spack/repos/builtin/packages/r-cdcfluview/package.py @@ -14,12 +14,14 @@ 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://cran.r-project.org/package=cdcfluview" - url = "https://cran.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cdcfluview" + 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" + version('0.9.0', sha256='1b2064886858cbb1790ef808d88fbab75d3a9cf55e720638221a3377ff8dd244') version('0.7.0', 'd592606fab3da3536f39a15c0fdbcd17') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) @@ -29,4 +31,3 @@ class RCdcfluview(RPackage): depends_on('r-readr', type=('build', 'run')) depends_on('r-mmwrweek', type=('build', 'run')) depends_on('r-units@0.4-6:', type=('build', 'run')) - depends_on('r@3.2.0:', 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 8a9e55430c5..4f8205d51fe 100644 --- a/var/spack/repos/builtin/packages/r-cellranger/package.py +++ b/var/spack/repos/builtin/packages/r-cellranger/package.py @@ -10,11 +10,12 @@ class RCellranger(RPackage): """Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.""" - homepage = "https://cran.r-project.org/package=cellranger" - url = "https://cran.r-project.org/src/contrib/cellranger_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cellranger" + 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" version('1.1.0', '1abcfea6af5ab2e277cb99e86880456f') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rematch', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-checkmate/package.py b/var/spack/repos/builtin/packages/r-checkmate/package.py index 10e69d62c6c..df1abd2b6ba 100644 --- a/var/spack/repos/builtin/packages/r-checkmate/package.py +++ b/var/spack/repos/builtin/packages/r-checkmate/package.py @@ -11,10 +11,12 @@ class RCheckmate(RPackage): A substantial part of the package was written in C to minimize any worries about execution time overhead.""" - homepage = "https://cran.r-project.org/package=checkmate" - url = "https://cran.rstudio.com/src/contrib/checkmate_1.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/checkmate" + 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" + version('1.9.4', sha256='faa25754b757fe483b876f5d07b73f76f69a1baa971420892fadec4af4bbad21') version('1.8.4', '00bd2c464386614da208f82c4b21910b') - depends_on('r-backports', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-backports@1.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index f841bc8c9c8..258a7ee7677 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -12,11 +12,13 @@ class RCheckpoint(RPackage): install packages as they existed on CRAN on a specific snapshot date as if you had a CRAN time machine.""" - homepage = "https://cran.r-project.org/package=checkpoint" - url = "https://cran.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/checkpoint" + homepage = "https://cloud.r-project.org/package=checkpoint" + url = "https://cloud.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint" + version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') + version('0.4.3', sha256='c3e862f89f8838183d6028f7ed13683aec562e6dab77ad4b6a5e24ec653cfb64') version('0.3.18', '021d7faeb72c36167951e103b2b065ea') version('0.3.15', 'a4aa8320338f1434a330d984e97981ea') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py index 93fd4f5253e..d2854903d13 100644 --- a/var/spack/repos/builtin/packages/r-chemometrics/package.py +++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py @@ -10,9 +10,9 @@ class RChemometrics(RPackage): """R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).""" - homepage = "https://cran.r-project.org/web/packages/chemometrics/index.html" - url = "https://cran.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/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" version('1.4.2', '8137b0ca4004add9cc2ea81d2c54427f') version('1.4.1', '1e5a89442bb4a61db0da884eedd74fc2') @@ -29,3 +29,6 @@ class RChemometrics(RPackage): depends_on('r-pls', type=('build', 'run')) depends_on('r-som', type=('build', 'run')) depends_on('r-pcapp', type=('build', 'run')) + depends_on('r-class', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py index 71c15755773..3defd1653b4 100644 --- a/var/spack/repos/builtin/packages/r-chron/package.py +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -9,8 +9,12 @@ class RChron(RPackage): """Chronological objects which can handle dates and times.""" - homepage = "https://cran.r-project.org/package=chron" - url = "https://cran.r-project.org/src/contrib/chron_2.3-47.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/chron" + 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" + version('2.3-53', sha256='521814b46ba958eae28e29d8766aebd285da5e6fa16c5806603df3ae39f77309') + version('2.3-52', sha256='c47fcf4abb635babe6337604c876d4853d8a24639a98b71523746c56ce75b4a0') version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f') + + depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-circlize/package.py b/var/spack/repos/builtin/packages/r-circlize/package.py index 89148b74f7d..31dd662d76f 100644 --- a/var/spack/repos/builtin/packages/r-circlize/package.py +++ b/var/spack/repos/builtin/packages/r-circlize/package.py @@ -18,13 +18,15 @@ class RCirclize(RPackage): convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.""" - homepage = "https://cran.r-project.org/package=circlize" - url = "https://cran.r-project.org/src/contrib/circlize_0.4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/circlize" + 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" + version('0.4.6', sha256='cec88cfc5e512a111cc37177552c25698ccc0e9bbecb0d6e60657e7b115a56fa') version('0.4.1', '6818830654f485abbdc8c74ec9087377') version('0.4.0', '0dbf1b481930a759d6f413d17f8ae1c4') - depends_on('r-globaloptions', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-globaloptions@0.1.0:', type=('build', 'run')) depends_on('r-shape', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index aa31dfe6ef6..472c8dbd4aa 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -11,9 +11,11 @@ class RClass(RPackage): Learning Vector Quantization and Self-Organizing Maps.""" homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" - url = "https://cran.r-project.org/src/contrib/class_7.3-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/class" + 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" + version('7.3-15', sha256='f6bf33d610c726d58622b6cea78a808c7d6a317d02409d27c17741dfd1c730f4') version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-classint/package.py b/var/spack/repos/builtin/packages/r-classint/package.py index 3a9f11c66dd..fb859c3e7cf 100644 --- a/var/spack/repos/builtin/packages/r-classint/package.py +++ b/var/spack/repos/builtin/packages/r-classint/package.py @@ -10,11 +10,16 @@ class RClassint(RPackage): """Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.""" - homepage = "https://cran.r-project.org/package=classInt" - url = "https://cran.r-project.org/src/contrib/classInt_0.1-24.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/classInt" + 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" + version('0.4-1', sha256='39c63f8e37b379033d73d57929b5b8ea41b0023626cc1cec648d66bade5d0103') + version('0.3-3', sha256='a93e685ef9c40d5977bb91d7116505a25303b229897a20544722a94ea1365f30') + version('0.3-1', sha256='e2e6f857b544dfecb482b99346aa3ecfdc27b4d401c3537ee8fbaf91caca92b9') version('0.1-24', '45f1bde3ec7601ce17c99189be5c0fd5') + depends_on('r@2.2:', type=('build', 'run')) depends_on('r-e1071', type=('build', 'run')) depends_on('r-class', type=('build', 'run')) + depends_on('r-kernsmooth', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py index 883a34e8eb8..e841226979d 100644 --- a/var/spack/repos/builtin/packages/r-cli/package.py +++ b/var/spack/repos/builtin/packages/r-cli/package.py @@ -12,11 +12,13 @@ class RCli(RPackage): 'Unicode' symbols with 'ASCII' alternatives.""" homepage = "https://github.com/r-lib/cli#readme" - url = "https://cran.r-project.org/src/contrib/cli_1.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cli" + url = "https://cloud.r-project.org/src/contrib/cli_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/cli" + version('1.1.0', sha256='4fc00fcdf4fdbdf9b5792faee8c7cf1ed5c4f45b1221d961332cda82dbe60d0a') version('1.0.1', 'ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4') version('1.0.0', 'e6c4169541d394d6d435c4b430b1dd77') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) + depends_on('r-crayon@1.3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-clipr/package.py b/var/spack/repos/builtin/packages/r-clipr/package.py index fe2f21736a7..bd6a07923cc 100644 --- a/var/spack/repos/builtin/packages/r-clipr/package.py +++ b/var/spack/repos/builtin/packages/r-clipr/package.py @@ -11,11 +11,11 @@ class RClipr(RPackage): and X11 clipboards.""" homepage = "https://github.com/mdlincoln/clipr" - url = "https://cran.r-project.org/src/contrib/clipr_0.4.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.7.0', sha256='03a4e4b72ec63bd08b53fe62673ffc19a004cc846957a335be2b30d046b8c2e2') + version('0.5.0', sha256='fd303f8b7f29badcdf490bb2d579acdfc4f4e1aa9c90ac77ab9d05ce3d053dbf') version('0.4.0', '4012a31eb3b7a36bd3bac00f916e56a7') - depends_on('r-rstudioapi', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) 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 new file mode 100644 index 00000000000..057fa67b9bc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-clisymbols/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 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 RClisymbols(RPackage): + """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 ).""" + + 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" + + version('1.2.0', sha256='0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0') diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index be9fdccdde0..44a36e5b00f 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -11,10 +11,15 @@ class RCluster(RPackage): Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".""" - homepage = "https://cran.r-project.org/web/packages/cluster/index.html" - url = "https://cran.rstudio.com/src/contrib/cluster_2.0.7-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cluster" + 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" + version('2.1.0', sha256='eaf955bef8f616ea563351ec7f597c445aec43e65991ca975e382ef1fd70aa14') version('2.0.7-1', 'a37add21b91d3e4f3883d005331e0d45') version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a') version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-clustergeneration/package.py b/var/spack/repos/builtin/packages/r-clustergeneration/package.py index 4dbcc13bb6e..ccae368dde8 100644 --- a/var/spack/repos/builtin/packages/r-clustergeneration/package.py +++ b/var/spack/repos/builtin/packages/r-clustergeneration/package.py @@ -9,10 +9,11 @@ class RClustergeneration(RPackage): """Random Cluster Generation (with Specified Degree of Separation)""" - homepage = "https://cran.r-project.org/package=clusterGeneration" - url = "https://cran.r-project.org/src/contrib/clusterGeneration_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/clusterGeneration/" + 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/" version('1.3.4', sha256='7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa') + depends_on('r@2.9.1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py index 8c83b9d5daa..bc06676d85c 100644 --- a/var/spack/repos/builtin/packages/r-cner/package.py +++ b/var/spack/repos/builtin/packages/r-cner/package.py @@ -33,5 +33,5 @@ class RCner(RPackage): depends_on('r-annotate@1.50.0:', type=('build', 'run')) depends_on('r-go-db@3.3.0:', type=('build', 'run')) depends_on('r-keggrest@1.14.0:', type=('build', 'run')) - depends_on('r-utils@2.3.0:', type=('build', 'run')) + depends_on('r-r-utils@2.3.0:', type=('build', 'run')) depends_on('r@3.4.3:3.4.9', when='@1.14.0') diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py index e7c7c8c11b1..b69c0f5a80f 100644 --- a/var/spack/repos/builtin/packages/r-coda/package.py +++ b/var/spack/repos/builtin/packages/r-coda/package.py @@ -12,10 +12,13 @@ class RCoda(RPackage): diagnostic tests of convergence to the equilibrium distribution of the Markov chain.""" - homepage = "https://cran.r-project.org/web/packages/coda/index.html" - url = "https://cran.r-project.org/src/contrib/coda_0.19-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/coda" + 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" + version('0.19-3', sha256='d3df1fc848bcf1af8fae13d61eeab60e99a3d4b4db384bec4326f909f502c5d6') + version('0.19-2', sha256='678a7e6a87a2723089daeb780ea37ac3d4319b37eabe26928ea3fa9c9b1eda0d') version('0.19-1', '0d2aca6a5a3bdae9542708817c1ec001') + depends_on('r@2.14:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index 4e451ba8394..5ccaa4914cf 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -9,9 +9,12 @@ class RCodetools(RPackage): """Code analysis tools for R.""" - homepage = "https://cran.r-project.org/web/packages/codetools/index.html" - url = "https://cran.r-project.org/src/contrib/codetools_0.2-15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/codetools" + 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" + version('0.2-16', sha256='f67a66175cb5d8882457d1e9b91ea2f16813d554fa74f80c1fd6e17cf1877501') version('0.2-15', '37419cbc3de81984cf6d9b207d4f62d4') version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') + + depends_on('r@2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py index 81a8bf45d48..b52fff5e772 100644 --- a/var/spack/repos/builtin/packages/r-coin/package.py +++ b/var/spack/repos/builtin/packages/r-coin/package.py @@ -11,15 +11,19 @@ class RCoin(RPackage): including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.""" - homepage = "https://cran.r-project.org/package=coin" - url = "https://cran.r-project.org/src/contrib/coin_1.1-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/coin" + 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" + version('1.3-0', sha256='adcebb37e0a7dfddbf8ec1e09c12a809bd76d90b5b8ff2b1048a75252ba11ef8') + version('1.2-2', sha256='d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb') version('1.1-3', '97d3d21f1e4a5762e36dd718dd2d0661') - depends_on('r@2.14.0:') - + 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-survival', type=('build', 'run')) 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')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index ebe83745ccc..9aaec8933ec 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -12,9 +12,13 @@ class RColorspace(RPackage): Qualitative, sequential, and diverging color palettes based on HCL colors are provided.""" - homepage = "https://cran.r-project.org/web/packages/colorspace/index.html" - url = "https://cran.r-project.org/src/contrib/colorspace_1.3-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace" + homepage = "https://cloud.r-project.org/package=colorspace" + url = "https://cloud.r-project.org/src/contrib/colorspace_1.3-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/colorspace" + version('1.4-1', sha256='693d713a050f8bfecdb7322739f04b40d99b55aed168803686e43401d5f0d673') + version('1.4-0', sha256='ce003c5958dd704697959e9dc8a108c8cb568f8d78ece113235732afc5dff556') version('1.3-2', '63000bab81d995ff167df76fb97b2984') version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-combinat/package.py b/var/spack/repos/builtin/packages/r-combinat/package.py index 98d89fffbd7..7adf6669727 100644 --- a/var/spack/repos/builtin/packages/r-combinat/package.py +++ b/var/spack/repos/builtin/packages/r-combinat/package.py @@ -9,8 +9,8 @@ class RCombinat(RPackage): """routines for combinatorics""" - homepage = "https://cran.r-project.org/package=combinat" - url = "https://cran.r-project.org/src/contrib/combinat_0.0-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/combinat/" + 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/" 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 6cbafa742f4..27afc8cfea9 100644 --- a/var/spack/repos/builtin/packages/r-commonmark/package.py +++ b/var/spack/repos/builtin/packages/r-commonmark/package.py @@ -9,8 +9,8 @@ class RCommonmark(RPackage): """commonmark: CommonMark and Github Markdown Rendering in R""" - homepage = "https://cran.r-project.org/package=commonmark" - url = "https://cran.r-project.org/src/contrib/commonmark_1.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/commonmark/" + 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/" 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 1b5e22f4bd6..112af5a1e53 100644 --- a/var/spack/repos/builtin/packages/r-compositions/package.py +++ b/var/spack/repos/builtin/packages/r-compositions/package.py @@ -9,9 +9,9 @@ class RCompositions(RPackage): """Compositional Data Analysis""" - homepage = "https://cran.r-project.org/web/packages/compositions/index.html" - url = "https://cran.r-project.org/src/contrib/compositions_1.40-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/compositions" + 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" version('1.40-2', 'ad87efe2fb303d95472e73c8ca8d9a01') diff --git a/var/spack/repos/builtin/packages/r-construct/package.py b/var/spack/repos/builtin/packages/r-construct/package.py index 03f026dc2d7..1ec973752f1 100644 --- a/var/spack/repos/builtin/packages/r-construct/package.py +++ b/var/spack/repos/builtin/packages/r-construct/package.py @@ -10,9 +10,9 @@ class RConstruct(RPackage): """conStruct: Models Spatially Continuous and Discrete Population GeneticStructure""" - homepage = "https://cran.r-project.org/package=conStruct" - url = "https://cran.r-project.org/src/contrib/conStruct_1.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/conStruct" + 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" version('1.0.3', sha256='b449c133a944ad05a28f84f312ed4ccbc1574c4659aa09c678618d2ae9008310') @@ -27,3 +27,4 @@ class RConstruct(RPackage): depends_on('r-rstan@2.18.1:', type=('build', 'run')) depends_on('r-rstantools@1.5.0:', type=('build', 'run')) depends_on('r-stanheaders@2.18.0:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-convevol/package.py b/var/spack/repos/builtin/packages/r-convevol/package.py index ea8d4595ecd..398e9050162 100644 --- a/var/spack/repos/builtin/packages/r-convevol/package.py +++ b/var/spack/repos/builtin/packages/r-convevol/package.py @@ -9,12 +9,13 @@ class RConvevol(RPackage): """Quantifies and assesses the significance of convergent evolution""" - homepage = "https://cran.r-project.org/package=convevol" - url = "https://cran.r-project.org/src/contrib/convevol_1.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/convevol/" + 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/" version('1.3', sha256='d6b24b9796a559f5280e277746189d141151ade4b14cc6b4c2d9d496d7f314ac') + depends_on('r@3.5.0:', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-geiger', 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 7d1632d5ac1..41043b8a1ce 100644 --- a/var/spack/repos/builtin/packages/r-corhmm/package.py +++ b/var/spack/repos/builtin/packages/r-corhmm/package.py @@ -14,9 +14,9 @@ class RCorhmm(RPackage): states in a Markov process and various other functions for evaluating models of binary character evolution.""" - homepage = "https://cran.r-project.org/package=corHMM" - url = "https://cran.r-project.org/src/contrib/corHMM_1.22.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/corHMM/" + homepage = "https://cloud.r-project.org/package=corHMM" + url = "https://cloud.r-project.org/src/contrib/corHMM_1.22.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/corHMM/" version('1.22', sha256='d262fa1183eab32087afb70f1789fabae6fb49bec01d627974c54a088a48b10d') diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py index bbebf81c22b..36902848095 100644 --- a/var/spack/repos/builtin/packages/r-corpcor/package.py +++ b/var/spack/repos/builtin/packages/r-corpcor/package.py @@ -9,8 +9,10 @@ class RCorpcor(RPackage): """Efficient Estimation of Covariance and (Partial) Correlation""" - homepage = "https://cran.r-project.org/package=corpcor" - url = "https://cran.r-project.org/src/contrib/corpcor_1.6.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/corpcor" + 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" version('1.6.9', '7f447d9f389e5d7dedb5fe5baedca925') + + 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 702fe40fabf..71ded1da625 100644 --- a/var/spack/repos/builtin/packages/r-corrplot/package.py +++ b/var/spack/repos/builtin/packages/r-corrplot/package.py @@ -10,8 +10,9 @@ class RCorrplot(RPackage): """A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering.""" - homepage = "https://cran.r-project.org/package=corrplot" - url = "https://cran.r-project.org/src/contrib/corrplot_0.77.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/corrplot" + 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" + version('0.84', sha256='0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc') version('0.77', '2a5d54fd5c65618b9afba1a32f6b4542') diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py index 404543baa12..1f62a54c170 100644 --- a/var/spack/repos/builtin/packages/r-covr/package.py +++ b/var/spack/repos/builtin/packages/r-covr/package.py @@ -16,14 +16,20 @@ class RCovr(RPackage): or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.""" - homepage = "https://cran.r-project.org/package=covr" - url = "https://cran.r-project.org/src/contrib/covr_3.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/covr" + 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" + version('3.3.0', sha256='c0aa0bd7b2dc05effdc2367c59d45294f46858930d1b14efb393b205021fc65a') + version('3.2.1', sha256='ea90daa48011e4ac4431ae47ee02fad98f54b529fc3900281cbeef7a2edef0a0') + version('3.2.0', sha256='b26135306b1d6b14dd4deb481359dd919a7ca1e802ca5479fed394dcf35f0ef9') version('3.0.1', 'f88383f751fe5aa830a2b2e5c14aa66a') + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-digest', when='@3.2.0:', type=('build', 'run')) 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', type=('build', 'run')) + depends_on('r-withr@1.0.2:', type=('build', 'run')) + depends_on('r-yaml', when='@3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cowplot/package.py b/var/spack/repos/builtin/packages/r-cowplot/package.py index 150844ec438..3d3bd5549b8 100644 --- a/var/spack/repos/builtin/packages/r-cowplot/package.py +++ b/var/spack/repos/builtin/packages/r-cowplot/package.py @@ -15,18 +15,21 @@ class RCowplot(RPackage): theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot package.""" - homepage = "https://cran.r-project.org/package=cowplot" - url = "https://cran.rstudio.com/src/contrib/cowplot_0.8.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/cowplot" + 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" + version('1.0.0', sha256='70f9a7c46d10f409d1599f1afc9fd3c947051cf2b430f01d903c64ef1e6c98a5') version('0.9.3', sha256='3e10475fd7506ea9297ed72eb1a3acf858c6fa99d26e46fc39654eba000c3dcb') version('0.9.2', sha256='8b92ce7f92937fde06b0cfb86c7634a39b3b2101e362cc55c4bec6b3fde1d28f') version('0.9.1', sha256='953fd9d6ff370472b9f5a9ee867a423bea3e26e406d08a2192ec1872a2e60047') version('0.9.0', sha256='d5632f78294c3678c08d3eb090abe1eec5cc9cd15cb5d96f9c43794ead098cb5') version('0.8.0', sha256='a617fde25030fe764f20967fb753a953d73b47745a2146c97c2565eb4d06700d') - depends_on('r@3.3.0:', type=('build', 'run')) - depends_on('r-ggplot2@2.1.0:', type=('build', 'run')) - depends_on('r-gtable@0.1.2:', type=('build', 'run')) - depends_on('r-plyr@1.8.2:', type=('build', 'run')) + 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:', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) + depends_on('r-plyr@1.8.2:', when='@:0.9.9', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) + depends_on('r-rlang', when='@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py index 843851a5921..4a5cd951453 100644 --- a/var/spack/repos/builtin/packages/r-crayon/package.py +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -13,9 +13,9 @@ class RCrayon(RPackage): New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.""" - homepage = "https://cran.r-project.org/package=sourcetools" - url = "https://cran.rstudio.com/src/contrib/crayon_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/crayon" + homepage = "https://github.com/r-lib/crayon#readme" + url = "https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/crayon" version('1.3.4', '77c7c2906c59a3141306d86c89ffc7d3') version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9') diff --git a/var/spack/repos/builtin/packages/r-crosstalk/package.py b/var/spack/repos/builtin/packages/r-crosstalk/package.py index 39119c3e26f..ad17c33aa6f 100644 --- a/var/spack/repos/builtin/packages/r-crosstalk/package.py +++ b/var/spack/repos/builtin/packages/r-crosstalk/package.py @@ -10,13 +10,15 @@ class RCrosstalk(RPackage): """Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files).""" - homepage = "https://cran.r-project.org/web/packages/crosstalk/index.html" - url = "https://cran.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz" + homepage = "https://cloud.r-project.org/package=crosstalk" + url = "https://cloud.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/crosstalk" version('1.0.0', 'c13c21b81af2154be3f08870fd3a7077') - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.3.5:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-shiny', type=('build', 'run')) + depends_on('r-shiny@0.11:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-crul/package.py b/var/spack/repos/builtin/packages/r-crul/package.py index 6ce56a55843..e2d4410ebc3 100644 --- a/var/spack/repos/builtin/packages/r-crul/package.py +++ b/var/spack/repos/builtin/packages/r-crul/package.py @@ -9,10 +9,11 @@ class RCrul(RPackage): """crul: HTTP Client""" - homepage = "https://cran.r-project.org/package=crul" - url = "https://cran.r-project.org/src/contrib/crul_0.7.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/crul" + 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" + version('0.8.4', sha256='dbd950ad3b68402e5a5955615b1abcb5c9bdc846c93aa25f96a7a58913d04c8b') version('0.7.4', sha256='c963dd666ae3fc89b661ce19fce2fa19a16fc3825e1502105cae98ceb92c6014') depends_on('r-curl@3.3:', type=('build', 'run')) @@ -20,3 +21,4 @@ class RCrul(RPackage): depends_on('r-mime', type=('build', 'run')) depends_on('r-r6@2.2.0:', type=('build', 'run')) depends_on('r-urltools@1.6.0:', type=('build', 'run')) + depends_on('r-jsonlite', when='@0.8.4:', 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 0b5a475b810..7ed968d5bc5 100644 --- a/var/spack/repos/builtin/packages/r-cubature/package.py +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -9,8 +9,12 @@ class RCubature(RPackage): """Adaptive multivariate integration over hypercubes""" - homepage = "https://cran.r-project.org/package=cubature" - url = "https://cran.r-project.org/src/contrib/cubature_1.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cubature" + 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" + version('2.0.3', sha256='79bf03ebdb64b0de1ef19d24051b9d922df9310254bee459bb47764522407a73') + version('2.0.2', sha256='641165c665ff490c523bccc05c42bb6851e42676b6b366b55fc442a51a8fbe8c') version('1.1-2', '5617e1d82baa803a3814d92461da45c9') + + depends_on('r-rcpp', when='@2.0.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py index 1a89f3c21f0..a41928e6639 100644 --- a/var/spack/repos/builtin/packages/r-cubist/package.py +++ b/var/spack/repos/builtin/packages/r-cubist/package.py @@ -9,10 +9,12 @@ class RCubist(RPackage): """Regression modeling using rules with added instance-based corrections""" - homepage = "https://cran.r-project.org/package=Cubist" - url = "https://cran.r-project.org/src/contrib/Cubist_0.0.19.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Cubist" + 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" + version('0.2.2', sha256='cd3e152cc72ab33f720a8fb6b8b6787171e1c037cfda48f1735ab692ed6d85d4') + version('0.2.1', sha256='b310c3f166f15fa3e16f8d110d39931b0bb1b0aa8d0c9ac2af5a9a45081588a3') version('0.0.19', 'bf9364f655536ec03717fd2ad6223a47') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index 785b4487c52..2a720b2a99a 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -18,14 +18,15 @@ class RCurl(RPackage): package with http specific tools and logic.""" homepage = "https://github.com/jeroenooms/curl" - url = "https://cran.r-project.org/src/contrib/curl_2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/curl" + url = "https://cloud.r-project.org/src/contrib/curl_2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/curl" + version('4.0', sha256='09a99c9c86666449188fbb211cb1e9fbdb5108ab56f0d09322cd0ae50e926171') version('3.3', sha256='0cb0b9a9280edc42ebed94708541ec86b4f48779e722171e45227eab8a88a5bd') version('3.0', '741202626eacd1f9c022b0a4d7be6d6a') version('2.3', '7250ee8caed98ba76906ab4d32da60f8') version('1.0', '93d34926d6071e1fba7e728b482f0dd9') version('0.9.7', 'a101f7de948cb828fef571c730f39217') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('curl') 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 4b669b8a76d..e9e2bc0440a 100644 --- a/var/spack/repos/builtin/packages/r-data-table/package.py +++ b/var/spack/repos/builtin/packages/r-data-table/package.py @@ -13,9 +13,11 @@ class RDataTable(RPackage): syntax, for faster development.""" homepage = "https://github.com/Rdatatable/data.table/wiki" - url = "https://cran.r-project.org/src/contrib/data.table_1.10.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/data.table" + url = "https://cloud.r-project.org/src/contrib/data.table_1.10.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/data.table" + version('1.12.2', sha256='db55c18f0d703a8bc1c806dd1f7551bb405cb867717f52ef9dd64405394d22f5') + version('1.12.0', sha256='611b112123dbd4ebd5200770fcdfaaeaab622adeb2b290d36018d3092742e3f7') version('1.11.8', sha256='dc427465599cadd848b28a78e2fce3362867847b44148252054385999fe566d9') version('1.11.6', sha256='ac6783c18e94d1bc05702ddec9fd87c542c744f640132f5ffc373348be84d9e9') version('1.11.4', sha256='fdccf1dec3f38bb344163163decf3ffa0c0f8e2c70daa1bec8aac422716e81d5') diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py index 866b19dd4c3..bd8e4289e3e 100644 --- a/var/spack/repos/builtin/packages/r-dbi/package.py +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -12,7 +12,11 @@ class RDbi(RPackage): virtual and need to be extended by the various R/DBMS implementations.""" homepage = "http://rstats-db.github.io/DBI" - url = "https://cran.rstudio.com/src/contrib/DBI_0.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DBI" + url = "https://cloud.r-project.org/src/contrib/DBI_0.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DBI" + + version('1.0.0', sha256='ff16f118eb3f759183441835e932b87358dd80ab9800ce576a8f3df1b6f01cf5') version('0.4-1', 'c7ee8f1c5037c2284e99c62698d0f087') version('0.7', '66065dd687d758b72d638adb6a8cab2e') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dbplyr/package.py b/var/spack/repos/builtin/packages/r-dbplyr/package.py index 5950fb4a025..2f88bb3fc8f 100644 --- a/var/spack/repos/builtin/packages/r-dbplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dbplyr/package.py @@ -14,21 +14,23 @@ class RDbplyr(RPackage): author.""" homepage = "https://github.com/tidyverse/dbplyr" - url = "https://cran.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dbplyr" + url = "https://cloud.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dbplyr" + version('1.4.2', sha256='b783f0da2c09a1e63f41168b02c0715b08820f02a351f7ab0aaa688432754de0') + version('1.4.1', sha256='cfe829f56acdc785c5af21bf3927cf08327504d78c4ae1477c405c81b131da95') version('1.2.2', sha256='9d410bb0055fffe10f1f8da55a5b24d98322c7b571d74df61427d5888332bc48') version('1.2.1', sha256='b348e7a02623f037632c85fb11be16c40c01755ae6ca02c8c189cdc192a699db') version('1.2.0', sha256='02a5fa8dcf8a81c061fdaefa74f17896bee913720418b44dbd226a0d6b30799d') version('1.1.0', sha256='7b1e456a2d1056fa6284582cd82d2df66d06b3eea92e9995f5a91a45f246f69d') - depends_on('r@3.2:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-assertthat@0.2.0:', type=('build', 'run')) - depends_on('r-dbi@0.7:', type=('build', 'run')) - depends_on('r-dplyr@0.7.4:', type=('build', 'run')) + depends_on('r-dbi@1.0.0:', type=('build', 'run')) + depends_on('r-dplyr@0.8.0:', type=('build', 'run')) depends_on('r-glue@1.2.0:', type=('build', 'run')) - depends_on('r-purrr@0.2.4:', type=('build', 'run')) + depends_on('r-purrr@0.2.5:', type=('build', 'run')) depends_on('r-r6@2.2.2:', type=('build', 'run')) - depends_on('r-rlang@0.1.6:', type=('build', 'run')) - depends_on('r-tibble@1.4.1:', type=('build', 'run')) - depends_on('r-tidyselect@0.2.2:', 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')) diff --git a/var/spack/repos/builtin/packages/r-debugme/package.py b/var/spack/repos/builtin/packages/r-debugme/package.py new file mode 100644 index 00000000000..590fe5f23a7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-debugme/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 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 RDebugme(RPackage): + """Specify debug messages as special string constants, and control + debugging of packages via environment variables.""" + + 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" + + version('1.1.0', sha256='4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1') + + depends_on('r-crayon', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py index 299ef640ac8..f206bc6a6bf 100644 --- a/var/spack/repos/builtin/packages/r-deldir/package.py +++ b/var/spack/repos/builtin/packages/r-deldir/package.py @@ -13,10 +13,12 @@ class RDeldir(RPackage): tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.""" - homepage = "https://CRAN.R-project.org/package=deldir" - url = "https://cran.r-project.org/src/contrib/deldir_0.1-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/deldir" + 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" + version('0.1-23', sha256='e0112bce9fc94daf73596a0fff9b3958b80872e3bbb487be73e157b13a6f201d') + version('0.1-21', sha256='b9dabcc1813c7a0f8edaf720a94bdd611a83baf3d3e52e861d352369e815690c') version('0.1-14', '6a22b13d962615cd9d51b6eae403409f') - depends_on('r@0.99:') + depends_on('r@0.99:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py index 3fe9677f902..b1e578164c1 100644 --- a/var/spack/repos/builtin/packages/r-dendextend/package.py +++ b/var/spack/repos/builtin/packages/r-dendextend/package.py @@ -9,15 +9,17 @@ class RDendextend(RPackage): """dendextend: Extending 'Dendrogram' Functionality in R""" - homepage = "https://CRAN.R-project.org/package=dendextend" - url = "https://cran.r-project.org/src/contrib/dendextend_1.5.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dendextend" + 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" + version('1.12.0', sha256='b487fed8c1878a23b9e28394ee11f16a1831b76c90793eb486e6963c7162fa55') + version('1.10.0', sha256='88f0fb3362d69144daf4f35d0ea09f32c2df1adf614e040327a42552a8fd3224') version('1.5.2', '1134869d94005727c63cf3037e2f1bbf') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-magrittr@1.0.1:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-fpc', type=('build', 'run')) - depends_on('r-whisker', 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-viridis', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py index 4a993a7185a..a17bd18179f 100644 --- a/var/spack/repos/builtin/packages/r-deoptim/package.py +++ b/var/spack/repos/builtin/packages/r-deoptim/package.py @@ -11,8 +11,9 @@ class RDeoptim(RPackage): """Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.""" - homepage = "https://cran.r-project.org/package=DEoptim" - url = "https://cran.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptim" + 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" + version('2.2-4', sha256='0a547784090d1e9b93efc53768110621f35bed3692864f6ce5c0dda2ebd6d482') version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326') diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py index 5c24834833a..a48e98af481 100644 --- a/var/spack/repos/builtin/packages/r-deoptimr/package.py +++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py @@ -11,8 +11,8 @@ class RDeoptimr(RPackage): Evolution stochastic algorithm for global optimization of nonlinear programming problems.""" - homepage = "https://cran.r-project.org/web/packages/DEoptimR/index.html" - url = "https://cran.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptimR" + 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" version('1.0-8', 'c85836a504fbe4166e3c8eba0efe705d') diff --git a/var/spack/repos/builtin/packages/r-desc/package.py b/var/spack/repos/builtin/packages/r-desc/package.py index 3aa442852fa..9504ed50523 100644 --- a/var/spack/repos/builtin/packages/r-desc/package.py +++ b/var/spack/repos/builtin/packages/r-desc/package.py @@ -9,9 +9,9 @@ class RDesc(RPackage): """desc: Manipulate DESCRIPTION Files""" - homepage = "https://cran.r-project.org/package=desc" - url = "https://cran.r-project.org/src/contrib/desc_1.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/desc/" + homepage = "https://cloud.r-project.org/package=desc" + url = "https://cloud.r-project.org/src/contrib/desc_1.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/desc/" version('1.2.0', sha256='e66fb5d4fc7974bc558abcdc107a1f258c9177a29dcfcf9164bc6b33dd08dae8') diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py index f26872629c0..466c8107ed4 100644 --- a/var/spack/repos/builtin/packages/r-desolve/package.py +++ b/var/spack/repos/builtin/packages/r-desolve/package.py @@ -12,8 +12,12 @@ class RDesolve(RPackage): equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations.""" - homepage = "https://cran.r-project.org/package=deSolve" - url = "https://cran.r-project.org/src/contrib/deSolve_1.20.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/deSolve" + 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" + version('1.24', sha256='3aa52c822abb0348a904d5bbe738fcea2b2ba858caab9f2831125d07f0d57b42') + version('1.21', sha256='45c372d458fe4c7c11943d4c409517849b1be6782dc05bd9a74b066e67250c63') version('1.20', '85c6a2d8568944ae8eef27ac7c35fb25') + + depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 8a4ed3db3ca..b5a11517027 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -10,19 +10,30 @@ class RDevtools(RPackage): """Collection of package development tools.""" homepage = "https://github.com/hadley/devtools" - url = "https://cran.r-project.org/src/contrib/devtools_1.12.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/devtools" + url = "https://cloud.r-project.org/src/contrib/devtools_1.12.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/devtools" + version('2.1.0', sha256='c1f75346a90adf0669b5508fe68cc78bd3b114c1303fa7d22bf90991edd9230d') + version('2.0.2', sha256='99a2fa957068254b8ecdb3fc2d50e2950230910ea31c314fc0e7d934e4bd1709') version('1.12.0', '73b46c446273566e5b21c9f5f72aeca3') version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') - depends_on('r@3.0.2:') - + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-httr@0.4:', type=('build', 'run')) depends_on('r-memoise@1.0.0:', type=('build', 'run')) - depends_on('r-whisker', type=('build', 'run')) + depends_on('r-whisker', when='@:1.9.9', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-rstudioapi@0.2.0:', type=('build', 'run')) + depends_on('r-rstudioapi@0.7.0:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-git2r@0.11.0:', type=('build', 'run')) + depends_on('r-git2r@0.23.0:', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) + depends_on('r-usethis@1.5.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-callr', when='@2.0.0:', type=('build', 'run')) + depends_on('r-cli', when='@2.0.0:', type=('build', 'run')) + depends_on('r-pkgbuild@1.0.3:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-pkgload@1.0.2:', when='@2.0.0:', 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-roxygen2@6.1.1:', when='@2.0.0:', 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')) diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py index 713740f1b09..23ad11daf88 100644 --- a/var/spack/repos/builtin/packages/r-diagrammer/package.py +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -10,15 +10,31 @@ class RDiagrammer(RPackage): """Create graph diagrams and flowcharts using R.""" homepage = "https://github.com/rich-iannone/DiagrammeR" - url = "https://cran.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.0.1', sha256='ccee8acf608fc909e73c6de4374cef5a570cb62e5f454ac55dda736f22f3f013') + version('1.0.0', sha256='2b186dae1b19018681b979e9444bf16559c42740d8382676fbaf3b0f8a44337e') version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a') - depends_on('r-htmlwidgets', type=('build', 'run')) - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-influencer', type=('build', 'run')) - depends_on('r-rstudioapi@0.6:', type=('build', 'run')) - depends_on('r-stringr', type=('build', 'run')) - depends_on('r-visnetwork', type=('build', 'run')) - depends_on('r-scales', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.9.2:', type=('build', 'run')) + depends_on('r-htmlwidgets@1.0:', type=('build', 'run')) + depends_on('r-igraph@1.1.2:', type=('build', 'run')) + depends_on('r-influencer@0.1.0:', type=('build', 'run')) + depends_on('r-rstudioapi@0.7:', type=('build', 'run')) + depends_on('r-stringr@1.3.0:', type=('build', 'run')) + depends_on('r-visnetwork@2.0.3:', type=('build', 'run')) + depends_on('r-scales@0.5.0:', type=('build', 'run')) + depends_on('r-dplyr@0.7.4:', when='@1.0.0:', 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-htmltools@0.3.6:', when='@1.0.0:', 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-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-rgexf@0.15.3:', when='@1.0.0:', 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-viridis@0.5.0:', when='@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dicekriging/package.py b/var/spack/repos/builtin/packages/r-dicekriging/package.py index 4372047e893..0f00d6ea5ad 100644 --- a/var/spack/repos/builtin/packages/r-dicekriging/package.py +++ b/var/spack/repos/builtin/packages/r-dicekriging/package.py @@ -11,7 +11,8 @@ class RDicekriging(RPackage): functions : km, print.km, plot.km, predict.km.""" homepage = "http://dice.emse.fr/" - url = "https://cran.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DiceKriging" + 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" + version('1.5.6', sha256='25466d2db9f17083d1c7b9545e5ec88f630be934f9373c2f7b36c38de4e64e92') version('1.5.5', 'ee3e2d7a91d4a712467ef4f0b69c2844') diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py index aced5190383..cda69069013 100644 --- a/var/spack/repos/builtin/packages/r-dichromat/package.py +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -10,8 +10,10 @@ class RDichromat(RPackage): """Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.""" - homepage = "https://cran.r-project.org/web/packages/dichromat/index.html" - url = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat" + 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" version('2.0-0', '84e194ac95a69763d740947a7ee346a6') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diffusionmap/package.py b/var/spack/repos/builtin/packages/r-diffusionmap/package.py index eac95871551..84fb7c20841 100644 --- a/var/spack/repos/builtin/packages/r-diffusionmap/package.py +++ b/var/spack/repos/builtin/packages/r-diffusionmap/package.py @@ -11,16 +11,17 @@ class RDiffusionmap(RPackage): computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.""" - homepage = "https://cran.r-project.org/web/packages/diffusionMap/index.html" - url = "https://cran.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/diffusionMap" + 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" + version('1.1-0.1', sha256='b24cf841af2566ac36f4ede2885f2ff355a7905398444d6d89747315d99a8486') version('1.1-0', 'cc7d728087ba08d9299ae3a64a8d8919') version('1.0-0', 'bca462e6efe45c5eaa48d38621f0bd6f') version('0.0-2', 'b599f47ebf30127e34ce2219dc3e43ae') version('0.0-1', '20c2cc2fffb5237d5c0216207016c2a1') - depends_on('r@3.4.0:3.4.9') + depends_on('r@2.4.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-scatterplot3d', type=('build', 'run')) depends_on('r-igraph', 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 d69645f7ee3..feb608e7f42 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -25,11 +25,14 @@ class RDigest(RPackage): used.""" homepage = "http://dirk.eddelbuettel.com/code/digest.html" - url = "https://cran.r-project.org/src/contrib/digest_0.6.12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/digest" + url = "https://cloud.r-project.org/src/contrib/digest_0.6.12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/digest" + version('0.6.20', sha256='05674b0b5d888461ff770176c67b10a11be062b0fee5dbd9298f25a9a49830c7') + version('0.6.19', sha256='28d159bd589ecbd01b8da0826eaed417f5c1bf5a11b79e76bf67ce8d935cccf4') version('0.6.12', '738efd4d9a37c5a4001ae66e954ce07e') version('0.6.11', '52a864f55846b48b3cab0b5d0304a82a') version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') - depends_on('r@2.4.1:') + depends_on('r@2.4.1:', when='@:0.6.15', type=('build', 'run')) + depends_on('r@3.1.0:', when='@0.6.16:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py index b7b25d82151..0e5edc21eff 100644 --- a/var/spack/repos/builtin/packages/r-diptest/package.py +++ b/var/spack/repos/builtin/packages/r-diptest/package.py @@ -9,8 +9,8 @@ class RDiptest(RPackage): """diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected""" - homepage = "https://CRAN.R-project.org/package=diptest" - url = "https://cran.r-project.org/src/contrib/diptest_0.75-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/diptest" + 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" version('0.75-7', '1a4a958fda763f7c99cb485dbe5954ab') diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py index 3876f1aa85e..4fb5e5e321a 100644 --- a/var/spack/repos/builtin/packages/r-dismo/package.py +++ b/var/spack/repos/builtin/packages/r-dismo/package.py @@ -11,8 +11,9 @@ class RDismo(RPackage): entire geographic distributions form occurrences at a number of sites and the environment at these sites.""" - homepage = "https://cran.r-project.org/package=dismo" - url = "https://cran.r-project.org/src/contrib/dismo_1.1-4.tar.gz" + 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" version('1.1-4', sha256='f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8') diff --git a/var/spack/repos/builtin/packages/r-diversitree/package.py b/var/spack/repos/builtin/packages/r-diversitree/package.py index 9578bbb4ece..bb2c27dac64 100644 --- a/var/spack/repos/builtin/packages/r-diversitree/package.py +++ b/var/spack/repos/builtin/packages/r-diversitree/package.py @@ -19,9 +19,10 @@ class RDiversitree(RPackage): rate 'speciation' and extinction.""" homepage = "http://www.zoology.ubc.ca/prog/diversitree" - url = "https://cran.r-project.org/src/contrib/diversitree_0.9-10.tar.gz" + 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" + version('0.9-11', sha256='4caa6a468f93de9f1c8c30e4457f34bb8346e1acdaf74f684005bfa86a950ecb') version('0.9-10', sha256='e7df5910c8508a5c2c2d6d3deea53dd3f947bb762196901094c32a7033cb043e') depends_on('r@2.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py index 8228866515f..9488d31952a 100644 --- a/var/spack/repos/builtin/packages/r-domc/package.py +++ b/var/spack/repos/builtin/packages/r-domc/package.py @@ -10,13 +10,13 @@ class RDomc(RPackage): """Provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.""" - homepage = "https://cran.r-project.org/package=doMC" - url = "https://cran.r-project.org/src/contrib/doMC_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/doMC" + 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" + version('1.3.6', sha256='2977fc9e2dc54d85d45b4a36cd286dff72834fbc73f38b6ee45a6eb8557fc9b2') version('1.3.4', 'f965b09add9056e84f99a831dc3af7d1') - depends_on('r@2.14.0:') - + depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-foreach@1.2.0:', type=('build', 'run')) depends_on('r-iterators@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py index 5db870b699e..250e396dfbb 100644 --- a/var/spack/repos/builtin/packages/r-doparallel/package.py +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -10,12 +10,14 @@ class RDoparallel(RPackage): """Provides a parallel backend for the %dopar% function using the parallel package.""" - homepage = "https://cran.r-project.org/web/packages/doParallel/index.html" - url = "https://cran.r-project.org/src/contrib/doParallel_1.0.10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/doParallel" + 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" + version('1.0.15', sha256='71ad7ea69616468996aefdd8d02a4a234759a21ddde9ed1657e3c537145cd86e') version('1.0.11', 'd7822f0efd7bdf7582d8b43c986be86c') version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43') - depends_on('r-foreach', type=('build', 'run')) - depends_on('r-iterators', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-foreach@1.2.0:', type=('build', 'run')) + depends_on('r-iterators@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dorng/package.py b/var/spack/repos/builtin/packages/r-dorng/package.py index 9e8baa6a776..a493805a36f 100644 --- a/var/spack/repos/builtin/packages/r-dorng/package.py +++ b/var/spack/repos/builtin/packages/r-dorng/package.py @@ -15,13 +15,15 @@ class RDorng(RPackage): independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.""" - homepage = "https://cran.rstudio.com/web/packages/doRNG/index.html" - url = "https://cran.rstudio.com/src/contrib/doRNG_1.6.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/doRNG" + 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" + version('1.7.1', sha256='27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9') version('1.6.6', 'ffb26024c58c8c99229470293fbf35cf') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) - depends_on('r-rngtools', type=('build', 'run')) + depends_on('r-rngtools@1.3:', type=('build', 'run')) depends_on('r-iterators', type=('build', 'run')) - depends_on('r-pkgmaker', type=('build', 'run')) + depends_on('r-pkgmaker@0.20:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dosnow/package.py b/var/spack/repos/builtin/packages/r-dosnow/package.py new file mode 100644 index 00000000000..7ad841b4317 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dosnow/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 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 RDosnow(RPackage): + """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" + + version('1.0.18', sha256='70e7bd82186e477e3d1610676d4c6a75258ac08f104ecf0dcc971550ca174766') + + depends_on('r@2.5.0:', type=('build', 'run')) + depends_on('r-foreach@1.2.0:', type=('build', 'run')) + depends_on('r-iterators@1.0.0:', type=('build', 'run')) + depends_on('r-snow@0.3.0:', 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 9a410e7972f..7b59089be6c 100644 --- a/var/spack/repos/builtin/packages/r-downloader/package.py +++ b/var/spack/repos/builtin/packages/r-downloader/package.py @@ -14,9 +14,9 @@ class RDownloader(RPackage): compiled with external dependencies. This package has no external dependencies, so it is much easier to install.""" - homepage = "https://cran.rstudio.com/web/packages/downloader/index.html" - url = "https://cran.rstudio.com/src/contrib/downloader_0.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/downloader" + 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" version('0.4', 'f26daf8fbeb29a1882bf102f62008594') diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index b2aed2c6262..a7ed7868d76 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -10,10 +10,12 @@ class RDplyr(RPackage): """A fast, consistent tool for working with data frame like objects, both in memory and out of memory.""" - homepage = "https://cran.r-project.org/package=dplyr" - url = "https://cran.r-project.org/src/contrib/dplyr_0.7.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dplyr" + homepage = "https://cloud.r-project.org/package=dplyr" + url = "https://cloud.r-project.org/src/contrib/dplyr_0.7.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dplyr" + version('0.8.3', sha256='68b4aac65a69ea6390e90991d9c7ce7a011a07e5db439d60cce911a078424c0c') + version('0.8.2', sha256='e2b6d5b30d04d86f270374623da426541cee8e33ce446fcab6cd7862abf8e18b') version('0.7.7', sha256='0553db5a55f0e6f5d2d111e88422c6d26e9d54cb36b860ad2ca28e3826e3d4a4') version('0.7.6', sha256='d489cc8b53854ec30737bb7d39b331b67ca35f4275ad19e97420d7a247808330') version('0.7.5', sha256='2fbd8f316a59670076d43a0fe854654621941ee5f621ea5f0185a3f5daafda50') @@ -24,14 +26,17 @@ class RDplyr(RPackage): version('0.7.0', sha256='27b3593c09da5e99c0c4fb19ea826edd2cab619f8aaefd0cfd2a4140a0bd9410') version('0.5.0', sha256='93d3b829f1c2d38e14a4f2fa7d6398fc6c1a9e4189b3e78bc38a0eb0e864454f') + depends_on('r@3.1.2:', when='@:0.8.0.1', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.8.1:', type=('build', 'run')) depends_on('r-assertthat@0.2.0:', type=('build', 'run')) - depends_on('r-bindrcpp@0.2.0:', type=('build', 'run')) - depends_on('r-glue@1.1.1:', type=('build', 'run')) + depends_on('r-bindrcpp@0.2.0:', when='@:0.7.9', type=('build', 'run')) + depends_on('r-glue@1.3.0:', type=('build', 'run')) depends_on('r-magrittr@1.5:', type=('build', 'run')) - depends_on('r-pkgconfig@2.0.1:', type=('build', 'run')) - depends_on('r-r6@2.2.2:', type=('build', 'run')) - depends_on('r-rcpp@0.12.19:', type=('build', 'run')) - depends_on('r-rlang@0.3.0:', type=('build', 'run')) - depends_on('r-tibble@1.4.2:', type=('build', 'run')) - depends_on('r-tidyselect@0.2.3:', type=('build', 'run')) - depends_on('r-bh@1.58.0-1:', type=('build', 'run')) + depends_on('r-pkgconfig', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rcpp@1.0.1:', type=('build', 'run')) + depends_on('r-rlang@0.4.0:', type=('build', 'run')) + depends_on('r-tibble@2.0.0:', type=('build', 'run')) + depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) + depends_on('r-bh', type=('build', 'run')) + depends_on('r-plogr@0.2.0:', when='@0.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dqrng/package.py b/var/spack/repos/builtin/packages/r-dqrng/package.py new file mode 100644 index 00000000000..ebb82b942c6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dqrng/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 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 RDqrng(RPackage): + """Several fast random number generators are provided as C++ header only + libraries: The PCG family by O'Neill (2014 + ) as well as Xoroshiro128+ + and Xoshiro256+ by Blackman and Vigna (2018 ). In + addition fast functions for generating random numbers according to a + uniform, normal and exponential distribution are included. The latter two + use the Ziggurat algorithm originally proposed by Marsaglia and Tsang + (2000, ). These functions are exported to R and + as a C++ interface and are enabled for use with the default 64 bit + generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the + 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011 + ) 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" + + version('0.2.1', sha256='e149c105b1db31e7f46b1aebf31d911a109e380923f3696fc56a53197fc1e866') + + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.16:', type=('build', 'run')) + depends_on('r-bh@1.64.0-1:', type=('build', 'run')) + depends_on('r-sitmo@2.0.0:', 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 b419985173a..141b40006bb 100644 --- a/var/spack/repos/builtin/packages/r-dt/package.py +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -13,9 +13,12 @@ class RDt(RPackage): abbreviation of 'DataTables'.""" homepage = "http://rstudio.github.io/DT" - url = "https://cran.r-project.org/src/contrib/DT_0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DT" + url = "https://cloud.r-project.org/src/contrib/DT_0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DT" + version('0.8', sha256='90195054148806cf31c7db5c41f72d5389c75adc0b1183606a9babd2c6ae8e21') + version('0.7', sha256='1de3f170deccd9e3aaefc057dd87c498e3b3f7f88eff645cf165ac34ffe3de2c') + version('0.6', sha256='2ed68e9d161559171fa74b6105eee87b98acf755eae072b38ada60a83d427916') version('0.4', sha256='3daa96b819ca54e5fbc2c7d78cb3637982a2d44be58cea0683663b71cfc7fa19') version('0.3', sha256='ef42b24c9ea6cfa1ce089687bf858d773ac495dc80756d4475234e979bd437eb') version('0.2', sha256='a1b7f9e5c31a241fdf78ac582499f346e915ff948554980bbc2262c924b806bd') @@ -25,3 +28,5 @@ class RDt(RPackage): depends_on('r-htmlwidgets@1.3:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-crosstalk', type=('build', 'run')) + depends_on('r-promises', when='@0.5:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', when='@0.8:', 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 bb820358975..f963965161f 100644 --- a/var/spack/repos/builtin/packages/r-dtw/package.py +++ b/var/spack/repos/builtin/packages/r-dtw/package.py @@ -11,15 +11,16 @@ class RDtw(RPackage): in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series.""" - homepage = "https://cran.r-project.org/web/packages/dtw/index.html" - url = "https://cran.r-project.org/src/contrib/dtw_1.18-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dtw" + 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" + version('1.20-1', sha256='43ca1a47a7c81a2b5d5054da1be8b8af79a85d6f9ce7b4512e9ed91f790f60f0') version('1.18-1', '5e9995a198a62f28045c29461265d536') version('1.17-1', 'e8be988fe528acd6b44afdf5aa06b745') version('1.16', '260bd22d9db429394eb39739db4a4686') version('1.15', 'd3b6fdb0b866ff2e5b178c37bcfc7c55') version('1.14-3', 'a7b878e8dda7a61df22356d0a81540c5') - depends_on('r@3.4.0:3.4.9') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-proxy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py index ce17c9dd6d5..f286e5363f3 100644 --- a/var/spack/repos/builtin/packages/r-dygraphs/package.py +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -13,13 +13,17 @@ class RDygraphs(RPackage): axis-display and interactive features like zoom/pan and series/point highlighting.""" - homepage = "https://cran.r-project.org/web/packages/dygraphs/index.html" - url = "https://cran.r-project.org/src/contrib/dygraphs_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dygraphs" + 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" + version('1.1.1.6', sha256='c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208') + version('1.1.1.5', sha256='274035988fdd6833121fd5831692355d383acc828d540788dbcecaf88eb2d72d') version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-htmlwidgets', type=('build', 'run')) - depends_on('r-zoo', type=('build', 'run')) - depends_on('r-xts', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py index 39e3dde2278..856e6efb89c 100644 --- a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py +++ b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py @@ -10,9 +10,9 @@ class RDynamictreecut(RPackage): """dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms""" - homepage = "https://cran.r-project.org/package=dynamicTreeCut" - url = "https://cran.r-project.org/src/contrib/dynamicTreeCut_1.63-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dynamicTreeCut/" + 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/" 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 c09473fe79c..41ada9809e1 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -11,10 +11,12 @@ class RE1071(RPackage): clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...""" - homepage = "https://cran.r-project.org/package=e1071" - url = "https://cran.r-project.org/src/contrib/e1071_1.6-7.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/e1071" + 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" + version('1.7-2', sha256='721c299ce83047312acfa3e0c4b3d4c223d84a4c53400c73465cca2c92913752') + version('1.7-1', sha256='5c5f04a51c1cd2c7dbdf69987adef9bc07116804c63992cd36d804a1daf89dfe') version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py index 5dd67a34150..abd9783b0f1 100644 --- a/var/spack/repos/builtin/packages/r-ellipse/package.py +++ b/var/spack/repos/builtin/packages/r-ellipse/package.py @@ -10,10 +10,11 @@ class REllipse(RPackage): """This package contains various routines for drawing ellipses and ellipse-like confidence regions.""" - homepage = "https://cran.r-project.org/package=ellipse" - url = "https://cran.r-project.org/src/contrib/ellipse_0.3-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ellipse" + 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" + version('0.4.1', sha256='1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d') version('0.3-8', '385f5ec5e49bcda4317ca9dffd33f771') - depends_on('r@2.0.0:') + depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ellipsis/package.py b/var/spack/repos/builtin/packages/r-ellipsis/package.py new file mode 100644 index 00000000000..89457220684 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ellipsis/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 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 REllipsis(RPackage): + """The ellipsis is a powerful tool for extending functions. Unfortunately + this power comes at a cost: misspelled arguments will be silently ignored. + The ellipsis package provides a collection of functions to catch problems + and alert the user.""" + + homepage = "https://github.com/r-lib/ellipsis" + url = "https://cloud.r-project.org/src/contrib/ellipsis_0.2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ellipsis" + + version('0.2.0.1', sha256='0e6528c5e8016c3617cc1cfcdb5a4bfeb073e0bd5ea76b43e56b0c3208a0a943') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-emmli/package.py b/var/spack/repos/builtin/packages/r-emmli/package.py index 249f3c3f6d2..974bb81c8ba 100644 --- a/var/spack/repos/builtin/packages/r-emmli/package.py +++ b/var/spack/repos/builtin/packages/r-emmli/package.py @@ -11,8 +11,8 @@ class REmmli(RPackage): on results. Fit models with a single within-module correlation or with separate within-module correlations fitted to each module.""" - homepage = "https://cran.r-project.org/package=EMMLi" - url = "https://cran.r-project.org/src/contrib/EMMLi_0.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/EMMLi" + 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" 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 897e96a8ade..ab2ef621dee 100644 --- a/var/spack/repos/builtin/packages/r-energy/package.py +++ b/var/spack/repos/builtin/packages/r-energy/package.py @@ -9,11 +9,13 @@ class REnergy(RPackage): """E-Statistics: Multivariate Inference via the Energy of Data""" - homepage = "https://cran.r-project.org/web/packages/energy/index.html" - url = "https://cran.r-project.org/src/contrib/energy_1.7-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/energy" + 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" + version('1.7-6', sha256='900edbb28e1f1bccd78580828470628cf75eb6333b63e1a58e4da7fc5c5fa89a') version('1.7-5', 'd13c76c26b5221ba29aade6a824f32d6') + 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')) diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py index 36c251cfa0c..9fedc0c078c 100644 --- a/var/spack/repos/builtin/packages/r-ergm/package.py +++ b/var/spack/repos/builtin/packages/r-ergm/package.py @@ -12,16 +12,26 @@ class RErgm(RPackage): part of the "statnet" suite of packages for network analysis.""" homepage = "http://statnet.org" - url = "https://cran.r-project.org/src/contrib/ergm_3.7.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ergm" + 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" + version('3.10.4', sha256='885f0b1a23c5a2c1947962350cfab66683dfdfd1db173c115e90396d00831f22') + version('3.10.1', sha256='a2ac249ff07ba55b3359242f20389a892543b4fff5956d74143d2d41fa6d4beb') version('3.7.1', '431ae430c76b2408988f469831d80126') - depends_on('r-robustbase@0.9-10:', type=('build', 'run')) - depends_on('r-coda@0.18-1:', type=('build', 'run')) - depends_on('r-trust', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-lpsolve', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) - depends_on('r-statnet-common@3.3:', type=('build', 'run')) - depends_on('r-network@1.13:', type=('build', 'run')) + depends_on('r-robustbase@0.93-5:', type=('build', 'run')) + depends_on('r-coda@0.19-2:', type=('build', 'run')) + depends_on('r-trust@0.1.7:', type=('build', 'run')) + depends_on('r-matrix@1.2-17:', type=('build', 'run')) + depends_on('r-lpsolve@5.6.13:', type=('build', 'run')) + depends_on('r-mass@7.3-51.4:', type=('build', 'run')) + depends_on('r-statnet-common@4.3.0:', type=('build', 'run')) + depends_on('r-network@1.15:', 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:', type=('build', 'run')) + # 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 + # appropriate options in the R script. diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index 4df731967b4..c56425716d5 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -10,14 +10,14 @@ class REvaluate(RPackage): """Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.""" - homepage = "https://cran.r-project.org/package=evaluate" - url = "https://cran.rstudio.com/src/contrib/evaluate_0.10.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/evaluate" + 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" + version('0.14', sha256='a8c88bdbe4e60046d95ddf7e181ee15a6f41cdf92127c9678f6f3d328a3c5e28') version('0.10.1', '1dde5a35e2b9d57f1b1bb16791b35ff5') version('0.10', 'c49326babf984a8b36e7e276da370ad2') version('0.9', '877d89ce8a9ef7f403b1089ca1021775') - depends_on('r@3.0.2:') - - depends_on('r-stringr@0.6.2:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-stringr@0.6.2:', when='@:0.11', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-expint/package.py b/var/spack/repos/builtin/packages/r-expint/package.py index 39d01fe50de..4bce63d28a6 100644 --- a/var/spack/repos/builtin/packages/r-expint/package.py +++ b/var/spack/repos/builtin/packages/r-expint/package.py @@ -10,9 +10,9 @@ class RExpint(RPackage): """expint: Exponential Integral and Incomplete Gamma Function""" - homepage = "https://cran.r-project.org/package=expint" - url = "https://cran.r-project.org/src/contrib/expint_0.1-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/expint" + 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" 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 c576ec912fd..f7e5588e4ed 100644 --- a/var/spack/repos/builtin/packages/r-expm/package.py +++ b/var/spack/repos/builtin/packages/r-expm/package.py @@ -10,8 +10,12 @@ class RExpm(RPackage): """Computation of the matrix exponential, logarithm, sqrt, and related quantities.""" - homepage = "http://R-Forge.R-project.org/projects/expm" - url = "https://cran.r-project.org/src/contrib/expm_0.999-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/expm" + homepage = "http://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" + version('0.999-4', sha256='58d06427a08c9442462b00a5531e2575800be13ed450c5a1546261251e536096') + version('0.999-3', sha256='511bac5860cc5b3888bca626cdf23241b6118eabcc82d100935386039e516412') version('0.999-2', 'e05fa3f995754af92bd03227625da984') + + depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py index 47e442cbc7e..562dc81c951 100644 --- a/var/spack/repos/builtin/packages/r-factoextra/package.py +++ b/var/spack/repos/builtin/packages/r-factoextra/package.py @@ -11,18 +11,19 @@ class RFactoextra(RPackage): Analyses""" homepage = "http://www.sthda.com/english/rpkgs/factoextra" - url = "https://cran.r-project.org/src/contrib/factoextra_1.0.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.0.5', sha256='8177a3f5107883ae248b2cd0afa388a1794741f5155a9455b3883788cf44d5d0') version('1.0.4', 'aa4c81ca610f17fdee0c9f3379e35429') - depends_on('r@3.1.0:') + depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) depends_on('r-abind', type=('build', 'run')) - # depends_on('r-cluster', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) depends_on('r-dendextend', type=('build', 'run')) depends_on('r-factominer', type=('build', 'run')) - depends_on('r-ggpubr', type=('build', 'run')) + depends_on('r-ggpubr@0.1.5:', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-ggrepel', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-factominer/package.py b/var/spack/repos/builtin/packages/r-factominer/package.py index 71d6f34415f..a5723eff146 100644 --- a/var/spack/repos/builtin/packages/r-factominer/package.py +++ b/var/spack/repos/builtin/packages/r-factominer/package.py @@ -10,9 +10,10 @@ class RFactominer(RPackage): """FactoMineR: Multivariate Exploratory Data Analysis and Data Mining""" homepage = "http://factominer.free.fr" - url = "https://cran.r-project.org/src/contrib/FactoMineR_1.35.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/FactoMineR" + url = "https://cloud.r-project.org/src/contrib/FactoMineR_1.35.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/FactoMineR" + version('1.42', sha256='4cd9efb3681767c3bd48ddc3504ebead1493fcbbc0a9f759a00955b16c3481fa') version('1.41', sha256='a9889d69e298b8a01e8d0a5a54260730e742c95681e367d759829aad9a8740c0') version('1.40', sha256='68cb778fe7581b55666a5ae4aa7a5e7fa3ecbd133ae8cff1b2371a737b6d95e8') version('1.39', sha256='b0bb1d6d7d1f3cb11a4b63c377321e10078a36f29bc78dfa3b80c7c149f4a08a') @@ -20,7 +21,7 @@ class RFactominer(RPackage): version('1.36', sha256='2198c3facaa41a23df6f9373d4ccb636b98a8810896e379e5deb686ab31b36de') version('1.35', sha256='afe176fe561d1d16c5965ecb2b80ec90a56d0fbcd75c43ec8025a401a5b715a9') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-car', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-ellipse', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fansi/package.py b/var/spack/repos/builtin/packages/r-fansi/package.py index 41695ebc72c..ff24e351bf3 100644 --- a/var/spack/repos/builtin/packages/r-fansi/package.py +++ b/var/spack/repos/builtin/packages/r-fansi/package.py @@ -10,12 +10,14 @@ class RFansi(RPackage): """Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.""" - homepage = "https://cran.r-project.org/package=fansi" - url = "https://cran.r-project.org/src/contrib/fansi_0.4.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fansi" + homepage = "https://cloud.r-project.org/package=fansi" + url = "https://cloud.r-project.org/src/contrib/fansi_0.4.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fansi" version('0.4.0', sha256='e104e9d01c7ff8a847f6b332ef544c0ef912859f9c6a514fe2e6f3b34fcfc209') version('0.3.0', sha256='dd6401d5c91ff4c45d752cceddd5379d1ae39a8a1196f236b0bc0ec6d691b88c') version('0.2.3', sha256='db6dfef8bfe6682d58b654b6a6a1d59cb07225ca41755176b465ab8611fd96c9') version('0.2.2', sha256='71dfdda467985a4d630ecf93d4bc60446a8a78d69dbd7ac24cc45822329d4bce') version('0.2.1', sha256='abe709d69ddd6610aaa24e049c7a97c16a2c2dbe0873d4e3b8af57e486ef05c5') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fastcluster/package.py b/var/spack/repos/builtin/packages/r-fastcluster/package.py index 0ec80c72078..d08a5ddb669 100644 --- a/var/spack/repos/builtin/packages/r-fastcluster/package.py +++ b/var/spack/repos/builtin/packages/r-fastcluster/package.py @@ -19,8 +19,8 @@ class RFastcluster(RPackage): the 'Python' files, see the file INSTALL in the source distribution.""" homepage = "http://danifold.net/fastcluster.html" - url = "https://cran.r-project.org/src/contrib/fastcluster_1.1.25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fastcluster/" + 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/" version('1.1.25', sha256='f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205') diff --git a/var/spack/repos/builtin/packages/r-fastmatch/package.py b/var/spack/repos/builtin/packages/r-fastmatch/package.py index 0257a475de0..88ef290d707 100644 --- a/var/spack/repos/builtin/packages/r-fastmatch/package.py +++ b/var/spack/repos/builtin/packages/r-fastmatch/package.py @@ -13,7 +13,7 @@ class RFastmatch(RPackage): subsequent lookup as it keeps the hash table in memory.""" homepage = "http://www.rforge.net/fastmatch" - url = "https://cran.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.1-0', '900c2363c15059ac9d63c4c71ea2d6b2') diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py index 76056bca94b..6b352a20085 100644 --- a/var/spack/repos/builtin/packages/r-ff/package.py +++ b/var/spack/repos/builtin/packages/r-ff/package.py @@ -11,9 +11,11 @@ class RFf(RPackage): fast access functions.""" homepage = "http://ff.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/ff_2.2-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ff" + 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" + version('2.2-14', sha256='1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0') version('2.2-13', '4adf8840d24cb6e2927a3ef885c86fcd') - depends_on('r-bit', type=('build', 'run')) + depends_on('r@2.10.1:', type=('build', 'run')) + depends_on('r-bit@1.1-13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fftwtools/package.py b/var/spack/repos/builtin/packages/r-fftwtools/package.py index 9d0a427a3ed..418347cd8e9 100644 --- a/var/spack/repos/builtin/packages/r-fftwtools/package.py +++ b/var/spack/repos/builtin/packages/r-fftwtools/package.py @@ -16,9 +16,10 @@ class RFftwtools(RPackage): the redundant complex conjugate when the input is real data.""" homepage = "https://github.com/krahim/fftwtools" - url = "https://cran.r-project.org/src/contrib/fftwtools_0.9-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.9-8', '2d1258fbaf0940b57ed61c8d6cd6694d') - depends_on('fftw') + depends_on('r@2.15.2:', type=('build', 'run')) + depends_on('fftw@3.1.2:') diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index e2c6b42ddc7..8a44c29f703 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -17,8 +17,12 @@ class RFilehash(RPackage): are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.""" - homepage = 'https://cran.r-project.org/' - url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/filehash" + 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" + version('2.4-2', sha256='b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93') + version('2.4-1', sha256='d0e087d338d89372c251c18fc93b53fb24b1750ea154833216ff16aff3b1eaf4') version('2.3', '01fffafe09b148ccadc9814c103bdc2f') + + depends_on('r@3.0.0:', 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 736ff0cb4c9..acfc903c335 100644 --- a/var/spack/repos/builtin/packages/r-findpython/package.py +++ b/var/spack/repos/builtin/packages/r-findpython/package.py @@ -10,9 +10,11 @@ class RFindpython(RPackage): """Package designed to find an acceptable python binary.""" homepage = "https://github.com/trevorld/findpython" - url = "https://cran.r-project.org/src/contrib/findpython_1.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.0.5', sha256='3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145') + version('1.0.4', sha256='a58fb46d53d3bdea1e00b2f4f9bdb5e98be9329ea9d8e2fe150d91462e6bccfd') version('1.0.3', sha256='5486535ae2f0a123b630d8eabf93a61b730765f55dfcc8ef4f6e56e7c49408f8') depends_on('python', type='run') 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 c15c7701e7c..3f1619d2e2b 100644 --- a/var/spack/repos/builtin/packages/r-fit-models/package.py +++ b/var/spack/repos/builtin/packages/r-fit-models/package.py @@ -9,9 +9,9 @@ class RFitModels(RPackage): """Compare Fitted Models""" - homepage = "https://cran.r-project.org/package=fit.models" - url = "https://cran.r-project.org/src/contrib/fit.models_0.5-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fit.models" + 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" version('0.5-14', '159b5c57953db4c917bc186ddacdff51') version('0.5-13', 'c9ff87e98189bcc3be597e3833408497') diff --git a/var/spack/repos/builtin/packages/r-fitdistrplus/package.py b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py new file mode 100644 index 00000000000..7a0cdfb107b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 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 RFitdistrplus(RPackage): + """Extends the fitdistr() function (of the MASS package) with several + functions to help the fit of a parametric distribution to non-censored or + censored data. Censored data may contain left censored, right censored and + interval censored values, with several lower and upper bounds. In addition + to maximum likelihood estimation (MLE), the package provides moment + matching (MME), quantile matching (QME) and maximum goodness-of-fit + estimation (MGE) methods (available only for non-censored data). Weighted + 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" + + version('1.0-14', sha256='85082590f62aa08d99048ea3414c5cc1e5b780d97b3779d2397c6cb435470083') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) + depends_on('r-npsurv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py index 4b322189433..6564e50a2bc 100644 --- a/var/spack/repos/builtin/packages/r-flashclust/package.py +++ b/var/spack/repos/builtin/packages/r-flashclust/package.py @@ -9,10 +9,10 @@ class RFlashclust(RPackage): """flashClust: Implementation of optimal hierarchical clustering""" - homepage = "https://CRAN.R-project.org/package=flashClust" - url = "https://cran.r-project.org/src/contrib/flashClust_1.01-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/flashClust" + 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" version('1.01-2', '23409aeeef98bf35d0b3d5dd755fdeff') - depends_on('r@2.3.0:') + depends_on('r@2.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flexclust/package.py b/var/spack/repos/builtin/packages/r-flexclust/package.py index b37f42e906b..324839aa7d3 100644 --- a/var/spack/repos/builtin/packages/r-flexclust/package.py +++ b/var/spack/repos/builtin/packages/r-flexclust/package.py @@ -15,11 +15,14 @@ class RFlexclust(RPackage): centroids, ...), and bootstrap methods for the analysis of cluster stability.""" - homepage = "https://cran.r-project.org/package=flexclust" - url = "https://cran.rstudio.com/src/contrib/flexclust_1.3-5.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/flexclust" + 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" + version('1.4-0', sha256='82fe445075a795c724644864c7ee803c5dd332a89ea9e6ccf7cd1ae2d1ecfc74') version('1.3-5', '90226a0e3a4f256f392a278e9543f8f4') + depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-modeltools', type=('build', 'run')) + depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py index 6eb90aa44bd..a8d3e03d9a6 100644 --- a/var/spack/repos/builtin/packages/r-flexmix/package.py +++ b/var/spack/repos/builtin/packages/r-flexmix/package.py @@ -9,13 +9,14 @@ class RFlexmix(RPackage): """flexmix: Flexible Mixture Modeling""" - homepage = "https://CRAN.R-project.org/package=flexmix" - url = "https://cran.r-project.org/src/contrib/flexmix_2.3-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/flexmix" + 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" + version('2.3-15', sha256='ba444c0bfe33ab87d440ab590c06b03605710acd75811c1622253171bb123f43') version('2.3-14', '5be4f7764e6a697f4586e60c2bf6e960') - depends_on('r@2.15.0:') - # depends_on('r-lattice', type=('build', 'run')) + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) depends_on('r-modeltools@0.2-16:', type=('build', 'run')) - # depends_on('r-nnet', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py index 4061e49108c..02afb622d2e 100644 --- a/var/spack/repos/builtin/packages/r-fnn/package.py +++ b/var/spack/repos/builtin/packages/r-fnn/package.py @@ -11,10 +11,12 @@ class RFnn(RPackage): related applications including KNN classification, regression and information measures are implemented.""" - homepage = "https://cran.r-project.org/web/packages/FNN/index.html" - url = "https://cran.r-project.org/src/contrib/FNN_1.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/FNN" + 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" + version('1.1.3', sha256='de763a25c9cfbd19d144586b9ed158135ec49cf7b812938954be54eb2dc59432') + version('1.1.2.2', sha256='b51a60fbbeff58c48cc90c2023c48972d5082d68efd02284c17ccd9820986326') version('1.1', '8ba8f5b8be271785593e13eae7b8c393') version('1.0', 'e9a47dc69d1ba55165be0877b8443fe0') version('0.6-4', '1c105df9763ceb7b13989cdbcb542fcc') @@ -22,5 +24,3 @@ class RFnn(RPackage): version('0.6-2', '20648ba934ea32b1b00dafb75e1a830c') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r-mvtnorm', type=('build', 'run')) - depends_on('r-chemometrics', 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 769bbe47979..e6cf5b73e2d 100644 --- a/var/spack/repos/builtin/packages/r-forcats/package.py +++ b/var/spack/repos/builtin/packages/r-forcats/package.py @@ -13,10 +13,15 @@ class RForcats(RPackage): rare levels into other, 'anonymising', and manually 'recoding').""" homepage = "http://forcats.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/forcats_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/forcats" + url = "https://cloud.r-project.org/src/contrib/forcats_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/forcats" + version('0.4.0', sha256='7c83cb576aa6fe1379d7506dcc332f7560068b2025f9e3ab5cd0a5f28780d2b2') + version('0.3.0', sha256='95814610ec18b8a8830eba63751954387f9d21400d6ab40394ed0ff22c0cb657') version('0.2.0', 'e4ba2c0a59dcdfcc02274c519bf3dbfc') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-ellipsis', when='@0.4.0:', type=('build', 'run')) + depends_on('r-rlang', when='@0.4.0:', 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 091b970299f..37baf00b4b2 100644 --- a/var/spack/repos/builtin/packages/r-foreach/package.py +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -15,11 +15,13 @@ class RForeach(RPackage): evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.""" - homepage = "https://cran.r-project.org/web/packages/foreach/index.html" - url = "https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/foreach" + 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" + version('1.4.7', sha256='95632c0b1182fc01490718d82fa3b2bce864f2a011ae53282431c7c2a3f5f160') version('1.4.3', 'ef45768126661b259f9b8994462c49a0') + depends_on('r@2.5.0:', type=('build', 'run')) depends_on('r-codetools', type=('build', 'run')) depends_on('r-iterators', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-forecast/package.py b/var/spack/repos/builtin/packages/r-forecast/package.py index b1d32d57108..6b33bdd1eb9 100644 --- a/var/spack/repos/builtin/packages/r-forecast/package.py +++ b/var/spack/repos/builtin/packages/r-forecast/package.py @@ -11,20 +11,24 @@ class RForecast(RPackage): series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.""" - homepage = "https://cran.r-project.org/package=forecast" - url = "https://cran.r-project.org/src/contrib/forecast_8.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/forecast" + 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" + version('8.8', sha256='d077074d77d3ea00e9215c828b3689a8c841a16af1e6859bb2dfdede081c2c1d') + version('8.6', sha256='4279e4f700e26310bae39419ab4a9b5918a850148667a5e577a4807d53eb4d02') version('8.2', '3ef095258984364c100b771b3c90d15e') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggplot2@2.2.1:', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) depends_on('r-nnet', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-fracdiff', type=('build', 'run')) depends_on('r-tseries', type=('build', 'run')) depends_on('r-lmtest', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) depends_on('r-timedate', type=('build', 'run')) - depends_on('r-rcpparmadillo', type=('build', 'run')) + depends_on('r-rcpparmadillo@0.2.35:', type=('build', 'run')) + depends_on('r-urca', when='@8.6:', 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 928d9df0ce1..9bba9e81a02 100644 --- a/var/spack/repos/builtin/packages/r-foreign/package.py +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -11,8 +11,12 @@ class RForeign(RPackage): Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.""" - homepage = "https://cran.r-project.org/web/packages/foreign/index.html" - url = "https://cran.r-project.org/src/contrib/foreign_0.8-66.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/foreign" + 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" + version('0.8-72', sha256='439c17c9cd387e180b1bb640efff3ed1696b1016d0f7b3b3b884e89884488c88') + version('0.8-70.2', sha256='ae82fad68159860b8ca75b49538406ef3d2522818e649d7ccc209c18085ef179') version('0.8-66', 'ff12190f4631dca31e30ca786c2c8f62') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 8d55e6c96c4..15914e209f8 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -14,14 +14,13 @@ class RFormatr(RPackage): human-readable and tidy. There is also a Shiny app as a user interface in this package.""" - homepage = "https://cran.r-project.org/package=formatR" - url = "https://cran.r-project.org/src/contrib/formatR_1.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/formatR" + 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" + version('1.7', sha256='a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb') + version('1.6', sha256='f5c98f0c3506ca51599671a2cdbc17738d0f326e8e3bb18b7a38e9f172122229') version('1.5', 'ac735515b8e4c32097154f1b68c5ecc7') version('1.4', '98b9b64b2785b35f9df403e1aab6c73c') - depends_on('r-codetools', type=('build', 'run')) - depends_on('r-shiny', type=('build', 'run')) - depends_on('r-testit', type=('build', 'run')) - # depends_on('r-knitr', type=('build', 'run')) - mutual dependency + depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py index cbe9071086b..38b50015d9f 100644 --- a/var/spack/repos/builtin/packages/r-formula/package.py +++ b/var/spack/repos/builtin/packages/r-formula/package.py @@ -11,9 +11,12 @@ class RFormula(RPackage): """Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side.""" - homepage = "https://cran.r-project.org/package=Formula" - url = "https://cran.rstudio.com/src/contrib/Formula_1.2-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Formula" + 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" + version('1.2-3', sha256='1411349b20bd09611a9fd0ee6d15f780c758ad2b0e490e908facb49433823872') version('1.2-2', 'c69bb0522811cf8eb9f1cc6c3d182b6e') version('1.2-1', '2afb31e637cecd0c1106317aca1e4849') + + depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py index ddc3ea3fea4..fd20c495dcc 100644 --- a/var/spack/repos/builtin/packages/r-fpc/package.py +++ b/var/spack/repos/builtin/packages/r-fpc/package.py @@ -10,20 +10,22 @@ class RFpc(RPackage): """fpc: Flexible Procedures for Clustering""" homepage = "http://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cran.r-project.org/src/contrib/fpc_2.1-10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fpc" + 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" + version('2.2-3', sha256='8100a74e6ff96b1cd65fd22494f2d200e54ea5ea533cfca321fa494914bdc3b7') + version('2.2-2', sha256='b6907019eb161d5c8c814cf02a4663cc8aae6322699932881ce5b02f45ecf8d3') version('2.1-10', '75e5340e416cd13d7751e06f1c07866b') - depends_on('r@2.0.0:') - # depends_on('r-mass', type=('build', 'run')) - # depends_on('r-cluster', type=('build', 'run')) + depends_on('r@2.0.0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) depends_on('r-flexmix', type=('build', 'run')) depends_on('r-prabclus', type=('build', 'run')) - # depends_on('r-class', type=('build', 'run')) + depends_on('r-class', type=('build', 'run')) depends_on('r-diptest', type=('build', 'run')) - depends_on('r-mvtnorm', type=('build', 'run')) + depends_on('r-mvtnorm', when='@:2.2-2', type=('build', 'run')) depends_on('r-robustbase', type=('build', 'run')) depends_on('r-kernlab', type=('build', 'run')) - depends_on('r-trimcluster', type=('build', 'run')) + depends_on('r-trimcluster', when='@:2.1-10', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fracdiff/package.py b/var/spack/repos/builtin/packages/r-fracdiff/package.py index 5f947244ed8..8f902428ec9 100644 --- a/var/spack/repos/builtin/packages/r-fracdiff/package.py +++ b/var/spack/repos/builtin/packages/r-fracdiff/package.py @@ -11,8 +11,8 @@ class RFracdiff(RPackage): fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989).""" - homepage = "https://cran.r-project.org/package=fracdiff" - url = "https://cran.r-project.org/src/contrib/fracdiff_1.4-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fracdiff" + 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" version('1.4-2', '6a6977d175ad963d9675736a8f8d41f7') diff --git a/var/spack/repos/builtin/packages/r-fs/package.py b/var/spack/repos/builtin/packages/r-fs/package.py new file mode 100644 index 00000000000..59d581838e6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fs/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 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 RFs(RPackage): + """A cross-platform interface to file system operations, built on top of + the 'libuv' C library.""" + + homepage = "http://fs.r-lib.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" + + version('1.3.1', sha256='d6934dca8f835d8173e3fb9fd4d5e2740c8c04348dd2bcc57df1b711facb46bc') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('gmake', type='build') 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 88a9471526a..d45418aa72b 100644 --- a/var/spack/repos/builtin/packages/r-futile-logger/package.py +++ b/var/spack/repos/builtin/packages/r-futile-logger/package.py @@ -11,11 +11,12 @@ class RFutileLogger(RPackage): futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.""" - homepage = "https://cran.rstudio.com/web/packages/futile.logger/index.html" - url = "https://cran.rstudio.com/src/contrib/futile.logger_1.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/futile.logger" + 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" version('1.4.3', 'ba0e8d2dfb5a970b51c21907bbf8bfc2') - depends_on('r-lambda-r', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-lambda-r@1.1.0:', type=('build', 'run')) depends_on('r-futile-options', type=('build', 'run')) 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 0325508c091..c493ac0ea6e 100644 --- a/var/spack/repos/builtin/packages/r-futile-options/package.py +++ b/var/spack/repos/builtin/packages/r-futile-options/package.py @@ -9,8 +9,11 @@ class RFutileOptions(RPackage): """A scoped options management framework""" - homepage = "https://cran.rstudio.com/web/packages/futile.options/index.html" - url = "https://cran.rstudio.com/src/contrib/futile.options_1.0.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/futile.options" + 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" + version('1.0.1', sha256='7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570') version('1.0.0', '8fd845774bbce56f41f7c43c3b4c13ba') + + depends_on('r@2.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-future-apply/package.py b/var/spack/repos/builtin/packages/r-future-apply/package.py new file mode 100644 index 00000000000..a0fd59e473e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-future-apply/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 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 RFutureApply(RPackage): + """Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), + replicate(), sapply(), tapply(), and vapply() that can be resolved using + any future-supported backend, e.g. parallel on the local machine or + distributed on a compute cluster. These future_*apply() functions come with + the same pros and cons as the corresponding base-R *apply() functions but + 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" + + 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-globals@0.12.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-future/package.py b/var/spack/repos/builtin/packages/r-future/package.py new file mode 100644 index 00000000000..d3778bb2c24 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-future/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2019 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 RFuture(RPackage): + """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. + Extensions to this package implement additional backends for processing + futures via compute cluster schedulers etc. Because of its unified API, + there is no need to modify any code in order switch from sequential on the + local machine to, say, distributed processing on a remote compute cluster. + Another strength of this package is that global variables and functions are + automatically identified and exported as needed, making it straightforward + to tweak existing code to make use of futures.""" + + homepage = "https://github.com/HenrikBengtsson/future" + url = "https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/future" + + version('1.14.0', sha256='0a535010d97a01b21aaf9d863603e44359335e273019c1e1980bbb5b2917dbcb') + + depends_on('r-digest', type=('build', 'run')) + depends_on('r-globals@0.12.4:', type=('build', 'run')) + depends_on('r-listenv@0.7.0:', type=('build', 'run')) 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 186654cc171..25b9fde1a54 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-data/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-data/package.py @@ -9,10 +9,12 @@ class RGamlssData(RPackage): """gamlss.data: GAMLSS Data""" - homepage = "https://cran.r-project.org/package=gamlss.data" - url = "https://cran.r-project.org/src/contrib/gamlss.data_5.1-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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/" + 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')) 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 4f08a156572..107dacdea61 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-dist/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-dist/package.py @@ -10,10 +10,12 @@ class RGamlssDist(RPackage): """gamlss.dist: Distributions for Generalized Additive Models for Location Scale and Shape""" - homepage = "https://cran.r-project.org/package=gamlss.dist" - url = "https://cran.r-project.org/src/contrib/gamlss.dist_5.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gamlss.dist/" + 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/" + version('5.1-4', sha256='343c6ca0fd8a1c1dfdf9ffc65c95d4dae0c6c80b3e60fccba003e5171f3d287e') + version('5.1-3', sha256='87fd643c82579519b67c66c1d87383fa1e203e8b09f607649ee7bce142bda404') version('5.1-1', sha256='44f999ff74ee516757eb39c8308c48aa850523aad2f38e622268313a13dda0b1') depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gamlss/package.py b/var/spack/repos/builtin/packages/r-gamlss/package.py index 0b04d2af532..0215a7fc195 100644 --- a/var/spack/repos/builtin/packages/r-gamlss/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss/package.py @@ -9,10 +9,12 @@ class RGamlss(RPackage): """gamlss: Generalised Additive Models for Location Scale and Shape""" - homepage = "https://cran.r-project.org/package=gamlss" - url = "https://cran.r-project.org/src/contrib/gamlss_5.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gamlss/" + 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/" + version('5.1-4', sha256='e2fc36fe6ca3a69d69cdafd9533a4ff35090fdfb01df126f6a49156f4aa3376c') + version('5.1-3', sha256='d37d121bc2acdbacc20cea04a1ed4489a575079e2a7b17b4a9823ee283857317') version('5.1-2', sha256='0d404e74768a8f98c6a5e9a48bd2cf4280125831a5dcd8c7f7b57922f57e016b') depends_on('r@3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gbm/package.py b/var/spack/repos/builtin/packages/r-gbm/package.py index 2c5b4e8f91f..1846290c448 100644 --- a/var/spack/repos/builtin/packages/r-gbm/package.py +++ b/var/spack/repos/builtin/packages/r-gbm/package.py @@ -9,10 +9,14 @@ class RGbm(RPackage): """Generalized Boosted Regression Models.""" - homepage = "https://cran.rstudio.com/web/packages/gbm/index.html" - url = "https://cran.rstudio.com/src/contrib/gbm_2.1.3.tar.gz" + 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" + version('2.1.5', sha256='06fbde10639dfa886554379b40a7402d1f1236a9152eca517e97738895a4466f') version('2.1.3', '9b2f32c892c6e31b01c1162e3b16b3f4') + depends_on('r@2.9.0:', type=('build', 'run')) + depends_on('r-gridextra', when='@2.1.5:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gbrd/package.py b/var/spack/repos/builtin/packages/r-gbrd/package.py new file mode 100644 index 00000000000..0dfe6081db4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gbrd/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 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 RGbrd(RPackage): + """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" + + version('0.4-11', sha256='0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b') diff --git a/var/spack/repos/builtin/packages/r-gdalutils/package.py b/var/spack/repos/builtin/packages/r-gdalutils/package.py index d8adeae4435..96f5e2f59bb 100644 --- a/var/spack/repos/builtin/packages/r-gdalutils/package.py +++ b/var/spack/repos/builtin/packages/r-gdalutils/package.py @@ -9,15 +9,16 @@ class RGdalutils(RPackage): """gdalUtils: Wrappers for the Geospatial Data Abstraction Library""" - homepage = "https://cran.r-project.org/package=gdalUtils" - url = "https://cran.r-project.org/src/contrib/gdalUtils_2.0.1.14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gdalUtils" + 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" version('2.0.1.14', sha256='890a502b2eb5f1b23655fab94caad5d32adca05b93f5db1d96d9dcde3f0e7737') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) - depends_on('r-utils', type=('build', 'run')) + depends_on('r-r-utils', type=('build', 'run')) depends_on('r-raster', type=('build', 'run')) depends_on('r-rgdal', type=('build', 'run')) + depends_on('gdal') diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py index f23f96165f2..40f27d4e009 100644 --- a/var/spack/repos/builtin/packages/r-gdata/package.py +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -25,11 +25,13 @@ class RGdata(RPackage): ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').""" - homepage = "https://cran.r-project.org/package=gdata" - url = "https://cran.r-project.org/src/contrib/gdata_2.18.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gdata" + 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" version('2.18.0', 'f831019aa743fe11dcf0a051e4280921') version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f') + depends_on('r@2.3.0:', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) + depends_on('perl@5.10.0:') diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py index 23453b776c9..2225c7051ee 100644 --- a/var/spack/repos/builtin/packages/r-geiger/package.py +++ b/var/spack/repos/builtin/packages/r-geiger/package.py @@ -9,18 +9,21 @@ class RGeiger(RPackage): """Methods for fitting macroevolutionary models to phylogenetic trees.""" - homepage = "https://cran.r-project.org/package=geiger" - url = "https://cran.r-project.org/src/contrib/geiger_2.0.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geiger" + homepage = "https://cloud.r-project.org/package=geiger" + url = "https://cloud.r-project.org/src/contrib/geiger_2.0.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/geiger" + version('2.0.6.2', sha256='9153047b608d652821251206d1450bb3f517c8884379f498a695315574ae001d') + version('2.0.6.1', sha256='2a95e20a3a90c096343b014344dd97e699e954da99c151c17fc6c245c77dba0b') version('2.0.6', 'e5e1a407ea56805227d0f91bf6d95afc') - depends_on('r-ape@3.0:', type=('build', 'run')) + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-ape@3.0-6:', type=('build', 'run')) depends_on('r-mvtnorm', type=('build', 'run')) depends_on('r-subplex', type=('build', 'run')) depends_on('r-desolve@1.7:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-rcpp@0.9.0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) depends_on('r-ncbit', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-generics/package.py b/var/spack/repos/builtin/packages/r-generics/package.py new file mode 100644 index 00000000000..0b9e1f681e8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-generics/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 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 RGenerics(RPackage): + """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" + url = "https://cloud.r-project.org/src/contrib/generics_0.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/generics" + + version('0.0.2', sha256='71b3d1b719ce89e71dd396ac8bc6aa5f1cd99bbbf03faff61dfbbee32fec6176') + + depends_on('r@3.1:', 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 e8dc6394947..e93e9ce9cb4 100644 --- a/var/spack/repos/builtin/packages/r-gensa/package.py +++ b/var/spack/repos/builtin/packages/r-gensa/package.py @@ -12,9 +12,9 @@ class RGensa(RPackage): Performs search for global minimum of a very complex non-linear objective function with a very large number of optima.""" - homepage = "https://cran.r-project.org/package=GenSA" - url = "https://cran.r-project.org/src/contrib/GenSA_1.1.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GenSA/" + 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/" version('1.1.7', sha256='9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f') diff --git a/var/spack/repos/builtin/packages/r-geomorph/package.py b/var/spack/repos/builtin/packages/r-geomorph/package.py index 3d33e648372..32049e61e34 100644 --- a/var/spack/repos/builtin/packages/r-geomorph/package.py +++ b/var/spack/repos/builtin/packages/r-geomorph/package.py @@ -12,10 +12,11 @@ class RGeomorph(RPackage): analyses, and provide graphical depictions of shapes and patterns of shape variation.""" - homepage = "https://cran.r-project.org/package=geomorph" - url = "https://cran.r-project.org/src/contrib/geomorph_3.0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geomorph" + 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" + version('3.1.2', sha256='29cf1c484f756cb44808cfdbc20137a6fbc4bd0c5c6f98c6c3f397c5aebda8f1') version('3.1.1', sha256='8eb222011433100860b308beef6f02ade7c421785f575ab4461ee25e38dfa1bd') version('3.0.7', sha256='68f8942e1a5bc3f0298c9f5b8f69c4702c8e12ecb2275d740fda4d04d66d38e1') version('3.0.5', '240e69fe260ca3ef4d84b4281d61396c') @@ -24,6 +25,6 @@ class RGeomorph(RPackage): depends_on('r-rgl', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) depends_on('r-jpeg', type=('build', 'run')) - depends_on('r-geiger', type=('build', 'run')) - depends_on('r-matrix', 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-rrpp', type=('build', 'run'), when='@3.0.7:') diff --git a/var/spack/repos/builtin/packages/r-geonames/package.py b/var/spack/repos/builtin/packages/r-geonames/package.py index 1d138cfc167..c8de77d062a 100644 --- a/var/spack/repos/builtin/packages/r-geonames/package.py +++ b/var/spack/repos/builtin/packages/r-geonames/package.py @@ -9,9 +9,9 @@ class RGeonames(RPackage): """geonames: Interface to the "Geonames" Spatial Query Web Service""" - homepage = "https://cran.r-project.org/package=geonames" - url = "https://cran.r-project.org/src/contrib/geonames_0.999.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geonames" + 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" 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 daa827c9392..2c499a19b83 100644 --- a/var/spack/repos/builtin/packages/r-geor/package.py +++ b/var/spack/repos/builtin/packages/r-geor/package.py @@ -10,9 +10,9 @@ class RGeor(RPackage): """Geostatistical analysis including traditional, likelihood-based and Bayesian methods.""" - homepage = "https://cran.r-project.org/web/packages/geoR/" - url = "https://cran.r-project.org/src/contrib/geoR_1.7-5.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geoR" + 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" version('1.7-5.2.1', 'a50f477bea1bec9070a4de01f69b831c') diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py index 58d3da5aeab..689e2f3c1d3 100644 --- a/var/spack/repos/builtin/packages/r-geosphere/package.py +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -11,10 +11,13 @@ class RGeosphere(RPackage): distances and related measures for angular (longitude/latitude) locations.""" - homepage = "https://cran.r-project.org/package=geosphere" - url = "https://cran.r-project.org/src/contrib/geosphere_1.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geosphere" + 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" + version('1.5-10', sha256='56cd4f787101e2e18f19ddb83794154b58697e63cad81168f0936f60ab7eb497') + version('1.5-7', sha256='9d9b555e2d59a5ae174ae654652121f169fbc3e9cf66c2491bfbe0684b6dd8a0') version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-getopt/package.py b/var/spack/repos/builtin/packages/r-getopt/package.py index 302f1f145c3..08c8b97611c 100644 --- a/var/spack/repos/builtin/packages/r-getopt/package.py +++ b/var/spack/repos/builtin/packages/r-getopt/package.py @@ -14,8 +14,9 @@ class RGetopt(RPackage): values, positional argument support, etc.""" homepage = "https://github.com/trevorld/getopt" - url = "https://cran.r-project.org/src/contrib/getopt_1.20.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.20.3', sha256='531f5fdfdcd6b96a73df2b39928418de342160ac1b0043861e9ea844f9fbf57f') version('1.20.2', sha256='3d6c12d32d6cd4b2909be626e570e158b3ed960e4739510e3a251e7f172de38e') version('1.20.1', '323cf2846e306f49236b8174bc3d4e47') diff --git a/var/spack/repos/builtin/packages/r-getoptlong/package.py b/var/spack/repos/builtin/packages/r-getoptlong/package.py index f7726bb23e6..e6064611e5f 100644 --- a/var/spack/repos/builtin/packages/r-getoptlong/package.py +++ b/var/spack/repos/builtin/packages/r-getoptlong/package.py @@ -12,12 +12,17 @@ class RGetoptlong(RPackage): use in R. It also provides a simple way for variable interpolation in R.""" - homepage = "https://cran.rstudio.com/web/packages/GetoptLong/index.html" - url = "https://cran.rstudio.com/src/contrib/GetoptLong_0.1.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GetoptLong" + 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" + version('0.1.7', sha256='b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba') version('0.1.6', 'e4b964d0817cb6c6a707297b21405749') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rjson', type=('build', 'run')) - depends_on('r-globaloptions', type=('build', 'run')) + depends_on('r-globaloptions@0.1.0:', type=('build', 'run')) + + # The CRAN site lists SystemRequirments as: Perl, Getopt::Long. The + # Getop::Long package will be installed with Perl so just depend on perl. depends_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 16f54d4744d..7ccb73a1285 100644 --- a/var/spack/repos/builtin/packages/r-ggally/package.py +++ b/var/spack/repos/builtin/packages/r-ggally/package.py @@ -14,15 +14,19 @@ class RGgally(RPackage): group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.""" - homepage = "https://cran.r-project.org/package=GGally" - url = "https://cran.r-project.org/src/contrib/GGally_1.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GGally" + homepage = "https://cloud.r-project.org/package=GGally" + url = "https://cloud.r-project.org/src/contrib/GGally_1.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GGally" + version('1.4.0', sha256='9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe') version('1.3.2', 'efe58133ba8431198af7afb6bcb76264') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-gtable', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + depends_on('r-gtable@0.2.0:', type=('build', 'run')) + depends_on('r-plyr@1.8.3:', type=('build', 'run')) depends_on('r-progress', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-reshape', 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('openssl', when='@1.4.0:') diff --git a/var/spack/repos/builtin/packages/r-ggdendro/package.py b/var/spack/repos/builtin/packages/r-ggdendro/package.py index e429a319b8f..87052809cc7 100644 --- a/var/spack/repos/builtin/packages/r-ggdendro/package.py +++ b/var/spack/repos/builtin/packages/r-ggdendro/package.py @@ -16,11 +16,11 @@ class RGgdendro(RPackage): The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.""" - homepage = "https://cran.r-project.org/package=ggdendro" - url = "https://cran.rstudio.com/src/contrib/ggdendro_0.1-20.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ggdendro" + 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" version('0.1-20', '787552e346432c758633d8f4b2675eb6') - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggplot2@0.9.2:', type=('build', 'run')) depends_on('r-mass', 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 df34c9513dd..3262750b38c 100644 --- a/var/spack/repos/builtin/packages/r-ggjoy/package.py +++ b/var/spack/repos/builtin/packages/r-ggjoy/package.py @@ -10,14 +10,15 @@ class RGgjoy(RPackage): """Joyplots provide a convenient way of visualizing changes in distributions over time or space.""" - homepage = "https://cran.r-project.org/web/packages/ggjoy/index.html" - url = "https://cran.r-project.org/src/contrib/ggjoy_0.4.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ggjoy" + 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" + version('0.4.1', sha256='d2f778bc40203d7fbb7c81b40beed8614c36ea10448e911663cc6109aa685504') version('0.4.0', 'c63782e2395a9cfc435d08e078e6596b') version('0.3.0', '59bd34a846270d43f2eeb1e90b03a127') version('0.2.0', '8584cd154e228f8505b324e91d2e50d7') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.2:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-ggridges', type=('build', 'run')) + depends_on('r-ggridges@0.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py index cc7e0a4e3d3..a468f4b18cc 100644 --- a/var/spack/repos/builtin/packages/r-ggmap/package.py +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -13,20 +13,32 @@ class RGgmap(RPackage): geolocation and routing.""" homepage = "https://github.com/dkahle/ggmap" - url = "https://cran.r-project.org/src/contrib/ggmap_2.6.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('3.0.0', sha256='96c24ffdc0710d0633ac4721d599d2c06f43a29c59d1e85c94ff0af30dfdb58d') + version('2.6.2', sha256='4e9cf53ab108fc70805d971dadb69b26fe67ea289c23c38adf6e30b198379d90') version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-proto', type=('build', 'run')) + 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', 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', 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', 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')) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index 1d0591e85b5..59e9b46b350 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -16,19 +16,25 @@ class RGgplot2(RPackage): documentation and examples.""" homepage = "http://ggplot2.org/" - url = "https://cran.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggplot2" + url = "https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggplot2" + version('3.2.0', sha256='31b6897fb65acb37913ff6e2bdc1b57f652360098ae3aa660abdcf54f84d73b3') + version('3.1.1', sha256='bfde297f3b4732e7f560078f4ce131812a70877e6b5b1d41a772c394939e0c79') version('2.2.1', '14c5a3507bc123c6e7e9ad3bef7cee5c') version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') - depends_on('r@3.1:') - + 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-digest', type=('build', 'run')) depends_on('r-gtable@0.1.1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r-plyr@1.7.1:', type=('build', 'run')) + depends_on('r-plyr@1.7.1:', when='@:3.1.1', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-scales@0.4.1:', type=('build', 'run')) + depends_on('r-scales@0.5.0:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-lazyeval', 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-viridislite', when='@3.0.0:', type=('build', 'run')) + depends_on('r-withr@2.0.0:', when='@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py index 4184d2e4e37..fcd2fc9e93b 100644 --- a/var/spack/repos/builtin/packages/r-ggpubr/package.py +++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py @@ -10,13 +10,27 @@ class RGgpubr(RPackage): """ggpubr: 'ggplot2' Based Publication Ready Plots""" homepage = "http://www.sthda.com/english/rpkgs/ggpubr" - url = "https://cran.r-project.org/src/contrib/ggpubr_0.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggpubr" + url = "https://cloud.r-project.org/src/contrib/ggpubr_0.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggpubr" + version('0.2.2', sha256='1c93dc6d1f08680dd00a10b6842445700d1fccb11f18599fbdf51e70c6b6b364') + version('0.2.1', sha256='611e650da9bd15d7157fdcdc4e926fee3b88df3aba87410fdb1c8a7294d98d28') + version('0.2', sha256='06c3075d8c452840662f5d041c3d966494b87254a52a858c849b9e1e96647766') version('0.1.2', '42a5749ae44121597ef511a7424429d1') - depends_on('r@3.1.0:') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) depends_on('r-ggrepel', type=('build', 'run')) depends_on('r-ggsci', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) + depends_on('r-plyr', when='@:0.1.2', type=('build', 'run')) + depends_on('r-tidyr', when='@0.2:', type=('build', 'run')) + depends_on('r-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')) diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py index 84f811e28b6..aca5c2fee38 100644 --- a/var/spack/repos/builtin/packages/r-ggrepel/package.py +++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py @@ -10,12 +10,14 @@ class RGgrepel(RPackage): """ggrepel: Repulsive Text and Label Geoms for 'ggplot2'""" homepage = "http://github.com/slowkow/ggrepel" - url = "https://cran.r-project.org/src/contrib/ggrepel_0.6.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.8.1', sha256='d5d03a77ab6d8c831934bc46e840cc4e3df487272ab591fa72767ad42bcb7283') + version('0.8.0', sha256='6386606e716d326354a29fcb6cd09f9b3d3b5e7c5ba0d5f7ff35416b1a4177d4') version('0.6.5', '7e2732cd4840efe2dc9e4bc689cf1ee5') - depends_on('r@3.0.0:') - depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) + 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-scales@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggridges/package.py b/var/spack/repos/builtin/packages/r-ggridges/package.py index 5968ced805e..c63fc86b41a 100644 --- a/var/spack/repos/builtin/packages/r-ggridges/package.py +++ b/var/spack/repos/builtin/packages/r-ggridges/package.py @@ -10,12 +10,17 @@ class RGgridges(RPackage): """Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space.""" - homepage = "https://cran.r-project.org/web/packages/ggridges/index.html" - url = "https://cran.r-project.org/src/contrib/ggridges_0.4.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ggridges" + 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" + version('0.5.1', sha256='01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36') + version('0.5.0', sha256='124bc84044e56728fa965682f8232fc868f2af7d3eb7276f6b0df53be8d2dbfe') version('0.4.1', '21d53b3f7263beb17f629f0ebfb7b67a') version('0.4.0', 'da94ed1ee856a7fa5fb87712c84ec4c9') - depends_on('r@3.4.0:3.4.9') - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py index d7f263c38b8..fa4fe4130f6 100644 --- a/var/spack/repos/builtin/packages/r-ggsci/package.py +++ b/var/spack/repos/builtin/packages/r-ggsci/package.py @@ -11,11 +11,13 @@ class RGgsci(RPackage): 'ggplot2'""" homepage = "https://github.com/road2stat/ggsci" - url = "https://cran.r-project.org/src/contrib/ggsci_2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.9', sha256='4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c') + version('2.8', sha256='b4ce7adce7ef23edf777866086f98e29b2b45b58fed085bbd1ffe6ab52d74ae8') version('2.4', '8e5dc2fcf84352cacbb91363e26c7175') - depends_on('r@3.0.2:') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggsignif/package.py b/var/spack/repos/builtin/packages/r-ggsignif/package.py new file mode 100644 index 00000000000..4a2e8cb5444 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggsignif/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 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 RGgsignif(RPackage): + """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" + + version('0.6.0', sha256='6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e') + + depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 1543f23dd2d..bf4b902e1d4 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -12,16 +12,18 @@ class RGgvis(RPackage): and web graphics from 'vega'.""" homepage = "http://ggvis.rstudio.com/" - url = "https://cran.rstudio.com/src/contrib/ggvis_0.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis" + 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" + version('0.4.4', sha256='1332ea122b768688c8a407a483be80febc4576de0ec8929077738421b27cafaf') version('0.4.3', '30297d464278a7974fb125bcc7d84e77') version('0.4.2', '039f45e5c7f1e0652779163d7d99f922') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-shiny', type=('build', 'run')) + depends_on('r-jsonlite@0.9.11:', type=('build', 'run')) + depends_on('r-shiny@0.11.1:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-dplyr@0.4.0:', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.2.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gh/package.py b/var/spack/repos/builtin/packages/r-gh/package.py new file mode 100644 index 00000000000..779e3e649ea --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gh/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 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 RGh(RPackage): + """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" + + version('1.0.1', sha256='f3c02b16637ae390c3599265852d94b3de3ef585818b260d00e7812595b391d2') + + depends_on('r-ini', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-httr', 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 a5769db25f3..ca1d6127ca2 100644 --- a/var/spack/repos/builtin/packages/r-gistr/package.py +++ b/var/spack/repos/builtin/packages/r-gistr/package.py @@ -16,13 +16,15 @@ class RGistr(RPackage): requests require authentication and some do not.""" homepage = "https://github.com/ropensci/gistr" - url = "https://cran.r-project.org/src/contrib/gistr_0.3.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.4.2', sha256='43c00c7f565732125f45f6c067724771ba1b337d6dd3a6e301639fe16e11032e') + version('0.4.0', sha256='51771a257379a17552d0c88ada72ca6263954bbe896997f8a66cde3bf0b83ce0') version('0.3.6', '49d548cb3eca0e66711aece37757a2c0') - depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-httr', type=('build', 'run')) + depends_on('r-jsonlite@1.4:', type=('build', 'run')) + depends_on('r-httr@1.2.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) depends_on('r-knitr', 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 2306bf9b08a..0e6ce008710 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -12,13 +12,15 @@ class RGit2r(RPackage): data and running some basic 'Git' commands.""" homepage = "https://github.com/ropensci/git2r" - url = "https://cran.r-project.org/src/contrib/git2r_0.18.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.26.1', sha256='13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435') + version('0.26.0', sha256='56671389c3a50591e1dae3be8c3b0112d06d291f897d7fe14db17aea175616cf') version('0.18.0', 'fb5741eb490c3d6e23a751a72336f24d') version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') - depends_on('r@3.0.2:') - + depends_on('r@3.1:', type=('build', 'run')) depends_on('zlib') depends_on('openssl') + depends_on('libgit2') diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py index 21cb2a59860..0e98d4ff0d2 100644 --- a/var/spack/repos/builtin/packages/r-glmnet/package.py +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -14,11 +14,13 @@ class RGlmnet(RPackage): 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://cran.rstudio.com/web/packages/glmnet/index.html" - url = "https://cran.rstudio.com/src/contrib/glmnet_2.0-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/glmnet" + 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" + + version('2.0-18', sha256='e8dce9d7b8105f9cc18ba981d420de64a53b09abee219660d3612915d554256b') version('2.0-13', '1dd5636388df5c3a29207d0bf1253343') version('2.0-5', '049b18caa29529614cd684db3beaec2a') - depends_on('r-matrix', type=('build', 'run')) + depends_on('r-matrix@1.0-6:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-globaloptions/package.py b/var/spack/repos/builtin/packages/r-globaloptions/package.py index d1b0d3d8a01..6831b436bf5 100644 --- a/var/spack/repos/builtin/packages/r-globaloptions/package.py +++ b/var/spack/repos/builtin/packages/r-globaloptions/package.py @@ -10,12 +10,12 @@ class RGlobaloptions(RPackage): """It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.""" - homepage = "https://cran.r-project.org/package=GlobalOptions" - url = "https://cran.rstudio.com/src/contrib/GlobalOptions_0.0.12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GlobalOptions" + 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" + version('0.1.0', sha256='567a0a51f6b7b14127302f00e6e4944befd4964c069f96a9e61256e8c3c79ef2') version('0.0.12', '6c268b3b27874918ba62eb0f6aa0a3e5') - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-markdown', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-globals/package.py b/var/spack/repos/builtin/packages/r-globals/package.py new file mode 100644 index 00000000000..cb3eaad8183 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-globals/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 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 RGlobals(RPackage): + """Identifies global ("unknown" or "free") objects in R expressions by code + inspection using various strategies, e.g. conservative or liberal. The + objective of this package is to make it as simple as possible to identify + 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" + + version('0.12.4', sha256='7985356ad75afa1f795f8267a20dee847020c0207252dc075c614cef55d8fe6b') + + depends_on('r@3.1.2:', type=('build', 'run')) + depends_on('r-codetools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py index 7e60a323fb1..c4886be7a44 100644 --- a/var/spack/repos/builtin/packages/r-glue/package.py +++ b/var/spack/repos/builtin/packages/r-glue/package.py @@ -14,7 +14,11 @@ class RGlue(RPackage): manual/strings/#triple-quoted-string-literals>.""" homepage = "https://github.com/tidyverse/glue" - url = "https://cran.r-project.org/src/contrib/glue_1.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.3.1', sha256='4fc1f2899d71a634e1f0adb7942772feb5ac73223891abe30ea9bd91d3633ea8') + version('1.3.0', sha256='789e5a44c3635c3d3db26666e635e88adcf61cd02b75465125d95d7a12291cee') version('1.2.0', '77d06b6d86abc882fa1c0599e457c5e2') + + depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py index 3baa8c73588..6eee5281566 100644 --- a/var/spack/repos/builtin/packages/r-gmodels/package.py +++ b/var/spack/repos/builtin/packages/r-gmodels/package.py @@ -10,10 +10,12 @@ class RGmodels(RPackage): """Various R programming tools for model fitting.""" homepage = "http://www.sf.net/projects/r-gregmisc" - url = "https://cran.r-project.org/src/contrib/gmodels_2.16.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gmodels" + 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" + version('2.18.1', sha256='626140a34eb8c53dd0a06511a76c71bc61c48777fa76fcc5e6934c9c276a1369') version('2.16.2', 'f13e5feb2a8b9f0cd47fdf25ddc74228') - depends_on('r@1.9:') + depends_on('r@1.9.0:', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py index c3c99c76760..0070a61fdf3 100644 --- a/var/spack/repos/builtin/packages/r-gmp/package.py +++ b/var/spack/repos/builtin/packages/r-gmp/package.py @@ -12,9 +12,12 @@ class RGmp(RPackage): using the C library GMP (GNU Multiple Precision Arithmetic).""" homepage = "http://mulcyber.toulouse.inra.fr/projects/gmp" - url = "https://cran.r-project.org/src/contrib/gmp_0.5-13.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.5-13.5', sha256='f681ab2ff3d1e379ba8ac44a8abddd08d08170723e885abc0b469b6fa8fe5510') + version('0.5-13.4', sha256='f05605b40fc39fc589e3a4d2f526a591a649faa45eef7f95c096e1bff8775196') version('0.5-13.1', '4a45d45e53bf7140720bd44f10b075ed') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('gmp@4.2.3:') diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py index 80774039126..5ac11e6a7aa 100644 --- a/var/spack/repos/builtin/packages/r-googlevis/package.py +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -14,9 +14,12 @@ class RGooglevis(RPackage): to Google.""" homepage = "https://github.com/mages/googleVis#googlevis" - url = "https://cran.r-project.org/src/contrib/googleVis_0.6.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.6.4', sha256='7dcaf0e9d5e5598c17e8bd474141708de37eeb2578b09788431b9d871edb7eb8') + version('0.6.3', sha256='17d104c5d4e6ab7b984df229cd51be19681e4726077afec7c61a33f6e4c0b6ef') version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-goplot/package.py b/var/spack/repos/builtin/packages/r-goplot/package.py index 4e41bcc8c32..fb94c72f3ec 100644 --- a/var/spack/repos/builtin/packages/r-goplot/package.py +++ b/var/spack/repos/builtin/packages/r-goplot/package.py @@ -17,8 +17,8 @@ class RGoplot(RPackage): (circle plot, chord plot, cluster plot, Venn diagram, heatmap).""" homepage = "https://github.com/wencke/wencke.github.io/issues" - url = "https://cran.r-project.org/src/contrib/GOplot_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GOplot" + 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" 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 new file mode 100644 index 00000000000..72393b714b0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gower/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 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 RGower(RPackage): + """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" + + version('0.2.1', sha256='af3fbe91cf818c0841b2c0ec4ddf282c182a588031228c8d88f7291b2cdff100') diff --git a/var/spack/repos/builtin/packages/r-gplots/package.py b/var/spack/repos/builtin/packages/r-gplots/package.py index 6b61f87f904..3ba000a5ddd 100644 --- a/var/spack/repos/builtin/packages/r-gplots/package.py +++ b/var/spack/repos/builtin/packages/r-gplots/package.py @@ -11,10 +11,14 @@ class RGplots(RPackage): """Various R Programming Tools for Plotting Data.""" - homepage = "https://cran.r-project.org/package=gplots" - url = "https://cran.rstudio.com/src/contrib/gplots_3.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gplots" + 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" + + version('3.0.1.1', sha256='7db103f903a25d174cddcdfc7b946039b61e236c95084b90ad17f1a41da3770c') version('3.0.1', '6116822401d55add044beb120ca93d14') + + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) depends_on('r-catools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-grbase/package.py b/var/spack/repos/builtin/packages/r-grbase/package.py index e1f00f410c2..cb057aef3c3 100644 --- a/var/spack/repos/builtin/packages/r-grbase/package.py +++ b/var/spack/repos/builtin/packages/r-grbase/package.py @@ -10,8 +10,8 @@ class RGrbase(RPackage): """gRbase: A Package for Graphical Modelling in R""" homepage = "http://people.math.aau.dk/~sorenh/software/gR/" - url = "https://cran.r-project.org/src/contrib/gRbase_1.8-3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gRbase" + 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" version('1.8-3.4', sha256='d35f94c2fb7cbd4ce3991570424dfe6723a849658da32e13df29f53b6ea2cc2c') diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py index 6c2acf087d8..38d7b684a22 100644 --- a/var/spack/repos/builtin/packages/r-gridbase/package.py +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -9,8 +9,10 @@ class RGridbase(RPackage): """Integration of base and grid graphics.""" - homepage = "https://cran.r-project.org/web/packages/gridBase/index.html" - url = "https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gridBase" + 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" version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f') + + depends_on('r@2.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index 8486e2c23d6..3f26f2ef564 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -10,9 +10,9 @@ class RGridextra(RPackage): """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://cran.r-project.org/package=gridExtra" - url = "https://cran.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gridExtras" + 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" version('2.3', '01e0ea88610756a0fd3b260e83c9bd43') version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2') diff --git a/var/spack/repos/builtin/packages/r-gsa/package.py b/var/spack/repos/builtin/packages/r-gsa/package.py new file mode 100644 index 00000000000..aa27d7a2284 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gsa/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 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 RGsa(RPackage): + """Gene Set Analysis.""" + + homepage = "http://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" + + version('1.03.1', sha256='e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917') diff --git a/var/spack/repos/builtin/packages/r-gss/package.py b/var/spack/repos/builtin/packages/r-gss/package.py index 26018c242eb..0c652099fc8 100644 --- a/var/spack/repos/builtin/packages/r-gss/package.py +++ b/var/spack/repos/builtin/packages/r-gss/package.py @@ -10,8 +10,11 @@ class RGss(RPackage): """A comprehensive package for structural multivariate function estimation using smoothing splines.""" - homepage = "https://cran.r-project.org/package=gss" - url = "https://cran.rstudio.com/src/contrib/gss_2.1-7.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/gss" + 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" + version('2.1-10', sha256='26c47ecae6a9b7854a1b531c09f869cf8b813462bd8093e3618e1091ace61ee2') version('2.1-7', '4a6bd96339d22b40c932895b64504fb2') + + depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gsubfn/package.py b/var/spack/repos/builtin/packages/r-gsubfn/package.py index 1a7ecb919fe..b5c9d95eff8 100644 --- a/var/spack/repos/builtin/packages/r-gsubfn/package.py +++ b/var/spack/repos/builtin/packages/r-gsubfn/package.py @@ -21,10 +21,11 @@ class RGsubfn(RPackage): sql calls that may involve strings where substitution is desirable.""" - homepage = "https://cran.r-project.org/package=gsubfn" - url = "https://cran.r-project.org/src/contrib/gsubfn_0.6-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gsubfn" + 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" + version('0.7', sha256='89351df9e65722d2862f26a0a3985666de3c86e8400808ced8a6eb6e165a4602') version('0.6-6', '94195ff3502706c736d9c593c07252bc') depends_on('r-proto', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py index fec5fdbb751..6df80edc585 100644 --- a/var/spack/repos/builtin/packages/r-gtable/package.py +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -9,8 +9,11 @@ class RGtable(RPackage): """Tools to make it easier to work with "tables" of 'grobs'.""" - homepage = "https://cran.r-project.org/web/packages/gtable/index.html" - url = "https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gtable" + 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" + version('0.3.0', sha256='fd386cc4610b1cc7627dac34dba8367f7efe114b968503027fb2e1265c67d6d3') version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab') + + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py index 2103df512f2..752dd44437f 100644 --- a/var/spack/repos/builtin/packages/r-gtools/package.py +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -40,8 +40,9 @@ class RGtools(RPackage): """ - homepage = "https://cran.r-project.org/package=gtools" - url = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gtools" + 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" + version('3.8.1', sha256='051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38') version('3.5.0', '45f8800c0336d35046641fbacc56bdbb') diff --git a/var/spack/repos/builtin/packages/r-gwmodel/package.py b/var/spack/repos/builtin/packages/r-gwmodel/package.py index dfbcaf9b890..08e1cb9c1be 100644 --- a/var/spack/repos/builtin/packages/r-gwmodel/package.py +++ b/var/spack/repos/builtin/packages/r-gwmodel/package.py @@ -10,9 +10,11 @@ class RGwmodel(RPackage): """GWmodel: Geographically-Weighted Models""" homepage = "http://gwr.nuim.ie/" - url = "https://cran.r-project.org/src/contrib/GWmodel_2.0-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GWmodel" + 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" + version('2.1-3', sha256='3e1a36fddf8e64f61d548067bb043216f8d12069d814a4cbf07a9cae0b310af6') + version('2.1-1', sha256='91241b4e26d423a54c7c6784ef5159759058a5dafdff18a1ea8451faf979d1f3') version('2.0-9', sha256='b479af2c19d4aec30f1883d00193d52e342c609c1badcb51cc0344e4404cffa7') depends_on('r@3.0.0:', type=('build', 'run')) @@ -24,3 +26,4 @@ class RGwmodel(RPackage): depends_on('r-spacetime', type=('build', 'run')) depends_on('r-spatialreg', type=('build', 'run')) depends_on('r-spdep', type=('build', 'run')) + depends_on('r-fnn', when='@2.1-1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-haven/package.py b/var/spack/repos/builtin/packages/r-haven/package.py index e825ac5f79e..1ddb4e0bff1 100644 --- a/var/spack/repos/builtin/packages/r-haven/package.py +++ b/var/spack/repos/builtin/packages/r-haven/package.py @@ -11,13 +11,18 @@ class RHaven(RPackage): library, .""" homepage = "http://haven.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/haven_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/haven" + url = "https://cloud.r-project.org/src/contrib/haven_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/haven" + version('2.1.1', sha256='90bcb4e7f24960e7aa3e15c06b95cd897f08de149cec43fd8ba110b14526068a') + version('2.1.0', sha256='c0a1cf1b039549fb3ad833f9644ed3f142790236ad755d2ee7bd3d8109e3ae74') version('1.1.0', '8edd4b7683f8c36b5bb68582ac1b8733') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-readr', type=('build', 'run')) + 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-rcpp@0.11.4:', type=('build', 'run')) + depends_on('r-readr@0.1.0:', type=('build', 'run')) depends_on('r-hms', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) - depends_on('r-forcats', type=('build', 'run')) + depends_on('r-forcats@0.2.0:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-hdf5r/package.py b/var/spack/repos/builtin/packages/r-hdf5r/package.py new file mode 100644 index 00000000000..670d1acb63b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-hdf5r/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2019 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 RHdf5r(RPackage): + """'HDF5' is a data model, library and file format for storing and managing + large amounts of data. This package provides a nearly feature complete, + object oriented wrapper for the 'HDF5' API + using R6 + 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" + + version('1.2.0', sha256='58813e334fd3f9040038345a7186e5cb02090898883ac192477a76a5b8b4fe81') + + depends_on('r@3.2.2:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-bit64', type=('build', 'run')) + depends_on('hdf5@1.8.13:') + + def configure_args(self): + if 'mpi' in self.spec: + args = [ + '--with-hdf5={0}/h5pcc'.format(self.spec['hdf5'].prefix.bin), + ] + else: + args = [ + '--with-hdf5={0}/h5cc'.format(self.spec['hdf5'].prefix.bin), + ] + return args diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index 2f2a39554dc..adfec4c76bc 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -12,9 +12,12 @@ class RHexbin(RPackage): on grid graphics and formal (S4) classes and methods.""" homepage = "http://github.com/edzer/hexbin" - url = "https://cran.r-project.org/src/contrib/hexbin_1.27.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.27.3', sha256='7ea422a76542c2fc2840df601af1b7803aa96df4fee6d51dec456ac36940c191') + version('1.27.2', sha256='46d47b1efef75d6f126af686a4dd614228b60418b9a5bde9e9e5d11200a0ee52') version('1.27.1', '7590ed158f8a57a71901bf6ca26f81be') + depends_on('r@2.0.1:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py index 9824c1e55da..fb600dc5677 100644 --- a/var/spack/repos/builtin/packages/r-highr/package.py +++ b/var/spack/repos/builtin/packages/r-highr/package.py @@ -13,7 +13,12 @@ class RHighr(RPackage): Andre Simon's highlight package.""" homepage = "https://github.com/yihui/highr" - url = "https://cran.r-project.org/src/contrib/highr_0.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/highr" + url = "https://cloud.r-project.org/src/contrib/highr_0.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/highr" + version('0.8', sha256='4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657') + version('0.7', sha256='cabba5b6f2ea82024a49c5ced5f1aa476f864bc52bc129038e319e4e26b6f3b7') version('0.6', 'bf47388c5f57dc61962362fb7e1d8b16') + + depends_on('r@3.0.2:', when='@:0.7', type=('build', 'run')) + depends_on('r@3.2.3:', when='@0.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py index a7f4c5e4df7..1ef0b1aa917 100644 --- a/var/spack/repos/builtin/packages/r-hmisc/package.py +++ b/var/spack/repos/builtin/packages/r-hmisc/package.py @@ -15,21 +15,27 @@ class RHmisc(RPackage): code, and recoding variables.""" homepage = "http://biostat.mc.vanderbilt.edu/Hmisc" - url = "https://cran.rstudio.com/src/contrib/Hmisc_4.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Hmisc" + 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" + version('4.2-0', sha256='9e9614673288dd00295f250fa0bf96fc9e9fed692c69bf97691081c1a01411d9') version('4.1-1', 'd255611f2b108d3cc0212b8a98fef6e3') version('4.0-3', '7091924db1e473419d8116c3335f82da') depends_on('r-lattice', type=('build', 'run')) - depends_on('r-survival', type=('build', 'run')) + depends_on('r-survival@2.40-1:', type=('build', 'run')) depends_on('r-formula', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggplot2@2.2:', type=('build', 'run')) depends_on('r-latticeextra', type=('build', 'run')) depends_on('r-acepack', type=('build', 'run')) depends_on('r-gridextra', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-htmltable', type=('build', 'run')) + depends_on('r-htmltable@1.11.0:', type=('build', 'run')) depends_on('r-viridis', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) + depends_on('r-rpart', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) + depends_on('r-foreign', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hms/package.py b/var/spack/repos/builtin/packages/r-hms/package.py index 6e4b513799e..b39d7f4ee5d 100644 --- a/var/spack/repos/builtin/packages/r-hms/package.py +++ b/var/spack/repos/builtin/packages/r-hms/package.py @@ -10,8 +10,13 @@ class RHms(RPackage): """Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.""" - homepage = "https://cran.rstudio.com/web/packages/hms/index.html" - url = "https://cran.rstudio.com/src/contrib/hms_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/hms" + homepage = "https://cloud.r-project.org/package=hms" + url = "https://cloud.r-project.org/src/contrib/hms_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/hms" + version('0.5.0', sha256='a87872665c3bf3901f597d78c152e7805f7129e4dbe27397051de4cf1a76561b') version('0.3', '92c4a0cf0c402a35145b5bb57212873e') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-hoardr/package.py b/var/spack/repos/builtin/packages/r-hoardr/package.py index 2e00826bbeb..cbc9806c3e6 100644 --- a/var/spack/repos/builtin/packages/r-hoardr/package.py +++ b/var/spack/repos/builtin/packages/r-hoardr/package.py @@ -9,16 +9,12 @@ class RHoardr(RPackage): """hoardr: Manage Cached Files""" - homepage = "https://cran.r-project.org/package=hoardr" - url = "https://cran.r-project.org/src/contrib/hoardr_0.5.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/hoardr/" + 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/" version('0.5.2', sha256='819113f0e25da105f120a676b5173872a4144f2f6f354cad14b35f898e76dc54') depends_on('r-r6@2.2.0:', type=('build', 'run')) depends_on('r-rappdirs@0.3.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-roxygen2@6.0.1:', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rmarkdown', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-htmltable/package.py b/var/spack/repos/builtin/packages/r-htmltable/package.py index 09c77875bbc..8693a8d8cc2 100644 --- a/var/spack/repos/builtin/packages/r-htmltable/package.py +++ b/var/spack/repos/builtin/packages/r-htmltable/package.py @@ -15,10 +15,11 @@ class RHtmltable(RPackage): few text formatting functions that help outputting text compatible with HTML/'LaTeX'.""" - homepage = "https://CRAN.R-project.org/package=htmlTable" - url = "https://cran.rstudio.com/src/contrib/htmlTable_1.11.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/htmlTable" + 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" + version('1.13.1', sha256='689f32b65da6a57ad500e8d9ef3309d346401dca277c6b264a46c8d7c75884d0') version('1.11.2', '473e6d486e7714f8dd7f16a31480c896') version('1.9', '08c62c19e1ffe570e7d8fa57db5094b9') @@ -27,4 +28,5 @@ class RHtmltable(RPackage): depends_on('r-magrittr@1.5:', type=('build', 'run')) depends_on('r-checkmate', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r-htmltools', type=('build', 'run'), when="@1.11.0:") depends_on('r-rstudioapi@0.6:', type=('build', 'run'), when="@1.11.0:") diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 0f23d8df4e5..866f20fe56d 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -10,11 +10,12 @@ class RHtmltools(RPackage): """Tools for HTML generation and output.""" homepage = "https://github.com/rstudio/htmltools" - url = "https://cran.rstudio.com/src/contrib/htmltools_0.3.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools" + url = "https://cloud.r-project.org/src/contrib/htmltools_0.3.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/htmltools" version('0.3.6', '336419c2143f958862e01ef1bbc9c253') version('0.3.5', '5f001aff4a39e329f7342dcec5139724') + depends_on('r@2.14.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py index f6a42ac7338..aed9faa579b 100644 --- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -11,14 +11,15 @@ class RHtmlwidgets(RPackage): including the R console, 'R Markdown' documents, and 'Shiny' web applications.""" - homepage = "https://cran.r-project.org/package=htmlTable" - url = "https://cran.rstudio.com/src/contrib/htmlwidgets_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/htmlwidgets" + 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" + version('1.3', sha256='f1e4ffabc29e6cfe857f627da095be3cfcbe0e1f02ae75e572f10b4a026c5a12') version('0.9', 'b42730691eca8fc9a28903c272d11605') version('0.8', '06b0404a00e25736946607a36ee5351d') version('0.6', '7fa522d2eda97593978021bda9670c0e') - depends_on('r-htmltools', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-htmltools@0.3:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', type=('build', 'run')) depends_on('r-yaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-httpcode/package.py b/var/spack/repos/builtin/packages/r-httpcode/package.py index edbed0d2329..ffd772eee77 100644 --- a/var/spack/repos/builtin/packages/r-httpcode/package.py +++ b/var/spack/repos/builtin/packages/r-httpcode/package.py @@ -10,7 +10,7 @@ class RHttpcode(RPackage): """httpcode: 'HTTP' Status Code Helper""" homepage = "https://github.com/sckott/httpcode" - url = "https://cran.r-project.org/src/contrib/httpcode_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" 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 ea9461773ef..9bc6326d95e 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -16,12 +16,16 @@ class RHttpuv(RPackage): information.)""" homepage = "https://github.com/rstudio/httpuv" - url = "https://cran.rstudio.com/src/contrib/httpuv_1.3.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.5.1', sha256='b5bb6b3b2f1a6d792568a70f3f357d6b3a35a5e26dd0c668c61a31f2ae8f5710') version('1.3.5', '48d894ff0067148f41a651634fbb2012') version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') - depends_on('r@2.15.1:') - + 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('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index e1ba98698ef..7f79836f9aa 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -12,17 +12,20 @@ class RHttr(RPackage): request components (authenticate(), add_headers() and so on).""" homepage = "https://github.com/hadley/httr" - url = "https://cran.r-project.org/src/contrib/httr_1.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.4.1', sha256='675c7e07bbe82c48284ee1ab929bb14a6e653abae2860d854dc41a3c028de156') + version('1.4.0', sha256='d633f1425da514f65f3b8c034ae0a8b6911995009840c6bb9657ceedb99ddb48') version('1.3.1', '5acfb6b2a6f2f26cd6dfad0458fe3351') version('1.2.1', 'c469948dedac9ab3926f23cf484b33d9') version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') - depends_on('r@3.0.0:') - + depends_on('r@3.0.0:', when='@:1.3.1', 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-jsonlite', type=('build', 'run')) depends_on('r-mime', type=('build', 'run')) - depends_on('r-curl@0.9.1:', type=('build', 'run')) - depends_on('r-openssl', type=('build', 'run')) + depends_on('r-curl@3.0.0:', type=('build', 'run')) + depends_on('r-openssl@0.8:', type=('build', 'run')) depends_on('r-r6', 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 9fa89f91d66..de980bb2d58 100644 --- a/var/spack/repos/builtin/packages/r-hwriter/package.py +++ b/var/spack/repos/builtin/packages/r-hwriter/package.py @@ -10,7 +10,10 @@ class RHwriter(RPackage): """Easy-to-use and versatile functions to output R objects in HTML format.""" - homepage = "https://cran.rstudio.com/web/packages/hwriter/index.html" - url = "https://cran.rstudio.com/src/contrib/hwriter_1.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/hwriter" + 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" + version('1.3.2', '9eef49df2eb68bbf3a16b5860d933517') + + depends_on('r@2.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ica/package.py b/var/spack/repos/builtin/packages/r-ica/package.py index ef882eb51e0..aea4b44ead5 100644 --- a/var/spack/repos/builtin/packages/r-ica/package.py +++ b/var/spack/repos/builtin/packages/r-ica/package.py @@ -11,10 +11,10 @@ class RIca(RPackage): Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).""" - homepage = "https://cran.r-project.org/web/packages/ica/index.html" - url = "https://cran.r-project.org/src/contrib/ica_1.0-1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ica" + 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" - depends_on('r@3.4.0:3.4.9') + version('1.0-2', sha256='e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179') version('1.0-1', '15c8d5afeec2804beec55dd14abc585d') version('1.0-0', '3ade2b3b00eb39c348d802f24d2afd1d') diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py index 69c1d161e18..2dbc16b1738 100644 --- a/var/spack/repos/builtin/packages/r-igraph/package.py +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -12,15 +12,18 @@ class RIgraph(RPackage): graphs, graph visualization, centrality methods and much more.""" homepage = "http://igraph.org/" - url = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/igraph" + 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" + version('1.2.4.1', sha256='891acc763b5a4a4a245358a95dee69280f4013c342f14dd6a438e7bb2bf2e480') + version('1.2.4', sha256='1048eb26ab6b592815bc269c1d91e974c86c9ab827ccb80ae0a40042019592cb') version('1.1.2', 'ca1617aea272852d2856c4661ad1c7d8') version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065') depends_on('r-matrix', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-pkgconfig', type=('build', 'run')) - depends_on('r-irlba', 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('libxml2') + depends_on('glpk', when='@1.2.0:') diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py index b6f2c7eb62a..51447618501 100644 --- a/var/spack/repos/builtin/packages/r-influencer/package.py +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -17,10 +17,11 @@ class RInfluencer(RPackage): configured.""" homepage = "https://github.com/rcc-uchicago/influenceR" - url = "https://cran.r-project.org/src/contrib/influenceR_0.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5') - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-igraph@1.0.1:', type=('build', 'run')) + depends_on('r-matrix@1.1-4:', 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 new file mode 100644 index 00000000000..67edc74e657 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ini/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 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 RIni(RPackage): + """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" + + 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 88cb95a6960..6083319dbd7 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -11,8 +11,11 @@ class RInline(RPackage): inlined C, C++ or Fortran code supporting .C and .Call calling conventions.""" - homepage = "https://cran.r-project.org/web/packages/inline/index.html" - url = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/inline" + 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" + version('0.3.15', sha256='ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68') version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca') + + depends_on('r@2.4.0:', 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 3b384f772c7..52ce3e8ccff 100644 --- a/var/spack/repos/builtin/packages/r-intervals/package.py +++ b/var/spack/repos/builtin/packages/r-intervals/package.py @@ -10,8 +10,8 @@ class RIntervals(RPackage): """intervals: Tools for Working with Points and Intervals""" homepage = "http://github.com/edzer/intervals" - url = "https://cran.r-project.org/src/contrib/intervals_0.15.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" 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 new file mode 100644 index 00000000000..7376f998ffe --- /dev/null +++ b/var/spack/repos/builtin/packages/r-inum/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 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 RInum(RPackage): + """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" + + version('1.0-1', sha256='3c2f94c13c03607e05817e4859595592068b55e810fed94e29bc181ad248a099') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-libcoin@1.0-0:', 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 edd42b5645f..43d91530921 100644 --- a/var/spack/repos/builtin/packages/r-ipred/package.py +++ b/var/spack/repos/builtin/packages/r-ipred/package.py @@ -11,14 +11,15 @@ class RIpred(RPackage): classification, regression and survival problems as well as resampling based estimators of prediction error.""" - homepage = "https://cran.r-project.org/package=ipred" - url = "https://cran.r-project.org/src/contrib/ipred_0.9-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ipred" + 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" + version('0.9-9', sha256='0da87a70730d5a60b97e46b2421088765e7d6a7cc2695757eba0f9d31d86416f') + version('0.9-8', sha256='9c1d11c3cb0d72be7870e70a216e589e403bbfee38c796fe75cd0611d878ac07') version('0.9-5', 'ce8768547a7aa9554ad3650b18ea3cbd') - depends_on('r@2.10:') - + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rpart@3.1-8:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py index f908fff7784..c246abbae03 100644 --- a/var/spack/repos/builtin/packages/r-irdisplay/package.py +++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py @@ -13,8 +13,11 @@ class RIrdisplay(RPackage): session""" homepage = "https://irkernel.github.io" - url = "https://cran.rstudio.com/src/contrib/IRdisplay_0.4.4.tar.gz" + 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" + version('0.7.0', sha256='91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089') version('0.4.4', '5be672fb82185b90f23bd99ac1e1cdb6') + depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-repr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py index 466e75ee45a..46a5d712dc5 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -11,10 +11,12 @@ class RIrlba(RPackage): decompositions and principal component analysis of large sparse or dense matrices.""" - homepage = "https://cran.r-project.org/web/packages/irlba/index.html" - url = "https://cran.r-project.org/src/contrib/irlba_2.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/irlba" + 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" + version('2.3.3', sha256='6ee233697bcd579813bd0af5e1f4e6dd1eea971e8919c748408130d970fef5c0') + version('2.3.2', sha256='3fdf2d8fefa6ab14cd0992740de7958f9f501c71aca93229f5eb03c54558fc38') version('2.1.2', '290940abf6662ed10c0c5a8db1bc6e88') version('2.0.0', '557674cf8b68fea5b9f231058c324d26') diff --git a/var/spack/repos/builtin/packages/r-isdparser/package.py b/var/spack/repos/builtin/packages/r-isdparser/package.py index 83e9d92a845..bb5e038d04e 100644 --- a/var/spack/repos/builtin/packages/r-isdparser/package.py +++ b/var/spack/repos/builtin/packages/r-isdparser/package.py @@ -10,8 +10,8 @@ class RIsdparser(RPackage): """isdparser: Parse 'NOAA' Integrated Surface Data Files""" homepage = "https://github.com/ropensci/isdparser" - url = "https://cran.r-project.org/src/contrib/isdparser_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.3.0', sha256='6c9e1d7f3661802838010d659d7c77b964423dcc9a6623402df1fe3be627b7b9') diff --git a/var/spack/repos/builtin/packages/r-iso/package.py b/var/spack/repos/builtin/packages/r-iso/package.py index 4bbca3b0b65..9640af6cbf2 100644 --- a/var/spack/repos/builtin/packages/r-iso/package.py +++ b/var/spack/repos/builtin/packages/r-iso/package.py @@ -10,8 +10,11 @@ class RIso(RPackage): """Linear order and unimodal order (univariate) isotonic regression; bivariate isotonic regression with linear order on both variables.""" - homepage = "https://cran.r-project.org/package=Iso" - url = "https://cran.rstudio.com/src/contrib/Iso_0.0-17.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/Iso" + 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" + version('0.0-18', sha256='2d7e8c4452653364ee086d95cea620c50378e30acfcff129b7261e1756a99504') version('0.0-17', 'bf99821efb6a44fa75fdbf5e5c4c91e4') + + depends_on('r@1.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py index 397ba24644c..da880c792fc 100644 --- a/var/spack/repos/builtin/packages/r-iterators/package.py +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -10,8 +10,12 @@ class RIterators(RPackage): """Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.""" - homepage = "https://cran.r-project.org/web/packages/iterators/index.html" - url = "https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/iterators" + 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" + version('1.0.12', sha256='96bf31d60ebd23aefae105d9b7790715e63327eec0deb2ddfb3d543994ea9f4b') + version('1.0.9', sha256='de001e063805fdd124953b571ccb0ed2838c55e40cca2e9d283d8a90b0645e9b') version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee') + + depends_on('r@2.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-janitor/package.py b/var/spack/repos/builtin/packages/r-janitor/package.py index a48d57f8514..a754eb61ee5 100644 --- a/var/spack/repos/builtin/packages/r-janitor/package.py +++ b/var/spack/repos/builtin/packages/r-janitor/package.py @@ -20,11 +20,17 @@ class RJanitor(RPackage): for the fun stuff.""" homepage = "https://github.com/sfirke/janitor" - url = "https://cran.r-project.org/src/contrib/janitor_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.2.0', sha256='5e15a2292c65c5ddd6160289dec2604b05a813651a2be0d7854ace4548a32b8c') + version('1.1.1', sha256='404b41f56e571fab4c95ef62e79cb4f3bb34d5bb6e4ea737e748ff269536176b') version('0.3.0', '76036c54693b91aef19d468107ae066a') - depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-tidyr', type=('build', 'run')) + depends_on('r@3.1.2:', type=('build', 'run')) + depends_on('r-dplyr@0.7.0:', type=('build', 'run')) + depends_on('r-tidyr@0.7.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-snakecase@0.9.2:', when='@1.1.0:', 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')) diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py index 39eced15603..8fcbd881b25 100644 --- a/var/spack/repos/builtin/packages/r-jomo/package.py +++ b/var/spack/repos/builtin/packages/r-jomo/package.py @@ -15,11 +15,15 @@ class RJomo(RPackage): with the substantive model. """ - homepage = "https://cran.r-project.org/package=jomo" - url = "https://cran.r-project.org/src/contrib/jomo_2.6-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/jomo" + 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" + version('2.6-9', sha256='b90f47071e62b8863b00b1ae710a56ae6efbfe2baeb9963f8a91a10d6183cc9b') + version('2.6-7', sha256='6e83dab51103511038a3e9a3c762e00cc45ae7080c0a0f64e37bcea8c488db53') version('2.6-2', 'eff4a6c1a971708959d65b3224c98a25') 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')) diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py index ca834140493..53b986d6d64 100644 --- a/var/spack/repos/builtin/packages/r-jpeg/package.py +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -12,9 +12,10 @@ class RJpeg(RPackage): and in-memory raw vectors.""" homepage = "http://www.rforge.net/jpeg/" - url = "https://cran.r-project.org/src/contrib/jpeg_0.1-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.1-8', '696007451d14395b1ed1d0e9af667a57') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('jpeg') diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 81601f6dd69..6cbdf132a8b 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -19,9 +19,10 @@ class RJsonlite(RPackage): use with dynamic data in systems and applications.""" homepage = "https://github.com/jeroenooms/jsonlite" - url = "https://cran.rstudio.com/src/contrib/jsonlite_1.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.6', sha256='88c5b425229966b7409145a6cabc72db9ed04f8c37ee95901af0146bb285db53') version('1.5', '2a81c261a702fccbbd5d2b32df108f76') version('1.2', '80cd2678ae77254be470f5931db71c51') version('1.0', 'c8524e086de22ab39b8ac8000220cc87') diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py index 6c8694f3c80..3eedaac2795 100644 --- a/var/spack/repos/builtin/packages/r-kernlab/package.py +++ b/var/spack/repos/builtin/packages/r-kernlab/package.py @@ -12,10 +12,12 @@ class RKernlab(RPackage): reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.""" - homepage = "https://cran.r-project.org/package=kernlab" - url = "https://cran.r-project.org/src/contrib/kernlab_0.9-25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/kernlab" + 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" + version('0.9-27', sha256='f6add50ed4097f04d09411491625f8d46eafc4f003b1c1cff78a6fff8cc31dd4') + version('0.9-26', sha256='954940478c6fcf60433e50e43cf10d70bcb0a809848ca8b9d683bf371cd56077') version('0.9-25', '1182a2a336a79fd2cf70b4bc5a35353f') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py index 8910c12247f..d39ea1e4ff7 100644 --- a/var/spack/repos/builtin/packages/r-kernsmooth/package.py +++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py @@ -9,10 +9,10 @@ class RKernsmooth(RPackage): """Functions for kernel smoothing (and density estimation).""" - homepage = "https://cran.r-project.org/package=KernSmooth" - url = "https://cran.r-project.org/src/contrib/KernSmooth_2.23-15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/KernSmooth" + 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" version('2.23-15', '746cdf26dec72004cf19978e87dcc982') - depends_on('r@2.5.0:') + depends_on('r@2.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py index 4729ce905fa..c63bbf2d6ad 100644 --- a/var/spack/repos/builtin/packages/r-kknn/package.py +++ b/var/spack/repos/builtin/packages/r-kknn/package.py @@ -10,13 +10,12 @@ class RKknn(RPackage): """Weighted k-Nearest Neighbors for Classification, Regression and Clustering.""" - homepage = "https://cran.r-project.org/package=kknn" - url = "https://cran.r-project.org/src/contrib/kknn_1.3.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/kknn" + 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" version('1.3.1', '372cd84f618cd5005f8c4c5721755117') - depends_on('r@2.10:') - + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-igraph@1.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index f6fcb803982..90f3cbb334b 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -11,18 +11,25 @@ class RKnitr(RPackage): """Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.""" - homepage = "https://cran.r-project.org/package=knitr" - url = "https://cran.rstudio.com/src/contrib/knitr_1.14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/knitr" + homepage = "https://cloud.r-project.org/package=knitr" + url = "https://cloud.r-project.org/src/contrib/knitr_1.14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/knitr" + version('1.24', sha256='e80c2043b445a7e576b62ae8510cce89322660fe388881d799a706d35cd27b89') + version('1.23', sha256='063bfb3300fc9f3e7d223c346e19b93beced0e6784470b9bef2524868a206a99') version('1.17', '4407ccf8f2a51629800d6d5243cf3e70') version('1.14', 'ef0fbeaa9372f99ffbc57212a7781511') version('0.6', 'c67d6db84cd55594a9e870c90651a3db') - depends_on('r-evaluate', type=('build', 'run')) - depends_on('r-digest', type=('build', 'run')) - depends_on('r-formatr', type=('build', 'run')) + 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-evaluate@0.10:', type=('build', 'run')) + depends_on('r-digest@:1.17', type=('build', 'run')) + depends_on('r-formatr@:1.14', type=('build', 'run')) depends_on('r-highr', type=('build', 'run')) - depends_on('r-stringr', type=('build', 'run')) + depends_on('r-stringr@0.6:', type=('build', 'run')) depends_on('r-markdown', type=('build', 'run')) - depends_on('r-yaml', type=('build', 'run')) + depends_on('r-yaml@2.1.19:', type=('build', 'run')) + depends_on('r-xfun', when='@1.23:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ks/package.py b/var/spack/repos/builtin/packages/r-ks/package.py index ceab1b8eb0d..5ff34544a4d 100644 --- a/var/spack/repos/builtin/packages/r-ks/package.py +++ b/var/spack/repos/builtin/packages/r-ks/package.py @@ -9,13 +9,15 @@ class RKs(RPackage): """Kernel smoothers for univariate and multivariate data.""" - homepage = "https://cran.r-project.org/package=ks" - url = "https://cran.r-project.org/src/contrib/Archive/ks/ks_1.11.2.tar.gz" + 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" + version('1.11.5', sha256='4f65565376391b8a6dcce76168ef628fd4859dba8496910cbdd54e4f88e8d51b') + version('1.11.4', sha256='0beffaf8694819fba8c93af07a8782674a15fe00a04ad1d94d31238d0a41b134') version('1.11.2', sha256='9dfd485096e1e67abc7dfcb7b76a83de110dd15bcfeffe5c899605b3a5592961') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r-fnn@1.1:', type=('build', 'run')) depends_on('r-kernlab', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py index 061d10272ce..49b481f61c7 100644 --- a/var/spack/repos/builtin/packages/r-labeling/package.py +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -9,8 +9,8 @@ class RLabeling(RPackage): """Provides a range of axis labeling algorithms.""" - homepage = "https://cran.r-project.org/web/packages/labeling/index.html" - url = "https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/labeling" + 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" version('0.3', 'ccd7082ec0b211aba8a89d85176bb534') 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 bbc6b81ad45..459ac5a3416 100644 --- a/var/spack/repos/builtin/packages/r-lambda-r/package.py +++ b/var/spack/repos/builtin/packages/r-lambda-r/package.py @@ -11,8 +11,12 @@ class RLambdaR(RPackage): Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.""" - homepage = "https://cran.rstudio.com/web/packages/lambda.r/index.html" - url = "https://cran.rstudio.com/src/contrib/lambda.r_1.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/lambda.r" + 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" + version('1.2.3', sha256='0cd8e37ba1a0960888016a85d492da51a57df54bd65ff920b08c79a3bfbe8631') version('1.2', 'bda49898b85ad5902880a31f43b432e2') + + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-formatr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py index a07c84a32c4..60bfe0ba76a 100644 --- a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py +++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py @@ -12,7 +12,11 @@ class RLaplacesdemon(RPackage): describes the history of the package development process.""" homepage = "https://github.com/LaplacesDemonR/LaplacesDemon" - url = "https://cran.r-project.org/src/contrib/LaplacesDemon_16.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('16.1.1', sha256='779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77') + version('16.1.0', sha256='41d99261e8fc33c977b43ecf66ebed8ef1c84d9bd46b271609e9aadddc2ca8bb') version('16.0.1', '1e4dab2dd0e27251734d68b0bfdbe911') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py index 82fbc6fd798..e2595d3c3ac 100644 --- a/var/spack/repos/builtin/packages/r-lars/package.py +++ b/var/spack/repos/builtin/packages/r-lars/package.py @@ -10,9 +10,9 @@ class RLars(RPackage): """Efficient procedures for fitting an entire lasso sequence with the cost of a single least squares fit.""" - homepage = "https://cran.r-project.org/web/packages/lars/index.html" - url = "https://cran.r-project.org/src/contrib/lars_1.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/lars" + 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" version('1.2', '2571bae325f6cba1ad0202ea61695b8c') version('1.1', 'e94f6902aade09b13ec25ba2381384e5') diff --git a/var/spack/repos/builtin/packages/r-later/package.py b/var/spack/repos/builtin/packages/r-later/package.py new file mode 100644 index 00000000000..1a1f2fa6796 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-later/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 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 RLater(RPackage): + """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" + + 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')) diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index 4c040d88e59..c47360d7017 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -13,8 +13,11 @@ class RLattice(RPackage): handle most nonstandard requirements. See ?Lattice for an introduction.""" homepage = "http://lattice.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/lattice_0.20-35.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lattice" + 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" + version('0.20-38', sha256='fdeb5e3e50dbbd9d3c5e2fa3eef865132b3eef30fbe53a10c24c7b7dfe5c0a2d') version('0.20-35', '07f1814623b3da6278ca61554ff7bfe6') version('0.20-34', 'c2a648b22d4206ae7526fb70b8e90fed') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-latticeextra/package.py b/var/spack/repos/builtin/packages/r-latticeextra/package.py index b82f7a9f256..7cf8b7da490 100644 --- a/var/spack/repos/builtin/packages/r-latticeextra/package.py +++ b/var/spack/repos/builtin/packages/r-latticeextra/package.py @@ -13,10 +13,11 @@ class RLatticeextra(RPackage): functions.""" homepage = "http://latticeextra.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/latticeExtra_0.6-28.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/latticeExtra" + 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" version('0.6-28', '771938f25d0983763369b48a1153b26c') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) 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 01739d205ff..b9daaf2e3a5 100644 --- a/var/spack/repos/builtin/packages/r-lava/package.py +++ b/var/spack/repos/builtin/packages/r-lava/package.py @@ -9,13 +9,15 @@ class RLava(RPackage): """Estimation and simulation of latent variable models.""" - homepage = "https://cran.r-project.org/package=lava" - url = "https://cran.r-project.org/src/contrib/lava_1.4.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lava" + 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" + version('1.6.6', sha256='7abc84dd99cce450a45ac4f232812cde3a322e432da3472f43b057fb5c59ca59') + version('1.6.4', sha256='41c6eeb96eaef9e1bfb04b31f7203e250a5ea7e7860be4d95f7f96f2a8644718') version('1.4.7', '28039248a7039ba9281d172e4dbf9543') - depends_on('r@3.0:') - + depends_on('r@3.0:', type=('build', 'run')) 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')) diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py index ded81125a8f..5650181c562 100644 --- a/var/spack/repos/builtin/packages/r-lazyeval/package.py +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -11,8 +11,12 @@ class RLazyeval(RPackage): Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.""" - homepage = "https://cran.r-project.org/web/packages/lazyeval/index.html" - url = "https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lazyeval" + 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" + version('0.2.2', sha256='d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4') + version('0.2.1', sha256='83b3a43e94c40fe7977e43eb607be0a3cd64c02800eae4f2774e7866d1e93f61') version('0.2.0', 'df1daac908dcf02ae7e12f4335b1b13b') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py index 4c88c497121..3a436e009ab 100644 --- a/var/spack/repos/builtin/packages/r-leaflet/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -12,12 +12,16 @@ class RLeaflet(RPackage): the R console, from 'RStudio', in Shiny apps and R Markdown documents.""" homepage = "http://rstudio.github.io/leaflet/" - url = "https://cran.r-project.org/src/contrib/leaflet_1.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.0.2', sha256='fa448d20940e01e953e0706fc5064b0fa347e69fa967792599eb03c52b2e3114') + version('2.0.1', sha256='9876d5adf3235ea5683db79ec2435d3997c626774e8c4ec4ef14022e24dfcf06') version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df') + 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-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) @@ -25,5 +29,6 @@ class RLeaflet(RPackage): depends_on('r-png', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-raster', type=('build', 'run')) - depends_on('r-scales', 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')) diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py index ae0e7f79095..b02ab2cfe4c 100644 --- a/var/spack/repos/builtin/packages/r-leaps/package.py +++ b/var/spack/repos/builtin/packages/r-leaps/package.py @@ -9,8 +9,8 @@ class RLeaps(RPackage): """leaps: Regression Subset Selection""" - homepage = "https://CRAN.R-project.org/package=leaps" - url = "https://cran.r-project.org/src/contrib/leaps_3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/leaps" + 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" version('3.0', '30823138890680e0493d1491c8f43edc') diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py index 5a152d06ef5..71644b853b3 100644 --- a/var/spack/repos/builtin/packages/r-learnbayes/package.py +++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py @@ -15,8 +15,9 @@ class RLearnbayes(RPackage): for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.""" - homepage = "https://CRAN.R-project.org/package=LearnBayes" - url = "https://cran.r-project.org/src/contrib/LearnBayes_2.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/LearnBayes" + 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" + version('2.15.1', sha256='9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532') version('2.15', '213713664707bc79fd6d3a109555ef76') diff --git a/var/spack/repos/builtin/packages/r-leiden/package.py b/var/spack/repos/builtin/packages/r-leiden/package.py new file mode 100644 index 00000000000..3079ce3ba6d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-leiden/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 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 RLeiden(RPackage): + """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: + Traag et al (2018) From Louvain + to Leiden: guaranteeing well-connected communities. + .""" + + 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" + + version('0.3.1', sha256='17fa1e49667fdd30ef5166506181c8514ae406f68f0878a026ee111bff11f8a5') + + depends_on('r-reticulate', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lhs/package.py b/var/spack/repos/builtin/packages/r-lhs/package.py index a0b5a7f4df2..da10bff6586 100644 --- a/var/spack/repos/builtin/packages/r-lhs/package.py +++ b/var/spack/repos/builtin/packages/r-lhs/package.py @@ -11,7 +11,13 @@ class RLhs(RPackage): Samples.""" homepage = "http://lhs.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/lhs_0.16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lhs" + url = "https://cloud.r-project.org/src/contrib/lhs_0.16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lhs" + version('1.0.1', sha256='a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53') + version('1.0', sha256='38c53482b360bdea89ddcfadf6d45476c80b99aee8902f97c5e97975903e2745') version('0.16', '088e593e5283414951e7e541a50ec2d1') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-libcoin/package.py b/var/spack/repos/builtin/packages/r-libcoin/package.py new file mode 100644 index 00000000000..69e70f4c8fa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-libcoin/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 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 RLibcoin(RPackage): + """Basic infrastructure for linear test statistics and permutation + inference in the framework of Strasser and Weber (1999) + . 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" + + version('1.0-4', sha256='91dcbaa0ab8c2109aa54c3eda29ad0acd67c870efcda208e27acce9d641c09c5') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-mvtnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-listenv/package.py b/var/spack/repos/builtin/packages/r-listenv/package.py new file mode 100644 index 00000000000..ef931f2612d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-listenv/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 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 RListenv(RPackage): + """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" + + version('0.7.0', sha256='6126020b111870baea08b36afa82777cd578e88c17db5435cd137f11b3964555') + + depends_on('r@3.1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index 0f6d6bbb0b9..64a021616cf 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -13,16 +13,21 @@ class RLme4(RPackage): numerical linear algebra and 'RcppEigen' "glue".""" homepage = "https://github.com/lme4/lme4/" - url = "https://cran.r-project.org/src/contrib/lme4_1.1-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lme4" + url = "https://cloud.r-project.org/src/contrib/lme4_1.1-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lme4" + version('1.1-21', sha256='7f5554b69ff8ce9bac21e8842131ea940fb7a7dfa2de03684f236d3e3114b20c') + version('1.1-20', sha256='44f45f5cd20ec6a50bf96a939b1db44b1a180dbc871a5e3042baf7a107016b2c') version('1.1-12', 'da8aaebb67477ecb5631851c46207804') - depends_on('r-matrix', type=('build', 'run')) + 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-matrix@1.2-1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) - depends_on('r-nlme', type=('build', 'run')) - depends_on('r-minqa', type=('build', 'run')) - depends_on('r-nloptr', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + 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-rcpp@0.10.5:', type=('build', 'run')) depends_on('r-rcppeigen', type=('build', 'run')) + depends_on('r-boot', when='@1.1-21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py index eebc165b3fe..ad59ed29c7e 100644 --- a/var/spack/repos/builtin/packages/r-lmtest/package.py +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -11,10 +11,13 @@ class RLmtest(RPackage): in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.""" - homepage = "https://cran.r-project.org/package=lmtest" - url = "https://cran.r-project.org/src/contrib/lmtest_0.9-34.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lmtest" + 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" + version('0.9-37', sha256='ddc929f94bf055974832fa4a20fdd0c1eb3a84ee11f716c287936f2141d5ca0a') + version('0.9-36', sha256='be9f168d6554e9cd2be0f9d8fc3244f055dce90d1fca00f05bcbd01daa4ed56b') version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-zoo', 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 141b25fbead..ce7536500f3 100644 --- a/var/spack/repos/builtin/packages/r-locfit/package.py +++ b/var/spack/repos/builtin/packages/r-locfit/package.py @@ -9,10 +9,11 @@ class RLocfit(RPackage): """Local regression, likelihood and density estimation.""" - homepage = "https://cran.rstudio.com/web/packages/locfit/index.html" - url = "https://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/locfit" + 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" version('1.5-9.1', '38af7791c9cda78e2804020e65ac7fb4') + depends_on('r@2.0.1:', type=('build', 'run')) 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 66ea6a38cdc..82d73f3bf8a 100644 --- a/var/spack/repos/builtin/packages/r-log4r/package.py +++ b/var/spack/repos/builtin/packages/r-log4r/package.py @@ -10,10 +10,9 @@ class RLog4r(RPackage): """logr4 provides an object-oriented logging system that uses an API roughly equivalent to log4j and its related variants.""" - homepage = "https://cran.r-project.org/package=log4r" - url = "https://cran.rstudio.com/src/contrib/log4r_0.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/log4r" + 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" + version('0.3.0', sha256='8e5d0221298410e48bee9d9a983a23e1834ce88592f9d931471bfdb05f37a691') version('0.2', 'f3fcb7b1f48526c6543b2e00e278ff65') - - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-loo/package.py b/var/spack/repos/builtin/packages/r-loo/package.py index 6135d41ade1..9a41eec8bc2 100644 --- a/var/spack/repos/builtin/packages/r-loo/package.py +++ b/var/spack/repos/builtin/packages/r-loo/package.py @@ -11,11 +11,12 @@ class RLoo(RPackage): BayesianModels""" homepage = "https://mc-stan.org/loo" - url = "https://cran.r-project.org/src/contrib/loo_2.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('2.1.0', sha256='1bf4a1ef85d151577ff96d4cf2a29c9ef24370b0b1eb08c70dcf45884350e87d') depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-checkmate', type=('build', 'run')) depends_on('r-matrixstats@0.52:', type=('build', 'run')) + depends_on('pandoc@1.12.3:') diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py index ef132bc6326..c118b4ebfc0 100644 --- a/var/spack/repos/builtin/packages/r-lpsolve/package.py +++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py @@ -14,8 +14,10 @@ class RLpsolve(RPackage): problems, and transportation problems. This version calls lp_solve""" - homepage = "https://cran.r-project.org/web/packages/lpSolve/index.html" - url = "https://cran.r-project.org/src/contrib/lpSolve_5.6.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lpSolve" + 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" + version('5.6.13.2', sha256='75f0c0af5cbdc219ac29c792342ecd625903632ad86e581c408879958aa88539') + version('5.6.13.1', sha256='6ad8dc430f72a4698fc4a615bb5ecb73690b3c4520e84d9094af51a528f720b8') version('5.6.13', '8471654d9ae76e0f85ff3449433d4bc1') diff --git a/var/spack/repos/builtin/packages/r-lsei/package.py b/var/spack/repos/builtin/packages/r-lsei/package.py index 59e23c1e0e0..e23f0e2033f 100644 --- a/var/spack/repos/builtin/packages/r-lsei/package.py +++ b/var/spack/repos/builtin/packages/r-lsei/package.py @@ -15,8 +15,8 @@ class RLsei(RPackage): is public domain and available at .""" - homepage = "https://cran.r-project.org/package=lsei" - url = "https://cran.rstudio.com/src/contrib/lsei_1.2-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lsei" + 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" version('1.2-0', '18a9322d7a79ecb86b8788645c4b7e3c') diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 34466be118b..675cdaf0987 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -14,12 +14,15 @@ class RLubridate(RPackage): a consistent and memorable syntax that makes working with dates easy and fun.""" - homepage = "https://cran.r-project.org/web/packages/lubridate/index.html" - url = "https://cran.r-project.org/src/contrib/lubridate_1.7.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lubridate" + homepage = "https://cloud.r-project.org/package=lubridate" + url = "https://cloud.r-project.org/src/contrib/lubridate_1.7.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lubridate" + version('1.7.4', sha256='510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891') + version('1.7.3', sha256='2cffbf54afce1d068e65241fb876a77b10ee907d5a19d2ffa84d5ba8a2c3f3df') version('1.7.1', '17dcb4c6a95189941bbdcffecf61b83b') version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') - depends_on('r-rcpp@0.11:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.13:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index d65fa443dc8..c4a04edc8d8 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -12,10 +12,13 @@ class RMagic(RPackage): functions for the manipulation and analysis of arbitrarily dimensioned arrays.""" - homepage = "https://cran.r-project.org/" - url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/magic" + 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" + version('1.5-9', sha256='fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a') + version('1.5-8', sha256='7f8bc26e05003168e9d2dadf64eb9a34b51bc41beba482208874803dee7d6c20') version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-abind', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-magick/package.py b/var/spack/repos/builtin/packages/r-magick/package.py new file mode 100644 index 00000000000..66ae0496151 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-magick/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2019 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 RMagick(RPackage): + """Bindings to 'ImageMagick': the most comprehensive open-source image + processing library available. Supports many common formats (png, jpeg, + tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, + etc). All operations are vectorized via the Magick++ STL meaning they + operate either on a single frame or a series of frames for working with + layers, collages, or animation. In RStudio images are automatically + previewed when printed to the console, resulting in an interactive editing + environment. The latest version of the package includes a native graphics + 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" + + version('2.1', sha256='ef4fb8fc1c5a9cfcc36b22485a0e17d622f61e55803b1e7423fd15f0550de7df') + + depends_on('r-rcpp@0.12.12:', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-curl', type=('build', 'run')) + depends_on('image-magick') diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py index 2020a11689c..5f9cda54b49 100644 --- a/var/spack/repos/builtin/packages/r-magrittr/package.py +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -13,8 +13,8 @@ class RMagrittr(RPackage): support for the type of right-hand side expressions. For more information, see package vignette.""" - homepage = "https://cran.r-project.org/web/packages/magrittr/index.html" - url = "https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/magrittr" + 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" version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a') diff --git a/var/spack/repos/builtin/packages/r-maldiquant/package.py b/var/spack/repos/builtin/packages/r-maldiquant/package.py index 5e2ea009c1f..6e596d92b13 100644 --- a/var/spack/repos/builtin/packages/r-maldiquant/package.py +++ b/var/spack/repos/builtin/packages/r-maldiquant/package.py @@ -17,11 +17,12 @@ class RMaldiquant(RPackage): replicated measurements as well as allowing spectra with different resolutions.""" - homepage = "https://cran.r-project.org/package=MALDIquant" - url = "https://cran.r-project.org/src/contrib/MALDIquant_1.16.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MALDIquant" + 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" + version('1.19.3', sha256='a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c') + version('1.19.2', sha256='8c6efc4ae4f1af4770b079db29743049f2fd597bcdefeaeb16f623be43ddeb87') version('1.16.4', '83200e7496d05c5a99292e45d2b11c67') - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py index fa589df09bd..0f04db37d98 100644 --- a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py +++ b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py @@ -13,8 +13,8 @@ class RManipulatewidget(RPackage): chart created with package 'htmlwidgets'.""" homepage = "https://github.com/rte-antares-rpackage/manipulateWidget" - url = "https://cran.r-project.org/src/contrib/manipulateWidget_0.10.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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/" version('0.10.0', sha256='3d61a3d0cedf5c8a850a3e62ed6af38c600dc3f25b44c4ff07a5093bf9ca4ffd') diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py index 65206ca7bca..a30907c0558 100644 --- a/var/spack/repos/builtin/packages/r-mapproj/package.py +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -9,10 +9,13 @@ class RMapproj(RPackage): """Converts latitude/longitude into projected coordinates.""" - homepage = "https://cran.r-project.org/package=mapproj" - url = "https://cran.r-project.org/src/contrib/mapproj_1.2-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mapproj" + 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" + version('1.2.6', sha256='62a5aa97837ae95ef9f973d95fe45fe43dbbf482dfa922e9df60f3c510e7efe5') + version('1.2-5', sha256='f3026a3a69a550c923b44c18b1ccc60d98e52670a438250d13f3c74cf2195f66') version('1.2-4', '10e22bde1c790e1540672f15ddcaee71') - depends_on('r-maps', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-maps@2.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py index 090fcfec374..4e98fbbff46 100644 --- a/var/spack/repos/builtin/packages/r-maps/package.py +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -10,8 +10,12 @@ class RMaps(RPackage): """Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').""" - homepage = "https://cran.r-project.org/" - url = "https://cran.r-project.org/src/contrib/maps_3.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('3.3.0', sha256='199afe19a4edcef966ae79ef802f5dcc15a022f9c357fcb8cae8925fe8bd2216') + version('3.2.0', sha256='437abeb4fa4ad4a36af6165d319634b89bfc6bf2b1827ca86c478d56d670e714') version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py index fd5e62a93ac..131a57bf887 100644 --- a/var/spack/repos/builtin/packages/r-maptools/package.py +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -14,11 +14,14 @@ class RMaptools(RPackage): maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.""" homepage = "http://r-forge.r-project.org/projects/maptools/" - url = "https://cran.r-project.org/src/contrib/maptools_0.8-39.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.9-5', sha256='5d9511f09fb49d57a51f28495b02239800596a4fcfad7b03ee1074d793657bdd') + version('0.9-4', sha256='930875f598a516f0f9049fa2fae7391bc9bdf7e3e5db696059ab4ec2fc9ba39c') version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836') - depends_on('r-sp', type=('build', 'run')) - depends_on('r-foreign', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-sp@1.0-11:', type=('build', 'run')) + depends_on('r-foreign@0.8:', type=('build', 'run')) depends_on('r-lattice', 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 9629da7627d..b90967ce5ab 100644 --- a/var/spack/repos/builtin/packages/r-markdown/package.py +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -13,11 +13,16 @@ class RMarkdown(RPackage): http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.""" - homepage = "https://cran.r-project.org/package=markdown" - url = "https://cran.r-project.org/src/contrib/markdown_0.7.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.1', sha256='8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b') + version('1.0', sha256='172d8072d1829644ee6cdf54282a55718e2cfe9c9915d3589ca5f9a016f8d9a6') + version('0.9', sha256='3068c6a41ca7a76cbedeb93b7371798f4d8437eea69a23c0ed5204c716d1bf23') version('0.8', '5dde829a865ad65bab37a2b9d243b071') version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff') - depends_on('r-mime', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index a5dd34ec2d9..35356a63752 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -10,9 +10,13 @@ class RMass(RPackage): """Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).""" - homepage = "https://cran.r-project.org/web/packages/MASS/index.html" - url = "https://cran.r-project.org/src/contrib/MASS_7.3-47.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MASS" + 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" + version('7.3-51.4', sha256='9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74') + version('7.3-51.3', sha256='5b0e0e7704d43a94b08dcc4b3fe600b9723d1b3e446dd393e82d39ddf66608b6') version('7.3-47', '2ef69aa9e25c0a445661a9877e117594') version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py index 5277fdb7c48..47e2f782a62 100644 --- a/var/spack/repos/builtin/packages/r-matr/package.py +++ b/var/spack/repos/builtin/packages/r-matr/package.py @@ -15,11 +15,12 @@ class RMatr(RPackage): environment for statistical computing.""" homepage = "https://github.com/MG-RAST/matR" - url = "https://cran.r-project.org/src/contrib/matR_0.9.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/matR/matR_0.9.tar.gz" + 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" version('0.9.1', sha256='554aeff37b27d0f17ddeb62b2e1004aa1f29190300e4946b1bec1d7c2bde82e3') version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mgraster', type=('build', 'run')) depends_on('r-biom-utils', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index c39e209d0fe..c624e1c89e2 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -11,13 +11,16 @@ class RMatrix(RPackage): using 'LAPACK' and 'SuiteSparse'.""" homepage = "http://matrix.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/Matrix_1.2-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix" + url = "https://cloud.r-project.org/src/contrib/Matrix_1.2-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Matrix" + version('1.2-17', sha256='db43e6f0196fd5dfd05a7e88cac193877352c60d771d4ec8772763e645723fcc') version('1.2-14', 'b2babcf1515625196b75592c9b345bba') version('1.2-12', '0ade6e374716f08650cc8b8da99a313c') version('1.2-11', 'b7d2a639aa52228dfde7c3c3ee68b38e') version('1.2-8', '4a6406666bf97d3ec6b698eea5d9c0f5') version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') + depends_on('r@3.0.1:', when='@:1.2-12', type=('build', 'run')) + depends_on('r@3.2.0:', when='@1.2.13:', type=('build', 'run')) 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 de276c8c909..ced334ea4f3 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -11,9 +11,10 @@ class RMatrixmodels(RPackage): prediction and response module classes.""" homepage = "http://matrix.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MatrixModels" + 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" version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r-matrix@1.1-5:', 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 5d098bbc488..5918f8b8a5e 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -14,8 +14,11 @@ class RMatrixstats(RPackage): vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().""" - homepage = "https://cran.rstudio.com/web/packages/matrixStats/index.html" - url = "https://cran.rstudio.com/src/contrib/matrixStats_0.52.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/matrixStats" + homepage = "https://cloud.r-project.org/package=matrixStats" + url = "https://cloud.r-project.org/src/contrib/matrixStats_0.52.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/matrixStats" + version('0.54.0', sha256='8f0db4e181300a208b9aedbebfdf522a2626e6675d2662656efb8ba71b05a06f') version('0.52.2', '41b987d3ae96ee6895875c413adcba3c') + + depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py index 4b748d22d11..aca88d788f0 100644 --- a/var/spack/repos/builtin/packages/r-mclust/package.py +++ b/var/spack/repos/builtin/packages/r-mclust/package.py @@ -11,9 +11,11 @@ class RMclust(RPackage): Classification, and Density Estimation""" homepage = "http://www.stat.washington.edu/mclust" - url = "https://cran.r-project.org/src/contrib/mclust_5.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('5.4.5', sha256='75f2963082669485953e4306ffa93db98335ee6afdc1318b95d605d56cb30a72') + version('5.4.4', sha256='ccc31b0ad445e121a447b04988e73232a085c506fcc7ebdf11a3e0754aae3e0d') version('5.3', '74aac9fccdfc78373ce733c1a09176ef') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py index 79a93688eb4..4c952a3271c 100644 --- a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py +++ b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py @@ -9,10 +9,12 @@ class RMcmcglmm(RPackage): """MCMC Generalised Linear Mixed Models.""" - homepage = "https://cran.r-project.org/web/packages/MCMCglmm/index.html" - url = "https://cran.r-project.org/src/contrib/MCMCglmm_2.25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MCMCglmm" + 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" + version('2.29', sha256='13ba7837ea2049e892c04e7ec5c83d5b599a7e4820b9d875f55ec40fc2cc67b4') + version('2.28', sha256='7d92e6d35638e5e060a590b92c3b1bfc02a11386276a8ab99bceec5d797bfc2a') version('2.25', '260527ef6fecdd87f762fd07406d674a') depends_on('r-matrix', 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 4769f3a8792..a6cee70aa36 100644 --- a/var/spack/repos/builtin/packages/r-mco/package.py +++ b/var/spack/repos/builtin/packages/r-mco/package.py @@ -11,8 +11,10 @@ class RMco(RPackage): and related test problems""" homepage = "https://github.com/cran/mco" - url = "https://cran.r-project.org/src/contrib/mco_1.0-15.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.0-15.1', '1768dea61d0561d71be2bbc6ac3dccfa') version('1.0-15', '0b444e085c59d919611224e86b5637f8') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mda/package.py b/var/spack/repos/builtin/packages/r-mda/package.py index fcdda3baa2e..2568f2fc5bf 100644 --- a/var/spack/repos/builtin/packages/r-mda/package.py +++ b/var/spack/repos/builtin/packages/r-mda/package.py @@ -10,12 +10,12 @@ class RMda(RPackage): """Mixture and flexible discriminant analysis, multivariate adaptive regression splines (MARS), BRUTO.""" - homepage = "https://cran.r-project.org/package=mda" - url = "https://cran.r-project.org/src/contrib/mda_0.4-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mda" + 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" + version('0.4-10', sha256='7036bc622a8fea5b2de94fc19e6b64f5f0c27e5d743ae7646e116af08c9de6a5') version('0.4-9', '2ce1446c4a013e0ebcc1099a00269ad9') - depends_on('r@1.9.0:') - + depends_on('r@1.9.0:', type=('build', 'run')) 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 ec039cc08f6..627b4e16095 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -11,9 +11,9 @@ class RMemoise(RPackage): same arguments it returns the pre-computed value.""" homepage = "https://github.com/hadley/memoise" - url = "https://cran.rstudio.com/src/contrib/memoise_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.1.0', '493209ee04673f0fcab473c3dd80fb8c') version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac') - depends_on('r-digest', type=('build', 'run')) + depends_on('r-digest@0.6.3:', 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 new file mode 100644 index 00000000000..2b9ee109a61 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-metap/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 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 RMetap(RPackage): + """The canonical way to perform meta-analysis involves using effect sizes. + When they are not available this package provides a number of methods for + meta-analysis of significance values including the methods of Edgington, + Fisher, Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets + 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" + + version('1.1', sha256='20120428672d39dc15829c7e66850fc4350a34df290d48cef0b1cc78d13f7b82') + + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-rdpack', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index 5938192ddb4..c4e2d98b7a6 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -12,10 +12,12 @@ class RMgcv(RPackage): function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.""" - homepage = "https://cran.r-project.org/package=mgcv" - url = "https://cran.r-project.org/src/contrib/mgcv_1.8-16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv" + homepage = "https://cloud.r-project.org/package=mgcv" + url = "https://cloud.r-project.org/src/contrib/mgcv_1.8-16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mgcv" + version('1.8-28', sha256='b55ea8227cd5c263c266c3885fa3299aa6bd23b54186517f9299bf38a7bdd3ea') + version('1.8-27', sha256='c88b99fb518decd7e9cd17a4c267e74f98a78172f056784194b5b127ca0f7d1b') version('1.8-22', 'b42079b33b46de784f293a74c824b877') version('1.8-21', 'aae8262a07c8698ca8d6213065c4983f') version('1.8-20', '58eb94404aad7ff8a0cf11a2f098f8bf') @@ -25,5 +27,6 @@ class RMgcv(RPackage): version('1.8-16', '4c1d85e0f80b017bccb4b63395842911') version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') - depends_on('r-nlme', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + 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 25eba17c7d2..9aa0023095c 100644 --- a/var/spack/repos/builtin/packages/r-mgraster/package.py +++ b/var/spack/repos/builtin/packages/r-mgraster/package.py @@ -12,7 +12,8 @@ class RMgraster(RPackage): (DOE) Systems Biology Knowledge Base (KBase).""" homepage = "https://github.com/braithwaite/MGRASTer/" - url = "https://cran.r-project.org/src/contrib/MGRASTer_0.9.tar.gz" + url = "https://cloud.r-project.org/src/contrib/MGRASTer_0.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/MGRASTer" version('0.9', '902c7ad4180b858d6b6428ea26d7652a') diff --git a/var/spack/repos/builtin/packages/r-mice/package.py b/var/spack/repos/builtin/packages/r-mice/package.py index c785631bc15..daaefe5a9c5 100644 --- a/var/spack/repos/builtin/packages/r-mice/package.py +++ b/var/spack/repos/builtin/packages/r-mice/package.py @@ -20,12 +20,15 @@ class RMice(RPackage): variables. Various diagnostic plots are available to inspect the quality of the imputations.""" - homepage = "https://cran.r-project.org/package=mice" - url = "https://cran.r-project.org/src/contrib/mice_3.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mice" + 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" + version('3.6.0', sha256='7bc72bdb631bc9f67d8f76ffb48a7bb275228d861075e20c24c09c736bebec5d') + version('3.5.0', sha256='4fccecdf9e8d8f9f63558597bfbbf054a873b2d0b0820ceefa7b6911066b9e45') version('3.0.0', 'fb54a29679536c474c756cca4538d7e3') + 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-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index 41b42a18f7b..8c99d8d720f 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -11,8 +11,10 @@ class RMime(RPackage): from /etc/mime.types in UNIX-type systems.""" homepage = "https://github.com/yihui/mime" - url = "https://cran.r-project.org/src/contrib/mime_0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mime" + url = "https://cloud.r-project.org/src/contrib/mime_0.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mime" + version('0.7', sha256='11083ee44c92569aadbb9baf60a2e079ab7a721c849b74d102694975cc8d778b') + version('0.6', sha256='4775b605ab0117406bee7953c8af59eea8b35e67d1bd63f4007686a7097fc401') version('0.5', '87e00b6d57b581465c19ae869a723c4d') version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') diff --git a/var/spack/repos/builtin/packages/r-miniui/package.py b/var/spack/repos/builtin/packages/r-miniui/package.py index 1dc54ed86c8..5b7de8ba859 100644 --- a/var/spack/repos/builtin/packages/r-miniui/package.py +++ b/var/spack/repos/builtin/packages/r-miniui/package.py @@ -10,11 +10,11 @@ class RMiniui(RPackage): """Provides UI widget and layout functions for writing Shiny apps that work well on small screens.""" - homepage = "https://cran.r-project.org/package=miniUI" - url = "https://cran.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/miniUI/" + 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/" version('0.1.1.1', sha256='452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0') depends_on('r-shiny@0.13:', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py index bb54a7252ad..f579dbdf574 100644 --- a/var/spack/repos/builtin/packages/r-minqa/package.py +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -11,9 +11,10 @@ class RMinqa(RPackage): interface to Fortran implementations by M. J. D. Powell.""" homepage = "http://optimizer.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/minqa_1.2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/minqa" + 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" version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.9.10:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-misc3d/package.py b/var/spack/repos/builtin/packages/r-misc3d/package.py index e215a4fcb27..a4043961aee 100644 --- a/var/spack/repos/builtin/packages/r-misc3d/package.py +++ b/var/spack/repos/builtin/packages/r-misc3d/package.py @@ -9,8 +9,8 @@ class RMisc3d(RPackage): """A collection of miscellaneous 3d plots, including isosurfaces.""" - homepage = "https://cran.r-project.org/web/packages/misc3d/index.html" - url = "https://cran.r-project.org/src/contrib/misc3d_0.8-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/misc3d" + 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" version('0.8-4', 'aefa27e67a243c21a1046868540343fe') diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py index 88e6784c4da..4980a9e157b 100644 --- a/var/spack/repos/builtin/packages/r-mitml/package.py +++ b/var/spack/repos/builtin/packages/r-mitml/package.py @@ -12,9 +12,12 @@ class RMitml(RPackage): 'jomo', and several functions for visualization, data management and the analysis of multiply imputed data sets.""" - homepage = "https://cran.r-project.org/package=mitml" - url = "https://cran.r-project.org/src/contrib/mitml_0.3-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mitml" + 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" + + version('0.3-7', sha256='c6f796d0059f1b093b599a89d955982fa257de9c45763ecc2cbbce10fdec1e7b') + version('0.3-6', sha256='bc59bdc802eb882340393752535446560c716f12c6fca2b95f03c6af30d978de') version('0.3-5', '6f8659c33696915bf510241287b2a34d') depends_on('r-pan', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mitools/package.py b/var/spack/repos/builtin/packages/r-mitools/package.py new file mode 100644 index 00000000000..45a9f80c6e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mitools/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 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 RMitools(RPackage): + """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" + + version('2.4', sha256='f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30') + + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mixtools/package.py b/var/spack/repos/builtin/packages/r-mixtools/package.py index 5b2f9d912e7..f8180067545 100644 --- a/var/spack/repos/builtin/packages/r-mixtools/package.py +++ b/var/spack/repos/builtin/packages/r-mixtools/package.py @@ -12,14 +12,14 @@ class RMixtools(RPackage): Analyzes finite mixture models for various parametric and semiparametric settings.""" - homepage = "https://cran.r-project.org/web/packages/mixtools/index.html" - url = "https://cran.r-project.org/src/contrib/mixtools_1.1.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/mixtools" + 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" version('1.1.0', 'c7d59110dd42964d40593a05b98acd5f') version('1.0.4', 'c0e6ec44d16ec8914797fb74a651d3e5') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.2:', type=('build', 'run')) 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 c0bebc06724..f861d6a5476 100644 --- a/var/spack/repos/builtin/packages/r-mlbench/package.py +++ b/var/spack/repos/builtin/packages/r-mlbench/package.py @@ -10,12 +10,10 @@ class RMlbench(RPackage): """A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.""" - homepage = "https://cran.r-project.org/web/packages/mlbench/index.html" - url = "https://cran.r-project.org/src/contrib/mlbench_2.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mlbench" + 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" version('2.1-1', '9f06848b8e137b8a37417c92d8e57f3b') - depends_on('r@2.10:') - - depends_on('r-lattice', type=('build', 'run')) + 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 6994ace5d0c..34a8f8f1fdb 100644 --- a/var/spack/repos/builtin/packages/r-mlr/package.py +++ b/var/spack/repos/builtin/packages/r-mlr/package.py @@ -19,12 +19,16 @@ class RMlr(RPackage): resampling. Most operations can be parallelized.""" homepage = "https://github.com/mlr-org/mlr/" - url = "https://cran.r-project.org/src/contrib/mlr_2.12.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.15.0', sha256='a3c2c2bd65a87d90b5e5e877b1ef8e7712e76b4eb1660d3f69672a1860ca5324') + version('2.14.0', sha256='1f72184400678386c7c44297c4c92a448b50148de700df5ba0438d4e486e944a') + version('2.13', sha256='e8729be7acddc1ea124c44f9493a8b903c5f54b97e09c714366553aed733011d') version('2.12.1', 'abddfc9dfe95f290a233ecd97969a4ec') version('2.12', '94ee7495aeafb432c8af5a8bdd26c25f') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-paramhelpers@1.10:', type=('build', 'run')) depends_on('r-bbmisc@1.11:', type=('build', 'run')) depends_on('r-backports@1.1.0:', type=('build', 'run')) @@ -33,4 +37,5 @@ class RMlr(RPackage): depends_on('r-checkmate@1.8.2:', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-parallelmap@1.3:', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) depends_on('r-xml', 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 fcde2d6d8b7..3caeec50dcb 100644 --- a/var/spack/repos/builtin/packages/r-mlrmbo/package.py +++ b/var/spack/repos/builtin/packages/r-mlrmbo/package.py @@ -22,9 +22,10 @@ class RMlrmbo(RPackage): use cases.""" homepage = "https://github.com/mlr-org/mlrMBO/" - url = "https://cran.r-project.org/src/contrib/mlrMBO_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.1.2', sha256='8e84caaa5d5d443d7019128f88ebb212fb095870b3a128697c9b64fe988f3efe') version('1.1.1', '9a35b41ceb8754111af294dee0ae76e0') version('1.1.0', '9e27ff8498225d24863b8da758d2918e') diff --git a/var/spack/repos/builtin/packages/r-mmwrweek/package.py b/var/spack/repos/builtin/packages/r-mmwrweek/package.py index 83799560ae8..cb36d6e6fb6 100644 --- a/var/spack/repos/builtin/packages/r-mmwrweek/package.py +++ b/var/spack/repos/builtin/packages/r-mmwrweek/package.py @@ -14,8 +14,8 @@ class RMmwrweek(RPackage): functionality to convert Dates to MMWR day, week, and year and the reverse.""" - homepage = "https://cran.r-project.org/package=MMWRweek" - url = "https://cran.r-project.org/src/contrib/MMWRweek_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MMWRweek" + 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" version('0.1.1', 'a1245025126f8a96c72be8f7b06b0499') diff --git a/var/spack/repos/builtin/packages/r-mnormt/package.py b/var/spack/repos/builtin/packages/r-mnormt/package.py index cdea6845c32..e322a43d12a 100644 --- a/var/spack/repos/builtin/packages/r-mnormt/package.py +++ b/var/spack/repos/builtin/packages/r-mnormt/package.py @@ -15,7 +15,9 @@ class RMnormt(RPackage): of dimensions.""" homepage = "http://azzalini.stat.unipd.it/SW/Pkg-mnormt" - url = "https://cran.r-project.org/src/contrib/mnormt_1.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.5-5', '19b5be2e9ed33b92d7a716bfcca6b2c7') + + depends_on('r@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modelmetrics/package.py b/var/spack/repos/builtin/packages/r-modelmetrics/package.py index 106e90e330d..47e925e4da2 100644 --- a/var/spack/repos/builtin/packages/r-modelmetrics/package.py +++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py @@ -10,12 +10,14 @@ class RModelmetrics(RPackage): """Collection of metrics for evaluating models written in C++ using 'Rcpp'.""" - homepage = "https://cran.r-project.org/package=ModelMetrics" - url = "https://cran.r-project.org/src/contrib/ModelMetrics_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ModelMetrics" + 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" + version('1.2.2', sha256='66d6fc75658287fdbae4d437b51d26781e138b8baa558345fb9e5a2df86a0d95') + version('1.2.0', sha256='3021ae88733695a35d66e279e8e61861431f14c9916a341f0a562f675cf6ede9') version('1.1.0', 'd43175001f0531b8810d2802d76b7b44') - depends_on('r@3.2.2:') - + 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')) diff --git a/var/spack/repos/builtin/packages/r-modelr/package.py b/var/spack/repos/builtin/packages/r-modelr/package.py index f693fd7b2eb..b65d8ec3232 100644 --- a/var/spack/repos/builtin/packages/r-modelr/package.py +++ b/var/spack/repos/builtin/packages/r-modelr/package.py @@ -11,15 +11,21 @@ class RModelr(RPackage): into a pipeline of data manipulation and visualisation.""" homepage = "https://github.com/hadley/modelr" - url = "https://cran.r-project.org/src/contrib/modelr_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.1.5', sha256='45bbee387c6ba154f9f8642e9f03ea333cce0863c324ff15d23096f33f85ce5a') + version('0.1.4', sha256='b4da77c1244bbda512ce323751c8338741eeaa195283f172a0feec2917bcfdd9') + version('0.1.3', sha256='e536b247c17d6cacf10565dd8a1b744efc90a8815c70edd54371e413e6d1b423') version('0.1.1', 'ce5fd088fb7850228ab1e34d241a975d') + 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-magrittr', type=('build', 'run')) - depends_on('r-purrr', type=('build', 'run')) - depends_on('r-lazyeval', type=('build', 'run')) + depends_on('r-purrr@0.2.2:', type=('build', 'run')) + depends_on('r-lazyeval@0.2.0:', when='@:0.1.1', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-broom', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-tidyr', type=('build', 'run')) + depends_on('r-tidyr@0.8.0:', type=('build', 'run')) + depends_on('r-rlang@0.2.0:', when='@0.1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modeltools/package.py b/var/spack/repos/builtin/packages/r-modeltools/package.py index bbcfc99671f..16f2c631162 100644 --- a/var/spack/repos/builtin/packages/r-modeltools/package.py +++ b/var/spack/repos/builtin/packages/r-modeltools/package.py @@ -9,8 +9,9 @@ class RModeltools(RPackage): """A collection of tools to deal with statistical models.""" - homepage = "https://cran.r-project.org/package=modeltools" - url = "https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/modeltools" + 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" + version('0.2-22', sha256='256a088fc80b0d9182f984f9bd3d6207fb7c1e743f72e2ecb480e6c1d4ac34e9') version('0.2-21', '3bf56b2e7bf78981444385d87eeccdd7') diff --git a/var/spack/repos/builtin/packages/r-mpm/package.py b/var/spack/repos/builtin/packages/r-mpm/package.py index ce0b0d0e356..ef159313d9e 100644 --- a/var/spack/repos/builtin/packages/r-mpm/package.py +++ b/var/spack/repos/builtin/packages/r-mpm/package.py @@ -8,12 +8,15 @@ 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.""" + gene expression data with different projection methods: principal + component analysis, correspondence analysis, spectral map analysis.""" + + 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" - homepage = "https://cran.rstudio.com/web/packages/mpm/index.html" - url = "https://cran.rstudio.com/src/contrib/mpm_1.0-22.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mpm" version('1.0-22', '91885c421cafd89ce8893ccf827165a2') + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) depends_on('r-kernsmooth', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index 656b55a54d7..db2bf153129 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -14,12 +14,14 @@ class RMultcomp(RPackage): (Bretz, Hothorn, Westfall, 2010, CRC Press).""" homepage = "http://multcomp.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/multcomp_1.4-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/multcomp" + 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" + version('1.4-10', sha256='29bcc635c0262e304551b139cd9ee655ab25a908d9693e1cacabfc2a936df5cf') + version('1.4-8', sha256='a20876619312310e9523d67e9090af501383ce49dc6113c6b4ca30f9c943a73a') version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') - depends_on('r-mvtnorm@1.0-3:', type=('build', 'run')) + depends_on('r-mvtnorm@1.0-10:', type=('build', 'run')) depends_on('r-survival@2.39-4:', type=('build', 'run')) depends_on('r-th-data@1.0-2:', type=('build', 'run')) depends_on('r-sandwich@2.3-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multicool/package.py b/var/spack/repos/builtin/packages/r-multicool/package.py index 5d9548da2b2..c4e322f678a 100644 --- a/var/spack/repos/builtin/packages/r-multicool/package.py +++ b/var/spack/repos/builtin/packages/r-multicool/package.py @@ -9,8 +9,9 @@ class RMulticool(RPackage): """Permutations of multisets in cool-lex order.""" - homepage = "https://cran.r-project.org/package=multicool" - url = "https://cran.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz" + 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" 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 172c24dce52..8e31a39c398 100644 --- a/var/spack/repos/builtin/packages/r-multitaper/package.py +++ b/var/spack/repos/builtin/packages/r-multitaper/package.py @@ -10,9 +10,9 @@ class RMultitaper(RPackage): """multitaper: Spectral Analysis Tools using the Multitaper Method""" homepage = "https://github.com/krahim/multitaper/" - url = "https://cran.r-project.org/src/contrib/multitaper_1.0-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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/" version('1.0-14', sha256='c84c122541dc2874131446e23b212259b3b00590d701efee49e6740fd74a8d13') - depends_on('r@3.0:', type='build') + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index 20ba74f6f10..8a0678d5d43 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -13,10 +13,11 @@ class RMunsell(RPackage): utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.""" - homepage = "https://cran.r-project.org/web/packages/munsell/index.html" - url = "https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/munsell" + 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" + version('0.5.0', sha256='d0f3a9fb30e2b5d411fa61db56d4be5733a2621c0edf017d090bdfa5e377e199') version('0.4.3', 'ebd205323dc37c948f499ee08be9c476') depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index db6ef6d65a5..bd7b6eab461 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -11,8 +11,13 @@ class RMvtnorm(RPackage): deviates and densities.""" homepage = "http://mvtnorm.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm" + url = "https://cloud.r-project.org/src/contrib/mvtnorm_1.0-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mvtnorm" + version('1.0-11', sha256='0321612de99aa9bc75a45c7e029d3372736014223cbdefb80d8cae600cbc7252') + version('1.0-10', sha256='31df19cd8b4cab9d9a70dba00442b7684e625d4ca143a2c023c2c5872b07ad12') version('1.0-6', 'cb69426868fd3e330412b8491901d9d4') version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-nanotime/package.py b/var/spack/repos/builtin/packages/r-nanotime/package.py index 40eb209c4d0..8d0b6c7cc0c 100644 --- a/var/spack/repos/builtin/packages/r-nanotime/package.py +++ b/var/spack/repos/builtin/packages/r-nanotime/package.py @@ -11,12 +11,14 @@ class RNanotime(RPackage): nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type.""" - homepage = "https://cran.r-project.org/package=nanotime" - url = "https://cran.r-project.org/src/contrib/nanotime_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nanotime" + homepage = "https://cloud.r-project.org/package=nanotime" + url = "https://cloud.r-project.org/src/contrib/nanotime_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nanotime" + version('0.2.4', sha256='2dfb7e7435fec59634b87563a215467e7793e2711e302749c0533901c74eb184') + version('0.2.3', sha256='7d6df69a4223ae154f610b650e24ece38ce4aa706edfa38bec27d15473229f5d') version('0.2.0', '796b1f7d0bb43e2f3d98e3cc6f4b0657') depends_on('r-bit64', type=('build', 'run')) - depends_on('r-rcppcctz', type=('build', 'run')) + depends_on('r-rcppcctz@0.2.3:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py index ad8c2b79cf4..f01a2035dd4 100644 --- a/var/spack/repos/builtin/packages/r-ncbit/package.py +++ b/var/spack/repos/builtin/packages/r-ncbit/package.py @@ -10,8 +10,10 @@ class RNcbit(RPackage): """Making NCBI taxonomic data locally available and searchable as an R object.""" - homepage = "https://cran.r-project.org/package=ncbit" - url = "https://cran.r-project.org/src/contrib/ncbit_2013.03.29.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ncbit" + 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" version('2013.03.29', '29582d7e5c8bbf9683c57c4f6ac3e891') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index 21ce037fba2..a040454530b 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -23,9 +23,11 @@ class RNcdf4(RPackage): package does not provide an interface for netcdf version 4 files.""" homepage = "http://cirrus.ucsd.edu/~pierce/ncdf" - url = "https://cran.r-project.org/src/contrib/ncdf4_1.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ncdf4" + url = "https://cloud.r-project.org/src/contrib/ncdf4_1.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ncdf4" + version('1.16.1', sha256='0dde2d6d1e8474f4abd15a61af8a2f7de564f13da00f1a01d7a479ab88587a20') + version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253') version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a') - depends_on('netcdf') + depends_on('netcdf@4.1:') diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py index ef59109a023..03f728256fe 100644 --- a/var/spack/repos/builtin/packages/r-network/package.py +++ b/var/spack/repos/builtin/packages/r-network/package.py @@ -12,7 +12,13 @@ class RNetwork(RPackage): arbitrary vertex/edge/graph attributes.""" homepage = "https://statnet.org" - url = "https://cran.r-project.org/src/contrib/network_1.13.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/network" + url = "https://cloud.r-project.org/src/contrib/network_1.13.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/network" + version('1.15', sha256='5cbe5c0369e5f8363e33a86f14fd33ce8727166106381627ecd13b7452e14cb3') + version('1.14-377', sha256='013c02f8d97f1f87f2c421760534df9353d2a8c2277f20b46b59fb79822d3e46') version('1.13.0', 'd0b967d6f1aad43b6479d72f29b705de') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py index 4db5c88274d..976f313fcdc 100644 --- a/var/spack/repos/builtin/packages/r-networkd3/package.py +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -10,12 +10,15 @@ class RNetworkd3(RPackage): """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.""" - homepage = "http://cran.r-project.org/package=networkD3" - url = "https://cran.r-project.org/src/contrib/networkD3_0.2.12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/networkD3" + 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" + version('0.4', sha256='33b82585f1eec6233303ec14033a703d0b17def441c7a0a67bf7e6764c9c9d0b') + version('0.3', sha256='6f9d6b35bb1562883df734bef8fbec166dd365e34c6e656da7be5f8a8d42343c') version('0.2.12', '356fe4be59698e6fb052644bd9659d84') - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-htmlwidgets@0.3.2:', 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-nleqslv/package.py b/var/spack/repos/builtin/packages/r-nleqslv/package.py index 97d29e4bfcf..75dda5930df 100644 --- a/var/spack/repos/builtin/packages/r-nleqslv/package.py +++ b/var/spack/repos/builtin/packages/r-nleqslv/package.py @@ -9,8 +9,8 @@ class RNleqslv(RPackage): """nleqslv: Solve Systems of Nonlinear Equations""" - homepage = "https://cran.r-project.org/package=nleqslv" - url = "https://cran.r-project.org/src/contrib/nleqslv_3.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nleqslv" + 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" 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 1356f73967a..bd13d96c202 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -9,12 +9,18 @@ class RNlme(RPackage): """Fit and compare Gaussian linear and nonlinear mixed-effects models.""" - homepage = "https://cran.r-project.org/package=nlme" - url = "https://cran.r-project.org/src/contrib/nlme_3.1-130.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nlme" + homepage = "https://cloud.r-project.org/package=nlme" + url = "https://cloud.r-project.org/src/contrib/nlme_3.1-130.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nlme" + version('3.1-141', sha256='910046260a03d8f776ac7b0766b5adee91556829d0d8a70165b2c695ce038056') + version('3.1-139', sha256='0460fc69d85122177e7ef01bad665d56bcaf63d31bdbfdbdfdcba2c082085739') version('3.1-131', '0f1215ec4d4e3bca939282d122f4d1fa') version('3.1-130', '1935d6e308a8018ed8e45d25c8731288') version('3.1-128', '3d75ae7380bf123761b95a073eb55008') + 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-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 13a8469e0e9..f6f7502524e 100644 --- a/var/spack/repos/builtin/packages/r-nloptr/package.py +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -16,13 +16,13 @@ class RNloptr(RPackage): During installation on Unix the NLopt code is downloaded and compiled from the NLopt website.""" - homepage = "https://cran.r-project.org/package=nloptr" - url = "https://cran.rstudio.com/src/contrib/nloptr_1.0.4.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/nloptr" + homepage = "https://cloud.r-project.org/package=nloptr" + url = "https://cloud.r-project.org/src/contrib/nloptr_1.0.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nloptr" + version('1.2.1', sha256='1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97') version('1.0.4', 'f2775dfb4f7f5552d46937a04c062b0d') - depends_on('r-testthat', type=('build', 'run')) depends_on('nlopt') def configure_args(self): diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index 854aafd636f..91c356d794f 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -15,16 +15,18 @@ class RNmf(RPackage): computations on multicore machines..""" homepage = "http://renozao.github.io/NMF" - url = "https://cran.r-project.org/src/contrib/NMF_0.20.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/NMF" + url = "https://cloud.r-project.org/src/contrib/NMF_0.20.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" + version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') version('0.20.6', '81df07b3bf710a611db5af24730ff3d0') - depends_on('r-pkgmaker', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-pkgmaker@0.20:', type=('build', 'run')) depends_on('r-registry', type=('build', 'run')) - depends_on('r-rngtools', type=('build', 'run')) + depends_on('r-rngtools@1.2.3:', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) - depends_on('r-stringr', type=('build', 'run')) + depends_on('r-stringr@1.0.0:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-gridbase', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nmof/package.py b/var/spack/repos/builtin/packages/r-nmof/package.py new file mode 100644 index 00000000000..ccd3061f122 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nmof/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 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 RNmof(RPackage): + """Functions, examples and data from the book "Numerical Methods and + Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2011), + ISBN 978-0123756626. The package provides implementations of several + optimisation heuristics, such as Differential Evolution, Genetic Algorithms + and Threshold Accepting. There are also functions for the valuation of + 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" + + version('1.6-0', sha256='5484cd43c28aaf23d560c2dde8bcd8dd440a205d2214eb50e02fe0bb42ec2755') + + depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py index 5f5c8cc759c..dada76423e1 100644 --- a/var/spack/repos/builtin/packages/r-nnet/package.py +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -11,7 +11,9 @@ class RNnet(RPackage): and for multinomial log-linear models.""" homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" - url = "https://cran.r-project.org/src/contrib/nnet_7.3-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nnet" + url = "https://cloud.r-project.org/src/contrib/nnet_7.3-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nnet" version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e') + + depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nnls/package.py b/var/spack/repos/builtin/packages/r-nnls/package.py index 548dc480c92..815f35b925f 100644 --- a/var/spack/repos/builtin/packages/r-nnls/package.py +++ b/var/spack/repos/builtin/packages/r-nnls/package.py @@ -11,8 +11,8 @@ class RNnls(RPackage): algorithm for non-negative least squares (NNLS). Also allows the combination of non-negative and non-positive constraints.""" - homepage = "https://cran.r-project.org/package=nnls" - url = "https://cran.rstudio.com/src/contrib/nnls_1.4.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/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" version('1.4', 'cdb3640120f73e0ccb6079108e0ef361') diff --git a/var/spack/repos/builtin/packages/r-nor1mix/package.py b/var/spack/repos/builtin/packages/r-nor1mix/package.py index 14543b4571f..050252b7e39 100644 --- a/var/spack/repos/builtin/packages/r-nor1mix/package.py +++ b/var/spack/repos/builtin/packages/r-nor1mix/package.py @@ -13,8 +13,9 @@ class RNor1mix(RPackage): generation and graphics; now fitting to data by ML (Maximum Likelihood) or EM estimation.""" - homepage = "https://CRAN.R-project.org/package=nor1mix" - url = "https://cran.rstudio.com/src/contrib/nor1mix_1.2-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nor1mix" + 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" + version('1.3-0', sha256='9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0') version('1.2-3', '60eb5cc1ea6b366f53042087a080b105') diff --git a/var/spack/repos/builtin/packages/r-nortest/package.py b/var/spack/repos/builtin/packages/r-nortest/package.py index 5407eb97219..c93b8b79bbc 100644 --- a/var/spack/repos/builtin/packages/r-nortest/package.py +++ b/var/spack/repos/builtin/packages/r-nortest/package.py @@ -11,8 +11,8 @@ class RNortest(RPackage): Five omnibus tests for testing the composite hypothesis of normality.""" - homepage = "https://cran.r-project.org/package=nortest" - url = "https://cran.r-project.org/src/contrib/nortest_1.0-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nortest" + 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" 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 f076e4d8085..0a7e9835355 100644 --- a/var/spack/repos/builtin/packages/r-np/package.py +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -16,10 +16,14 @@ class RNp(RPackage): Research Computing Network (SHARCNET:www.sharcnet.ca).""" homepage = "https://github.com/JeffreyRacine/R-Package-np/" - url = "https://cran.r-project.org/src/contrib/np_0.60-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.60-9', sha256='fe31a8985f0b1a576a7775022b7131093b1c9a8337734136d5fcad85fa6592fc') + version('0.60-8', sha256='924c342feb2a862fa3871a45db5f8434dbbfb900cfc40c001a0872108a3a069e') version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389') 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')) diff --git a/var/spack/repos/builtin/packages/r-npsurv/package.py b/var/spack/repos/builtin/packages/r-npsurv/package.py new file mode 100644 index 00000000000..6ef60c6345b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-npsurv/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 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 RNpsurv(RPackage): + """Contains functions for non-parametric survival analysis of exact and + interval-censored observations.""" + + homepage = "https://www.stat.auckland.ac.nz/~yongwang" + url = "https://cloud.r-project.org/src/contrib/npsurv_0.4-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/npsurv" + + version('0.4-0', sha256='404cf7135dc40a04e9b81224a543307057a8278e11109ba1fcaa28e87c6204f3') + + depends_on('r-lsei', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-numderiv/package.py b/var/spack/repos/builtin/packages/r-numderiv/package.py index 16342ff5c52..d234dca5386 100644 --- a/var/spack/repos/builtin/packages/r-numderiv/package.py +++ b/var/spack/repos/builtin/packages/r-numderiv/package.py @@ -10,10 +10,11 @@ class RNumderiv(RPackage): """Methods for calculating (usually) accurate numerical first and second order derivatives.""" - homepage = "https://cran.r-project.org/package=numDeriv" - url = "https://cran.r-project.org/src/contrib/numDeriv_2016.8-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/numDeriv" + 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" + version('2016.8-1.1', sha256='d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345') version('2016.8-1', '30e486298d5126d86560095be8e8aac1') - depends_on('r@2.11.1:') + depends_on('r@2.11.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index a11bb4546a4..72ef2426672 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -18,12 +18,15 @@ class ROpenssl(RPackage): generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.""" - homepage = "https://CRAN.R-project.org/package=openssl" - url = "https://cran.r-project.org/src/contrib/openssl_0.9.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/openssl" + homepage = "https://cloud.r-project.org/package=openssl" + url = "https://cloud.r-project.org/src/contrib/openssl_0.9.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/openssl" + version('1.4.1', sha256='f7fbecc75254fc43297a95a4338c674ab9ba2ec056b59e027d16d23122161fc6') + version('1.3', sha256='1c83f4d529adc1f5ec40e477c690a8d5b0a42422f3e542f1fc39062dcfaca4bf') version('0.9.7', '86773824dce7d3d79abfef574ce2531a') version('0.9.6', '7ef137929d9dd07db690d35db242ba4b') version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') + depends_on('r-askpass', when='@1.2:', type=('build', 'run')) depends_on('openssl@1.0.1:') diff --git a/var/spack/repos/builtin/packages/r-openxlsx/package.py b/var/spack/repos/builtin/packages/r-openxlsx/package.py new file mode 100644 index 00000000000..cd375247e59 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-openxlsx/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 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 ROpenxlsx(RPackage): + """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" + + version('4.1.0.1', sha256='8b7011debe14714de035ef42797c8caa923162d5dc3cc3c2a299fc10eff3d4d1') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-zip', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-optparse/package.py b/var/spack/repos/builtin/packages/r-optparse/package.py index 6bbe628b6b1..be8c989605d 100644 --- a/var/spack/repos/builtin/packages/r-optparse/package.py +++ b/var/spack/repos/builtin/packages/r-optparse/package.py @@ -11,10 +11,12 @@ class ROptparse(RPackage): with Rscript to write "#!" shebang scripts that accept short and long flag/options""" - homepage = "https://cran.r-project.org/package=optparse" - url = "https://cran.r-project.org/src/contrib/optparse_1.6.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/optparse" + homepage = "https://cloud.r-project.org/package=optparse" + url = "https://cloud.r-project.org/src/contrib/optparse_1.6.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/optparse" + version('1.6.2', sha256='b5a5a49ae05005f20359868329b73daac83d50f5e088981dcf5c41399534377f') + version('1.6.1', sha256='819be3eff54cb7f3f18703eed9714fc655290ab8e169f87605433d069b597e13') version('1.6.0', '8d0bd89b2e25cc1580437cdeeb1faac2') depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ordinal/package.py b/var/spack/repos/builtin/packages/r-ordinal/package.py new file mode 100644 index 00000000000..ad837a34112 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ordinal/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 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 ROrdinal(RPackage): + """Implementation of cumulative link (mixed) models also known as ordered + regression models, proportional odds models, proportional hazards models + for grouped survival times and ordered logit/probit/... models. Estimation + is via maximum likelihood and mixed models are fitted with the Laplace + approximation and adaptive Gauss-Hermite quadrature. Multiple random effect + terms are allowed and they may be nested, crossed or partially + nested/crossed. Restrictions of symmetry and equidistance can be imposed on + the thresholds (cut-points/intercepts). Standard model methods are + available (summary, anova, drop-methods, step, confint, predict etc.) in + 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" + + version('2019.4-25', sha256='2812ad7a123cae5dbe053d1fe5f2d9935afc799314077eac185c844e3c9d79df') + + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-ucminf', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-numderiv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py index a871964a0e9..427843d0806 100644 --- a/var/spack/repos/builtin/packages/r-packrat/package.py +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -11,8 +11,12 @@ class RPackrat(RPackage): and reproducible way.""" homepage = "https://github.com/rstudio/packrat/" - url = "https://cran.r-project.org/src/contrib/packrat_0.4.7-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/packrat" + url = "https://cloud.r-project.org/src/contrib/packrat_0.4.7-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/packrat" + version('0.5.0', sha256='d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7') + version('0.4.9-3', sha256='87299938a751defc54eb00a029aecd3522d6349d900aaa8b3e1aa6bf31e98234') version('0.4.8-1', '14e82feba55fcda923396282fc490038') version('0.4.7-1', '80c2413269b292ade163a70ba5053e84') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py index a65db10103b..fef678b671a 100644 --- a/var/spack/repos/builtin/packages/r-pacman/package.py +++ b/var/spack/repos/builtin/packages/r-pacman/package.py @@ -12,12 +12,15 @@ class RPacman(RPackage): 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://cran.r-project.org/package=pacman" - url = "https://cran.r-project.org/src/contrib/pacman_0.4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pacman" + 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" + version('0.5.1', sha256='9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c') + version('0.5.0', sha256='61294757212ab0aa0153219d7d031f58be6f30ead88d84859001d58caa76603d') version('0.4.1', 'bf18fe6d1407d31e00b337d9b07fb648') - depends_on('r@3.0.2:') - - depends_on('r-devtools', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-paleotree/package.py b/var/spack/repos/builtin/packages/r-paleotree/package.py index 9a4f31c8722..f14ea30f0ce 100644 --- a/var/spack/repos/builtin/packages/r-paleotree/package.py +++ b/var/spack/repos/builtin/packages/r-paleotree/package.py @@ -13,12 +13,16 @@ class RPaleotree(RPackage): extinct (i.e. fossil) lineages""" homepage = "https://github.com/dwbapst/paleotree" - url = "https://cran.r-project.org/src/contrib/paleotree_3.1.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/paleotree" + url = "https://cloud.r-project.org/src/contrib/paleotree_3.1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/paleotree" + version('3.3.0', sha256='f8f6b0228dd5290b251cad3a8626689442b5aa793d8f072c8c2c7813a063df90') version('3.1.3', sha256='4c1cc8a5e171cbbbd88f78914f86d5e6d144ae573816fbeeff2ab54a814ec614') depends_on('r@3.0.0:', type=('build', 'run')) 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')) diff --git a/var/spack/repos/builtin/packages/r-pamr/package.py b/var/spack/repos/builtin/packages/r-pamr/package.py index c56459b865b..f4697f4c179 100644 --- a/var/spack/repos/builtin/packages/r-pamr/package.py +++ b/var/spack/repos/builtin/packages/r-pamr/package.py @@ -9,8 +9,13 @@ class RPamr(RPackage): """Some functions for sample classification in microarrays.""" - homepage = "https://cran.r-project.org/package=pamr" - url = "https://cran.rstudio.com/src/contrib/pamr_1.55.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pamr" + 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" + version('1.56.1', sha256='d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779') version('1.55', '108932d006a4de3a178b6f57f5d1a006') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py index 21c6155ba51..176104e3dff 100644 --- a/var/spack/repos/builtin/packages/r-pan/package.py +++ b/var/spack/repos/builtin/packages/r-pan/package.py @@ -9,8 +9,9 @@ class RPan(RPackage): """Multiple imputation for multivariate panel or clustered data.""" - homepage = "https://cran.r-project.org/package=pan" - url = "https://cran.r-project.org/src/contrib/pan_1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pan" + 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" + version('1.6', sha256='adc0df816ae38bc188bce0aef3aeb71d19c0fc26e063107eeee71a81a49463b6') version('1.4', 'cdead963110561fc42dc544a60ac44ed') diff --git a/var/spack/repos/builtin/packages/r-parallelmap/package.py b/var/spack/repos/builtin/packages/r-parallelmap/package.py index b5911996c8f..cc437937287 100644 --- a/var/spack/repos/builtin/packages/r-parallelmap/package.py +++ b/var/spack/repos/builtin/packages/r-parallelmap/package.py @@ -15,10 +15,12 @@ class RParallelmap(RPackage): this operation.""" homepage = "https://github.com/berndbischl/parallelMap" - url = "https://cran.r-project.org/src/contrib/parallelMap_1.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/parallelMap" + url = "https://cloud.r-project.org/src/contrib/parallelMap_1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/parallelMap" + version('1.4', sha256='fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b') version('1.3', 'dd62866b395847b0bd5b13bed98c0081') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-bbmisc@1.8:', type=('build', 'run')) - depends_on('r-checkmate@1.5.1:', type=('build', 'run')) + depends_on('r-checkmate@1.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-paramhelpers/package.py b/var/spack/repos/builtin/packages/r-paramhelpers/package.py index 5898de58fe9..2aa307b30de 100644 --- a/var/spack/repos/builtin/packages/r-paramhelpers/package.py +++ b/var/spack/repos/builtin/packages/r-paramhelpers/package.py @@ -14,10 +14,14 @@ class RParamhelpers(RPackage): function evaluations is also provided.""" homepage = "https://github.com/berndbischl/ParamHelpers" - url = "https://cran.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ParamHelpers" + url = "https://cloud.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ParamHelpers" + version('1.12', sha256='b54db9e6608ba530345c380c757a60cb2b78ab08992a890b1a41914ce7abcc14') + version('1.11', sha256='1614f4c0842cf822befc01228ab7263417f3423dd6a1dc24347b14f8491637a0') version('1.10', '36e9060488ebd484d62cd991a4693332') depends_on('r-bbmisc@1.10:', type=('build', 'run')) - depends_on('r-checkmate@1.8.1:', type=('build', 'run')) + depends_on('r-checkmate@1.8.2:', type=('build', 'run')) + depends_on('r-backports', when='@1.11:', type=('build', 'run')) + depends_on('r-fastmatch', when='@1.11:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-party/package.py b/var/spack/repos/builtin/packages/r-party/package.py index 73fc0c82335..db876b5faf0 100644 --- a/var/spack/repos/builtin/packages/r-party/package.py +++ b/var/spack/repos/builtin/packages/r-party/package.py @@ -9,16 +9,18 @@ class RParty(RPackage): """A computational toolbox for recursive partitioning.""" - homepage = "https://cran.r-project.org/web/packages/party/index.html" - url = "https://cran.r-project.org/src/contrib/party_1.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/party" + homepage = "https://cloud.r-project.org/package=party" + url = "https://cloud.r-project.org/src/contrib/party_1.1-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/party" + version('1.3-3', sha256='9f72eea02d43a4cee105790ae7185b0478deb6011ab049cc9d31a0df3abf7ce9') + version('1.3-2', sha256='9f350fa21114151c49bccc3d5f8536dbc5a608cfd88f60461c9805a4c630510b') version('1.1-2', '40a00336cf8418042d2ab616675c8ddf') - depends_on('r@2.14.0:') - + 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-mvtnorm@1.0-2:', type=('build', 'run')) - depends_on('r-modeltools@0.1-21:', type=('build', 'run')) + depends_on('r-modeltools@0.2-21:', type=('build', 'run')) depends_on('r-strucchange', type=('build', 'run')) depends_on('r-survival@2.37-7:', type=('build', 'run')) depends_on('r-coin@1.1-0:', 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 d01292d3073..1e914397a0a 100644 --- a/var/spack/repos/builtin/packages/r-partykit/package.py +++ b/var/spack/repos/builtin/packages/r-partykit/package.py @@ -18,10 +18,17 @@ class RPartykit(RPackage): provided based on the new infrastructure.""" homepage = "http://partykit.r-forge.r-project.org/partykit" - url = "https://cran.r-project.org/src/contrib/partykit_1.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/partykit" + url = "https://cloud.r-project.org/src/contrib/partykit_1.1-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/partykit" + version('1.2-5', sha256='f48e30790f93fa5d03e68e8ce71ce33d009d107d46d45d85da2016b38b27629c') + version('1.2-3', sha256='56749b246e283f94ac2ad2cdcfc0a477e05cd44b5e8f6e462c26f4dff818da35') version('1.1-1', '8fcb31d73ec1b8cd3bcd9789639a9277') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) - depends_on('r-formula', type=('build', 'run')) + depends_on('r-formula@1.2-1:', type=('build', 'run')) + depends_on('r-libcoin@1.0-0:', when='@1.2-0:', type=('build', 'run')) + depends_on('r-mvtnorm', when='@1.2-0:', type=('build', 'run')) + depends_on('r-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')) diff --git a/var/spack/repos/builtin/packages/r-pbapply/package.py b/var/spack/repos/builtin/packages/r-pbapply/package.py index 0a230ab7594..cc481c277a4 100644 --- a/var/spack/repos/builtin/packages/r-pbapply/package.py +++ b/var/spack/repos/builtin/packages/r-pbapply/package.py @@ -10,14 +10,16 @@ class RPbapply(RPackage): """A lightweight package that adds progress bar to vectorized R apply functions.""" - homepage = "https://cran.r-project.org/web/packages/pbapply/index.html" - url = "https://cran.r-project.org/src/contrib/pbapply_1.3-3.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/pbapply" + homepage = "https://cloud.r-project.org/package=pbapply" + url = "https://cloud.r-project.org/src/contrib/pbapply_1.3-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pbapply" + version('1.4-1', sha256='b3633349181db944e1dfc4422b4728a6562e454117a232cbb51633906cd27cad') + version('1.3-4', sha256='cdfdaf9b8aecbe48daac858aecaf65a766b74a363d1eb7cd6ebf27c0549f6552') version('1.3-3', '570db6795179a1439c174be881c77d18') version('1.3-2', 'd72a777bfe4a28ba4e1585e31680f82e') version('1.3-1', '13d64dead441426aa96a3bf3fde29daf') version('1.3-0', 'a3f93cd05054657a01893a3817fa1f08') version('1.2-2', '23e2bfe531c704b79308b0b5fbe1ace8') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index e0a8ef25ba0..48625786c1b 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -17,10 +17,14 @@ class RPbdzmq(RPackage): functions compatible with 'rzmq' are also provided.""" homepage = "http://r-pbd.org/" - url = "https://cran.r-project.org/src/contrib/pbdZMQ_0.2-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pbdZMQ" + url = "https://cloud.r-project.org/src/contrib/pbdZMQ_0.2-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pbdZMQ" + version('0.3-3', sha256='ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca') + version('0.3-2', sha256='ece2a2881c662f77126e4801ba4e01c991331842b0d636ce5a2b591b9de3fc37') version('0.2-4', 'e5afb70199aa54d737ee7a0e26bde060') - depends_on('r-r6', type=('build', 'run')) - depends_on('zeromq') + depends_on('r@3.0.0:', when='@:0.2-5', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run')) + depends_on('r-r6', when='@:0.2-6', type=('build', 'run')) + depends_on('zeromq@4.0.4:') diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index 42cca11729b..a696abf87af 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -14,14 +14,15 @@ class RPbkrtest(RPackage): models.""" homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/" - url = "https://cran.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest" + url = "https://cloud.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pbkrtest" + version('0.4-7', sha256='5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea') version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') version('0.4-4', '5e54b1b1b35413dd1d24ef15735ec645') - depends_on('r@3.2.3:') - + depends_on('r@3.0.2:', when='@:0.4-5', type=('build', 'run')) + depends_on('r@3.2.3:', when='@0.4-6:', type=('build', 'run')) depends_on('r-lme4@1.1.10:', type=('build', 'run')) depends_on('r-matrix@1.2.3:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py index 4e49bd47aa7..bcc1b7a4722 100644 --- a/var/spack/repos/builtin/packages/r-pcapp/package.py +++ b/var/spack/repos/builtin/packages/r-pcapp/package.py @@ -7,16 +7,18 @@ class RPcapp(RPackage): - """Provides functions for robust PCA by projection pursuit.""" + """Provides functions for robust PCA by projection pursuit.""" - homepage = "https://cran.r-project.org/web/packages/pcaPP/index.html" - url = "https://cran.r-project.org/src/contrib/pcaPP_1.9-72.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/pcaPP" + 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" - version('1.9-72', '87c08f8ecab69311bba395c026bbc91c') - version('1.9-70', '3fcc809ec1cdc910f10e9ebf372888e8') - version('1.9-61', '1bd5bc3aff968b168493e8c523d726ea') - version('1.9-60', '23dd468abb9fedc11e40166446df1017') - version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3') + version('1.9-73', sha256='ca4566b0babfbe83ef9418283b08a12b3420dc362f93c6562f265df7926b53fc') + version('1.9-72.1', sha256='a9e39ee15a650930c07672092f9f0c431807869b68b5471037eb7290a4d65bd5') + version('1.9-72', '87c08f8ecab69311bba395c026bbc91c') + version('1.9-70', '3fcc809ec1cdc910f10e9ebf372888e8') + version('1.9-61', '1bd5bc3aff968b168493e8c523d726ea') + version('1.9-60', '23dd468abb9fedc11e40166446df1017') + version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3') - depends_on('r-mvtnorm', type=('build', 'run')) + depends_on('r-mvtnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py index 4798b844efa..a386df053b4 100644 --- a/var/spack/repos/builtin/packages/r-permute/package.py +++ b/var/spack/repos/builtin/packages/r-permute/package.py @@ -16,9 +16,10 @@ class RPermute(RPackage): (and later) by Cajo ter Braak.""" homepage = "https://github.com/gavinsimpson/permute" - url = "https://cran.r-project.org/src/contrib/permute_0.9-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.9-5', sha256='d2885384a07497e8df273689d6713fc7c57a7c161f6935f3572015e16ab94865') version('0.9-4', '569fc2442d72a1e3b7e2d456019674c9') - depends_on('r@2.14:') + depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phangorn/package.py b/var/spack/repos/builtin/packages/r-phangorn/package.py index b147d5c9f1c..3b0c34fb7e3 100644 --- a/var/spack/repos/builtin/packages/r-phangorn/package.py +++ b/var/spack/repos/builtin/packages/r-phangorn/package.py @@ -12,12 +12,15 @@ class RPhangorn(RPackage): and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.""" - homepage = "https://cran.r-project.org/package=phangorn" - url = "https://cran.r-project.org/src/contrib/phangorn_2.3.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/phangorn" + 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" + version('2.5.5', sha256='c58dc1ace26cb4358619a15da3ea4765dbdde1557acccc5103c85589a7571346') + version('2.5.3', sha256='a306585a0aabe7360a2adaf9116ae2993fb5ceff641b198f2e01e4329d3768af') version('2.3.1', '85e7309900d061432508ab6f7e3e627e') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-ape@5.0:', type=('build', 'run')) depends_on('r-quadprog', type=('build', 'run')) depends_on('r-igraph@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phytools/package.py b/var/spack/repos/builtin/packages/r-phytools/package.py index 385e76ff365..718e54cb4bd 100644 --- a/var/spack/repos/builtin/packages/r-phytools/package.py +++ b/var/spack/repos/builtin/packages/r-phytools/package.py @@ -10,9 +10,10 @@ class RPhytools(RPackage): """Phylogenetic Tools for Comparative Biology (and Other Things)""" homepage = "http://github.com/liamrevell/phytools" - url = "https://cran.r-project.org/src/contrib/phytools_0.6-60.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/phytools/" + url = "https://cloud.r-project.org/src/contrib/phytools_0.6-60.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/phytools/" + version('0.6-99', sha256='2ef532cba77c5f73803bd34582bef05709705311a0b50e42316e69944567390f') version('0.6-60', sha256='55cad759510d247ebbf03a53a46caddadd3bf87584ccf7fcd6dd06d44516b377') depends_on('r@3.2.0:', type=('build', 'run')) @@ -30,3 +31,4 @@ 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-gtools', when='@0.6-99:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-picante/package.py b/var/spack/repos/builtin/packages/r-picante/package.py index e9e20b030ff..6cfa91cfc2d 100644 --- a/var/spack/repos/builtin/packages/r-picante/package.py +++ b/var/spack/repos/builtin/packages/r-picante/package.py @@ -9,10 +9,12 @@ class RPicante(RPackage): """R tools for integrating phylogenies and ecology""" - homepage = "https://cran.r-project.org/package=picante" - url = "https://cran.r-project.org/src/contrib/picante_1.6-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/picante" + homepage = "https://cloud.r-project.org/package=picante" + url = "https://cloud.r-project.org/src/contrib/picante_1.6-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/picante" + version('1.8', sha256='81a6308dbb53c9cdab30c1f9ac727abee76314351823b3a2142c21ed8e1498ad') + version('1.7', sha256='75e4d73080db67e776562a1d58685438461cbde39af46900c7838da56aef0a62') version('1.6-2', 'e3eba6ef254068d2cfa9e96760bcd7a3') version('1.6-1', '73d86b90eceda582654e995d47236d6e') diff --git a/var/spack/repos/builtin/packages/r-pillar/package.py b/var/spack/repos/builtin/packages/r-pillar/package.py index d23c6eb662d..213a2658db3 100644 --- a/var/spack/repos/builtin/packages/r-pillar/package.py +++ b/var/spack/repos/builtin/packages/r-pillar/package.py @@ -10,10 +10,12 @@ class RPillar(RPackage): """Provides a 'pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals.""" - homepage = "https://cran.r-project.org/package=pillar" - url = "https://cran.r-project.org/src/contrib/pillar_1.3.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pillar" + homepage = "https://cloud.r-project.org/package=pillar" + url = "https://cloud.r-project.org/src/contrib/pillar_1.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pillar" + version('1.4.2', sha256='bababb76b6db06dc32ccd947dbad6c164a1749ff5b558c6783ad03570f010825') + version('1.4.1', sha256='f571ca7a3ef0927747510b972da31a26da24b9da68990fe1bbc9d4ae58028c55') version('1.3.1', sha256='b338b55f956dd7134f379d39bb94dfb25e13cf27999d6a6e6dc9f292755acbf6') version('1.3.0', sha256='aed845ae4888be9a7340eed57536e3fe6cb46e89d905897fb9b0635797cfcae0') version('1.2.3', sha256='c81d1b5c6b55d789a6717dc3c7be1200eb0efbcfc5013db00d553d9cafd6f0e7') @@ -25,7 +27,8 @@ class RPillar(RPackage): version('1.0.0', sha256='7478d0765212c5f0333b8866231a6fe350393b7fa49840e6fed3516ac64540dc') depends_on('r-cli', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) + depends_on('r-crayon@1.3.4:', type=('build', 'run')) depends_on('r-fansi', type=('build', 'run')) - depends_on('r-rlang', type=('build', 'run')) - depends_on('r-utf8', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', type=('build', 'run')) + depends_on('r-utf8@1.1.0:', type=('build', 'run')) + depends_on('r-vctrs', when='@1.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgbuild/package.py b/var/spack/repos/builtin/packages/r-pkgbuild/package.py index 723180c3332..2e4dedfa1b8 100644 --- a/var/spack/repos/builtin/packages/r-pkgbuild/package.py +++ b/var/spack/repos/builtin/packages/r-pkgbuild/package.py @@ -9,18 +9,20 @@ class RPkgbuild(RPackage): """pkgbuild: Find Tools Needed to Build R Packages""" - homepage = "https://cran.r-project.org/package=pkgbuild" - url = "https://cran.r-project.org/src/contrib/pkgbuild_1.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgbuild/" + 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/" + version('1.0.4', sha256='2934efa5ff9ccfe1636d360aedec36713f3bb3128a493241dbb728d842ea3b5f') version('1.0.3', sha256='c93aceb499886e42bcd61eb7fb59e47a76c9ba5ab5349a426736d46c8ce21f4d') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r-callr', 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-cli', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) depends_on('r-desc', type=('build', 'run')) depends_on('r-prettyunits', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) depends_on('r-rprojroot', type=('build', 'run')) - depends_on('r-withr', type=('build', 'run')) + depends_on('r-withr@2.1.2:', 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 1f589b5b61d..947d6f4ee53 100644 --- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py @@ -11,9 +11,9 @@ class RPkgconfig(RPackage): given package only apply to that package, other packages are unaffected.""" - homepage = "https://cran.rstudio.com/web/packages/pkgconfig/index.html" - url = "https://cran.rstudio.com/src/contrib/pkgconfig_2.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgconfig" + homepage = "https://cloud.r-project.org/package=pkgconfig" + url = "https://cloud.r-project.org/src/contrib/pkgconfig_2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgconfig" version('2.0.2', sha256='25997754d1adbe7a251e3bf9879bb52dced27dd8b84767d558f0f644ca8d69ca') version('2.0.1', 'a20fd9588e37995995fa62dc4828002e') diff --git a/var/spack/repos/builtin/packages/r-pkgload/package.py b/var/spack/repos/builtin/packages/r-pkgload/package.py index e1a579adafc..fa6d0aa6350 100644 --- a/var/spack/repos/builtin/packages/r-pkgload/package.py +++ b/var/spack/repos/builtin/packages/r-pkgload/package.py @@ -9,9 +9,9 @@ class RPkgload(RPackage): """pkgload: Simulate Package Installation and Attach""" - homepage = "https://cran.r-project.org/package=pkgload" - url = "https://cran.r-project.org/src/contrib/pkgload_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgload/" + 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/" version('1.0.2', sha256='3186564e690fb05eabe76e1ac0bfd4312562c3ac8794b29f8850399515dcf27c') diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index 29628b68e79..b89ec59b809 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -16,8 +16,8 @@ class RPkgmaker(RPackage): changes in the interface(s) are more than likely to happen.""" homepage = "https://renozao.github.io/pkgmaker" - url = "https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgmaker" + url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4') @@ -32,11 +32,3 @@ class RPkgmaker(RPackage): depends_on('r-xtable', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) depends_on('r-bibtex@0.4:', type=('build', 'run')) - depends_on('r-devtools@0.8:', type=('build', 'run')) - depends_on('r-roxygen2', type=('build', 'run')) - depends_on('r-runit', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rmarkdown', type=('build', 'run')) - depends_on('r-yaml', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plogr/package.py b/var/spack/repos/builtin/packages/r-plogr/package.py index b85fdaf2b0d..c35e0900e4c 100644 --- a/var/spack/repos/builtin/packages/r-plogr/package.py +++ b/var/spack/repos/builtin/packages/r-plogr/package.py @@ -11,9 +11,9 @@ class RPlogr(RPackage): 'LinkingTo: plogr' to 'DESCRIPTION', and '#include ' in your C++ modules to use it.""" - homepage = "https://cran.r-project.org/package=plogr" - url = "https://cran.r-project.org/src/contrib/plogr_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/plogr" + 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" version('0.2.0', sha256='0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29') version('0.1-1', '5ee46ed21b5c571d02900219098517c0') diff --git a/var/spack/repos/builtin/packages/r-plot3d/package.py b/var/spack/repos/builtin/packages/r-plot3d/package.py index b856601463b..8e338d123bc 100644 --- a/var/spack/repos/builtin/packages/r-plot3d/package.py +++ b/var/spack/repos/builtin/packages/r-plot3d/package.py @@ -11,10 +11,11 @@ class RPlot3d(RPackage): slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.""" - homepage = "https://CRAN.R-project.org/package=plot3D" - url = "https://cran.r-project.org/src/contrib/plot3D_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/plot3D" + homepage = "https://cloud.r-project.org/package=plot3D" + url = "https://cloud.r-project.org/src/contrib/plot3D_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plot3D" version('1.1.1', '5135aa1f3cf6106f2ded3f393a24e75d') + depends_on('r@2.15:', type=('build', 'run')) depends_on('r-misc3d', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plotly/package.py b/var/spack/repos/builtin/packages/r-plotly/package.py index 7b7cc8999d7..29d1ea37a59 100644 --- a/var/spack/repos/builtin/packages/r-plotly/package.py +++ b/var/spack/repos/builtin/packages/r-plotly/package.py @@ -10,25 +10,38 @@ class RPlotly(RPackage): """Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R.""" - homepage = "https://cran.r-project.org/web/packages/plotly/index.html" - url = "https://cran.r-project.org/src/contrib/plotly_4.7.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/plotly" + homepage = "https://cloud.r-project.org/package=plotly" + url = "https://cloud.r-project.org/src/contrib/plotly_4.7.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plotly" + version('4.9.0', sha256='f761148338231f210fd7fe2f8325ffe9cfdaaaeddd7b933b65c44ebb4f85e2cf') + version('4.8.0', sha256='78f90282c831bbbb675ed4811fb506a98dd05e37251fabd42ebc263c80bae8a6') version('4.7.1', '4799c8b429291d4c52fb904380806548') version('4.7.0', '5bd52d515c01af7ff291c30a6cf23bec') version('4.6.0', '27ff3de288bacfaad6e6694752ea2929') version('4.5.6', 'e6e00177fa64dc6b1a199facfd73f585') version('4.5.2', '7eb11b24a9faa9a572657fd89ed72fa5') - depends_on('r@3.4.0:3.4.9') - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.3.6:', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r-htmlwidgets@1.3:', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-hexbin', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-crosstalk', type=('build', 'run')) + depends_on('r-crosstalk', when='@4.6.0:', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) + depends_on('r-jsonlite@1.6:', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-viridislite', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-lazyeval@0.2.0:', type=('build', 'run')) + depends_on('r-rcolorbrewer', when='@4.6.0:', type=('build', 'run')) + depends_on('r-data-table', when='@4.7.0:', type=('build', 'run')) + depends_on('r-rlang', when='@4.8.0:', type=('build', 'run')) + depends_on('r-promises', when='@4.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index 6ef26073428..a03e77b93af 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -9,9 +9,13 @@ class RPlotrix(RPackage): """Lots of plots, various labeling, axis and color scaling functions.""" - homepage = "https://cran.r-project.org/package=plotrix" - url = "https://cran.r-project.org/src/contrib/plotrix_3.6-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/plotrix" + homepage = "https://cloud.r-project.org/package=plotrix" + url = "https://cloud.r-project.org/src/contrib/plotrix_3.6-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plotrix" + version('3.7-6', sha256='83d5f7574592953288b4fe39c4c0dd7670d097598ad7f6bddbb0687a32954e46') + version('3.7-5', sha256='b22f3f9d93961d23ad46e41597d1e45d2665ced04dcad8c40f6806a67cded14c') version('3.6-4', 'efe9b9b093d8903228a9b56c46d943fa') version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') + + depends_on('r@3.5.0:', when='@3.7-6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py index 706448e19d6..d310c5d5fb8 100644 --- a/var/spack/repos/builtin/packages/r-pls/package.py +++ b/var/spack/repos/builtin/packages/r-pls/package.py @@ -11,10 +11,12 @@ class RPls(RPackage): Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).""" - homepage = "https://cran.r-project.org/package=pls" - url = "https://cran.r-project.org/src/contrib/pls_2.6-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pls" + 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" + version('2.7-1', sha256='f8fd817fc2aa046970c49a9a481489a3a2aef8b6f09293fb1f0218f00bfd834b') + version('2.7-0', sha256='5ddc1249a14d69a7a39cc4ae81595ac8c0fbb1e46c911af67907baddeac35875') version('2.6-0', '04e02e8e46d983c5ed53c1f952b329df') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index 077c331b504..c5fc1bf68d5 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -16,9 +16,10 @@ class RPlyr(RPackage): Dickinson'.""" homepage = "http://had.co.nz/plyr" - url = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pmcmr/package.py b/var/spack/repos/builtin/packages/r-pmcmr/package.py index 25936e929bd..3097e0861f8 100644 --- a/var/spack/repos/builtin/packages/r-pmcmr/package.py +++ b/var/spack/repos/builtin/packages/r-pmcmr/package.py @@ -21,8 +21,11 @@ class RPmcmr(RPackage): balanced incomplete block design (BIBD) is also given in this package.""" - homepage = "https://cran.r-project.org/package=PMCMR" - url = "https://cran.rstudio.com/src/contrib/PMCMR_4.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/PMCMR" + 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" + version('4.3', sha256='328a2880dd614dc412e8dca21d29ed9d5eea29ccbe0eff98c8068100856c7b25') version('4.1', 'b9c0c4e4cb4f73ae36f45a47abae986a') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py index 80689773af2..a9bdc3318ba 100644 --- a/var/spack/repos/builtin/packages/r-png/package.py +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -12,9 +12,10 @@ class RPng(RPackage): and in-memory raw vectors.""" homepage = "http://www.rforge.net/png/" - url = "https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('libpng') diff --git a/var/spack/repos/builtin/packages/r-polynom/package.py b/var/spack/repos/builtin/packages/r-polynom/package.py new file mode 100644 index 00000000000..4244a2a4ea8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-polynom/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 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 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" + + version('1.4-0', sha256='c5b788b26f7118a18d5d8e7ba93a0abf3efa6603fa48603c70ed63c038d3d4dd') diff --git a/var/spack/repos/builtin/packages/r-popgenome/package.py b/var/spack/repos/builtin/packages/r-popgenome/package.py index de573b59f56..70ca45e3b42 100644 --- a/var/spack/repos/builtin/packages/r-popgenome/package.py +++ b/var/spack/repos/builtin/packages/r-popgenome/package.py @@ -12,9 +12,10 @@ class RPopgenome(RPackage): genomes.""" homepage = "https://popgenome.weebly.com" - url = "https://cran.r-project.org/src/contrib/PopGenome_2.6.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/PopGenome" + url = "https://cloud.r-project.org/src/contrib/PopGenome_2.6.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/PopGenome" + version('2.7.1', sha256='a84903b151528fa026ccaba42ada22cd89babbc1824afd40269b7204e488a5fa') version('2.6.1', sha256='7a2922ed505fa801117a153e479d246bcf4854b91c6ab0241acc620a9d779b1c') depends_on('r@2.14.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-popvar/package.py b/var/spack/repos/builtin/packages/r-popvar/package.py index c5398eb1bf5..15e1c036459 100644 --- a/var/spack/repos/builtin/packages/r-popvar/package.py +++ b/var/spack/repos/builtin/packages/r-popvar/package.py @@ -10,9 +10,9 @@ class RPopvar(RPackage): """PopVar: Genomic Breeding Tools: Genetic Variance Prediction andCross- Validation""" - homepage = "https://cran.r-project.org/package=PopVar" - url = "https://cran.r-project.org/src/contrib/PopVar_1.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/PopVar" + 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" version('1.2.1', sha256='5e3df79634ab63708a431e4b8e6794675972ac6c58d2bc615726aa0f142f5f25') diff --git a/var/spack/repos/builtin/packages/r-powerlaw/package.py b/var/spack/repos/builtin/packages/r-powerlaw/package.py index f406a2f56a0..0ee38127a04 100644 --- a/var/spack/repos/builtin/packages/r-powerlaw/package.py +++ b/var/spack/repos/builtin/packages/r-powerlaw/package.py @@ -13,9 +13,12 @@ class RPowerlaw(RPackage): is used to estimate the lower cut-off for the scaling region.""" homepage = "https://github.com/csgillespie/poweRlaw" - url = "https://cran.rstudio.com/src/contrib/poweRlaw_0.70.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/poweRlaw" + url = "https://cloud.r-project.org/src/contrib/poweRlaw_0.70.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/poweRlaw" + version('0.70.2', sha256='240f1454389b1a00ad483fb63e5b53243cc9367f21a3e7253ab2c293673459ab') version('0.70.1', '4117cb95c37f72441f320ea12f553065') + depends_on('r@3.1.0:', when='@:0.70.1', type=('build', 'run')) + depends_on('r@3.4.0:', when='@0.70.2:', type=('build', 'run')) depends_on('r-vgam', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py index 124049d0cad..fd12aaddee5 100644 --- a/var/spack/repos/builtin/packages/r-prabclus/package.py +++ b/var/spack/repos/builtin/packages/r-prabclus/package.py @@ -11,11 +11,13 @@ class RPrabclus(RPackage): Multilocus Genetic Data""" homepage = "http://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cran.r-project.org/src/contrib/prabclus_2.2-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/prabclus" + url = "https://cloud.r-project.org/src/contrib/prabclus_2.2-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/prabclus" + version('2.3-1', sha256='ef3294767d43bc3f72478fdaf0d1f13c8de18881bf9040c9f1add68af808b3c0') + version('2.2-7.1', sha256='2c5bf3bbb0d225e04c53bb0e11e9c2a6809f0e46d95b8f6dc14b9dd6a2452975') version('2.2-6', '7f835dcc113243e1db74aad28ce93d11') - depends_on('r@2.1.0:') - # depends_on('r-mass', type=('build', 'run')) + depends_on('r@2.1.0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) depends_on('r-mclust', 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 be0785716bc..830b9cfc00c 100644 --- a/var/spack/repos/builtin/packages/r-praise/package.py +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -11,7 +11,7 @@ class RPraise(RPackage): something good, or they just need it to feel better.""" homepage = "https://github.com/gaborcsardi/praise" - url = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.0.0', '9318724cec0454884b5f762bee2da6a1') diff --git a/var/spack/repos/builtin/packages/r-prettyunits/package.py b/var/spack/repos/builtin/packages/r-prettyunits/package.py index 3a3a3bf0299..00d903db5c9 100644 --- a/var/spack/repos/builtin/packages/r-prettyunits/package.py +++ b/var/spack/repos/builtin/packages/r-prettyunits/package.py @@ -11,9 +11,9 @@ class RPrettyunits(RPackage): 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.""" - homepage = "https://cran.r-project.org/package=prettyunits" - url = "https://cran.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/prettyunits" + homepage = "https://cloud.r-project.org/package=prettyunits" + url = "https://cloud.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/prettyunits" version('1.0.2', '0a091a297e8b37df54e7fcf28697ee50') diff --git a/var/spack/repos/builtin/packages/r-processx/package.py b/var/spack/repos/builtin/packages/r-processx/package.py index 86a2a3e73c2..d6661875b40 100644 --- a/var/spack/repos/builtin/packages/r-processx/package.py +++ b/var/spack/repos/builtin/packages/r-processx/package.py @@ -10,17 +10,19 @@ class RProcessx(RPackage): """Tools to run system processes in the background""" homepage = "https://github.com/r-lib/processx" - url = "https://cran.r-project.org/src/contrib/processx_3.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/processx/processx_3.1.0.tar.gz" + url = "https://cloud.r-project.org/src/contrib/processx_3.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/processx" + version('3.4.1', sha256='f1abddb48fa78f2b176552e2ec5d808d4d87d79ce72e9b3d25c9a7d715bbd1bc') + version('3.3.1', sha256='6123dbdf9f3bb6e5e8678980fb4587dcefb56d2190adf2ef494d7cd199720bae') version('3.2.0', sha256='c4ba602fcbdc032ae9d94701b3e6b83a2dab1b53d0b4f9937b07a84eae22fddf') version('3.1.0', sha256='11ac120ab4e4aa0e99c9b2eda87d07bc683bab735f1761e95e5ddacd311b5972') version('3.0.3', sha256='53781dba3c538605a02e28b3b577e7de79e2064bfc502025f7ec0e5945e302bf') version('2.0.0.1', sha256='8f61b2952d0f2d13c74465bfba174ce11eee559475c2f7b9be6bcb9e2e1d827b') version('2.0.0', sha256='8325b56a60a276909228756281523cda9256bc754c5f3ca03b41c5c17cc398ad') - depends_on('r-assertthat', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) - depends_on('r-ps', 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-ps@1.2.0:', when='@3.2.0:', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) - depends_on('r-utils', type=('build', 'run')) + depends_on('r-debugme', when='@:3.0.9', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py index 157fa3b832d..e945333a1cf 100644 --- a/var/spack/repos/builtin/packages/r-prodlim/package.py +++ b/var/spack/repos/builtin/packages/r-prodlim/package.py @@ -11,14 +11,15 @@ class RProdlim(RPackage): user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.""" - homepage = "https://cran.r-project.org/package=prodlim" - url = "https://cran.r-project.org/src/contrib/prodlim_1.5.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/prodlim" + 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" + version('2018.04.18', sha256='4b22b54fdf712439309be0ff74f63cde9080464667b00e19823372ac0fc254ab') + version('1.6.1', sha256='3f2665257118a3db8682731a500b1ae4d669af344672dc2037f987bee3cca154') version('1.5.9', 'e0843053c9270e41b657a733d6675dc9') - depends_on('r@2.9.0:') - + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.5:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-kernsmooth', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-progress/package.py b/var/spack/repos/builtin/packages/r-progress/package.py index 44955975ae5..1d74872e341 100644 --- a/var/spack/repos/builtin/packages/r-progress/package.py +++ b/var/spack/repos/builtin/packages/r-progress/package.py @@ -13,10 +13,15 @@ class RProgress(RPackage): The package also provides a 'C++' 'API', that works with or without 'Rcpp'.""" - homepage = "https://cran.r-project.org/package=progress" - url = "https://cran.r-project.org/src/contrib/progress_1.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/progress" + 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" + version('1.2.2', sha256='b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35') + version('1.2.1', sha256='7401e86ff76bef4d26508b74ee8bd169a0377b2738d9ec79ebff0b7fd5c55326') version('1.1.2', 'b3698672896125137e0077bc97132428') + 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')) diff --git a/var/spack/repos/builtin/packages/r-promises/package.py b/var/spack/repos/builtin/packages/r-promises/package.py new file mode 100644 index 00000000000..6b0f6bf679a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-promises/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 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 RPromises(RPackage): + """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" + + version('1.0.1', sha256='c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558') + + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-later', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py index 2b8aa7211a2..d2f5012ccb2 100644 --- a/var/spack/repos/builtin/packages/r-proto/package.py +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -11,8 +11,8 @@ class RProto(RPackage): prototype-based, rather than class-based object oriented ideas.""" homepage = "http://r-proto.googlecode.com/" - url = "https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/proto" + 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" version('1.0.0', sha256='9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1') version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212') diff --git a/var/spack/repos/builtin/packages/r-proxy/package.py b/var/spack/repos/builtin/packages/r-proxy/package.py index 99ffc64571c..94c954f821a 100644 --- a/var/spack/repos/builtin/packages/r-proxy/package.py +++ b/var/spack/repos/builtin/packages/r-proxy/package.py @@ -11,7 +11,12 @@ class RProxy(RPackage): auto- and cross-proximities, along with implementations of the most popular ones.""" - homepage = "https://cran.r-project.org/package=proxy" - url = "https://cran.rstudio.com/src/contrib/proxy_0.4-19.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/proxy" + homepage = "https://cloud.r-project.org/package=proxy" + url = "https://cloud.r-project.org/src/contrib/proxy_0.4-19.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/proxy" + + version('0.4-23', sha256='9dd4eb0978f40e4fcb55c8a8a26266d32eff9c63ac9dfe70cf1f664ca9c3669d') version('0.4-19', '279a01a1cc12ed50208c98196d78a5d7') + + depends_on('r@3.3.2:', when='@:0.4-20', type=('build', 'run')) + depends_on('r@3.4.0:', when='@0.4-21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py index d0d504a2482..a3ba60d71e3 100644 --- a/var/spack/repos/builtin/packages/r-pryr/package.py +++ b/var/spack/repos/builtin/packages/r-pryr/package.py @@ -12,10 +12,14 @@ class RPryr(RPackage): at a deeper level.""" homepage = "https://github.com/hadley/pryr" - url = "https://cran.r-project.org/src/contrib/pryr_0.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.1.4', sha256='d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b') + version('0.1.3', sha256='6acd88341dde4fe247a5cafd3949b281dc6742b7d60f68b57c1feb84b96739ac') version('0.1.2', '66b597a762aa15a3b7037779522983b6') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-codetools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ps/package.py b/var/spack/repos/builtin/packages/r-ps/package.py index dc10f7b1a0d..6c75998ed57 100644 --- a/var/spack/repos/builtin/packages/r-ps/package.py +++ b/var/spack/repos/builtin/packages/r-ps/package.py @@ -10,8 +10,12 @@ class RPs(RPackage): """Manipulate processes on Windows, Linux and MacOS""" homepage = "https://github.com/r-lib/ps" - url = "https://cran.r-project.org/src/contrib/ps_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ps/ps_1.0.0.tar.gz" + url = "https://cloud.r-project.org/src/contrib/ps_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ps" + version('1.3.0', sha256='289193d0ccd2db0b6fe8702e8c5711e935219b17f90f01a6e9684982413e98d1') + version('1.2.1', sha256='bd7207164e6557a9e4213c4b00dc5dc23d7705ab290569765998640b16a3beff') version('1.1.0', sha256='5d5240d5bf1d48c721b3fdf47cfc9dbf878e388ea1f057b764db05bffdc4a9fe') version('1.0.0', sha256='9bdaf64aaa44ae11866868402eb75bf56c2e3022100476d9b9dcd16ca784ffd8') + + depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-psych/package.py b/var/spack/repos/builtin/packages/r-psych/package.py index b5fc1085ca4..e98d427f3d7 100644 --- a/var/spack/repos/builtin/packages/r-psych/package.py +++ b/var/spack/repos/builtin/packages/r-psych/package.py @@ -25,11 +25,14 @@ class RPsych(RPackage): page.""" homepage = "http://personality-project.org/r/psych" - url = "https://cran.r-project.org/src/contrib/psych_1.7.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/psych" + url = "https://cloud.r-project.org/src/contrib/psych_1.7.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/psych" + version('1.8.12', sha256='6e175e049bc1ee5b79a9e51ccafb22b962b4e6c839ce5c9cfa1ad83967037743') + version('1.8.10', sha256='e8901ddab14729bfccbd82a8824fbb6523c10c2cd8fb7199b1ca56a7ffcb6e58') version('1.7.8', 'db37f2f85ff5470ee40bbc0a58ebe22b') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mnormt', type=('build', 'run')) depends_on('r-foreign', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ptw/package.py b/var/spack/repos/builtin/packages/r-ptw/package.py index b0d8b89d50a..a571c31e308 100644 --- a/var/spack/repos/builtin/packages/r-ptw/package.py +++ b/var/spack/repos/builtin/packages/r-ptw/package.py @@ -18,10 +18,11 @@ class RPtw(RPackage): error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported.""" - homepage = "https://cran.r-project.org/package=ptw" - url = "https://cran.rstudio.com/src/contrib/ptw_1.9-12.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ptw" + homepage = "https://cloud.r-project.org/package=ptw" + url = "https://cloud.r-project.org/src/contrib/ptw_1.9-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ptw" + version('1.9-13', sha256='7855e74a167db3d3eba9df9d9c3daa25d7cf487cbcfe8b095f16d96eba862f46') version('1.9-12', 'ddff887752d789ea72db3ee235ae7c67') depends_on('r-nloptr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py index 67ab921aecd..5e80aec44e3 100644 --- a/var/spack/repos/builtin/packages/r-purrr/package.py +++ b/var/spack/repos/builtin/packages/r-purrr/package.py @@ -10,11 +10,14 @@ class RPurrr(RPackage): """A complete and consistent functional programming toolkit for R.""" homepage = "http://purrr.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/purrr_0.2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/purrr" + 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" + version('0.3.2', sha256='27c74dd9e4f6f14bf442473df22bcafc068822f7f138f0870326532f143a9a31') + version('0.3.1', sha256='c2a3c9901192efd8a04976676f84885a005db88deb1432e4750900c7b3b7883b') version('0.2.4', 'd9a11e6c14771beb3ebe8f4771a552f3') - depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-rlang', type=('build', 'run')) - depends_on('r-tibble', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-qtl/package.py b/var/spack/repos/builtin/packages/r-qtl/package.py index fcacfb58af7..010b95665ce 100644 --- a/var/spack/repos/builtin/packages/r-qtl/package.py +++ b/var/spack/repos/builtin/packages/r-qtl/package.py @@ -10,8 +10,8 @@ class RQtl(RPackage): """qtl: Tools for Analyzing QTL Experiments""" homepage = "http://rqtl.org" - url = "https://cran.r-project.org/src/contrib/qtl_1.44-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/qtl" + url = "https://cloud.r-project.org/src/contrib/qtl_1.44-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/qtl" version('1.44-9', 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 4991cf03b73..d9ff67e8040 100644 --- a/var/spack/repos/builtin/packages/r-quadprog/package.py +++ b/var/spack/repos/builtin/packages/r-quadprog/package.py @@ -10,8 +10,12 @@ class RQuadprog(RPackage): """This package contains routines and documentation for solving quadratic programming problems.""" - homepage = "https://cran.r-project.org/web/packages/quadprog/index.html" - url = "https://cran.r-project.org/src/contrib/quadprog_1.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/quadprog" + homepage = "https://cloud.r-project.org/package=quadprog" + url = "https://cloud.r-project.org/src/contrib/quadprog_1.5-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/quadprog" + version('1.5-7', sha256='1af41e57df6f2d08ee8b72a1a5ada137beadb36c7ec9ab9bdb7c05226e8ae76d') + version('1.5-6', sha256='1443e5ffdf884b13dd454e4f6aa260fce6ec47e6845d85b62238c206ce57dcba') version('1.5-5', '8442f37afd8d0b19b12e77d63e6515ad') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py index 972fe3e71de..9fb04ff133f 100644 --- a/var/spack/repos/builtin/packages/r-quantmod/package.py +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -11,13 +11,16 @@ class RQuantmod(RPackage): strategies.""" homepage = "http://www.quantmod.com/" - url = "https://cran.r-project.org/src/contrib/quantmod_0.4-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/quantmod" + url = "https://cloud.r-project.org/src/contrib/quantmod_0.4-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/quantmod" + version('0.4-15', sha256='7ef2e798d4d8e4d2af0a5b2b9fecebec30568087afbd24bfd923cdeb8b53df53') + version('0.4-14', sha256='d95b1acf73328d675bbad18a93fa3c40faf58959e0401458ad21cf6b9f9254b3') version('0.4-10', 'e4119c673567801eee16dcbbd0265de8') version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631') - depends_on('r-xts', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.4-11:', type=('build', 'run')) + depends_on('r-xts@0.9-0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) - depends_on('r-ttr', type=('build', 'run')) + depends_on('r-ttr@0.2:', type=('build', 'run')) depends_on('r-curl', 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 deaffa31f37..65b538146e1 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -14,13 +14,17 @@ class RQuantreg(RPackage): selection methods based on expected shortfall risk are also included.""" - homepage = "https://cran.r-project.org/package=quantreg" - url = "https://cran.r-project.org/src/contrib/quantreg_5.29.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg" + homepage = "https://cloud.r-project.org/package=quantreg" + url = "https://cloud.r-project.org/src/contrib/quantreg_5.29.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/quantreg" + version('5.51', sha256='df1330d245f66ee6d924b209bd4c15d44ff8cce52667959ec0d299975428bdb1') + version('5.42.1', sha256='4cc2b0883c52694e58fcfde83e30e4a54be9f4d9cbcf6138f6498cc8e0b3ccab') + version('5.40', sha256='86e310a235009ab85635dfb8803c175f80a35892e237db2525c4ef37a98936eb') version('5.29', '643ca728200d13f8c2e62365204e9907') version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') + depends_on('r@2.6:', type=('build', 'run')) depends_on('r-sparsem', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-matrixmodels', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-methodss3/package.py b/var/spack/repos/builtin/packages/r-r-methodss3/package.py similarity index 73% rename from var/spack/repos/builtin/packages/r-methodss3/package.py rename to var/spack/repos/builtin/packages/r-r-methodss3/package.py index f52de95e12e..e2887c572d8 100644 --- a/var/spack/repos/builtin/packages/r-methodss3/package.py +++ b/var/spack/repos/builtin/packages/r-r-methodss3/package.py @@ -6,7 +6,7 @@ from spack import * -class RMethodss3(RPackage): +class RRMethodss3(RPackage): """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 @@ -17,8 +17,10 @@ class RMethodss3(RPackage): a cross-platform package implemented in pure R that generates standard S3 methods.""" - homepage = "https://cran.r-project.org/package=R.methodsS3" - url = "https://cran.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R.methodsS3" + 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" version('1.7.1', 'c88e815837f268affd4f2a39c737d969') + + depends_on('r@2.13.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-oo/package.py b/var/spack/repos/builtin/packages/r-r-oo/package.py similarity index 67% rename from var/spack/repos/builtin/packages/r-oo/package.py rename to var/spack/repos/builtin/packages/r-r-oo/package.py index cef0f76cd80..8dc62a1b166 100644 --- a/var/spack/repos/builtin/packages/r-oo/package.py +++ b/var/spack/repos/builtin/packages/r-r-oo/package.py @@ -6,7 +6,7 @@ from spack import * -class ROo(RPackage): +class RROo(RPackage): """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 @@ -16,9 +16,11 @@ class ROo(RPackage): standard S3 classes without any tricks.""" homepage = "https://github.com/HenrikBengtsson/R.oo" - url = "https://cran.rstudio.com/src/contrib/R.oo_1.21.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.22.0', sha256='c0862e4608fb2b8f91ec4494d46c2f3ba7bc44999f9aa3d7b9625d3792e7dd4c') version('1.21.0', 'f0062095c763faaeba30558303f68bc3') - depends_on('r-methodss3', type=('build', 'run')) + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r-utils/package.py b/var/spack/repos/builtin/packages/r-r-utils/package.py new file mode 100644 index 00000000000..9318bdc1d9c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-r-utils/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 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 RRUtils(RPackage): + """Utility functions useful when programming and + developing R packages.""" + + homepage = "https://github.com/HenrikBengtsson/R.utils" + url = "https://cloud.r-project.org/src/contrib/R.utils_2.5.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/R.utils" + + version('2.9.0', sha256='b2aacc5a55d3ea86c41ac576d2583e446af145f4cb1103ad7b6f95b09ab09ff0') + version('2.5.0', 'a728ef3ceb35cafc4c39ea577cecc38b') + + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-r-oo@1.22.0:', type=('build', 'run')) + depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py index 2e8209fd5ef..983cabee2de 100644 --- a/var/spack/repos/builtin/packages/r-r6/package.py +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -15,11 +15,12 @@ class RR6(RPackage): classes are defined in different packages.""" homepage = "https://github.com/wch/R6/" - url = "https://cran.rstudio.com/src/contrib/R6_2.2.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R6" + url = "https://cloud.r-project.org/src/contrib/R6_2.2.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/R6" + version('2.4.0', sha256='70be110174fbf5f5304049b186a6f9c05b77bfaec6d8caf980fcef5da6e0abce') version('2.2.2', '635b58c65bff624a1fab69c6b1989801') version('2.2.0', '659d83b2d3f7a308a48332b4cfbdab49') version('2.1.2', 'b6afb9430e48707be87638675390e457') - depends_on('r@3.0:') + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomfields/package.py b/var/spack/repos/builtin/packages/r-randomfields/package.py index b8a6232842e..815eba35570 100644 --- a/var/spack/repos/builtin/packages/r-randomfields/package.py +++ b/var/spack/repos/builtin/packages/r-randomfields/package.py @@ -11,12 +11,14 @@ class RRandomfields(RPackage): are provided, as well as methods for the simulation of extreme value random fields.""" - homepage = "https://cran.r-project.org/web/packages/RandomFields" - url = "https://cran.r-project.org/src/contrib/RandomFields_3.1.50.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RandomFields" + homepage = "https://cloud.r-project.org/package=RandomFields" + url = "https://cloud.r-project.org/src/contrib/RandomFields_3.1.50.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFields" + version('3.3.6', sha256='51b7bfb4e5bd7fd0ce1207c77f428508a6cd3dfc9de01545a8724dfd9c050213') + version('3.3.4', sha256='a340d4f3ba7950d62acdfa19b9724c82e439d7b1a9f73340124038b7c90c73d4') version('3.1.50', 'fd91aea76365427c0ba3b25fb3af43a6') - depends_on('r@3.3:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) - depends_on('r-randomfieldsutils@0.3.25:', type=('build', 'run')) + depends_on('r-randomfieldsutils@0.5.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index cbd01992570..fa51ba6c9ab 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -12,10 +12,12 @@ class RRandomfieldsutils(RPackage): checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.""" - homepage = "https://cran.r-project.org/web/packages/RandomFieldsUtils" - url = "https://cran.r-project.org/src/contrib/RandomFieldsUtils_0.3.25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RandomFieldsUtils" + homepage = "https://cloud.r-project.org/package=RandomFieldsUtils" + url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.3.25.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFieldsUtils" + version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') + version('0.5.1', sha256='a95aab4e2025c4247503ff513570a65aa3c8e63cb7ce2979c9317a2798dfaca2') version('0.3.25', '026c15a23296c9726012135891f016d5') - depends_on('r@3.3:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py index b2e99873936..b24defd121c 100644 --- a/var/spack/repos/builtin/packages/r-randomforest/package.py +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -11,7 +11,11 @@ class RRandomforest(RPackage): inputs.""" homepage = "https://www.stat.berkeley.edu/~breiman/RandomForests/" - url = "https://cran.r-project.org/src/contrib/randomForest_4.6-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/randomForest" + 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" + version('4.6-14', sha256='f4b88920419eb0a89d0bc5744af0416d92d112988702dc726882394128a8754d') version('4.6-12', '071c03af974198e861f1475c5bab9e7a') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-randomglm/package.py b/var/spack/repos/builtin/packages/r-randomglm/package.py index 47e513968d7..817d6467b40 100644 --- a/var/spack/repos/builtin/packages/r-randomglm/package.py +++ b/var/spack/repos/builtin/packages/r-randomglm/package.py @@ -10,8 +10,8 @@ class RRandomglm(RPackage): """randomGLM: Random General Linear Model Prediction""" homepage = "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/" - url = "https://cran.r-project.org/src/contrib/randomGLM_1.02-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/randomGLM" + 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" version('1.02-1', sha256='3bf7c1dbdacc68125f8ae3014b9bc546dd3328d04ad015d154781bdf3f1a230c') diff --git a/var/spack/repos/builtin/packages/r-ranger/package.py b/var/spack/repos/builtin/packages/r-ranger/package.py index 0a95a556351..a8cf0f0d0af 100644 --- a/var/spack/repos/builtin/packages/r-ranger/package.py +++ b/var/spack/repos/builtin/packages/r-ranger/package.py @@ -10,17 +10,19 @@ class RRanger(RPackage): """A fast implementation of Random Forests, particularly suited for high dimensional data.""" - homepage = "https://cran.r-project.org/web/packages/ranger/index.html" - url = "https://cran.r-project.org/src/contrib/ranger_0.8.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ranger" + homepage = "https://cloud.r-project.org/package=ranger" + url = "https://cloud.r-project.org/src/contrib/ranger_0.8.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ranger" + version('0.11.2', sha256='13ac8a9433fdd92f62f66de44abc52477dcbb436b2045c1947951a266bffbeeb') + version('0.11.1', sha256='999fb114602e27601ff0fe8ab461c39d667c6f5e8434e7feb3d21c7caf0dcffb') version('0.8.0', '1501380f418e784a6159bc1fb06fd32c') version('0.7.0', 'c7fbcbab7c195bc8e65b1ceb3baeb87f') version('0.6.0', '047ad26289c9b528b7476aa4811b4111') version('0.5.0', 'd45001c8ff58d3078de7353971219927') version('0.4.0', 'd404d8a9142372e3c77482b6b7dc469b') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.2:', type=('build', 'run')) depends_on('r-rcppeigen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rann/package.py b/var/spack/repos/builtin/packages/r-rann/package.py new file mode 100644 index 00000000000..bbe014ee45a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rann/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 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 RRann(RPackage): + """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" + + version('2.6.1', sha256='b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182') diff --git a/var/spack/repos/builtin/packages/r-rappdirs/package.py b/var/spack/repos/builtin/packages/r-rappdirs/package.py index 49e24bf0d54..5366f074940 100644 --- a/var/spack/repos/builtin/packages/r-rappdirs/package.py +++ b/var/spack/repos/builtin/packages/r-rappdirs/package.py @@ -11,9 +11,9 @@ class RRappdirs(RPackage): you should use to save data, caches and logs. A port of Python's 'Appdirs' to R.""" - homepage = "https://cran.r-project.org/package=rappdirs" - url = "https://cran.rstudio.com/src/contrib/rappdirs_0.3.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rappdirs" + homepage = "https://cloud.r-project.org/package=rappdirs" + url = "https://cloud.r-project.org/src/contrib/rappdirs_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rappdirs" version('0.3.1', 'fbbdceda2aa49374e61c7d387bf9ea21') diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py index e0cc4a95554..912f9c17e05 100644 --- a/var/spack/repos/builtin/packages/r-raster/package.py +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -11,11 +11,14 @@ class RRaster(RPackage): spatial data. The package implements basic and high-level functions. Processing of very large files is supported.""" - homepage = "http://cran.r-project.org/package=raster" - url = "https://cran.r-project.org/src/contrib/raster_2.5-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/raster" + homepage = "https://cloud.r-project.org/package=raster" + url = "https://cloud.r-project.org/src/contrib/raster_2.5-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/raster" + version('2.9-23', sha256='90aaec9e3b1e3e6015d9993ea7491e008f2f71990f8abb8610f979c4e28b38af') + version('2.9-22', sha256='8107d95f1aa85cea801c8101c6aa391becfef4b5b915d9bc7a323531fee26128') version('2.5-8', '2a7db931c74d50516e82d04687c0a577') - depends_on('r-sp', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-sp@1.2-0:', type=('build', 'run')) depends_on('r-rcpp', 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 332de772ba5..b0e8e510f76 100644 --- a/var/spack/repos/builtin/packages/r-rbokeh/package.py +++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py @@ -12,12 +12,12 @@ class RRbokeh(RPackage): Analytics.""" homepage = "https://hafen.github.io/rbokeh" - url = "https://cran.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rbokeh" + url = "https://cloud.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rbokeh" version('0.5.0', '4e14778c3fbd9286460ca28c68f57d10') - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r-htmlwidgets@0.5:', type=('build', 'run')) depends_on('r-maps', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcmdcheck/package.py b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py new file mode 100644 index 00000000000..c64a59bc977 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2019 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 RRcmdcheck(RPackage): + """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" + + 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-desc@1.2.0:', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-pkgbuild', type=('build', 'run')) + depends_on('r-prettyunits', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rprojroot', type=('build', 'run')) + depends_on('r-sessioninfo@1.1.1:', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) + depends_on('r-xopen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py index 287e846c7cf..b2cb38aa1f2 100644 --- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -11,7 +11,9 @@ class RRcolorbrewer(RPackage): Brewer as described at http://colorbrewer2.org""" homepage = "http://colorbrewer2.org" - url = "https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RColorBrewer" + 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" version('1.1-2', '66054d83eade4dff8a43ad4732691182') + + depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 3ee436d104f..e2abba3b833 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -18,9 +18,10 @@ class RRcpp(RPackage): last two.""" homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" - url = "https://cran.rstudio.com/src/contrib/Rcpp_0.12.13.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/Rcpp" + url = "https://cloud.r-project.org/src/contrib/Rcpp_0.12.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rcpp" + version('1.0.2', sha256='ad9338d6fc89dd116a3e2c5ecef1956e4be63b6c6aa1b21b2e5f249d65a5129c') version('1.0.0', sha256='b7378bf0dda17ef72aa3f2a318a9cb5667bef50b601dc1096431e17426e18bc2') version('0.12.19', sha256='63aeb6d4b58cd2899ded26f38a77d461397d5b0dc5936f187d3ca6cd958ab582') version('0.12.18', sha256='fcecd01e53cfcbcf58dec19842b7235a917b8d98988e4003cc090478c5bbd300') diff --git a/var/spack/repos/builtin/packages/r-rcppannoy/package.py b/var/spack/repos/builtin/packages/r-rcppannoy/package.py new file mode 100644 index 00000000000..64ee9a72aa0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcppannoy/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 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 RRcppannoy(RPackage): + """'Annoy' is a small C++ library for Approximate Nearest Neighbors written + for efficient memory usage as well an ability to load from / save to disk. + This package provides an R interface by relying on the 'Rcpp' package, + exposing the same interface as the original Python wrapper to 'Annoy'. See + for more on 'Annoy'. 'Annoy' is released + 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" + + version('0.0.12', sha256='8f736cbbb4a32c80cb08ba4e81df633846d725f27867e983af2012966eac0eac') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-rcpp@0.11.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py index 51ef1b3daf5..55f412a45c9 100644 --- a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py +++ b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py @@ -10,10 +10,13 @@ class RRcpparmadillo(RPackage): """'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library.""" - homepage = "https://cran.r-project.org/package=RcppArmadillo" - url = "https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.100.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RcppArmadillo" + homepage = "https://cloud.r-project.org/package=RcppArmadillo" + url = "https://cloud.r-project.org/src/contrib/RcppArmadillo_0.8.100.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppArmadillo" + version('0.9.600.4.0', sha256='2057b7aa965a4c821dd734276d8e6a01cd59a1b52536b65cb815fa7e8c114f1e') + version('0.9.400.3.0', sha256='56936d501fe8e6f8796ae1a6badb9294d7dad98a0b557c3b3ce6bd4ecaad13b0') version('0.8.100.1.0', 'a79c0ee967f502702414bc3c80c88f56') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@3.3.0:', when='@0.8.500.0:', type=('build', 'run')) + 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 d2161ceaa2d..e9af43aded0 100644 --- a/var/spack/repos/builtin/packages/r-rcppblaze/package.py +++ b/var/spack/repos/builtin/packages/r-rcppblaze/package.py @@ -35,12 +35,12 @@ class RRcppblaze(RPackage): the most compilers and system.""" homepage = "https://github.com/Chingchuan-chen/RcppBlaze" - url = "https://cran.rstudio.com/src/contrib/RcppBlaze_0.2.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/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" version('0.2.2', '22ecae73cf1bebce06ed6387d49f2c77') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-matrix@1.1-0:', type=('build', 'run')) depends_on('r-bh@1.54.0-2:', type=('build', 'run')) - depends_on('r@3.0.2:') diff --git a/var/spack/repos/builtin/packages/r-rcppcctz/package.py b/var/spack/repos/builtin/packages/r-rcppcctz/package.py index ad2b03965bd..d4f48d3a5c1 100644 --- a/var/spack/repos/builtin/packages/r-rcppcctz/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcctz/package.py @@ -14,9 +14,11 @@ class RRcppcctz(RPackage): for more details.""" homepage = "https://github.com/eddelbuettel/rcppcctz" - url = "https://cran.r-project.org/src/contrib/RcppCCTZ_0.2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.2.6', sha256='0e9a76055d29da24cd4c4069c78c1f44998f3461be60c7a6c3e7a35059fb79ae') + version('0.2.4', sha256='98b6867d38abe03957fe803e88b6cc2d122b85a68ef07fa86f7e1009d6c00819') version('0.2.3', '7635014a1cc696a3f00a7619fb5d7008') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py index 1344d5931fe..dc517e90603 100644 --- a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py @@ -10,11 +10,11 @@ class RRcppcnpy(RPackage): """Rcpp bindings for NumPy files.""" homepage = "https://github.com/eddelbuettel/rcppcnpy" - url = "https://cran.r-project.org/src/contrib/RcppCNPy_0.2.9.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/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" + version('0.2.10', sha256='77d6fbc86520a08da40d44c0b82767099f8f719ca95870d91efff1a9cab1ab9c') version('0.2.9', '7f63354d15928b6716830c2975b3baf0') depends_on('r@3.1.0:', type=('build', 'run')) - depends_on('cnpy') depends_on('r-rcpp', 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 1f07972974e..221a998383d 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -22,12 +22,15 @@ class RRcppeigen(RPackage): GNU GPL version 2 or later, as is the rest of 'Rcpp'.""" homepage = "http://eigen.tuxfamily.org/" - url = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen" + url = "https://cloud.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppEigen" + version('0.3.3.5.0', sha256='e5c6af17770c5f57b7cf2fba04ad1a519901b446e8138bfff221952458207f05') + version('0.3.3.4.0', sha256='11020c567b299b1eac95e8a4d57abf0315931286907823dc7b66c44d0dd6dad4') version('0.3.3.3.1', '1a5ae17828813e40e6b3e7400e408a2b') version('0.3.2.9.0', '14a7786882a5d9862d53c4b2217df318') version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@2.15.1:', type=('build', 'run')) + depends_on('r-matrix@1.1-0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppparallel/package.py b/var/spack/repos/builtin/packages/r-rcppparallel/package.py new file mode 100644 index 00000000000..ad723a0de54 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcppparallel/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 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 RRcppparallel(RPackage): + """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 = "http://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" + + version('4.4.3', sha256='7a04929ecab97e46c0b09fe5cdbac9d7bfa17ad7d111f1a9787a9997f45fa0fa') + + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rcppprogress/package.py b/var/spack/repos/builtin/packages/r-rcppprogress/package.py index 5ef2b4ea1f2..4680b00964e 100644 --- a/var/spack/repos/builtin/packages/r-rcppprogress/package.py +++ b/var/spack/repos/builtin/packages/r-rcppprogress/package.py @@ -11,14 +11,15 @@ class RRcppprogress(RPackage): computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.""" - homepage = "https://cran.r-project.org/web/packages/RcppProgress/index.html" - url = "https://cran.r-project.org/src/contrib/RcppProgress_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RcppProgress" + 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" + version('0.4.1', sha256='11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a') + version('0.4', sha256='706e14360dbc5976db05c2ac6692c3279c0f8c95e72bf9d4becd9e1348025e3e') version('0.3', '3cd527af84bc6fcb3c77422e0ff09dba') version('0.2.1', 'c9cd69759ff457acfee0b52353f9af1b') version('0.2', '9522c962ecddd4895b5636e7a499bda5') version('0.1', '34afefe0580ca42b6353533fe758d5bf') - depends_on('r@3.4.0:3.4.9') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.9.4:', when='@:0.4', 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 2c88de66fe4..0af3d5275ea 100644 --- a/var/spack/repos/builtin/packages/r-rcurl/package.py +++ b/var/spack/repos/builtin/packages/r-rcurl/package.py @@ -18,11 +18,14 @@ class RRcurl(RPackage): SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.""" - homepage = "https://cran.rstudio.com/web/packages/RCurl/index.html" - url = "https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl" + 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" + version('1.95-4.12', sha256='393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4') version('1.95-4.8', '9c8aaff986eb2792c89dd3ae54d21580') + depends_on('r@3.0.0:', type=('build', 'run')) 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 3dc929a13ad..4cdbe65ac05 100644 --- a/var/spack/repos/builtin/packages/r-rda/package.py +++ b/var/spack/repos/builtin/packages/r-rda/package.py @@ -10,8 +10,12 @@ class RRda(RPackage): """Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.""" - homepage = "https://cran.r-project.org/web/packages/rda/index.html" - url = "https://cran.r-project.org/src/contrib/rda_1.0.2-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rda" + 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" + version('1.0.2-2.1', sha256='6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8') + version('1.0.2-2', sha256='52ee41249b860af81dc692eee38cd4f8f26d3fbe34cb274f4e118de0013b58bc') version('1.0.2-1', '78060c5e054a63a2df4ae4002d7247bc') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rdpack/package.py b/var/spack/repos/builtin/packages/r-rdpack/package.py new file mode 100644 index 00000000000..2febe781863 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rdpack/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 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 RRdpack(RPackage): + """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" + + version('0.11-0', sha256='8fb449c80fbe931cdce51f728fb03a1978009ccce66fd6b9edacdc6ff4118d85') + + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-bibtex@0.4.0:', type=('build', 'run')) + depends_on('r-gbrd', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-readr/package.py b/var/spack/repos/builtin/packages/r-readr/package.py index 1b6753916ba..586d0d95285 100644 --- a/var/spack/repos/builtin/packages/r-readr/package.py +++ b/var/spack/repos/builtin/packages/r-readr/package.py @@ -12,14 +12,20 @@ class RReadr(RPackage): flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.""" - homepage = "https://cran.rstudio.com/web/packages/readr/index.html" - url = "https://cran.rstudio.com/src/contrib/readr_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/readr/" + homepage = "https://cloud.r-project.org/package=readr" + url = "https://cloud.r-project.org/src/contrib/readr_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/readr" + version('1.3.1', sha256='33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3') version('1.1.1', 'cffb6669664f6a0f6fe172542e64cb47') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@3.0.2:', when='@:1.2.1', type=('build', 'run')) + depends_on('r@3.1:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.0.5:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) - depends_on('r-hms', type=('build', 'run')) + depends_on('r-hms@0.4.1:', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) depends_on('r-bh', type=('build', 'run')) + depends_on('r-clipr', when='@1.2.0:', type=('build', 'run')) + depends_on('r-crayon', when='@1.3.1:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-readxl/package.py b/var/spack/repos/builtin/packages/r-readxl/package.py index f01cc790ff0..599534113d3 100644 --- a/var/spack/repos/builtin/packages/r-readxl/package.py +++ b/var/spack/repos/builtin/packages/r-readxl/package.py @@ -14,12 +14,15 @@ class RReadxl(RPackage): without external dependencies.""" homepage = "http://readxl.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/readxl_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/readxl/readxl_1.0.0.tar.gz" + 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" + version('1.3.1', sha256='24b441713e2f46a3e7c6813230ad6ea4d4ddf7e0816ad76614f33094fbaaaa96') + version('1.3.0', sha256='8379d1026dcfc662d073eb1c69ed1d90aa6439d6cb3c6fc1b5d1db4f51b3fadc') version('1.1.0', sha256='b63d21fc6510acb373e96deaec45e966a523ec75cbec75a089529297ed443116') version('1.0.0', '030c47ae1af5dd4168087160c29131e4') - depends_on('r-tibble', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-recipes/package.py b/var/spack/repos/builtin/packages/r-recipes/package.py new file mode 100644 index 00000000000..12c00f66136 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-recipes/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2019 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 RRecipes(RPackage): + """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" + + version('0.1.6', sha256='51e0db72de171d58d13ad8ffcf1dea402ab8f82100d161722041b6fd014cbfd9') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-generics', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run')) + depends_on('r-gower', type=('build', 'run')) + depends_on('r-ipred', type=('build', 'run')) + depends_on('r-lubridate', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-purrr@0.2.3:', type=('build', 'run')) + 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-tidyselect@0.2.5:', type=('build', 'run')) + depends_on('r-timedate', type=('build', 'run')) + 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 4c6acb2624c..457908f4dfd 100644 --- a/var/spack/repos/builtin/packages/r-registry/package.py +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -9,8 +9,12 @@ class RRegistry(RPackage): """Provides a generic infrastructure for creating and using registries.""" - homepage = "https://cran.r-project.org/web/packages/registry/index.html" - url = "https://cran.r-project.org/src/contrib/registry_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/registry" + 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" + version('0.5-1', sha256='dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc') + version('0.5', sha256='5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb') version('0.3', '85345b334ec81eb3da6edcbb27c5f421') + + depends_on('r@2.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rematch/package.py b/var/spack/repos/builtin/packages/r-rematch/package.py index 00f5d75da55..2887630876a 100644 --- a/var/spack/repos/builtin/packages/r-rematch/package.py +++ b/var/spack/repos/builtin/packages/r-rematch/package.py @@ -11,10 +11,8 @@ class RRematch(RPackage): captured groups from the match of a regular expression to a character vector.""" - homepage = "https://cran.r-project.org/package=rematch" - url = "https://cran.r-project.org/src/contrib/rematch_1.0.1.tar.gz" + 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" version('1.0.1', '5271666295e232931f21499522489dd3') - - depends_on('r-covr', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-remotes/package.py b/var/spack/repos/builtin/packages/r-remotes/package.py new file mode 100644 index 00000000000..9c4a790dcb1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-remotes/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 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 RRemotes(RPackage): + """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" + + version('2.1.0', sha256='8944c8f6fc9f0cd0ca04d6cf1221b716eee08facef9f4b4c4d91d0346d6d68a7') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reordercluster/package.py b/var/spack/repos/builtin/packages/r-reordercluster/package.py index d1ed897d0ee..5d63690aa80 100644 --- a/var/spack/repos/builtin/packages/r-reordercluster/package.py +++ b/var/spack/repos/builtin/packages/r-reordercluster/package.py @@ -11,10 +11,12 @@ class RReordercluster(RPackage): that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.""" - homepage = "https://cran.r-project.org/package=ReorderCluster" - url = "https://cran.rstudio.com/src/contrib/ReorderCluster_1.0.tar.gz" + 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" version('1.0', '67ba34acb15dda75389a822bd2fdd31a') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-gplots', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py index eed19834ad6..de4930c4c80 100644 --- a/var/spack/repos/builtin/packages/r-reportingtools/package.py +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -41,7 +41,7 @@ class RReportingtools(RPackage): depends_on('r-gseabase', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) - depends_on('r-utils', type=('build', 'run')) + depends_on('r-r-utils', type=('build', 'run')) depends_on('r-deseq2', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-ggbio', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py index ca7f3a37e69..90da8713f61 100644 --- a/var/spack/repos/builtin/packages/r-repr/package.py +++ b/var/spack/repos/builtin/packages/r-repr/package.py @@ -12,7 +12,15 @@ class RRepr(RPackage): mime types.""" homepage = "https://github.com/IRkernel/repr" - url = "https://cran.r-project.org/src/contrib/repr_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.0.1', sha256='ecde22c17fd800e1ff5c2b2962689119aa486fba40fbc6f2c50e8d4cc61bc44b') + version('1.0.0', sha256='98b2eb1058c1cb2caa8f98708b63726f5564b45de03d38b95ff6b963a8261f49') version('0.9', 'db5ff74893063b492f684e42283070bd') + + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r-htmltools', when='@0.13:', type=('build', 'run')) + depends_on('r-base64enc', 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')) diff --git a/var/spack/repos/builtin/packages/r-reprex/package.py b/var/spack/repos/builtin/packages/r-reprex/package.py index c0c0393f737..7a0f5063891 100644 --- a/var/spack/repos/builtin/packages/r-reprex/package.py +++ b/var/spack/repos/builtin/packages/r-reprex/package.py @@ -16,13 +16,21 @@ class RReprex(RPackage): formats, such as copy/paste from an R session.""" homepage = "https://github.com/jennybc/reprex" - url = "https://cran.r-project.org/src/contrib/reprex_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/reprex" + url = "https://cloud.r-project.org/src/contrib/reprex_0.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/reprex" + version('0.3.0', sha256='203c2ae6343f6ff887e7a5a3f5d20bae465f6e8d9745c982479f5385f4effb6c') + version('0.2.1', sha256='5d234ddfbcadc5a5194a58eb88973c51581e7e2e231f146974af8f42747b45f3') version('0.1.1', 'fcd89995d7b35a2ddd4269973937bde3') - depends_on('r-callr', type=('build', 'run')) - depends_on('r-clipr', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) + depends_on('r@3.0.2:', when='@:0.1.2', type=('build', 'run')) + depends_on('r@3.1:', when='@0.2.0:', type=('build', 'run')) + depends_on('r-callr@2.0.0:', type=('build', 'run')) + depends_on('r-clipr@0.4.0:', type=('build', 'run')) + depends_on('r-knitr', when='@:0.1.9', type=('build', 'run')) depends_on('r-rmarkdown', type=('build', 'run')) depends_on('r-whisker', type=('build', 'run')) + depends_on('r-rlang', when='@0.2.0:', type=('build', 'run')) + depends_on('r-withr', when='@0.2.0:', type=('build', 'run')) + depends_on('r-fs', when='@0.2.1:', type=('build', 'run')) + depends_on('pandoc@1.12.3:') diff --git a/var/spack/repos/builtin/packages/r-reshape/package.py b/var/spack/repos/builtin/packages/r-reshape/package.py index 7e38c9fdc10..ed783c9def9 100644 --- a/var/spack/repos/builtin/packages/r-reshape/package.py +++ b/var/spack/repos/builtin/packages/r-reshape/package.py @@ -10,10 +10,12 @@ class RReshape(RPackage): """Flexibly restructure and aggregate data using just two functions: melt and cast.""" - homepage = "https://cran.r-project.org/package=reshape" - url = "https://cran.r-project.org/src/contrib/reshape_0.8.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/reshape" + 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" + version('0.8.8', sha256='4d5597fde8511e8fe4e4d1fd7adfc7ab37ff41ac68c76a746f7487d7b106d168') version('0.8.7', '0b0eececc5eb74dea9d59a985bce6211') + depends_on('r@2.6.1:', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index cd2a9d59b30..0a04e1b4edf 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -11,12 +11,14 @@ class RReshape2(RPackage): and dcast (or acast).""" homepage = "https://github.com/hadley/reshape" - url = "https://cran.r-project.org/src/contrib/reshape2_1.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/reshape2" + 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" + version('1.4.3', sha256='8aff94c935e75032344b52407593392ddd4e16a88bb206984340c816d42c710e') version('1.4.2', 'c851a0312191b8c5bab956445df7cf5f') version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') - depends_on('r-plyr', type=('build', 'run')) + depends_on('r@3.1:', when='@1.4.3:', type=('build', 'run')) + depends_on('r-plyr@1.8.1:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-rcpp', 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 new file mode 100644 index 00000000000..f1dc039491f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-reticulate/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 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 RReticulate(RPackage): + """Interface to 'Python' modules, classes, and functions. When calling into + 'Python', R data types are automatically converted to their equivalent + 'Python' types. When values are returned from 'Python' to R they are + 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" + + version('1.13', sha256='adbe41d556b667c4419d563680f8608a56b0f792b8bc427b3bf4c584ff819de3') + + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-rcpp@0.12.7:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('python@2.7.0:') diff --git a/var/spack/repos/builtin/packages/r-rex/package.py b/var/spack/repos/builtin/packages/r-rex/package.py index 968f4a09590..54d124d84a3 100644 --- a/var/spack/repos/builtin/packages/r-rex/package.py +++ b/var/spack/repos/builtin/packages/r-rex/package.py @@ -9,9 +9,9 @@ class RRex(RPackage): """A friendly interface for the construction of regular expressions.""" - homepage = "https://cran.r-project.org/package=rex" - url = "https://cran.r-project.org/src/contrib/rex_1.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rex" + 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" version('1.1.2', '8820b4d4fe3718f275847b6f2cf83689') diff --git a/var/spack/repos/builtin/packages/r-rgdal/package.py b/var/spack/repos/builtin/packages/r-rgdal/package.py index 1146e0ff583..39c95f3cb5f 100644 --- a/var/spack/repos/builtin/packages/r-rgdal/package.py +++ b/var/spack/repos/builtin/packages/r-rgdal/package.py @@ -17,13 +17,16 @@ class RRgdal(RPackage): Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.""" - homepage = "https://cran.r-project.org/package=rgdal" - url = "https://cran.rstudio.com/src/contrib/rgdal_1.3-9.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rgdal" + 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" + version('1.4-4', sha256='2532e76e0af27d145f799d70006a5dbecb2d3be698e3d0bbf580f4c41a34c5d7') version('1.3-9', sha256='3e44f88d09894be4c0abd8874d00b40a4a5f4542b75250d098ffbb3ba41e2654') version('1.2-16', 'de83bf08519a53de68a7632ecb7f2dc9') - depends_on('r-sp', type=('build', 'run')) - depends_on('gdal') - depends_on('proj@:5') + depends_on('r@3.3.0:', type=('build', 'run')) + 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:') diff --git a/var/spack/repos/builtin/packages/r-rgenoud/package.py b/var/spack/repos/builtin/packages/r-rgenoud/package.py index 7b836f82fb8..f5cc12720d0 100644 --- a/var/spack/repos/builtin/packages/r-rgenoud/package.py +++ b/var/spack/repos/builtin/packages/r-rgenoud/package.py @@ -10,7 +10,11 @@ class RRgenoud(RPackage): """A genetic algorithm plus derivative optimizer.""" homepage = "http://sekhon.berkeley.edu/rgenoud/" - url = "https://cran.r-project.org/src/contrib/rgenoud_5.8-1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('5.8-3.0', sha256='9beb11b5edab3ab3aa6001daa39668b240a8e0328be9d55db4e23ff88ce3235d') + version('5.8-2.0', sha256='106c4f6a6df5159578e929a0141b3cfbaa88141a70703ff59a1fc48a27e2d239') version('5.8-1.0', '85801093d2f1e6789683b46ab4a7d70f') + + depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgeos/package.py b/var/spack/repos/builtin/packages/r-rgeos/package.py index fb889dda960..fd982f99968 100644 --- a/var/spack/repos/builtin/packages/r-rgeos/package.py +++ b/var/spack/repos/builtin/packages/r-rgeos/package.py @@ -13,11 +13,13 @@ class RRgeos(RPackage): must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.""" - homepage = "https://cran.r-project.org/package=rgeos" - url = "https://cran.rstudio.com/src/contrib/rgeos_0.3-26.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rgeos" + 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" + version('0.5-1', sha256='8408973e7fe5648e39aa53f3d4bfe800638021a146a4e06f86496c0132e05488') version('0.3-26', '7d10a28011b49f68c5817b6fbca132df') - depends_on('r-sp', type=('build', 'run')) - depends_on('geos') + 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:') diff --git a/var/spack/repos/builtin/packages/r-rgexf/package.py b/var/spack/repos/builtin/packages/r-rgexf/package.py new file mode 100644 index 00000000000..3a98d900359 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rgexf/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 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 RRgexf(RPackage): + """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 = "http://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" + + version('0.15.3', sha256='2e8a7978d1fb977318e6310ba65b70a9c8890185c819a7951ac23425c6dc8147') + + depends_on('r-xml', type=('build', 'run')) + depends_on('r-rook', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgl/package.py b/var/spack/repos/builtin/packages/r-rgl/package.py index 372833f8ab5..2195923a6e0 100644 --- a/var/spack/repos/builtin/packages/r-rgl/package.py +++ b/var/spack/repos/builtin/packages/r-rgl/package.py @@ -15,27 +15,30 @@ class RRgl(RPackage): including PNG, Postscript, SVG, PGF.""" homepage = "https://r-forge.r-project.org/projects/rgl" - url = "https://cran.r-project.org/src/contrib/rgl_0.99.16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.100.26', sha256='e1889c2723ad458b39fdf9366fdaf590d7657d3762748f8534a8491ef754e740') + version('0.100.24', sha256='1233a7bdc5a2b908fc64d5f56e92a0e123e8f7c0b9bac93dfd005608b78fa35a') version('0.99.16', sha256='692a545ed2ff0f5e15289338736f0e3c092667574c43ac358d8004901d7a1a61') version('0.98.1', 'bd69e1d33f1590feb4b6dc080b133e5b') - depends_on('r@3.2:3.9') - depends_on('zlib', type=('link')) - depends_on('libpng', type=('link')) - depends_on('libx11') - depends_on('freetype', type=('link')) - depends_on('gl') - depends_on('glu') + depends_on('r@3.2:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-knitr', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + 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', type=('build', 'run'), when='@0.99.16:') - depends_on('r-manipulatewidget', type=('build', 'run'), when='@0.99.16:') + 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('zlib', type='link') + depends_on('libpng@1.2.9:', type='link') + depends_on('libx11') + depends_on('freetype', type='link') + depends_on('gl') + depends_on('glu') + depends_on('pandoc@1.14:', type='build') def configure_args(self): args = ['--x-includes=%s' % self.spec['libx11'].prefix.include, diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py index 5450d5dd8e1..1c615f7e777 100644 --- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -12,11 +12,14 @@ class RRgooglemaps(RPackage): background image to overlay plots within R. This requires proper coordinate scaling.""" - homepage = "https://cran.r-project.org/package=RgoogleMaps" - url = "https://cran.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RgoogleMaps" + 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" + version('1.4.3', sha256='44cb62bcd23e5b4807e91c5825352eb8d38aaaeb3b38a8271ca9f21c1e1d4b19') + version('1.4.2', sha256='b479996fcb72f067644a7ea7f00325e44e76efd202e84aaab022753c4a6d5584') version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) - depends_on('r-rjsonio', type=('build', 'run')) + depends_on('r-rjsonio', when='@1.2.0.5:1.2.0.7', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rhmmer/package.py b/var/spack/repos/builtin/packages/r-rhmmer/package.py index 4fe328f7393..23854fb2b15 100644 --- a/var/spack/repos/builtin/packages/r-rhmmer/package.py +++ b/var/spack/repos/builtin/packages/r-rhmmer/package.py @@ -9,9 +9,9 @@ class RRhmmer(RPackage): """rhmmer: Utilities Parsing 'HMMER' Results""" - homepage = "https://cran.r-project.org/package=rhmmer" - url = "https://cran.r-project.org/src/contrib/rhmmer_0.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rhmmer/" + 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/" version('0.1.0', sha256='5022cefc9ba335160c1ad8d1b614610ae0ad48287c9fdbaf8f8966149358e520') @@ -21,5 +21,3 @@ class RRhmmer(RPackage): depends_on('r-dplyr', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-covr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py index 7ed751394ee..5681e87113f 100644 --- a/var/spack/repos/builtin/packages/r-rinside/package.py +++ b/var/spack/repos/builtin/packages/r-rinside/package.py @@ -23,11 +23,12 @@ class RRinside(RPackage): available at the 'RInside' website as well.""" homepage = "http://dirk.eddelbuettel.com/code/rinside.html" - url = "https://cran.r-project.org/src/contrib/RInside_0.2.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RInside" + 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" version('0.2.15', '3b8c13dc53c6958c1f82c0a25dd6c211') version('0.2.14', 'fc72761e22b1f597433eb53d6eb122ff') version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rio/package.py b/var/spack/repos/builtin/packages/r-rio/package.py new file mode 100644 index 00000000000..5b4934f4294 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rio/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 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 RRio(RPackage): + """Streamlined data import and export by making assumptions that the user + is probably willing to make: 'import()' and 'export()' determine the data + structure from the file extension, reasonable defaults are used for data + import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is + natively supported (including from SSL/HTTPS), compressed files can be read + directly without explicit decompression, and fast import packages are used + where appropriate. An additional convenience function, 'convert()', + provides a simple method for converting between file types.""" + + homepage = "https://github.com/leeper/rio" + url = "https://cloud.r-project.org/src/contrib/rio_0.5.16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rio" + + version('0.5.16', sha256='d3eb8d5a11e0a3d26169bb9d08f834a51a6516a349854250629072d59c29d465') + + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-foreign', type=('build', 'run')) + 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')) + depends_on('r-readxl@0.1.1:', type=('build', 'run')) + depends_on('r-openxlsx', type=('build', 'run')) + depends_on('r-tibble', 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 dc66dd0c39a..0b86c0e8e67 100644 --- a/var/spack/repos/builtin/packages/r-rjags/package.py +++ b/var/spack/repos/builtin/packages/r-rjags/package.py @@ -11,15 +11,16 @@ class RRjags(RPackage): """Interface to the JAGS MCMC library. Usage: $ spack load r-rjags """ - homepage = "https://cran.r-project.org/web/packages/rjags/index.html" - url = "https://cran.r-project.org/src/contrib/rjags_4-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rjags/" + 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/" version('4-8', sha256='1529827ab11493fb5f05552e239d700ae2f818995d86d3c9e4c92523f594b59f') version('4-6', 'c26b7cc8e8ddcdb55e14cba28df39f4c') - depends_on('jags', type=('link')) - depends_on('r-coda', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-coda@0.13:', type=('build', 'run')) + depends_on('jags@4.0.0:4.999.999', type=('link')) def configure_args(self): args = ['--with-jags-lib=%s' % self.spec['jags'].prefix.lib, diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index 8148ed2d748..cc6bb3cdfba 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -11,10 +11,12 @@ class RRjava(RPackage): Allows creation of objects, calling methods and accessing fields.""" homepage = "http://www.rforge.net/rJava/" - url = "https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.9-11', sha256='c28ae131456a98f4d3498aa8f6eac9d4df48727008dacff1aa561fc883972c69') version('0.9-8', '51ae0d690ceed056ebe7c4be71fc6c7a') - depends_on('java') + depends_on('r@2.5:', type=('build', 'run')) + depends_on('java@1.2:') + 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 b6c928ad06b..9c2c7a14095 100644 --- a/var/spack/repos/builtin/packages/r-rjson/package.py +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -9,8 +9,12 @@ class RRjson(RPackage): """Converts R object into JSON objects and vice-versa.""" - homepage = "https://cran.r-project.org/package=rjson" - url = "https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rjson" + 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" + version('0.2.20', sha256='3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c') + version('0.2.19', sha256='5c2672461986f2b715416cab92ed262abe9875f31299bc8a1a072ef7c6dd49bc') version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py index 2f68f67596f..b981fa80fe0 100644 --- a/var/spack/repos/builtin/packages/r-rjsonio/package.py +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -23,8 +23,10 @@ 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://cran.r-project.org/package=RJSONIO" - url = "https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RJSONIO" + 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" + version('1.3-1.2', sha256='550e18f7c04186376d67747b8258f529d205bfc929da9194fe45ec384e092d7e') + version('1.3-1.1', sha256='c72493b441758cd1e3e9d91296b9ea31068e71104649f46ad84c854a02c09693') version('1.3-0', '72c395622ba8d1435ec43849fd32c830') diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py index 2fada492907..f7a5344ba42 100644 --- a/var/spack/repos/builtin/packages/r-rlang/package.py +++ b/var/spack/repos/builtin/packages/r-rlang/package.py @@ -10,10 +10,12 @@ class RRlang(RPackage): """A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.""" - homepage = "https://cran.r-project.org/package=rlang" - url = "https://cran.r-project.org/src/contrib/rlang_0.2.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rlang" + homepage = "https://cloud.r-project.org/package=rlang" + url = "https://cloud.r-project.org/src/contrib/rlang_0.2.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rlang" + version('0.4.0', sha256='9748a4a217548bbe5631c18fd88c94811950446f798ff21fb327703aebaa150d') + version('0.3.4', sha256='4e467f7b0dcbde91b60c292137d2c69cecaa713a6e4c9b7157ef6fd5453b7ade') version('0.3.1', sha256='30427b2be2288e88acd30c4ea348ee06043a649fd73623a63148b1ad96317151') version('0.3.0.1', sha256='29451db0a3cabd75761d32df47a5d43ccadbde07ecb693ffdd73f122a0b9f348') version('0.3.0', sha256='9ab10ea3e19b2d60a289602ebbefa83509f430db1c8161e523896c374241b893') @@ -21,3 +23,6 @@ class RRlang(RPackage): version('0.1.4', 'daed5104d557c0cbfb4a654ec8ffb579') version('0.1.2', '170f8cf7b61898040643515a1746a53a') version('0.1.1', '38a51a0b8f8487eb52b4f3d986313682') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py index 30c61e67707..aec117f37a7 100644 --- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py +++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py @@ -11,20 +11,25 @@ class RRmarkdown(RPackage): """Convert R Markdown documents into a variety of formats.""" homepage = "http://rmarkdown.rstudio.com/" - url = "https://cran.r-project.org/src/contrib/rmarkdown_1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rmarkdown" + url = "https://cloud.r-project.org/src/contrib/rmarkdown_1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rmarkdown" + version('1.14', sha256='f636b1048c5be56e06aa0b2b4342ad5c8192734f1e9b27468fef62be672edc61') + version('1.13', sha256='96fb6b08d27bbb8054145e0a55721f905341941d4f6691480a2a234e2d5a63ef') version('1.7', '477c50840581ba7947b3d905c67a511b') version('1.0', '264aa6a59e9680109e38df8270e14c58') - depends_on('r-knitr@1.14:', type=('build', 'run')) - depends_on('r-yaml@2.1.5:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-knitr@1.22:', type=('build', 'run')) + depends_on('r-yaml@2.1.19:', type=('build', 'run')) depends_on('r-htmltools@0.3.5:', type=('build', 'run')) - depends_on('r-evaluate@0.8:', type=('build', 'run')) + depends_on('r-evaluate@0.13:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-rprojroot', type=('build', 'run')) - depends_on('r-mime', type=('build', 'run')) - depends_on('r-stringr@1.2.0:', type=('build', 'run')) - depends_on('r-catools', type=('build', 'run')) - depends_on('r@3.0:') + depends_on('r-rprojroot', when='@1.3:1.7', type=('build', 'run')) + depends_on('r-mime', when='@1.8:', type=('build', 'run')) + depends_on('r-stringr@1.2.0:', when='@1.6:', type=('build', 'run')) + depends_on('r-catools', when='@:1.7', type=('build', 'run')) + depends_on('r-tinytex@0.11:', when='@1.10:', type=('build', 'run')) + depends_on('r-xfun', when='@1.13:', type=('build', 'run')) + depends_on('pandoc@1.12.3:') diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py index 08b8ea7aa3c..92b99dd9f7d 100644 --- a/var/spack/repos/builtin/packages/r-rminer/package.py +++ b/var/spack/repos/builtin/packages/r-rminer/package.py @@ -12,8 +12,8 @@ class RRminer(RPackage): and coherent set of functions.""" homepage = "http://www3.dsi.uminho.pt/pcortez/rminer.html" - url = "https://cran.r-project.org/src/contrib/rminer_1.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rminer" + 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" version('1.4.2', '7d5d90f4ae030cf647d67aa962412c05') diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py index 54d9238265f..840a4f3f205 100644 --- a/var/spack/repos/builtin/packages/r-rmpfr/package.py +++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py @@ -14,10 +14,16 @@ class RRmpfr(RPackage): is based on the GMP (GNU Multiple Precision) Library.""" homepage = "http://rmpfr.r-forge.r-project.org" - url = "https://cran.r-project.org/src/contrib/Rmpfr_0.6-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Rmpfr" + 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" + version('0.7-2', sha256='ec1da6ec5292ea6ac95495c6a299591d367e520ae324719817fb884c865603ff') + version('0.7-1', sha256='9b3021617a22b0710b0f1acc279290762317ff123fd9e8fd03f1449f4bbfe204') version('0.6-1', '55d4ec257bd2a9233bafee9e444d0265') + depends_on('r@3.0.1:', when='@:0.6-1', 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-gmp@0.5-8:', type=('build', 'run')) depends_on('mpfr@3.0.0:') + depends_on('gmp@4.2.3:') diff --git a/var/spack/repos/builtin/packages/r-rmpi/package.py b/var/spack/repos/builtin/packages/r-rmpi/package.py index 614e7be67eb..fe43add7b86 100644 --- a/var/spack/repos/builtin/packages/r-rmpi/package.py +++ b/var/spack/repos/builtin/packages/r-rmpi/package.py @@ -11,12 +11,15 @@ class RRmpi(RPackage): manager and worker environment.""" homepage = "http://www.stats.uwo.ca/faculty/yu/Rmpi" - url = "https://cran.r-project.org/src/contrib/Rmpi_0.6-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Rmpi" + 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" + version('0.6-9', sha256='b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6') + version('0.6-8', sha256='9b453ce3bd7284eda33493a0e47bf16db6719e3c48ac5f69deac6746f5438d96') version('0.6-6', 'a6fa2ff5e1cd513334b4e9e9e7a2286f') + + depends_on('r@2.15.1:', type=('build', 'run')) depends_on('mpi') - depends_on('r@2.15.1:') # The following MPI types are not supported conflicts('^intel-mpi') diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 4e73352019d..6739bdb1043 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -10,11 +10,13 @@ class RRmysql(RPackage): """Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.""" homepage = "https://github.com/rstats-db/rmysql" - url = "https://cran.r-project.org/src/contrib/RMySQL_0.10.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.10.17', sha256='754df4fce159078c1682ef34fc96aa5ae30981dc91f4f2bada8d1018537255f5') version('0.10.9', '3628200a1864ac3005cfd55cc7cde17a') depends_on('r-dbi@0.4:', type=('build', 'run')) - depends_on('mariadb@:5.5.56') + depends_on('mariadb@:5.5') + + depends_on('r@2.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index 4ab784813fd..ea11d03f0fb 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -14,12 +14,17 @@ class RRngtools(RPackage): the way current RNG settings can be changed.""" homepage = "https://renozao.github.io/rngtools" - url = "https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rngtools" + url = "https://cloud.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rngtools" + version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') + version('1.3.1.1', sha256='99e1a8fde6b81128d0946746c1ef84ec5b6c2973ad843a080098baf73aa3364c') version('1.3.1', sha256='763fc493cb821a4d3e514c0dc876d602a692c528e1d67f295dde70c77009e224') version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') - depends_on('r-pkgmaker', type=('build', 'run')) + depends_on('r@3.0.0:', when='@:1.3.1', type=('build', 'run')) + depends_on('r@3.6.0:', when='@1.3.1.1', type=('build', 'run')) + depends_on('r@3.2.0:', when='@1.4:', type=('build', 'run')) + depends_on('r-pkgmaker@0.20:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rnoaa/package.py b/var/spack/repos/builtin/packages/r-rnoaa/package.py index 0eabbc65852..7434fb58bab 100644 --- a/var/spack/repos/builtin/packages/r-rnoaa/package.py +++ b/var/spack/repos/builtin/packages/r-rnoaa/package.py @@ -10,8 +10,8 @@ class RRnoaa(RPackage): """rnoaa: 'NOAA' Weather Data from R""" homepage = "https://github.com/ropensci/rnoaa" - url = "https://cran.r-project.org/src/contrib/rnoaa_0.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.8.4', sha256='fb9ae771111dd5f638c1eff3290abad2ff9cc7e68a6678bf2414433ebed2dbbf') diff --git a/var/spack/repos/builtin/packages/r-robust/package.py b/var/spack/repos/builtin/packages/r-robust/package.py index 3e83224ead0..b49de8879f2 100644 --- a/var/spack/repos/builtin/packages/r-robust/package.py +++ b/var/spack/repos/builtin/packages/r-robust/package.py @@ -10,10 +10,11 @@ class RRobust(RPackage): """robust: Port of the S+ Robust Library """ - homepage = "https://cran.r-project.org/package=robust" - url = "https://cran.r-project.org/src/contrib/robust_0.4-18.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/robust/" + 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/" + version('0.4-18.1', sha256='de31901882873ef89748bb6863caf55734431df5b3eb3c6663ed17ee2e4a4077') version('0.4-18', sha256='e4196f01bb3b0d768759d4411d524238b627eb8dc213d84cb30014e75480f8ac') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py index f8b96ddcf0a..6b8c510639d 100644 --- a/var/spack/repos/builtin/packages/r-robustbase/package.py +++ b/var/spack/repos/builtin/packages/r-robustbase/package.py @@ -14,9 +14,13 @@ class RRobustbase(RPackage): by 'Maronna, Martin and Yohai'; Wiley 2006.""" homepage = "https://robustbase.r-forge.r-project.org" - url = "https://cran.r-project.org/src/contrib/robustbase_0.92-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/robustbase" + 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" + version('0.93-5', sha256='bde564dbd52f04ab32f9f2f9dd09b9578f3ccd2541cf5f8ff430da42a55e7f56') + version('0.93-4', sha256='ea9e03d484ef52ea805803477ffc48881e4c8c86ffda4eea56109f8b23f0a6e0') version('0.92-7', 'db3c8d12f9729b35bad17abf09e80b72') + 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-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 02d3b7e3674..4952136ac5d 100644 --- a/var/spack/repos/builtin/packages/r-rocr/package.py +++ b/var/spack/repos/builtin/packages/r-rocr/package.py @@ -23,9 +23,9 @@ class RRocr(RPackage): mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.""" - homepage = "https://cran.r-project.org/package=ROCR" - url = "https://cran.rstudio.com/src/contrib/ROCR_1.0-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ROCR" + 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" version('1.0-7', '46cbd43ae87fc4e1eff2109529a4820e') 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 4eb0f0d0179..a21269c1ef6 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -9,10 +9,13 @@ class RRodbc(RPackage): """An ODBC database interface.""" - homepage = "https://cran.rstudio.com/web/packages/RODBC/" - url = "https://cran.rstudio.com/src/contrib/RODBC_1.3-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RODBC/" + 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/" + version('1.3-15', sha256='c43e5a2f0aa2f46607e664bfc0bb3caa230bbb779f4ff084e01727642da136e1') version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e') depends_on('unixodbc') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rook/package.py b/var/spack/repos/builtin/packages/r-rook/package.py new file mode 100644 index 00000000000..4d3b1dbda97 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rook/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 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 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.""" + + 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" + + version('1.1-1', sha256='00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903') + + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-brew', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py index f85b27187cd..3958ab12984 100644 --- a/var/spack/repos/builtin/packages/r-roxygen2/package.py +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -11,12 +11,14 @@ class RRoxygen2(RPackage): 'NAMESPACE' files.""" homepage = "https://github.com/klutometis/roxygen" - url = "https://cran.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/roxygen2" + 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" version('6.1.1', sha256='ed46b7e062e0dfd8de671c7a5f6d120fb2b720982e918dbeb01e6985694c0273') version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7') + depends_on('r@3.0.2:', when='@:6.0.1', type=('build', 'run')) + depends_on('r@3.1:', when='@6.1.0:', type=('build', 'run')) depends_on('r-brew', type=('build', 'run')) depends_on('r-commonmark', type=('build', 'run')) depends_on('r-desc@1.2.0:', type=('build', 'run')) 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 59a74efa904..4671e1078a1 100644 --- a/var/spack/repos/builtin/packages/r-rpart-plot/package.py +++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py @@ -10,10 +10,14 @@ class RRpartPlot(RPackage): """Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.""" - homepage = "https://cran.r-project.org/package=rpart.plot" - url = "https://cran.r-project.org/src/contrib/rpart.plot_2.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rpart.plot" + 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" + version('3.0.7', sha256='04e7fcadfa907507b74529c3ecfae4a0c782badf55e87d9c62dbd9a536ea9144') + version('3.0.6', sha256='1c584290c8f58ded5c3f0638790a0da63408eca3ecd5d5c4d8c46954de9f4b02') version('2.1.0', 'fb0f8edfe22c464683ee82aa429136f9') - depends_on('r-rpart@4.1-0:', type=('build', 'run')) + 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-rpart@4.1-10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpart/package.py b/var/spack/repos/builtin/packages/r-rpart/package.py index 1679317b6d2..4c309ba4ab3 100644 --- a/var/spack/repos/builtin/packages/r-rpart/package.py +++ b/var/spack/repos/builtin/packages/r-rpart/package.py @@ -10,11 +10,13 @@ class RRpart(RPackage): """Recursive partitioning for classification, regression and survival trees.""" - homepage = "https://cran.r-project.org/package=rpart" - url = "https://cran.r-project.org/src/contrib/rpart_4.1-10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rpart" + 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" + version('4.1-15', sha256='2b8ebe0e9e11592debff893f93f5a44a6765abd0bd956b0eb1f70e9394cfae5c') + version('4.1-13', sha256='8e11a6552224e0fbe23a85aba95acd21a0889a3fe48277f3d345de3147c7494c') version('4.1-11', 'f77b37cddf7e9a7b5993a52a750b8817') version('4.1-10', '15873cded4feb3ef44d63580ba3ca46e') - depends_on('r@2.15.0:') + depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 3aa969bed4f..a5c9e119745 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -18,10 +18,12 @@ class RRpostgresql(RPackage): https://code.google.com/p/rpostgresql/.""" homepage = "https://code.google.com/p/rpostgresql/" - url = "https://cran.r-project.org/src/contrib/RPostgreSQL_0.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RPostgreSQL" + 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" + version('0.6-2', sha256='080118647208bfa2621bcaac0d324891cc513e07618fa22e3c50ec2050e1b0d5') version('0.4-1', 'e7b22e212afbb2cbb88bab937f93e55a') - depends_on('r-dbi', type=('build', 'run')) + depends_on('r@2.9.0:', type=('build', 'run')) + depends_on('r-dbi@0.3:', type=('build', 'run')) depends_on('postgresql') diff --git a/var/spack/repos/builtin/packages/r-rprojroot/package.py b/var/spack/repos/builtin/packages/r-rprojroot/package.py index 56ddb40aa0c..b1ec14200d8 100644 --- a/var/spack/repos/builtin/packages/r-rprojroot/package.py +++ b/var/spack/repos/builtin/packages/r-rprojroot/package.py @@ -11,11 +11,12 @@ class RRprojroot(RPackage): 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://cran.r-project.org/package=rprojroot" - url = "https://cran.rstudio.com/src/contrib/rprojroot_1.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rprojroot" + 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" + version('1.3-2', sha256='df5665834941d8b0e377a8810a04f98552201678300f168de5f58a587b73238b') version('1.2', 'c1a0574aaac2a43a72f804abbaea19c3') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-backports', type=('build', 'run')) - depends_on('r@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-rrblup/package.py b/var/spack/repos/builtin/packages/r-rrblup/package.py index 882711f3927..b165e2a527e 100644 --- a/var/spack/repos/builtin/packages/r-rrblup/package.py +++ b/var/spack/repos/builtin/packages/r-rrblup/package.py @@ -10,8 +10,8 @@ class RRrblup(RPackage): """rrBLUP: Ridge Regression and Other Kernels for Genomic Selection""" homepage = "http://potatobreeding.cals.wisc.edu/software" - url = "https://cran.r-project.org/src/contrib/rrBLUP_4.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rrBLUP" + url = "https://cloud.r-project.org/src/contrib/rrBLUP_4.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rrBLUP" 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 78a0b65d461..7b1d3bd74a6 100644 --- a/var/spack/repos/builtin/packages/r-rrcov/package.py +++ b/var/spack/repos/builtin/packages/r-rrcov/package.py @@ -9,9 +9,9 @@ class RRrcov(RPackage): """rrcov: Scalable Robust Estimators with High Breakdown Point""" - homepage = "https://cran.r-project.org/package=rrcov" - url = "https://cran.r-project.org/src/contrib/rrcov_1.4-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rrcov" + 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" version('1.4-7', sha256='cbd08ccce8b583a2f88946a3267c8fc494ee2b44ba749b9296a6e3d818f6f293') @@ -21,5 +21,3 @@ class RRrcov(RPackage): depends_on('r-lattice', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-pcapp', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) - depends_on('r-ellipse', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rrpp/package.py b/var/spack/repos/builtin/packages/r-rrpp/package.py index c20f2008459..a2448a36361 100644 --- a/var/spack/repos/builtin/packages/r-rrpp/package.py +++ b/var/spack/repos/builtin/packages/r-rrpp/package.py @@ -23,7 +23,9 @@ class RRrpp(RPackage): other fields, as well.""" homepage = "https://github.com/mlcollyer/RRPP" - url = "https://cran.r-project.org/src/contrib/RRPP_0.3.0.tar.gz" + 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" + version('0.4.2', sha256='21a4ebb549d21f66ee9107adf762eee630e478bc740f232f384ba1a6b1cd3bf4') + version('0.4.1', sha256='d7cd3b089240d7f7e13f65f0259487669a378ffae062aee33d4dc6ab0f86f899') version('0.3.0', sha256='34fea6ce7a78e4f38398d3b99585bab11a8171bc8b9a4e461b6d984ed1373739') diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py index 4bde5a8680b..1fdc9326525 100644 --- a/var/spack/repos/builtin/packages/r-rsnns/package.py +++ b/var/spack/repos/builtin/packages/r-rsnns/package.py @@ -17,9 +17,12 @@ class RRsnns(RPackage): and learning algorithms integrate seamlessly into R.""" homepage = "http://sci2s.ugr.es/dicits/software/RSNNS" - url = "https://cran.r-project.org/src/contrib/RSNNS_0.4-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.4-11', sha256='87943126e98ae47f366e3025d0f3dc2f5eb0aa2924508fd9ee9a0685d7cb477c') + version('0.4-10.1', sha256='38bb3d172390bd01219332ec834744274b87b01f94d23b29a9d818c2bca04071') version('0.4-7', 'ade7736611c456effb5f72e0ce0a1e6f') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-rcpp@0.8.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py index 65ecf288ec3..03c24b0b468 100644 --- a/var/spack/repos/builtin/packages/r-rsolnp/package.py +++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py @@ -10,10 +10,11 @@ class RRsolnp(RPackage): """General Non-linear Optimization Using Augmented Lagrange Multiplier Method.""" - homepage = "https://cran.r-project.org/package=Rsolnp" - url = "https://cran.rstudio.com/src/contrib/Rsolnp_1.16.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/Rsolnp" + 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" version('1.16', '507e1e1a64f5f1d32b7e4e12ed19599f') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-truncnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rspectra/package.py b/var/spack/repos/builtin/packages/r-rspectra/package.py new file mode 100644 index 00000000000..460a649c253 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rspectra/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2019 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 RRspectra(RPackage): + """R interface to the 'Spectra' library for + large-scale eigenvalue and SVD problems. It is typically used to compute a + few eigenvalues/vectors of an n by n matrix, e.g., the k largest + eigenvalues, which is usually more efficient than eigen() if k << n. This + package provides the 'eigs()' function that does the similar job as in + 'Matlab', 'Octave', 'Python SciPy' and 'Julia'. It also provides the + 'svds()' function to calculate the largest k singular values and + corresponding singular vectors of a real matrix. The matrix to be computed + 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" + + version('0.15-0', sha256='1ad5698201007044a0420cb10b7c48e94312a8a1d22b9d946d5de1c6743969a9') + + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-matrix@1.1-0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) + depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index 9afd523511e..d9e018304d2 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -11,17 +11,20 @@ class RRsqlite(RPackage): interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.""" - homepage = "https://cran.rstudio.com/web/packages/RSQLite/index.html" - url = "https://cran.r-project.org/src/contrib/RSQLite_2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RSQLite" + 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" + version('2.1.2', sha256='66dad425d22b09651c510bf84b7fc36375ce537782f02585cf1c6856ae82d9c6') + version('2.1.0', sha256='ad6081be2885be5921b1a44b1896e6a8568c8cff40789f43bfaac9f818767642') version('2.0', '63842410e78ccdfc52d4ee97992521d5') - depends_on('r-dbi', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-dbi@1.0.0:', type=('build', 'run')) depends_on('r-bit64', type=('build', 'run')) - depends_on('r-blob', type=('build', 'run')) + depends_on('r-blob@1.2.0:', type=('build', 'run')) depends_on('r-memoise', type=('build', 'run')) depends_on('r-pkgconfig', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.12.7:', type=('build', 'run')) depends_on('r-bh', type=('build', 'run')) - depends_on('r-plogr', type=('build', 'run')) + depends_on('r-plogr@0.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 9bebbc38a2b..6e8bc944586 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -18,24 +18,26 @@ class RRstan(RPackage): the need to derive the partial derivatives.""" homepage = "http://mc-stan.org/" - url = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.19.2', sha256='31e4ceb9c327cd62873225097ffa538c2ac4cb0547c52271e52e4c7652d508da') version('2.18.2', sha256='4d75dad95610d5a1d1c89a4ddbaf4326462e4ffe0ad28aed2129f2d9292e70ff') version('2.17.2', '60f4a0284c58f5efc1b1cbf488d7edda') version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-stanheaders', type=('build', 'run')) + depends_on('r@3.0.2:', when='@:2.17.3', type=('build', 'run')) + depends_on('r@3.4.0:', when='@2.18.1:', type=('build', 'run')) + depends_on('r-stanheaders@2.18.1:', type=('build', 'run')) + depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) depends_on('r-inline', type=('build', 'run')) - depends_on('r-gridextra', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-rcppeigen', type=('build', 'run')) - depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run'), when='@2.17.2:') - depends_on('r-bh', 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-loo@2.0.0:', when='@2.18:', type=('build', 'run')) + depends_on('r-pkgbuild', when='@2.18:', type=('build', 'run')) + depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run')) + depends_on('r-bh@1.69.0:', type=('build', 'run')) + depends_on('gmake', type='build') + depends_on('pandoc', type='build') - depends_on('r-bh@1.66:', type=('build', 'run'), when='@2.18:') - depends_on('r-loo@2.0.0:', type=('build', 'run'), when='@2.18:') - depends_on('r-pkgbuild', type=('build', 'run'), when='@2.18:') - depends_on('r-stanheaders@2.18.0:', type=('build', 'run'), when='@2.18:') 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 a50941c9d6c..08f2e968bbc 100644 --- a/var/spack/repos/builtin/packages/r-rstantools/package.py +++ b/var/spack/repos/builtin/packages/r-rstantools/package.py @@ -10,7 +10,9 @@ class RRstantools(RPackage): """rstantools: Tools for Developing R Packages Interfacing with 'Stan'""" homepage = "http://discourse.mc-stan.org/" - url = "https://cran.r-project.org/src/contrib/rstantools_1.5.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rstantools" + 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" version('1.5.1', sha256='5cab16c132c12e84bd08e18cd6ef25ba39d67a04ce61015fc4490659c7cfb485') + + depends_on('pandoc', type='build') diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index 13f4d0c10c9..9a7779f063e 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -10,10 +10,12 @@ class RRstudioapi(RPackage): """Access the RStudio API (if available) and provide informative error messages when it's not.""" - homepage = "https://cran.r-project.org/web/packages/rstudioapi/index.html" - url = "https://cran.r-project.org/src/contrib/rstudioapi_0.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi" + 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" + version('0.10', sha256='80c5aa3063bcab649904cb92f0b164edffa2f6b0e6a8f7ea28ae317b80e1ab96') + version('0.9.0', sha256='5149a2830ae7134c396ce64764b263cf9f348d4399f53da3804f40d7d5bec13e') version('0.7', 'ee4ab567a7a9fdfac1a6fd01fe38de4a') version('0.6', 'fdb13bf46aab02421557e713fceab66b') version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') diff --git a/var/spack/repos/builtin/packages/r-rsvd/package.py b/var/spack/repos/builtin/packages/r-rsvd/package.py new file mode 100644 index 00000000000..554824aea57 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rsvd/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 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 RRsvd(RPackage): + """Low-rank matrix decompositions are fundamental tools and widely used for + data analysis, dimension reduction, and data compression. Classically, + highly accurate deterministic matrix algorithms are used for this task. + However, the emergence of large-scale data has severely challenged our + computational ability to analyze big data. The concept of randomness has + been demonstrated as an effective strategy to quickly produce approximate + answers to familiar problems such as the singular value decomposition + (SVD). The rsvd package provides several randomized matrix algorithms such + as the randomized singular value decomposition (rsvd), randomized principal + component analysis (rpca), randomized robust principal component analysis + (rrpca), randomized interpolative decomposition (rid), and the randomized + CUR decomposition (rcur). In addition several plot functions are provided. + The methods are discussed in detail by Erichson et al. (2016) + .""" + + 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" + + version('1.0.2', sha256='c8fe5c18bf7bcfe32604a897e3a7caae39b49e47e93edad9e4d07657fc392a3a') + + depends_on('r@3.2.2:', type=('build', 'run')) + 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 80909001a23..be053b293f4 100644 --- a/var/spack/repos/builtin/packages/r-rtsne/package.py +++ b/var/spack/repos/builtin/packages/r-rtsne/package.py @@ -10,13 +10,13 @@ class RRtsne(RPackage): """An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation.""" - homepage = "https://CRAN.R-project.org/package=Rtsne" - url = "https://cran.r-project.org/src/contrib/Rtsne_0.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Rtsne" + 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" + version('0.15', sha256='56376e4f0a382fad3d3d40e2cb0562224be5265b827622bcd235e8fc63df276c') version('0.13', 'ea1d2ef2bda16735bbf219ffda5b0661') version('0.11', '9a1eaa9b71d67cc27a55780e6e9df733') version('0.10', 'c587e1b76fdcea2629424f74c6e92340') - depends_on('r@3.4.0:3.4.9') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-runit/package.py b/var/spack/repos/builtin/packages/r-runit/package.py index 246c189cb27..03452d630e8 100644 --- a/var/spack/repos/builtin/packages/r-runit/package.py +++ b/var/spack/repos/builtin/packages/r-runit/package.py @@ -9,11 +9,10 @@ class RRunit(RPackage): """RUnit: R Unit Test Framework""" - homepage = "https://cran.r-project.org/package=RUnit" - url = "https://cran.r-project.org/src/contrib/RUnit_0.4.32.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RUnit/" + 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/" version('0.4.32', sha256='23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1') depends_on('r@2.5.0:', type=('build', 'run')) - depends_on('r-xml@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rvcheck/package.py b/var/spack/repos/builtin/packages/r-rvcheck/package.py index bd0fd37ed2a..9adfd8d31d2 100644 --- a/var/spack/repos/builtin/packages/r-rvcheck/package.py +++ b/var/spack/repos/builtin/packages/r-rvcheck/package.py @@ -10,8 +10,13 @@ class RRvcheck(RPackage): """Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').""" - homepage = "https://cran.r-project.org/package=rvcheck" - url = "https://cran.rstudio.com/src/contrib/rvcheck_0.0.9.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rvcheck" + 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" + version('0.1.3', sha256='0b59986c1ccc5b89f8aca8fa7cf62d0b875719addb40e08dbda1791cfd334fc4') version('0.0.9', '7e9821de754577f94fdcbf7b02a20edc') + + 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-rlang', when='@0.1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rvest/package.py b/var/spack/repos/builtin/packages/r-rvest/package.py index 18353fe750e..1872315f773 100644 --- a/var/spack/repos/builtin/packages/r-rvest/package.py +++ b/var/spack/repos/builtin/packages/r-rvest/package.py @@ -11,12 +11,17 @@ class RRvest(RPackage): download, then manipulate, HTML and XML.""" homepage = "https://github.com/hadley/rvest" - url = "https://cran.r-project.org/src/contrib/rvest_0.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rvest" + url = "https://cloud.r-project.org/src/contrib/rvest_0.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rvest" + version('0.3.4', sha256='413e171b9e89b7dc4e8b41165027cf19eb97cd73e149c252237bbdf0d0a4254a') + version('0.3.3', sha256='b10a87fa2d733f7c0fc567242ef0ab10a1a77d58d51796996cc0fd81381a556f') version('0.3.2', '78c88740850e375fc5da50d37734d1b2') + 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-xml2', type=('build', 'run')) - depends_on('r-httr', type=('build', 'run')) + depends_on('r-httr@0.5:', type=('build', 'run')) depends_on('r-selectr', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index fb6f0f5634b..8b800c4b5fb 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -11,9 +11,12 @@ class RRzmq(RPackage): """Interface to the ZeroMQ lightweight messaging kernel.""" homepage = "http://github.com/armstrtw/rzmq" - url = "https://cran.r-project.org/src/contrib/rzmq_0.7.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.9.6', sha256='80a3fc6eb6f7851224c4cd5e219ca4db0286551ad429359d4df853ccb9234316') + version('0.9.4', sha256='03fbda756d823c11fba359b94a6213c3440e61973331668eaac35779717f73ad') version('0.7.7', '8ba18fd1c222d1eb25bb622ccd2897e0') - depends_on('zeromq') + depends_on('r@3.1.0:', when='@0.9.0:', type=('build', 'run')) + depends_on('zeromq@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-samr/package.py b/var/spack/repos/builtin/packages/r-samr/package.py index 79ae1762c7c..5ebc81a468e 100644 --- a/var/spack/repos/builtin/packages/r-samr/package.py +++ b/var/spack/repos/builtin/packages/r-samr/package.py @@ -9,10 +9,15 @@ class RSamr(RPackage): """Significance Analysis of Microarrays.""" - homepage = "https://cran.r-project.org/package=samr" - url = "https://cran.rstudio.com/src/contrib/samr_2.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/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', 'e8f50b8b25069d03d42c2c61c72b0da0') 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')) diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index 68feab8e3ca..d303fe56cf2 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -10,12 +10,13 @@ class RSandwich(RPackage): """Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.""" - homepage = "https://cran.r-project.org/package=sandwich" - url = "https://cran.r-project.org/src/contrib/sandwich_2.3-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sandwich" + 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" + version('2.5-1', sha256='dbef6f4d12b83e166f9a2508b7c732b04493641685d6758d29f3609e564166d6') + version('2.5-0', sha256='6cc144af20739eb23e5539010d3833d7c7fc53cbca2addb583ab933167c11399') version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') - depends_on('r@2.0.0:') - + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index fbc6d69d814..0ea8442689f 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -11,17 +11,20 @@ class RScales(RPackage): automatically determining breaks and labels for axes and legends.""" homepage = "https://github.com/hadley/scales" - url = "https://cran.r-project.org/src/contrib/scales_0.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.0.0', sha256='0c1f4a14edd336a404da34a3cc71a6a9d0ca2040ba19360c41a79f36e06ca30c') version('0.5.0', '435f6bd826c5cf8df703ffb8a6750fd1') version('0.4.1', '3fb2218866a7fe4c1f6e66790876f85a') version('0.4.0', '7b5602d9c55595901192248bca25c099') + depends_on('r@2.13:', when='@:0.5.0', type=('build', 'run')) + depends_on('r@3.1:', when='@1.0.0:', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-dichromat', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-munsell', 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-munsell@0.5:', type=('build', 'run')) depends_on('r-labeling', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py index 2c53d967451..e4bb9abbc6e 100644 --- a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py +++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py @@ -9,10 +9,11 @@ class RScatterplot3d(RPackage): """scatterplot3d: 3D Scatter Plot""" - homepage = "https://CRAN.R-project.org/package=scatterplot3d" - url = "https://cran.r-project.org/src/contrib/scatterplot3d_0.3-40.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/scatterplot3d" + 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" + version('0.3-41', sha256='4c8326b70a3b2d37126ca806771d71e5e9fe1201cfbe5b0d5a0a83c3d2c75d94') version('0.3-40', '67b9ab6131d244d7fc1db39dcc911dfe') - depends_on('r@2.7.0:') + depends_on('r@2.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sctransform/package.py b/var/spack/repos/builtin/packages/r-sctransform/package.py new file mode 100644 index 00000000000..7dd0b4e703d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sctransform/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 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 RSctransform(RPackage): + """A normalization method for single-cell UMI count data using a variance + stabilizing transformation. The transformation is based on a negative + binomial regression model with regularized parameters. As part of the same + regression framework, this package also provides functions for batch + correction, and data correction. See Hafemeister and Satija 2019 + 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" + + version('0.2.0', sha256='d7f4c7958693823454f1426b23b0e1e9c207ad61a7a228602a1885a1318eb3e4') + + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-future', type=('build', 'run')) + depends_on('r-future-apply', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-rcppeigen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sdmtools/package.py b/var/spack/repos/builtin/packages/r-sdmtools/package.py index 46acd8c8a6b..e6dd23d74d9 100644 --- a/var/spack/repos/builtin/packages/r-sdmtools/package.py +++ b/var/spack/repos/builtin/packages/r-sdmtools/package.py @@ -13,15 +13,15 @@ class RSdmtools(RPackage): This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises.""" - homepage = "https://cran.r-project.org/web/packages/SDMTools/index.html" - url = "https://cran.r-project.org/src/contrib/SDMTools_1.1-221.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/SDMTools" + 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" + version('1.1-221.1', sha256='3825856263bdb648ca018b27dc6ab8ceaef24691215c197f8d5cd17718b54fbb') version('1.1-221', '3604da1783d0c6081b62b29d35a32c3c') version('1.1-20', '27cc8de63cfdd86d4ba9983012121c58') version('1.1-13', '0d6a14d985988a81b9ff06c635675143') version('1.1-12', 'a13d75e4024d908a57ea462112d8a437') version('1.1-11', 'cb890ee06eb862f97141b73c7390a0a9') - depends_on('r@3.4.0:3.4.9') - depends_on('r-utils', type=('build', 'run')) + depends_on('r-r-utils', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py index 45bc7df141b..748d8811ef9 100644 --- a/var/spack/repos/builtin/packages/r-segmented/package.py +++ b/var/spack/repos/builtin/packages/r-segmented/package.py @@ -11,9 +11,11 @@ class RSegmented(RPackage): one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.""" - homepage = "https://CRAN.R-project.org/package=segmented" - url = "https://cran.r-project.org/src/contrib/segmented_0.5-1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/segmented" + 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" + version('1.0-0', sha256='eeadc89b4bb4744bbd1e4e6c3b6536ff96fc7ee09016228dfdc0a8ebdc74fac5') + version('0.5-4.0', sha256='7ff63a19915cbd1e190d3a4875892b4c7bd97890b0dc2909126348a19aec4071') version('0.5-2.2', '1511ec365aea289d5f0a574f6d10d2d6') version('0.5-1.4', 'f9d76ea9e22ef5f40aa126b697351cae') diff --git a/var/spack/repos/builtin/packages/r-selectr/package.py b/var/spack/repos/builtin/packages/r-selectr/package.py index 5b57993a855..628ee221f99 100644 --- a/var/spack/repos/builtin/packages/r-selectr/package.py +++ b/var/spack/repos/builtin/packages/r-selectr/package.py @@ -15,12 +15,13 @@ class RSelectr(RPackage): ().""" homepage = "https://sjp.co.nz/projects/selectr" - url = "https://cran.r-project.org/src/contrib/selectr_0.3-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.4-1', sha256='8bd42f167629344e485e586f9b05fed342746132489079084d82133d7b3ee2ca') + version('0.4-0', sha256='40cd51bfe499954b300742c49f92167a68964b974268a7f47ca8864f32020ece') version('0.3-1', '7190fcdea1823ad7ef429cab6938e960') - depends_on('r-testthat', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-xml2', type=('build', 'run')) + depends_on('r-r6', when='@0.4-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py index a685f86a147..ab7685fc475 100644 --- a/var/spack/repos/builtin/packages/r-seqinr/package.py +++ b/var/spack/repos/builtin/packages/r-seqinr/package.py @@ -12,13 +12,13 @@ class RSeqinr(RPackage): data management under the ACNUC system.""" homepage = "http://seqinr.r-forge.r-project.org" - url = "https://cran.r-project.org/src/contrib/seqinr_3.3-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/seginr" + 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" version('3.4-5', 'd550525dcea754bbd5b83cb46b4124cc') version('3.3-6', '73023d627e72021b723245665e1ad055') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-ade4', type=('build', 'run')) depends_on('r-segmented', type=('build', 'run')) depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/r-sessioninfo/package.py b/var/spack/repos/builtin/packages/r-sessioninfo/package.py new file mode 100644 index 00000000000..f8770c7f193 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sessioninfo/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 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 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.""" + + 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" + + version('1.1.1', sha256='166b04678448a7decd50f24afabe5e2ad613e3c55b180ef6e8dd7a870a1dae48') + + depends_on('r-cli', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-seurat/package.py b/var/spack/repos/builtin/packages/r-seurat/package.py index abb49e06280..c3e5de9dce2 100644 --- a/var/spack/repos/builtin/packages/r-seurat/package.py +++ b/var/spack/repos/builtin/packages/r-seurat/package.py @@ -11,44 +11,79 @@ class RSeurat(RPackage): single cell RNA-seq data.""" homepage = "http://satijalab.org/seurat/" - url = "https://cran.r-project.org/src/contrib/Seurat_2.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('3.1.0', sha256='d8d3fad2950a8f791376e3d20c72ea07c68bf8d82d800661cab5ce696db39d45') + version('3.0.2', sha256='16df5dec6b41d49320c5bf5ce30eb3b7dedeea69b054b55b77528f2f2b7bce04') + version('3.0.1', sha256='8c467bdbfdb9aff51bde6a897ff98a7389941f688639d8f1d36c71dde076a257') version('2.1.0', '46427837bb739883f9b7addd08fccee5') version('2.0.1', 'a77794891e93b9fa1ef41735fe8424ea') - depends_on('r@3.4.0:3.4.9') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-gplots', type=('build', 'run')) - depends_on('r-reshape2', type=('build', 'run')) + 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-ggplot2@3.0.0:', 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', type=('build', 'run')) - depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-caret', type=('build', 'run')) - depends_on('r-gdata', type=('build', 'run')) - depends_on('r-glue', type=('build', 'run')) - depends_on('r-pkgconfig', type=('build', 'run')) - depends_on('r-plogr', type=('build', 'run')) - depends_on('r-gridextra', 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-cowplot', type=('build', 'run')) depends_on('r-rocr', type=('build', 'run')) - depends_on('r-hmisc', type=('build', 'run')) - depends_on('r-nmf', 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-irlba', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) - depends_on('r-fpc', type=('build', 'run')) + depends_on('r-fpc', when='@:2.3.4', type=('build', 'run')) depends_on('r-rcppprogress', type=('build', 'run')) - depends_on('r-lars', type=('build', 'run')) - depends_on('r-dtw', type=('build', 'run')) - depends_on('r-mixtools', 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-ica', type=('build', 'run')) - depends_on('r-diffusionmap', type=('build', 'run')) + depends_on('r-diffusionmap', when='@:2.3.3', type=('build', 'run')) depends_on('r-tsne', type=('build', 'run')) depends_on('r-rtsne', type=('build', 'run')) - depends_on('r-ranger', type=('build', 'run')) + depends_on('r-ranger', when='@:2.3.2', type=('build', 'run')) depends_on('r-pbapply', type=('build', 'run')) - depends_on('r-ggjoy', type=('build', 'run')) + depends_on('r-ggjoy', when='@:2.1.0', type=('build', 'run')) depends_on('r-plotly', type=('build', 'run')) depends_on('r-sdmtools', type=('build', 'run')) - depends_on('r-tclust', type=('build', 'run')) - depends_on('r-fnn', type=('build', 'run')) - depends_on('r-vgam', 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-matrix@1.2.14:', type=('build', 'run')) + depends_on('r-rcolorbrewer', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-rcppeigen', type=('build', 'run')) + depends_on('r-ggridges', when='@2.2.0:', 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:', type=('build', 'run')) + depends_on('r-cluster', when='@2.3.0:', type=('build', 'run')) + depends_on('r-fitdistrplus', when='@2.3.0:', type=('build', 'run')) + depends_on('r-png', when='@2.3.0:', type=('build', 'run')) + depends_on('r-lmtest', when='@2.3.0:', type=('build', 'run')) + depends_on('r-rann', when='@2.3.0:', type=('build', 'run')) + depends_on('r-reticulate', when='@2.3.1:', 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-httr', 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-future', when='@3.0.0:', type=('build', 'run')) + depends_on('r-future-apply', when='@3.0.0:', type=('build', 'run')) + depends_on('r-ggrepel', when='@3.0.0:', type=('build', 'run')) + depends_on('r-kernsmooth', when='@3.0.0:', type=('build', 'run')) + depends_on('r-rlang', when='@3.0.0:', type=('build', 'run')) + depends_on('r-rsvd', when='@3.0.0:', type=('build', 'run')) + depends_on('r-scales', when='@3.0.0:', type=('build', 'run')) + depends_on('r-sctransform@0.2.0:', when='@3.0.0:', type=('build', 'run')) + depends_on('r-leiden@0.3.1:', when='@3.1.0:', type=('build', 'run')) + depends_on('r-rcppannoy', when='@3.1.0:', type=('build', 'run')) + depends_on('r-uwot', when='@3.1.0:', type=('build', 'run')) + depends_on('java', when='@:2.3.0') diff --git a/var/spack/repos/builtin/packages/r-sf/package.py b/var/spack/repos/builtin/packages/r-sf/package.py index 711915fc6f7..bd79b7a4fd5 100644 --- a/var/spack/repos/builtin/packages/r-sf/package.py +++ b/var/spack/repos/builtin/packages/r-sf/package.py @@ -13,18 +13,20 @@ class RSf(RPackage): datum transformations.""" homepage = "https://github.com/r-spatial/sf/" - url = "https://cran.r-project.org/src/contrib/sf_0.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.7-7', sha256='d1780cb46a285b30c7cc41cae30af523fbc883733344e53f7291e2d045e150a4') + version('0.7-5', sha256='53ed0567f502216a116c4848f5a9262ca232810f82642df7b98e0541a2524868') version('0.5-5', '53ff32d0c9bf2844666c68ce7d75beb2') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-dbi@0.5:', type=('build', 'run')) - depends_on('r-units@0.4-6:', type=('build', 'run')) - depends_on('r-classint', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.18:', type=('build', 'run')) + depends_on('r-dbi@0.8:', type=('build', 'run')) + depends_on('r-units@0.6-0:', type=('build', 'run')) + depends_on('r-classint@0.2-1:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('gdal@2.0.0:') - depends_on('geos@3.3.0:') - # Since PROJ.4 and PROJ.6 have incompatible APIs, I'm assuming - # that since r-sf supports PROJ.4, it doesn't support PROJ.6 - depends_on('proj@4.8.0:5') + 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:', when='@0.7-4:') diff --git a/var/spack/repos/builtin/packages/r-sfsmisc/package.py b/var/spack/repos/builtin/packages/r-sfsmisc/package.py index 8b9707d7500..779d13959c6 100644 --- a/var/spack/repos/builtin/packages/r-sfsmisc/package.py +++ b/var/spack/repos/builtin/packages/r-sfsmisc/package.py @@ -11,8 +11,13 @@ class RSfsmisc(RPackage): ETH Zurich, quite a few related to graphics; some were ported from S-plus.""" - homepage = "https://cran.r-project.org/web/packages/sfsmisc/index.html" - url = "https://cran.r-project.org/src/contrib/sfsmisc_1.1-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sfsmisc" + 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" + version('1.1-4', sha256='44b6a9c859922e86b7182e54eb781d3264f3819f310343518ebc66f54f305c7d') + version('1.1-3', sha256='58eff7d4a9c79212321858efe98d2a6153630e263ff0218a31d5e104b8b545f8') version('1.1-0', '1ba4303076e2bbf018f7eecc7d04e178') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-shape/package.py b/var/spack/repos/builtin/packages/r-shape/package.py index f5cdc618583..67851868f13 100644 --- a/var/spack/repos/builtin/packages/r-shape/package.py +++ b/var/spack/repos/builtin/packages/r-shape/package.py @@ -10,9 +10,12 @@ class RShape(RPackage): """Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...""" - homepage = "https://cran.r-project.org/package=shape" - url = "https://cran.r-project.org/src/contrib/shape_1.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/shape" + 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" + version('1.4.4', sha256='f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41') version('1.4.3', '2a807bf95e7decc71478f805221852da') version('1.4.2', '75557c43a385b9cc0c4dff361af6e06c') + + depends_on('r@2.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index 4d6a9d83b10..3c1c3bcb478 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -13,17 +13,23 @@ class RShiny(RPackage): powerful applications with minimal effort.""" homepage = "http://shiny.rstudio.com/" - url = "https://cran.rstudio.com/src/contrib/shiny_1.0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/shiny" + 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" + version('1.3.2', sha256='28b851ae6c196ca845f6e815c1379247595ac123a4faa10a16533d1a9ce0c24f') version('1.0.5', '419dd5d3ea0bd87a07f8f0b1ef14fc13') version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611') - depends_on('r-httpuv', type=('build', 'run')) - depends_on('r-mime', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-httpuv@1.5.0:', type=('build', 'run')) + 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-htmltools', type=('build', 'run')) - depends_on('r-r6', type=('build', 'run')) + depends_on('r-htmltools@0.3.6:', type=('build', 'run')) + 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-promises@1.0.1:', when='@1.1.0:', 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')) diff --git a/var/spack/repos/builtin/packages/r-shinydashboard/package.py b/var/spack/repos/builtin/packages/r-shinydashboard/package.py index 5c71ff533a5..23733e9576e 100644 --- a/var/spack/repos/builtin/packages/r-shinydashboard/package.py +++ b/var/spack/repos/builtin/packages/r-shinydashboard/package.py @@ -9,13 +9,15 @@ class RShinydashboard(RPackage): """Create Dashboards with 'Shiny'""" - homepage = "https://cran.r-project.org/package=shinydashboard" - url = "https://cran.r-project.org/src/contrib/shinydashboard_0.7.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/shinydashboard" + 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" + version('0.7.1', sha256='51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e') version('0.7.0', 'a572695884e3b45320b0ab5a7b364ffd') version('0.6.1', '0f6ad0448237e10d53d4d27ade1c6863') - depends_on('r@3.3.0:', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-shinyfiles/package.py b/var/spack/repos/builtin/packages/r-shinyfiles/package.py new file mode 100644 index 00000000000..70b4864f406 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-shinyfiles/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 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 RShinyfiles(RPackage): + """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" + + version('0.7.3', sha256='710c8a6191aaf336379bc748daff1160d0d2858e2aee0d98e2ad48e7121d5a05') + + depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-shiny@1.1.0:', type=('build', 'run')) + depends_on('r-fs@1.2.6:', type=('build', 'run')) + depends_on('r-tibble@1.4.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sitmo/package.py b/var/spack/repos/builtin/packages/r-sitmo/package.py new file mode 100644 index 00000000000..eab70f5ac40 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sitmo/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 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 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 + 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 + the header files inside of 'sitmo' instead of including a copy of each + engine within their individual package. Lastly, the package contains + 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" + + version('2.0.1', sha256='0c90d357af334d5c99c8956739dc12623ddd87dda5efa59f4a43f7393c87ed2a') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.13:', 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 89de1cb4e9d..29a46acd058 100644 --- a/var/spack/repos/builtin/packages/r-sm/package.py +++ b/var/spack/repos/builtin/packages/r-sm/package.py @@ -12,9 +12,10 @@ class RSm(RPackage): Oxford University Press.""" homepage = "http://www.stats.gla.ac.uk/~adrian/sm" - url = "https://cran.r-project.org/src/contrib/sm_2.2-5.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.2-5.6', sha256='b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30') version('2.2-5.5', sha256='43e212a14c364b98b10018b56fe0a619ccffe4bde1294e6c45b3eafe7caf82e7') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-smoof/package.py b/var/spack/repos/builtin/packages/r-smoof/package.py index 839d5a1ce24..60520006b8c 100644 --- a/var/spack/repos/builtin/packages/r-smoof/package.py +++ b/var/spack/repos/builtin/packages/r-smoof/package.py @@ -14,8 +14,8 @@ class RSmoof(RPackage): functions.""" homepage = "http://github.com/jakobbossek/smoof" - url = "https://cran.r-project.org/src/contrib/smoof_1.5.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.5.1', 'c3e3b5dafed34608f933ae255cf49054') version('1.5', 'b371bde2724eade5a6d4d808fa3ad269') diff --git a/var/spack/repos/builtin/packages/r-sn/package.py b/var/spack/repos/builtin/packages/r-sn/package.py index 7b3fa2c3e93..61d84c1df29 100644 --- a/var/spack/repos/builtin/packages/r-sn/package.py +++ b/var/spack/repos/builtin/packages/r-sn/package.py @@ -12,16 +12,18 @@ class RSn(RPackage): related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.""" - homepage = "https://cran.r-project.org/web/packages/sn/index.html" - url = "https://cran.r-project.org/src/contrib/sn_1.5-0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/sn" + 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" + version('1.5-4', sha256='46677ebc109263a68f62b5cf53ec59916cda490e5bc5bbb08276757a677f8674') + version('1.5-3', sha256='cc21b97ddd674c9b1296260f2a72ffb085cdcb877c8332f0bfa96ff028517183') version('1.5-0', 'a3349773be950199d7f4c17954be56d1') version('1.4-0', 'cfa604317ea54224b06abd1cec179375') version('1.3-0', '84d02ba2ab5ca6f3644626013e7ce36d') version('1.2-4', 'bf3a47b05016326e910fdb4cc4967e4d') version('1.2-3', '290ae511d974a6beb4c3c79c0106858f') - depends_on('r@3.4.0:3.4.9') - depends_on('r-mnormt', type=('build', 'run')) + depends_on('r@2.15.3:', type=('build', 'run')) + depends_on('r-mnormt@1.5-4:', type=('build', 'run')) depends_on('r-numderiv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snakecase/package.py b/var/spack/repos/builtin/packages/r-snakecase/package.py new file mode 100644 index 00000000000..fddcd2c56c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-snakecase/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 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 RSnakecase(RPackage): + """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" + + version('0.11.0', sha256='998420a58391ac85785e60bcdf6fd6927c82758ad2859a9a73a0e57299e8c1cf') + + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-stringr', type=('build', 'run')) + depends_on('r-stringi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py index ada2cfaefaa..e7173b4c356 100644 --- a/var/spack/repos/builtin/packages/r-snow/package.py +++ b/var/spack/repos/builtin/packages/r-snow/package.py @@ -9,11 +9,11 @@ class RSnow(RPackage): """Support for simple parallel computing in R.""" - homepage = "https://cran.r-project.org/web/packages/snow/index.html" - url = "https://cran.r-project.org/src/contrib/snow_0.4-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/snow" + 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" + version('0.4-3', sha256='8512537daf334ea2b8074dbb80cf5e959a403a78d68bc1e97664e8a4f64576d8') version('0.4-2', 'afc7b0dfd4518aedb6fc81712fd2ac70') - depends_on('r-rmpi', type='run') depends_on('r@2.13.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snowfall/package.py b/var/spack/repos/builtin/packages/r-snowfall/package.py index 880b8523d73..fbc86513af7 100644 --- a/var/spack/repos/builtin/packages/r-snowfall/package.py +++ b/var/spack/repos/builtin/packages/r-snowfall/package.py @@ -13,9 +13,11 @@ class RSnowfall(RPackage): present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.""" - homepage = "https://cran.r-project.org/web/packages/snowfall/index.html" - url = "https://cran.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz" + 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" version('1.84-6.1', '5ec38116aa9cac237d56f59ba5bd60e3') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-snow', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py index a2de57deb0c..f87b92c3675 100644 --- a/var/spack/repos/builtin/packages/r-som/package.py +++ b/var/spack/repos/builtin/packages/r-som/package.py @@ -9,9 +9,9 @@ class RSom(RPackage): """Self-Organizing Map (with application in gene clustering).""" - homepage = "https://cran.r-project.org/web/packages/som/index.html" - url = "https://cran.r-project.org/src/contrib/som_0.3-5.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/som" + 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" version('0.3-5.1', '802a5a80902579354ce3420faeeeb756') version('0.3-5', '72717499794c7aa945a768b742af8895') diff --git a/var/spack/repos/builtin/packages/r-sourcetools/package.py b/var/spack/repos/builtin/packages/r-sourcetools/package.py index 6a107c9d8e5..2df62d25d86 100644 --- a/var/spack/repos/builtin/packages/r-sourcetools/package.py +++ b/var/spack/repos/builtin/packages/r-sourcetools/package.py @@ -9,11 +9,12 @@ class RSourcetools(RPackage): """Tools for Reading, Tokenizing and Parsing R Code.""" - homepage = "https://cran.r-project.org/package=sourcetools" - url = "https://cran.r-project.org/src/contrib/sourcetools_0.1.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sourcetools" + 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" + version('0.1.7', sha256='47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca') version('0.1.6', 'c78a816384b168d04af41bd7ff4d909d') version('0.1.5', 'b4d7902ffafd9802e8fbff5ce824bb28') - depends_on('r-testthat', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py index 373c373e87a..2cdbaf6ffd5 100644 --- a/var/spack/repos/builtin/packages/r-sp/package.py +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -13,9 +13,12 @@ class RSp(RPackage): methods for retrieving coordinates, for subsetting, print, summary, etc.""" homepage = "https://github.com/edzer/sp/" - url = "https://cran.r-project.org/src/contrib/sp_1.2-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.3-1', sha256='57988b53ba8acc35f3912d62feba4b929a0f757c6b54080c623c5d805e0cb59f') + version('1.2-7', sha256='6d60e03e1abd30a7d4afe547d157ce3dd7a8c166fc5e407fd6d62ae99ff30460') version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spacetime/package.py b/var/spack/repos/builtin/packages/r-spacetime/package.py index 88037ed6996..e12bd4cc0b8 100644 --- a/var/spack/repos/builtin/packages/r-spacetime/package.py +++ b/var/spack/repos/builtin/packages/r-spacetime/package.py @@ -10,8 +10,8 @@ class RSpacetime(RPackage): """spacetime: Classes and Methods for Spatio-Temporal Data""" homepage = "http://github.com/edzer/spacetime" - url = "https://cran.r-project.org/src/contrib/spacetime_1.2-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('1.2-2', sha256='1e9d3f92e5c4614a69c82a58bf0b5c829b4ed262bf1250bef943ae286056ea2d') diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index bd280899111..e5974e19afc 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -12,8 +12,12 @@ class RSparsem(RPackage): subsetting and Kronecker products.""" homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html" - url = "https://cran.r-project.org/src/contrib/SparseM_1.74.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM" + url = "https://cloud.r-project.org/src/contrib/SparseM_1.74.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/SparseM" + version('1.77', sha256='a9329fef14ae4fc646df1f4f6e57efb0211811599d015f7bc04c04285495d45c') + version('1.76', sha256='c2c8e44376936a5fe6f09a37f3668016e66cbc687519cc952aa346a658a2b69b') version('1.74', 'a16c9b7db172dfd2b7b6508c48e81a5d') version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') + + depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatial/package.py b/var/spack/repos/builtin/packages/r-spatial/package.py index 6129cf58657..6673560c041 100644 --- a/var/spack/repos/builtin/packages/r-spatial/package.py +++ b/var/spack/repos/builtin/packages/r-spatial/package.py @@ -9,9 +9,9 @@ class RSpatial(RPackage): """spatial: Functions for Kriging and Point Pattern Analysis""" - homepage = "https://cran.r-project.org/package=spatial" - url = "https://cran.r-project.org/src/contrib/spatial_7.3-11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spatial" + 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" version('7.3-11', sha256='624448d2ac22e1798097d09fc5dc4605908a33f490b8ec971fc6ea318a445c11') diff --git a/var/spack/repos/builtin/packages/r-spatialreg/package.py b/var/spack/repos/builtin/packages/r-spatialreg/package.py index e99f955be80..bcbadc07a1a 100644 --- a/var/spack/repos/builtin/packages/r-spatialreg/package.py +++ b/var/spack/repos/builtin/packages/r-spatialreg/package.py @@ -9,9 +9,9 @@ class RSpatialreg(RPackage): """spatialreg: Spatial Regression Analysis""" - homepage = "https://cran.r-project.org/package=spatialreg" - url = "https://cran.r-project.org/src/contrib/spatialreg_1.1-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spatialreg" + 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" version('1.1-3', sha256='7609cdfcdfe427d2643a0db6b5360be3f6d60ede8229436ab52092d1c9cf0480') @@ -26,3 +26,4 @@ class RSpatialreg(RPackage): depends_on('r-nlme', type=('build', 'run')) depends_on('r-spdata', type=('build', 'run')) depends_on('r-spdep', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spdata/package.py b/var/spack/repos/builtin/packages/r-spdata/package.py index 1a40030c36f..0cfa061db64 100644 --- a/var/spack/repos/builtin/packages/r-spdata/package.py +++ b/var/spack/repos/builtin/packages/r-spdata/package.py @@ -10,8 +10,8 @@ class RSpdata(RPackage): """spData: Datasets for Spatial Analysis""" homepage = "https://github.com/Nowosad/spData" - url = "https://cran.r-project.org/src/contrib/spData_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.3.0', sha256='de24ea659541a6c795cd26a1f6a213e15061af9c97a24cba1c24ce30c6c24c98') diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py index 1ae0a16f0e1..2c0f9bc47b1 100644 --- a/var/spack/repos/builtin/packages/r-spdep/package.py +++ b/var/spack/repos/builtin/packages/r-spdep/package.py @@ -23,15 +23,24 @@ class RSpdep(RPackage): two stage least squares models.""" homepage = "https://r-forge.r-project.org/projects/spdep" - url = "https://cran.r-project.org/src/contrib/spdep_0.6-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.1-2', sha256='ba0ca3a0ad6b9cc1dc46cadd9e79259949ad38c88f738e98e482d6c06640b31a') + version('1.0-2', sha256='6f9efa4347d5c13b49922b75481ac403431c3c76a65a109af29954aa7bb138b2') version('0.6-13', 'bfc68b3016b4894b152ecec4b86f85d1') - depends_on('r@3.0:') + 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-sp@1.0:', type=('build', 'run')) depends_on('r-learnbayes', type=('build', 'run')) depends_on('r-deldir', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) depends_on('r-gmodels', type=('build', 'run')) depends_on('r-expm', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-boot@1.3-1:', type=('build', 'run')) + depends_on('r-nlme', 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')) diff --git a/var/spack/repos/builtin/packages/r-speedglm/package.py b/var/spack/repos/builtin/packages/r-speedglm/package.py index cd7e69ef2a7..2371b3090e5 100644 --- a/var/spack/repos/builtin/packages/r-speedglm/package.py +++ b/var/spack/repos/builtin/packages/r-speedglm/package.py @@ -10,9 +10,9 @@ class RSpeedglm(RPackage): """Fitting linear models and generalized linear models to large data sets by updating algorithms.""" - homepage = "https://cran.r-project.org/package=speedglm" - url = "https://cran.rstudio.com/src/contrib/speedglm_0.3-2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/speedglm" + 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" version('0.3-2', 'c4874d4c2a677d657a335186ebb63131') diff --git a/var/spack/repos/builtin/packages/r-splancs/package.py b/var/spack/repos/builtin/packages/r-splancs/package.py index 60cf5fa30e1..4ef99ef42ca 100644 --- a/var/spack/repos/builtin/packages/r-splancs/package.py +++ b/var/spack/repos/builtin/packages/r-splancs/package.py @@ -9,9 +9,9 @@ class RSplancs(RPackage): """Spatial and Space-Time Point Pattern Analysis""" - homepage = "https://cran.r-project.org/web/packages/splancs/index.html" - url = "https://cran.r-project.org/src/contrib/splancs_2.01-40.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/splancs" + 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" version('2.01-40', 'dc08a5c9a1fd2098d78459152f4917ce') diff --git a/var/spack/repos/builtin/packages/r-splitstackshape/package.py b/var/spack/repos/builtin/packages/r-splitstackshape/package.py index 8ceb1fe1b94..a314d22134a 100644 --- a/var/spack/repos/builtin/packages/r-splitstackshape/package.py +++ b/var/spack/repos/builtin/packages/r-splitstackshape/package.py @@ -19,10 +19,12 @@ class RSplitstackshape(RPackage): """ homepage = "http://github.com/mrdwab/splitstackshape" - url = "https://cran.r-project.org/src/contrib/splitstackshape_1.4.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('1.4.8', sha256='656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56') + version('1.4.6', sha256='b9888f9508babdb8e09f57674facaa8b158a06255ef1e61c8df813f58881860f') version('1.4.4', '54d2554fe92dfc4670a000b45baacc28') - depends_on('r-data-table@1.9.4:', type=('build', 'run')) depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-data-table@1.9.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sqldf/package.py b/var/spack/repos/builtin/packages/r-sqldf/package.py index dd9289fe0f6..da7d95aa310 100644 --- a/var/spack/repos/builtin/packages/r-sqldf/package.py +++ b/var/spack/repos/builtin/packages/r-sqldf/package.py @@ -18,13 +18,14 @@ class RSqldf(RPackage): files are larger than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported.""" - homepage = "https://cran.r-project.org/package=sqldf" - url = "https://cran.r-project.org/src/contrib/sqldf_0.4-11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sqldf" + 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" version('0.4-11', '85def6fe2418569370c24e53522d2c2d') - depends_on('r-gsubfn', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-gsubfn@0.6:', type=('build', 'run')) depends_on('r-proto', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-squarem/package.py b/var/spack/repos/builtin/packages/r-squarem/package.py new file mode 100644 index 00000000000..a4f0e9de369 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-squarem/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 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 RSquarem(RPackage): + """Algorithms for accelerating the convergence of slow, monotone sequences + from smooth, contraction mapping such as the EM algorithm. It can be used + to accelerate any smooth, linearly convergent acceleration scheme. A + tutorial style introduction to this package is available in a vignette on + the CRAN download page or, when the package is loaded in an R session, with + vignette("SQUAREM").""" + + homepage = "http://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" + + version('2017.10-1', sha256='9b89905b436f1cf3faa9e3dabc585a76299e729e85ca659bfddb4b7cba11b283') + + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-squash/package.py b/var/spack/repos/builtin/packages/r-squash/package.py index 580255de985..f38963c8d01 100644 --- a/var/spack/repos/builtin/packages/r-squash/package.py +++ b/var/spack/repos/builtin/packages/r-squash/package.py @@ -9,9 +9,9 @@ class RSquash(RPackage): """Color-Based Plots for Multivariate Visualization""" - homepage = "https://cran.r-project.org/package=squash" - url = "https://cran.r-project.org/src/contrib/squash_1.0.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/squash" + 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" version('1.0.8', '50d5743d306fa11cfa1a3c4daa75e508') version('1.0.7', '4ac381b17d4d7b77bdaa6f824fbb03ab') diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py index a1b2cb2e4c9..2cac7d0963c 100644 --- a/var/spack/repos/builtin/packages/r-stanheaders/package.py +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -24,9 +24,13 @@ class RStanheaders(RPackage): estimate, and analyze Stan models.""" homepage = "http://mc-stan.org/" - url = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders" + 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" + version('2.18.1-10', sha256='8a9f7e22105428e97d14f44f75395c37cf8c809de148d279c620024452b3565a') version('2.18.1', sha256='ce0d609a7cd11725b1203bdeae92acc54da3a48b8266eb9dbdb9d95b14df9209') version('2.17.1', '11d8770277dd18e563852852633c6c25') version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57') + + depends_on('r@3.4.0:', when='@2.18.0:', type=('build', 'run')) + depends_on('pandoc', type='build') diff --git a/var/spack/repos/builtin/packages/r-statmod/package.py b/var/spack/repos/builtin/packages/r-statmod/package.py index b48e62a9102..ceee29fceb4 100644 --- a/var/spack/repos/builtin/packages/r-statmod/package.py +++ b/var/spack/repos/builtin/packages/r-statmod/package.py @@ -16,8 +16,11 @@ class RStatmod(RPackage): that implement secure convergence, dispersion modeling and Tweedie power-law families.""" - homepage = "https://cran.r-project.org/package=statmod" - url = "https://cran.rstudio.com/src/contrib/statmod_1.4.30.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/statmod" + 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" + version('1.4.32', sha256='2f67a1cfa66126e6345f8a40564a3077d08f1748f17cb8c8fb05c94ed0f57e20') version('1.4.30', '34e60132ce3df38208f9dc0db0479151') + + depends_on('r@3.0.0:', type=('build', 'run')) 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 b1b68e65225..7ad4104329e 100644 --- a/var/spack/repos/builtin/packages/r-statnet-common/package.py +++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py @@ -11,7 +11,12 @@ class RStatnetCommon(RPackage): Statnet Project. They may also be of use to others.""" homepage = "http://www.statnet.org" - url = "https://cran.r-project.org/src/contrib/statnet.common_3.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/statnet.common" + 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" + version('4.3.0', sha256='834a3359eac967df0420eee416ae4983e3b502a3de56bb24f494a7ca4104e959') + version('4.2.0', sha256='1176c3303436ebe858d02979cf0a0c33e4e2d1f3637516b4761d573ccd132461') version('3.3.0', '36bc11098dcd3652a4beb05c156ad6c8') + + depends_on('r@3.5:', when='@4.2.0:', type=('build', 'run')) + depends_on('r-coda', when='@4.1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index 5e10fff5f9f..8c44256da8e 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -18,12 +18,15 @@ class RStringi(RPackage): etc.""" homepage = "http://www.gagolewski.com/software/stringi/" - url = "https://cran.r-project.org/src/contrib/stringi_1.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/stringi" + url = "https://cloud.r-project.org/src/contrib/stringi_1.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/stringi" + version('1.4.3', sha256='13cecb396b700f81af38746e97b550a1d9fda377ca70c78f6cdfc770d33379ed') + version('1.3.1', sha256='32df663bb6e9527e1ac265eec2116d26f7b7e62ea5ae7cc5de217cbb8defc362') version('1.1.5', '0d5ec30ae368ab1b87a36fee3e228e7b') version('1.1.3', '3b89cee3b5ef7c031077cd7707718e07') version('1.1.2', '0ec2faa62643e1900734c0eaf5096648') version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') - depends_on('icu4c') + depends_on('r@2.14:', type=('build', 'run')) + depends_on('icu4c@52:') diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index 54a43fe9b73..aa6bee349d5 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -13,13 +13,17 @@ class RStringr(RPackage): vectors in the same way, and the output from one function is easy to feed into the input of another.""" - homepage = "https://cran.r-project.org/web/packages/stringr/index.html" - url = "https://cran.r-project.org/src/contrib/stringr_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/stringr" + 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" + version('1.4.0', sha256='87604d2d3a9ad8fd68444ce0865b59e2ffbdb548a38d6634796bbd83eeb931dd') + version('1.3.1', sha256='7a8b8ea038e45978bd797419b16793f44f10c5355ad4c64b74d15276fef20343') version('1.2.0', '9054b1de91c578cc5cf454d656e9c697') version('1.1.0', '47973a33944c6d5db9524b1e835b8a5d') version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') - depends_on('r-stringi', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-strucchange/package.py b/var/spack/repos/builtin/packages/r-strucchange/package.py index 4cf073e9e1d..8e111a58d7d 100644 --- a/var/spack/repos/builtin/packages/r-strucchange/package.py +++ b/var/spack/repos/builtin/packages/r-strucchange/package.py @@ -10,13 +10,12 @@ class RStrucchange(RPackage): """Testing, monitoring and dating structural changes in (linear) regression models.""" - homepage = "https://cran.r-project.org/package=strucchange" - url = "https://cran.r-project.org/src/contrib/strucchange_1.5-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/strucchange" + 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" version('1.5-1', 'fc751fc011df9c8df82d577298cb8395') - depends_on('r@2.10.0:') - + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) depends_on('r-sandwich', 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 cc9efbfb24d..2ddbb19bf34 100644 --- a/var/spack/repos/builtin/packages/r-subplex/package.py +++ b/var/spack/repos/builtin/packages/r-subplex/package.py @@ -9,8 +9,12 @@ class RSubplex(RPackage): """Unconstrained Optimization using the Subplex Algorithm""" - homepage = "https://cran.r-project.org/package=subplex" - url = "https://cran.r-project.org/src/contrib/subplex_1.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/subplex" + 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" + version('1.5-4', sha256='ff94cf6b1560f78c31712c05bc2bc1b703339e09c7fc777ee94abf15fa7a8b81') + version('1.5-2', sha256='6f8c3ccadf1ccd7f11f3eae28cec16eed3695f14e351b864d807dbaba6cd3ded') version('1.4-1', '2ed963dbbb1dbef47ebec7003f39a117') + + depends_on('r@2.5.1:', 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 d0729c99960..a3f22495213 100644 --- a/var/spack/repos/builtin/packages/r-survey/package.py +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -16,7 +16,19 @@ class RSurvey(RPackage): sampling without replacement. Principal components, factor analysis.""" homepage = "http://r-survey.r-forge.r-project.org/survey/" - url = "https://cran.r-project.org/src/contrib/survey_3.30-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('3.36', sha256='90f32e9d2b52eacf881e6717a4b5edfc5a3beb5da516f8372293549589d79475') + version('3.35-1', sha256='11e5ddde9c8c21dfaed0b1247036e068ad32782c76ff71f7937eb7585dd364db') version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0') + + depends_on('r@2.14.0:', when='@:3.31-5', 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')) diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py index fec334728b5..34c23beca0a 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -11,12 +11,15 @@ class RSurvival(RPackage): Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.""" - homepage = "https://cran.r-project.org/package=survival" - url = "https://cran.r-project.org/src/contrib/survival_2.41-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/survival" + 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" + version('2.44-1.1', sha256='55b151e15fcd24ccb3acf60331c9a7ad82bc10f3841ab3be9bc2a37e9ee751b9') + version('2.44-1', sha256='82c44afa41fe4504295855f1da4a5940c3289dfd61bc664bf211bb67c051a909') version('2.41-3', '6edb8093d1177775685dc26f3ce78d73') version('2.40-1', 'a2474b656cd723791268e3114481b8a7') version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') + depends_on('r@2.13.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sys/package.py b/var/spack/repos/builtin/packages/r-sys/package.py new file mode 100644 index 00000000000..af8fb3ebbd4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sys/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 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 RSys(RPackage): + """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" + + version('3.2', sha256='2819498461fe2ce83d319d1a47844e86bcea6d01d10861818dba289e7099bbcc') diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py index a7ef6efd60d..3637255bf1b 100644 --- a/var/spack/repos/builtin/packages/r-tarifx/package.py +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -9,10 +9,11 @@ class RTarifx(RPackage): """A collection of various utility and convenience functions.""" - homepage = "https://cran.r-project.org/package=taRifx" - url = "https://cran.r-project.org/src/contrib/taRifx_1.0.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/taRifx" + 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" + version('1.0.6.1', sha256='d4c832b26d476a395ddf8349c42613270023c8bbf52a274d280be6284c11d7e2') version('1.0.6', '7e782e04bd69d929b29f91553382e6a2') depends_on('r-reshape2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-taxizedb/package.py b/var/spack/repos/builtin/packages/r-taxizedb/package.py index 384e90f63b9..973d75262bb 100644 --- a/var/spack/repos/builtin/packages/r-taxizedb/package.py +++ b/var/spack/repos/builtin/packages/r-taxizedb/package.py @@ -9,9 +9,9 @@ class RTaxizedb(RPackage): """taxizedb: Tools for Working with 'Taxonomic' Databases""" - homepage = "https://cran.r-project.org/package=taxizedb" - url = "https://cran.r-project.org/src/contrib/taxizedb_0.1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/taxizedb/" + 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/" version('0.1.4', sha256='5a40569a2b5abe56201f112a10220150353412df39b7e8d21ea8698f424cf295') @@ -24,5 +24,3 @@ class RTaxizedb(RPackage): 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-roxygen2@6.0.1:', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tclust/package.py b/var/spack/repos/builtin/packages/r-tclust/package.py index b2a0f2d5c68..e0534329818 100644 --- a/var/spack/repos/builtin/packages/r-tclust/package.py +++ b/var/spack/repos/builtin/packages/r-tclust/package.py @@ -9,18 +9,15 @@ class RTclust(RPackage): """Provides functions for robust trimmed clustering.""" - homepage = "https://cran.r-project.org/web/packages/tclust/index.html" - url = "https://cran.r-project.org/src/contrib/tclust_1.3-1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tclust" + 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" + version('1.4-1', sha256='4b0be612c8ecd7b4eb19a44ab6ac8f5d40515600ae1144c55989b6b41335ad9e') version('1.3-1', '5415d74682588d4a6fb8ce166fc75661') version('1.2-7', 'e32cd02819682cc944c7baaac3b6f2b7') version('1.2-3', '922abc1abd8da4c6ac9830e1f2f71e84') version('1.1-03', 'f1cc9278bdb068acce4623a9d98b7b62') version('1.1-02', '6f206501b0341fb5623208d145984f5a') - depends_on('r@3.4.0:3.4.9') - depends_on('r-cluster', type=('build', 'run')) - depends_on('r-mclust', type=('build', 'run')) - depends_on('r-mvtnorm', type=('build', 'run')) - depends_on('r-sn', type=('build', 'run')) + depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tensora/package.py b/var/spack/repos/builtin/packages/r-tensora/package.py index 6735fbb8294..4330b8c9651 100644 --- a/var/spack/repos/builtin/packages/r-tensora/package.py +++ b/var/spack/repos/builtin/packages/r-tensora/package.py @@ -11,8 +11,11 @@ class RTensora(RPackage): with tensors and computation with datasets of tensors on a higher level abstraction.""" - homepage = "https://cran.r-project.org/web/packages/tensorA/index.html" - url = "https://cran.r-project.org/src/contrib/tensorA_0.36.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tensorA" + 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" + version('0.36.1', sha256='c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c') version('0.36', '01c0613491d9b46600bf403d7e3bdd80') + + depends_on('r@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py index f83669a9e81..e4a9ae9db79 100644 --- a/var/spack/repos/builtin/packages/r-testit/package.py +++ b/var/spack/repos/builtin/packages/r-testit/package.py @@ -11,9 +11,11 @@ class RTestit(RPackage): """Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.""" - homepage = "https://cran.r-project.org/package=testit" - url = "https://cran.r-project.org/src/contrib/testit_0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/testit" + 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" + version('0.9', sha256='9cf6b3df9b2c700e4e7dcbd5b8cb64fabefe674e1f40346ccaf39fe7feda5e55') + version('0.8', sha256='08a9c19c962eae60f4ab58885a23e0bc239efc39da682290be436c066f8d97f7') version('0.7', 'cfc5f5c66aa644fbf53efc4b29d18e8c') version('0.5', 'f206d3cbdc5174e353d2d05ba6a12e59') diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py index 6b7c0489505..baf7fced96d 100644 --- a/var/spack/repos/builtin/packages/r-testthat/package.py +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -11,13 +11,20 @@ class RTestthat(RPackage): up.""" homepage = "https://github.com/hadley/testthat" - url = "https://cran.r-project.org/src/contrib/testthat_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.2.1', sha256='67ee0512bb312695c81fd74338bb8ce9e2e58763681ddbcdfdf35f52dfdb0b78') + version('2.1.0', sha256='cf5fa7108111b32b86e70819352f86b57ab4e835221bb1e83642d52a1fdbcdd4') version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) + depends_on('r-crayon@1.3.4:', type=('build', 'run')) depends_on('r-praise', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-r6', type=('build', 'run')) + depends_on('r-r6@2.2.0:', type=('build', 'run')) + depends_on('r-cli', when='@2.0.0:', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-withr@2.0.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-evaluate', when='@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py index 1a305242a09..8631d5d7269 100644 --- a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py +++ b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py @@ -16,9 +16,11 @@ class RTfmpvalue(RPackage): Algorithms Mol Biol:2, 15.""" homepage = "https://github.com/ge11232002/TFMPvalue" - url = "https://cran.rstudio.com/src/contrib/TFMPvalue_0.0.6.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/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" + version('0.0.8', sha256='6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841') version('0.0.6', '69fdf4f9b9a0f408a5cee9ce34bea261') + depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-rcpp@0.11.1:', type=('build', 'run')) 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 7460b5d4ee4..593cb7e6ae2 100644 --- a/var/spack/repos/builtin/packages/r-th-data/package.py +++ b/var/spack/repos/builtin/packages/r-th-data/package.py @@ -9,12 +9,15 @@ class RThData(RPackage): """Contains data sets used in other packages Torsten Hothorn maintains.""" - homepage = "https://cran.r-project.org/package=TH.data" - url = "https://cran.r-project.org/src/contrib/TH.data_1.0-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/TH.data" + 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" + version('1.0-10', sha256='618a1c67a30536d54b1e48ba3af46a6edcd6c2abef17935b5d4ba526a43aff55') + version('1.0-9', sha256='d8318a172ce2b9f7f284dc297c8a8d5093de8eccbb566c8e7580e70938dfae0f') version('1.0-8', '2cc20acc8b470dff1202749b4bea55c4') version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') + depends_on('r@2.10.0:', type=('build', 'run')) 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 c32f33acf93..604bbb9c2a5 100644 --- a/var/spack/repos/builtin/packages/r-threejs/package.py +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -11,11 +11,16 @@ class RThreejs(RPackage): 'three.js' visualization library ("http://threejs.org").""" homepage = "http://bwlewis.github.io/rthreejs" - url = "https://cran.r-project.org/src/contrib/threejs_0.2.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/threejs" + 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" + + version('0.3.1', sha256='71750b741672a435ecf749b69c72f0681aa8bb795e317f4e3056d5e33f6d79e8') version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b') - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-htmlwidgets@0.3.2:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-jsonlite', 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-igraph@1.0.0:', when='@0.3.1:', type=('build', 'run')) + depends_on('r-crosstalk', when='@0.3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 29b2f614cd4..9e2aa5cebbd 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -11,8 +11,10 @@ class RTibble(RPackage): capabilities than traditional data frames.""" homepage = "https://github.com/tidyverse/tibble" - url = "https://cran.rstudio.com/src/contrib/tibble_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tibble" + url = "https://cloud.r-project.org/src/contrib/tibble_1.3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tibble" + + version('2.1.3', sha256='9a8cea9e6b5d24a7e9bf5f67ab38c40b2b6489eddb0d0edb8a48a21ba3574e1a') version('2.0.1', sha256='7ab2cc295eecf00a5310993c99853cd6622ad468e7a60d004b8a73957a713d13') version('2.0.0', sha256='05ad2d62e949909548c4bb8ac596810321f11b330afa9717d0889dc35edd99ba') version('1.4.2', sha256='11670353ff7059a55066dd075d1534d6a27bc5c3583fb9bc291bf750a75c5b17') @@ -21,13 +23,14 @@ class RTibble(RPackage): version('1.2', 'bdbc3d67aa16860741add6d6ec20ea13') version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') - depends_on('r@3.1.2:') - - depends_on('r-assertthat', type=('build', 'run')) + depends_on('r@3.1.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r@3.1.2:', when='@:1.2', type=('build', 'run')) + 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', type=('build', 'run')) - depends_on('r-rlang', type=('build', 'run'), when='@1.3.1:') + depends_on('r-rcpp@0.12.3:', type=('build', 'run'), when='@:1.3.4') + depends_on('r-rlang@0.3.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-cli', type=('build', 'run'), when='@1.4.2:') - depends_on('r-crayon', type=('build', 'run'), when='@1.4.2:') - depends_on('r-pillar', type=('build', 'run'), when='@1.4.2:') - depends_on('r-pkgconfig', type=('build', 'run'), when='@1.4.2:') + depends_on('r-crayon@1.3.4:', type=('build', 'run'), when='@1.4.1:') + depends_on('r-pillar@1.3.1:', type=('build', 'run'), when='@1.4.1:') + depends_on('r-pkgconfig', type=('build', 'run'), when='@2.0.0:') + depends_on('r-fansi@0.4.0:', type=('build', 'run'), when='@2.0.0:') diff --git a/var/spack/repos/builtin/packages/r-tidycensus/package.py b/var/spack/repos/builtin/packages/r-tidycensus/package.py index c6e41da83d9..c6c52e3bd11 100644 --- a/var/spack/repos/builtin/packages/r-tidycensus/package.py +++ b/var/spack/repos/builtin/packages/r-tidycensus/package.py @@ -13,21 +13,23 @@ class RTidycensus(RPackage): data frames, and optionally returns a list-column with feature geometry for many geographies.""" - homepage = "https://cran.r-project.org/package=tidycensus" - url = "https://cran.rstudio.com/src/contrib/tidycensus_0.3.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tidycensus" + 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" + version('0.9.2', sha256='2454525301caff9eaaf6ebe14f58706ece1fbace6187ce8bf3fff04c842b9536') version('0.3.1', '420d046b5a408d321e775c3d410e7699') + depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-sf', type=('build', 'run')) - depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-dplyr@0.7.0:', type=('build', 'run')) depends_on('r-tigris', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-jsonlite', 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', type=('build', 'run')) + depends_on('r-tidyr@0.7.0:', type=('build', 'run')) depends_on('r-rappdirs', type=('build', 'run')) depends_on('r-readr', type=('build', 'run')) depends_on('r-xml2', 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 e3a5ac05e5e..456a6b79314 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -12,12 +12,15 @@ class RTidyr(RPackage): pipelines.""" homepage = "https://github.com/hadley/tidyr" - url = "https://cran.r-project.org/src/contrib/tidyr_0.7.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tidyr" + url = "https://cloud.r-project.org/src/contrib/tidyr_0.7.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidyr" + version('0.8.3', sha256='a18f54ec35124110058ab23f7e0a3c037a8d50f0405520cf5cc5443ec022cc37') + version('0.8.2', sha256='99a508d0539390364789c5f4835b36c4a383927f0ec1648e2a4636c1cc6e490f') version('0.7.2', '42d723bf04c5c1c59e27a8be14f3a6b6') version('0.5.1', '3cadc869510c054ed93d374ab44120bd') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-dplyr@0.7.0:', type=('build', 'run')) depends_on('r-stringi', type=('build', 'run')) @@ -25,5 +28,5 @@ class RTidyr(RPackage): depends_on('r-glue', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-tidyselect', type=('build', 'run')) + depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyselect/package.py b/var/spack/repos/builtin/packages/r-tidyselect/package.py index fbcad342646..89eba20d6d9 100644 --- a/var/spack/repos/builtin/packages/r-tidyselect/package.py +++ b/var/spack/repos/builtin/packages/r-tidyselect/package.py @@ -11,13 +11,16 @@ class RTidyselect(RPackage): easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.""" - homepage = "https://cran.r-project.org/package=tidyselect" - url = "https://cran.r-project.org/src/contrib/tidyselect_0.2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tidyselect" + homepage = "https://cloud.r-project.org/package=tidyselect" + url = "https://cloud.r-project.org/src/contrib/tidyselect_0.2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidyselect" + version('0.2.5', sha256='5ce2e86230fa35cfc09aa71dcdd6e05e1554a5739c863ca354d241bfccb86c74') + version('0.2.4', sha256='5cb30e56ad5c1ac59786969edc8d542a7a1735a129a474f585a141aefe6a2295') version('0.2.3', 'c9dbd895ad7ce209bacfad6d19de91c9') - depends_on('r-glue', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-glue@1.3.0:', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-rlang@0.1:', type=('build', 'run')) + depends_on('r-rlang@0.2.2:', type=('build', 'run')) depends_on('r-rcpp@0.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyverse/package.py b/var/spack/repos/builtin/packages/r-tidyverse/package.py index 1f8abb3d6fb..83027d7ff22 100644 --- a/var/spack/repos/builtin/packages/r-tidyverse/package.py +++ b/var/spack/repos/builtin/packages/r-tidyverse/package.py @@ -13,8 +13,8 @@ class RTidyverse(RPackage): packages in a single step.""" homepage = "http://tidyverse.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tidyverse" + url = "https://cloud.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidyverse" version('1.2.1', '7e2ca0b72ab668342c02fd0f52c082e1') @@ -43,4 +43,3 @@ class RTidyverse(RPackage): depends_on('r-tibble@1.3.4:', type=('build', 'run')) depends_on('r-tidyr@0.7.2:', type=('build', 'run')) depends_on('r-xml2@1.1.1:', type=('build', 'run')) - depends_on('r-rlang@0.1.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tiff/package.py b/var/spack/repos/builtin/packages/r-tiff/package.py index 596d0587541..b74693ac46e 100644 --- a/var/spack/repos/builtin/packages/r-tiff/package.py +++ b/var/spack/repos/builtin/packages/r-tiff/package.py @@ -12,10 +12,11 @@ class RTiff(RPackage): write both files and in-memory raw vectors.""" homepage = "http://www.rforge.net/tiff/" - url = "https://cran.rstudio.com/src/contrib/tiff_0.1-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.1-5', '5052990b8647c77d3e27bc0ecf064e0b') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on("jpeg") depends_on("libtiff") diff --git a/var/spack/repos/builtin/packages/r-tigris/package.py b/var/spack/repos/builtin/packages/r-tigris/package.py index 93ace4a3eeb..19c1cef79a1 100644 --- a/var/spack/repos/builtin/packages/r-tigris/package.py +++ b/var/spack/repos/builtin/packages/r-tigris/package.py @@ -10,16 +10,19 @@ class RTigris(RPackage): """Download TIGER/Line shapefiles from the United States Census Bureau and load into R as 'SpatialDataFrame' or 'sf' objects.""" - homepage = "https://cran.r-project.org/package=tigris" - url = "https://cran.rstudio.com/src/contrib/tigris_0.5.3.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tigris" + 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" + version('0.8.2', sha256='ed8d6ab25332c2cc800858d58324bd8264772d8a916a3f0a8d489250a7e7140e') version('0.5.3', 'c11cb459bf134d3deb1a641a60c86413') + 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-stringr', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-rgdal', type=('build', 'run')) - depends_on('r-rgeos', type=('build', 'run')) + depends_on('r-rgeos', when='@:0.5.3', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) depends_on('r-rappdirs', type=('build', 'run')) depends_on('r-maptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-timedate/package.py b/var/spack/repos/builtin/packages/r-timedate/package.py index ab31d415b00..2025d4af64f 100644 --- a/var/spack/repos/builtin/packages/r-timedate/package.py +++ b/var/spack/repos/builtin/packages/r-timedate/package.py @@ -10,8 +10,12 @@ class RTimedate(RPackage): """Environment for teaching "Financial Engineering and Computational Finance". Managing chronological and calendar objects.""" - homepage = "https://cran.r-project.org/package=timeDate" - url = "https://cran.r-project.org/src/contrib/timeDate_3012.100.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/timeDate" + 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" + version('3043.102', sha256='377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473') + version('3042.101', sha256='6c8d4c7689b31c6a43555d9c7258516556ba03b132e5643691e3e317b89a8c6d') version('3012.100', '9f69d3724efbf0e125e6b8e6d3475fe4') + + depends_on('r@2.15.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tinytex/package.py b/var/spack/repos/builtin/packages/r-tinytex/package.py new file mode 100644 index 00000000000..e8384c0285e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tinytex/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 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 RTinytex(RPackage): + """Helper functions to install and maintain the 'LaTeX' distribution named + 'TinyTeX' (), a lightweight, cross-platform, + portable, and easy-to-maintain version of 'TeX Live'. This package also + contains helper functions to compile 'LaTeX' documents, and install missing + 'LaTeX' packages automatically.""" + + homepage = "https://github.com/yihui/tinytex" + url = "https://cloud.r-project.org/src/contrib/tinytex_0.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tinytex" + + version('0.15', sha256='5d0988d3b7f763dfa65c722f177452a21344e428415a4b31aeb51478f0abad90') + + depends_on('r-xfun@0.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-triebeard/package.py b/var/spack/repos/builtin/packages/r-triebeard/package.py index f2d04924da6..a3521c9c1b3 100644 --- a/var/spack/repos/builtin/packages/r-triebeard/package.py +++ b/var/spack/repos/builtin/packages/r-triebeard/package.py @@ -10,8 +10,8 @@ class RTriebeard(RPackage): """triebeard: 'Radix' Trees in 'Rcpp'""" homepage = "https://github.com/Ironholds/triebeard/" - url = "https://cran.r-project.org/src/contrib/triebeard_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" 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 d918d314396..df73e3bf94e 100644 --- a/var/spack/repos/builtin/packages/r-trimcluster/package.py +++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py @@ -10,9 +10,10 @@ class RTrimcluster(RPackage): """trimcluster: Cluster analysis with trimming""" homepage = "http://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cran.r-project.org/src/contrib/trimcluster_0.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/trimcluster" + 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" + version('0.1-2.1', sha256='b64a872a6c2ad677dfeecc776c9fe5aff3e8bab6bc6a8c86957b5683fd5d2300') version('0.1-2', '7617920e224bd18f5b87db38a3116ec2') - depends_on('r@1.9.0:') + depends_on('r@1.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py index 28929fa1035..19d76beb064 100644 --- a/var/spack/repos/builtin/packages/r-truncnorm/package.py +++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py @@ -10,8 +10,10 @@ class RTruncnorm(RPackage): """Density, probability, quantile and random number generation functions for the truncated normal distribution.""" - homepage = "https://cran.r-project.org/package=truncnorm" - url = "https://cran.rstudio.com/src/contrib/truncnorm_1.0-8.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/truncnorm" + 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" version('1.0-8', 'c60cd6555be0dd2ea91e61757439282d') + + depends_on('r@3.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py index 2964eb6b7ea..221be990b55 100644 --- a/var/spack/repos/builtin/packages/r-trust/package.py +++ b/var/spack/repos/builtin/packages/r-trust/package.py @@ -11,7 +11,9 @@ class RTrust(RPackage): Guaranteed to converge to local minimum of objective function.""" homepage = "http://www.stat.umn.edu/geyer/trust" - url = "https://cran.r-project.org/src/contrib/trust_0.1-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.1-7', '7e218b3a6b33bd77bd7e86dc6360418d') + + depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tseries/package.py b/var/spack/repos/builtin/packages/r-tseries/package.py index 30554303401..e55c8c3b1a8 100644 --- a/var/spack/repos/builtin/packages/r-tseries/package.py +++ b/var/spack/repos/builtin/packages/r-tseries/package.py @@ -9,12 +9,15 @@ class RTseries(RPackage): """Time series analysis and computational finance.""" - homepage = "https://cran.r-project.org/package=tseries" - url = "https://cran.r-project.org/src/contrib/tseries_0.10-42.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tseries" + 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" + version('0.10-47', sha256='202377df56806fe611c2e12c4d9732c71b71220726e2defa7e568d2b5b62fb7b') + version('0.10-46', sha256='12940afd1d466401160e46f993ed4baf28a42cef98d3757b66ee15e916e07222') version('0.10-42', '3feaa5c463bc967d749323163d9bc836') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-quadprog', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) - depends_on('r-quantmod', type=('build', 'run')) + depends_on('r-quantmod@0.4-9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tsne/package.py b/var/spack/repos/builtin/packages/r-tsne/package.py index 11247374a92..a65ae8cfa20 100644 --- a/var/spack/repos/builtin/packages/r-tsne/package.py +++ b/var/spack/repos/builtin/packages/r-tsne/package.py @@ -9,12 +9,10 @@ class RTsne(RPackage): """A "pure R" implementation of the t-SNE algorithm.""" - homepage = "https://cran.r-project.org/web/packages/tsne/index.html" - url = "https://cran.r-project.org/src/contrib/tsne_0.1-3.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tnse" + 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" version('0.1-3', '00974d4b3fd5f1100d0ebd24e03b0af9') version('0.1-2', 'd96d8dce6ffeda68e2b25ec1ff52ea61') version('0.1-1', '8197e5c61dec916b7a31b74e658b632d') - - depends_on('r@3.4.0:3.4.9') diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py index 8e81f138251..08583bb6dbe 100644 --- a/var/spack/repos/builtin/packages/r-ttr/package.py +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -10,10 +10,13 @@ class RTtr(RPackage): """Functions and data to construct technical trading rules with R.""" homepage = "https://github.com/joshuaulrich/TTR" - url = "https://cran.r-project.org/src/contrib/TTR_0.23-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.23-4', sha256='eb17604da986213b3b924f0af65c3d089502a658a253ee34f6b8f6caccf6bfa2') + version('0.23-3', sha256='2136032c7a2cd2a82518a4412fc655ecb16597b123dbdebe5684caef9f15261f') version('0.23-1', '35f693ac0d97e8ec742ebea2da222986') - depends_on('r-xts', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-ucminf/package.py b/var/spack/repos/builtin/packages/r-ucminf/package.py new file mode 100644 index 00000000000..a0ddaaa7b11 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ucminf/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 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 RUcminf(RPackage): + """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" + + 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 b72b7224ab6..0adfcef4b3b 100644 --- a/var/spack/repos/builtin/packages/r-udunits2/package.py +++ b/var/spack/repos/builtin/packages/r-udunits2/package.py @@ -10,9 +10,10 @@ class RUdunits2(RPackage): """Provides simple bindings to Unidata's udunits library.""" homepage = "https://github.com/pacificclimate/Rudunits2" - url = "https://cran.r-project.org/src/contrib/udunits2_0.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/udunits2" + url = "https://cloud.r-project.org/src/contrib/udunits2_0.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/udunits2" version('0.13', 'c8717808c740ef70eed7aea93c7c4c7d') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('udunits2') diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py index 0dcf8c35d96..49ae88dcba8 100644 --- a/var/spack/repos/builtin/packages/r-units/package.py +++ b/var/spack/repos/builtin/packages/r-units/package.py @@ -15,9 +15,14 @@ class RUnits(RPackage): conversion.""" homepage = "https://github.com/edzer/units/" - url = "https://cran.r-project.org/src/contrib/units_0.4-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.6-3', sha256='03de88d9dcfe80d22dd3813413f33657c576aed24a8091dbfc7f68602020a64f') + version('0.6-2', sha256='5e286775d0712c8e15b6ae3a533d4c4349b0f6410c2d9d897ca519c3d0e5f170') version('0.4-6', '0bb90dde5dad7608fa6feb1599381bf2') - depends_on('r-udunits2', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-udunits2@0.13:', when='@:0.5-1', type=('build', 'run')) + depends_on('r-rcpp@0.12.10:', type=('build', 'run')) + depends_on('udunits2', when='@0.6-0:') diff --git a/var/spack/repos/builtin/packages/r-urca/package.py b/var/spack/repos/builtin/packages/r-urca/package.py new file mode 100644 index 00000000000..1dc5753a430 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-urca/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 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 RUrca(RPackage): + """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" + + version('1.3-0', sha256='621cc82398e25b58b4a16edf000ed0a1484d9a0bc458f734e97b6f371cc76aaa') + + depends_on('r@2.0.0:', type=('build', 'run')) + depends_on('r-nlme', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-urltools/package.py b/var/spack/repos/builtin/packages/r-urltools/package.py index 6c1b78deb29..5187a31288d 100644 --- a/var/spack/repos/builtin/packages/r-urltools/package.py +++ b/var/spack/repos/builtin/packages/r-urltools/package.py @@ -10,8 +10,8 @@ class RUrltools(RPackage): """urltools: Vectorised Tools for URL Handling and Parsing""" homepage = "https://github.com/Ironholds/urltools/" - url = "https://cran.r-project.org/src/contrib/urltools_1.7.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" 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 new file mode 100644 index 00000000000..4f7cfc743c0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-usethis/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2019 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 RUsethis(RPackage): + """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" + + version('1.5.1', sha256='9e3920a04b0df82adf59eef2c1b2b4d835c4a757a51b3c163b8fc619172f561d') + + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-clipr@0.3.0:', type=('build', 'run')) + depends_on('r-clisymbols', 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-fs@1.3.0:', type=('build', 'run')) + depends_on('r-gh', type=('build', 'run')) + depends_on('r-git2r@0.23:', type=('build', 'run')) + depends_on('r-glue@1.3.0:', type=('build', 'run')) + depends_on('r-purrr', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + 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-yaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-utf8/package.py b/var/spack/repos/builtin/packages/r-utf8/package.py index 2e40f83bfa2..8a00a26db69 100644 --- a/var/spack/repos/builtin/packages/r-utf8/package.py +++ b/var/spack/repos/builtin/packages/r-utf8/package.py @@ -10,12 +10,15 @@ class RUtf8(RPackage): """Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.""" - homepage = "https://cran.r-project.org/package=utf8" - url = "https://cran.r-project.org/src/contrib/utf8_1.1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/utf8" + 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" + version('1.1.4', sha256='f6da9cadfc683057d45f54b43312a359cf96ec2731c0dda18a8eae31d1e31e54') version('1.1.3', sha256='43b394c3274ba0f66719d28dc4a7babeb87187e766de8d8ca716e0548091440f') version('1.1.2', sha256='148517aadb75d82aba61f63afe2a30d254abebbdc7e32dd0830e12ff443915b9') version('1.1.1', sha256='0e30c824e43cdc0a3339f4688e3271737d02ea10768a46137e0e41936051cb3d') version('1.1.0', sha256='6a8ae2c452859800c3ef12993a55892588fc35df8fa1360f3d182ed97244dc4f') version('1.0.0', sha256='7562a80262cbc2017eee76c0d3c9575f240fab291f868a11724fa04a116efb80') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-utils/package.py b/var/spack/repos/builtin/packages/r-utils/package.py deleted file mode 100644 index 45caeafb935..00000000000 --- a/var/spack/repos/builtin/packages/r-utils/package.py +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 2013-2019 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 RUtils(RPackage): - """Utility functions useful when programming and - developing R packages.""" - - homepage = "https://github.com/HenrikBengtsson/R.utils" - url = "https://cran.rstudio.com/src/contrib/R.utils_2.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R.utils" - - version('2.5.0', 'a728ef3ceb35cafc4c39ea577cecc38b') - - depends_on('r-oo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py index d161948c050..d68b08fc994 100644 --- a/var/spack/repos/builtin/packages/r-uuid/package.py +++ b/var/spack/repos/builtin/packages/r-uuid/package.py @@ -12,6 +12,9 @@ class RUuid(RPackage): Identifiers).""" homepage = "http://www.rforge.net/uuid" - url = "https://cran.rstudio.com/src/contrib/uuid_0.1-2.tar.gz" + 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" version('0.1-2', 'f97d000c0b16bca455fb5bf2cd668ddf') + + depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-uwot/package.py b/var/spack/repos/builtin/packages/r-uwot/package.py new file mode 100644 index 00000000000..092288646dc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-uwot/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 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 RUwot(RPackage): + """An implementation of the Uniform Manifold Approximation and Projection + dimensionality reduction by McInnes et al. (2018) . It + also provides means to transform new data and to carry out supervised + dimensionality reduction. An implementation of the related LargeVis method + of Tang et al. (2016) is also provided. This is a + complete re-implementation in R (and C++, via the 'Rcpp' package): no + Python installation is required. See the uwot website + () 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" + + version('0.1.3', sha256='4936e6922444cae8a71735e945b6bb0828a1012232eb94568054f78451c406d7') + + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + 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-rcppparallel', type=('build', 'run')) + depends_on('r-irlba', type=('build', 'run')) + depends_on('r-rcppprogress', type=('build', 'run')) + depends_on('r-dqrng', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-varselrf/package.py b/var/spack/repos/builtin/packages/r-varselrf/package.py index b187f4a542a..03fedb632aa 100644 --- a/var/spack/repos/builtin/packages/r-varselrf/package.py +++ b/var/spack/repos/builtin/packages/r-varselrf/package.py @@ -15,8 +15,10 @@ class RVarselrf(RPackage): and other genomics and proteomics applications).""" homepage = "http://ligarto.org/rdiaz/Software/Software.html" - url = "https://cran.rstudio.com/src/contrib/varSelRF_0.7-8.tar.gz" + 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" version('0.7-8', '103c460d0734bd38ae13496c839d3435') + depends_on('r@2.0.0:', type=('build', 'run')) depends_on('r-randomforest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py index 6980e5459a2..f342ec57700 100644 --- a/var/spack/repos/builtin/packages/r-vcd/package.py +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -14,12 +14,15 @@ class RVcd(RPackage): the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).""" - homepage = "https://cran.r-project.org/package=vcd" - url = "https://cran.r-project.org/src/contrib/vcd_1.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/vcd" + 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" + version('1.4-4', sha256='a561adf120b5ce41b66e0c0c321542fcddc772eb12b3d7020d86e9cd014ce9d2') + version('1.4-3', sha256='17ce89927421d9cd01285b6093eeaaecb1e7252388007f66d3b9222e58cc5f15') version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02') + depends_on('r@2.4.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) depends_on('r-lmtest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vctrs/package.py b/var/spack/repos/builtin/packages/r-vctrs/package.py new file mode 100644 index 00000000000..0dc05227c53 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vctrs/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 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 RVctrs(RPackage): + """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" + url = "https://cloud.r-project.org/src/contrib/vctrs_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/vctrs" + + version('0.2.0', sha256='5bce8f228182ecaa51230d00ad8a018de9cf2579703e82244e0931fe31f20016') + + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-backports', type=('build', 'run')) + depends_on('r-ellipsis@0.2.0:', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run')) + depends_on('r-rlang@0.4.0:', type=('build', 'run')) + depends_on('r-zeallot', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py index 1410129e62e..2248bfd9e1e 100644 --- a/var/spack/repos/builtin/packages/r-vegan/package.py +++ b/var/spack/repos/builtin/packages/r-vegan/package.py @@ -11,10 +11,19 @@ class RVegan(RPackage): community and vegetation ecologists.""" homepage = "https://github.com/vegandevs/vegan" - url = "https://cran.r-project.org/src/contrib/vegan_2.4-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.5-5', sha256='876b5266f29f3034fed881020d16f476e62d145a00cb450a1a213e019e056971') + version('2.5-4', sha256='5116a440111fca49b5f95cfe888b180ff29a112e6301d5e2ac5cae0e628493e0') version('2.4-3', 'db17d4c4b9a4d421246abd5b36b00fec') - depends_on('r@3.0:') + depends_on('r@3.0.0:', when='@:2.4-6', 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-permute@0.9-0:', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) + depends_on('r-mgcv', 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 0e5d8c0a72f..d6c52c2c507 100644 --- a/var/spack/repos/builtin/packages/r-vfs/package.py +++ b/var/spack/repos/builtin/packages/r-vfs/package.py @@ -9,15 +9,12 @@ class RVfs(RPackage): """VFS: Vegetated Filter Strip and Erosion Model""" - homepage = "https://cran.r-project.org/package=VFS" - url = "https://cran.r-project.org/src/contrib/VFS_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/VFS" + 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" version('1.0.2', sha256='8ff7e7e13919ff21f10c7c693ef596a2c7b57c7ca37d79278e443ed122a21aad') depends_on('r@3.4.0:', type=('build', 'run')) depends_on('r-e1071', type=('build', 'run')) depends_on('r-nleqslv@3.3.0:', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rmarkdown', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vgam/package.py b/var/spack/repos/builtin/packages/r-vgam/package.py index 236de33f3af..3039bbbd6cc 100644 --- a/var/spack/repos/builtin/packages/r-vgam/package.py +++ b/var/spack/repos/builtin/packages/r-vgam/package.py @@ -10,16 +10,18 @@ class RVgam(RPackage): """An implementation of about 6 major classes of statistical regression models.""" - homepage = "https://cran.r-project.org/web/packages/VGAM/index.html" - url = "https://cran.r-project.org/src/contrib/VGAM_1.0-4.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/VGAM" + 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" + version('1.1-1', sha256='de192bd65a7e8818728008de8e60e6dd3b61a13616c887a43e0ccc8147c7da52') + version('1.0-6', sha256='121820a167411e847b41bdcb0028b55842d0ccc0c3471755c67449837e0fe3b9') version('1.0-4', '9d30736842db6d9dcec83df49f11d3c1') version('1.0-3', 'a158cd0a6ff956b4bf21d610df361b18') version('1.0-2', '813b303d5d956914cf8910db3fa1ba14') version('1.0-1', '778182585c774036ac3d10240cf63b40') version('1.0-0', '81da7b3a797b5e26b9e859dc2f373b7b') - depends_on('r@3.4.0:3.4.9') - depends_on('r-mass', type=('build', 'run')) - depends_on('r-mgcv', type=('build', 'run')) + depends_on('r@3.0.0:', when='@:1.0-1', 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')) diff --git a/var/spack/repos/builtin/packages/r-vipor/package.py b/var/spack/repos/builtin/packages/r-vipor/package.py index 354305221f5..e4deb92f860 100644 --- a/var/spack/repos/builtin/packages/r-vipor/package.py +++ b/var/spack/repos/builtin/packages/r-vipor/package.py @@ -9,9 +9,9 @@ class RVipor(RPackage): """Plot Categorical Data Using Quasirandom Noise and Density Estimates""" - homepage = "https://cran.r-project.org/package=vipor" - url = "https://cran.r-project.org/src/contrib/vipor_0.4.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/vipor" + 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" version('0.4.5', 'd08bc95b3aaf1574bf41b7eb41b67ce4') version('0.4.4', '834212e3971787809ba9737744d54dee') diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py index 5492e1451c4..82f5578b1a6 100644 --- a/var/spack/repos/builtin/packages/r-viridis/package.py +++ b/var/spack/repos/builtin/packages/r-viridis/package.py @@ -10,12 +10,14 @@ class RViridis(RPackage): """viridis: Default Color Maps from 'matplotlib'""" homepage = "https://github.com/sjmgarnier/viridis" - url = "https://cran.r-project.org/src/contrib/viridis_0.4.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.5.1', sha256='ddf267515838c6eb092938133035cee62ab6a78760413bfc28b8256165701918') + version('0.5.0', sha256='fea477172c1e11be40554545260b36d6ddff3fe6bc3bbed87813ffb77c5546cd') version('0.4.0', 'f874384cbedf459f6c309ddb40b354ea') - depends_on('r@2.1.0:') - depends_on('r-viridislite@0.2.0:', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-viridislite@0.3.0:', type=('build', 'run')) 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 8b73a9f6c09..5ff479d2f49 100644 --- a/var/spack/repos/builtin/packages/r-viridislite/package.py +++ b/var/spack/repos/builtin/packages/r-viridislite/package.py @@ -10,9 +10,10 @@ class RViridislite(RPackage): """viridisLite: Default Color Maps from 'matplotlib' (Lite Version)""" homepage = "https://github.com/sjmgarnier/viridisLite" - url = "https://cran.r-project.org/src/contrib/viridisLite_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/viridisLite" + url = "https://cloud.r-project.org/src/contrib/viridisLite_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/viridisLite" + version('0.3.0', sha256='780ea12e7c4024d5ba9029f3a107321c74b8d6d9165262f6e64b79e00aa0c2af') version('0.2.0', '04a04415cf651a2b5f964b261896c0fb') - depends_on('r@2.1.0:') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py index 80e254de0cf..bbf78d73723 100644 --- a/var/spack/repos/builtin/packages/r-visnetwork/package.py +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -11,11 +11,14 @@ class RVisnetwork(RPackage): allows an interactive visualization of networks.""" homepage = "https://github.com/datastorm-open/visNetwork" - url = "https://cran.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('2.0.7', sha256='15ad01636a3a19e1901be6743052805a5b6a9ac1240fb3dab765252b1e865128') + version('2.0.6', sha256='ec2478e6a2af446569ef2d5210a2bc6b2600bcb7fd9908cef8f8c80b01e9c8aa') version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-jsonlite', 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 5821e2949cf..987dd60c2c7 100644 --- a/var/spack/repos/builtin/packages/r-webshot/package.py +++ b/var/spack/repos/builtin/packages/r-webshot/package.py @@ -10,11 +10,12 @@ class RWebshot(RPackage): """webshot: Take Screenshots of Web Pages""" homepage = "https://github.com/wch/webshot/" - url = "https://cran.r-project.org/src/contrib/webshot_0.5.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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/" version('0.5.1', sha256='b9750d206c6fa0f1f16cc212b0a34f4f4bfa916962d2c877f0ee9a33620f4b23') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-callr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-wgcna/package.py b/var/spack/repos/builtin/packages/r-wgcna/package.py index 14c6d8b8a60..7b21e756edd 100644 --- a/var/spack/repos/builtin/packages/r-wgcna/package.py +++ b/var/spack/repos/builtin/packages/r-wgcna/package.py @@ -9,10 +9,12 @@ class RWgcna(RPackage): """WGCNA: Weighted Correlation Network Analysis""" - homepage = "https://cran.r-project.org/package=WGCNA" - url = "https://cran.r-project.org/src/contrib/WGCNA_1.66.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/WGCNA/" + homepage = "https://cloud.r-project.org/package=WGCNA" + url = "https://cloud.r-project.org/src/contrib/WGCNA_1.66.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/WGCNA/" + version('1.68', sha256='0a04f15a20817f9260ae1896eda3be83a7f4855a27a348df85c7f4d376f1efe8') + version('1.67', sha256='c9cc9989763b2c80835489eabd38d9ee35b204305044d115ca7c775a103f6824') version('1.64-1', sha256='961a890cda40676ba533cd6de2b1d4f692addd16363f874c82ba8b65dd2d0db6') depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py index 55b3a4f1ba0..951e64faba5 100644 --- a/var/spack/repos/builtin/packages/r-whisker/package.py +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -11,7 +11,7 @@ class RWhisker(RPackage): including R""" homepage = "http://github.com/edwindj/whisker" - url = "https://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6') diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index fffb8ee84a6..f1e50a2ec43 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -13,11 +13,11 @@ class RWithr(RPackage): dependencies to provide access to these functions.""" homepage = "http://github.com/jimhester/withr" - url = "https://cran.r-project.org/src/contrib/withr_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/withr" + url = "https://cloud.r-project.org/src/contrib/withr_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/withr" version('2.1.2', sha256='41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686') version('1.0.2', 'ca52b729af9bbaa14fc8b7bafe38663c') version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') - depends_on('r@3.0.2:') + depends_on('r@3.0.2:', 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 new file mode 100644 index 00000000000..9ffb8f618e4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xfun/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 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 RXfun(RPackage): + """Miscellaneous functions commonly used in other packages maintained by + 'Yihui Xie'.""" + + homepage = "https://github.com/yihui/xfun" + url = "https://cloud.r-project.org/src/contrib/xfun_0.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xfun" + + 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 581c442a05d..13cc2d6139f 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -18,14 +18,17 @@ class RXgboost(RPackage): users are also allowed to define their own objectives easily.""" homepage = "https://github.com/dmlc/xgboost" - url = "https://cran.r-project.org/src/contrib/xgboost_0.6-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" + version('0.90.0.2', sha256='240584c1b4d54a95b4fef9074480752fae9a5b096e8f84747457d641decfc9bf') + version('0.81.0.1', sha256='3e7ada32e66881ea5c90aeafdab948927014c76cfff60a8e3d7f9e1f8a9ed7ce') version('0.6-4', '86e517e3ce39f8a01de796920f6b425e') version('0.4-4', 'c24d3076058101a71de4b8af8806697c') - depends_on('r@3.3.0:') - + depends_on('r@2.10:', when='@:0.4-4', 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-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')) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 0d2b658537c..a6b1d4619db 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -11,11 +11,15 @@ class RXlconnect(RPackage): data.""" homepage = "http://miraisolutions.wordpress.com/" - url = "https://cran.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnect" + 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" + version('0.2-15', sha256='26e1d8db65974719adbc25f1327c584003eb562dc1bb2121bffc2550cf3178b3') + version('0.2-14', sha256='d1013ed26947572bad97d62a3d66346f74993cf96c6408d21d5b6ee567468819') version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') version('0.2-11', '9d1769a103cda05665df399cc335017d') - depends_on('r-xlconnectjars', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-xlconnectjars@0.2-15', type=('build', 'run')) depends_on('r-rjava', type=('build', 'run')) + depends_on('java@6:') diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index ce529fe6beb..57edc703aeb 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -10,10 +10,13 @@ class RXlconnectjars(RPackage): """Provides external JAR dependencies for the XLConnect package.""" homepage = "http://miraisolutions.wordpress.com/" - url = "https://cran.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnectJars" + 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" + version('0.2-15', sha256='bd6f48a72c3a02b7a5e9373bcfc671614bc793f41d7bb8f4f34115a89ff4f8c6') + version('0.2-14', sha256='c675f0ccff0c3e56b2b1cc00d4d28bf8fdfa508266ac0ffab5c0641151dd7332') version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') depends_on('r-rjava', type=('build', 'run')) + depends_on('java@6:') diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index af4ec6f7399..06f3b7e916a 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -11,9 +11,12 @@ class RXlsx(RPackage): 97/2000/XP/2003 file formats.""" homepage = "http://code.google.com/p/rexcel/" - url = "https://cran.rstudio.com/src/contrib/xlsx_0.5.7.tar.gz" + url = "https://cloud.r-project.org/src/contrib/xlsx_0.5.7.tar.gz" + listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" + version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') version('0.5.7', '36b1b16f29c54b6089b1dae923180dd5') depends_on('r-rjava', type=('build', 'run')) depends_on('r-xlsxjars', type=('build', 'run')) + depends_on('java@1.6:') diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index 541028a873d..ad383b3fef4 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -10,8 +10,9 @@ class RXlsxjars(RPackage): """The xlsxjars package collects all the external jars required for the xlxs package. This release corresponds to POI 3.10.1.""" - homepage = "https://cran.rstudio.com/web/packages/xlsxjars/index.html" - url = "https://cran.rstudio.com/src/contrib/xlsxjars_0.6.1.tar.gz" + 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" version('0.6.1', '5a1721d5733cb42f3a29e3f353e39166') diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py index 1454226466d..954c1c76334 100644 --- a/var/spack/repos/builtin/packages/r-xml/package.py +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -11,11 +11,15 @@ class RXml(RPackage): (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".""" - homepage = "https://cran.r-project.org/web/packages/XML/index.html" - url = "https://cran.r-project.org/src/contrib/XML_3.98-1.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XML" + 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" + + version('3.98-1.20', sha256='46af86376ea9a0fb1b440cf0acdf9b89178686a05c4b77728fcff1f023aa4858') + version('3.98-1.19', sha256='81b1c4a2df24c5747fa8b8ec2d76b4e9c3649b56ca94f6c93fbd106c8a72beab') version('3.98-1.9', '70dd9d711cf3cbd218eb2b870aee9503') version('3.98-1.5', 'd1cfcd56f7aec96a84ffca91aea507ee') version('3.98-1.4', '1a7f3ce6f264eeb109bfa57bedb26c14') - depends_on('libxml2') + depends_on('r@2.13.0:', type=('build', 'run')) + 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 80c748ef866..cf355c7f6ff 100644 --- a/var/spack/repos/builtin/packages/r-xml2/package.py +++ b/var/spack/repos/builtin/packages/r-xml2/package.py @@ -10,12 +10,15 @@ class RXml2(RPackage): """Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.""" - homepage = "https://cran.r-project.org/package=xml2" - url = "https://cran.r-project.org/src/contrib/xml2_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/xml2" + 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" + version('1.2.2', sha256='3050f147c4335be2925a576557bbda36bd52a5bba3110d47b740a2dd811a78f4') + version('1.2.1', sha256='5615bbc94607efc3bc192551992b349091df802ae34b855cfa817733f2690605') version('1.1.1', '768f7edc39c4baab6b6b9e7c7ec79fee') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-bh', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.12:', type=('build', 'run')) + depends_on('r-bh', when='@:1.1.1', type=('build', 'run')) depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/r-xnomial/package.py b/var/spack/repos/builtin/packages/r-xnomial/package.py index 348245d2678..609340c9665 100644 --- a/var/spack/repos/builtin/packages/r-xnomial/package.py +++ b/var/spack/repos/builtin/packages/r-xnomial/package.py @@ -11,11 +11,10 @@ class RXnomial(RPackage): """XNomial: Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities""" - homepage = "https://cran.r-project.org/package=XNomial" - url = "https://cran.r-project.org/src/contrib/XNomial_1.0.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XNomial/" + 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/" version('1.0.4', sha256='e6237f79d96f02bb30af1cf055ae9f70541abba34ce045a9d4359b5304189dd7') depends_on('r@2.14:', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xopen/package.py b/var/spack/repos/builtin/packages/r-xopen/package.py new file mode 100644 index 00000000000..4365dff7e10 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xopen/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 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 RXopen(RPackage): + """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" + + version('1.0.0', sha256='e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-processx', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py index 0265a5e3f29..96eeedcaba6 100644 --- a/var/spack/repos/builtin/packages/r-xtable/package.py +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -10,7 +10,11 @@ class RXtable(RPackage): """Coerce data to LaTeX and HTML tables.""" homepage = "http://xtable.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/xtable" + 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" + version('1.8-4', sha256='5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c') + version('1.8-3', sha256='53b2b0fff8d7a8bba434063c2a01b867f510a4389ded2691fbedbc845f08c325') version('1.8-2', '239e4825cd046156a67efae3aac01d86') + + depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py index 2e657117ea6..d698110be7f 100644 --- a/var/spack/repos/builtin/packages/r-xts/package.py +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -13,10 +13,10 @@ class RXts(RPackage): cross-class interoperability.""" homepage = "http://r-forge.r-project.org/projects/xts/" - url = "https://cran.r-project.org/src/contrib/xts_0.11-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/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" version('0.11-2', sha256='12772f6a66aab5b84b0665c470f11a3d8d8a992955c027261cfe8e6077ee13b8') version('0.9-7', 'a232e94aebfa654653a7d88a0503537b') - depends_on('r-zoo', type=('build', 'run')) + depends_on('r-zoo@1.7-12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py index a7d537e0949..9454402e20c 100644 --- a/var/spack/repos/builtin/packages/r-yaml/package.py +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -10,9 +10,11 @@ class RYaml(RPackage): """This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.""" - homepage = "https://cran.r-project.org/web/packages/yaml/index.html" - url = "https://cran.r-project.org/src/contrib/yaml_2.1.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/yaml" + 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" + version('2.2.0', sha256='55bcac87eca360ab5904914fcff473a6981a1f5e6d2215d2634344d0ac30c546') + version('2.1.19', sha256='e5db035693ac765e4b5fe1fc2e9711f8ca73e398e3f2bf27cc60def59ccd7f11') version('2.1.14', '2de63248e6a122c368f8e4537426e35c') version('2.1.13', 'f2203ea395adaff6bd09134666191d9a') diff --git a/var/spack/repos/builtin/packages/r-zeallot/package.py b/var/spack/repos/builtin/packages/r-zeallot/package.py new file mode 100644 index 00000000000..7276bff2553 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-zeallot/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 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 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.""" + + 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" + + 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 new file mode 100644 index 00000000000..13270d7b320 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-zip/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 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 RZip(RPackage): + """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" + + 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 50b38f8aa9b..fe845adea54 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -14,10 +14,14 @@ class RZoo(RPackage): methods to extend standard generics.""" homepage = "http://zoo.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/zoo_1.7-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/zoo" + 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" + version('1.8-6', sha256='2217a4f362f2201443b5fdbfd9a77d9a6caeecb05f02d703ee8b3b9bf2af37cc') + version('1.8-5', sha256='8773969973d28d7d1a48f74b73be1dbd97acb3b22a4668a102e8bb585a7de826') version('1.7-14', '8c577a7c1e535c899ab14177b1039c32') version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') - depends_on('r-lattice', type=('build', 'run')) + depends_on('r@2.10.0:', when='@:1.8-1', type=('build', 'run')) + depends_on('r@3.1.0:', when='@1.8-2:', type=('build', 'run')) + depends_on('r-lattice@0.20-27:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/swftools/configure.patch b/var/spack/repos/builtin/packages/swftools/configure.patch new file mode 100644 index 00000000000..fdaff87aa44 --- /dev/null +++ b/var/spack/repos/builtin/packages/swftools/configure.patch @@ -0,0 +1,17 @@ +--- a/configure 2019-08-07 20:44:13.708133253 -0500 ++++ b/configure 2019-08-07 20:44:27.334099579 -0500 +@@ -2640,10 +2640,10 @@ + + # ------------------------------------------------------------------ + +-if test "x${srcdir}" != "x."; then +- echo "--srcdir is not supported" +- exit 1 +-fi ++#if test "x${srcdir}" != "x."; then ++# echo "--srcdir is not supported" ++# exit 1 ++#fi + + WARNINGS="-Wimplicit -Wreturn-type -Wno-write-strings -Wformat" + if test "x$ENABLE_WARNINGS" '!=' "x";then diff --git a/var/spack/repos/builtin/packages/swftools/package.py b/var/spack/repos/builtin/packages/swftools/package.py new file mode 100644 index 00000000000..779358df74a --- /dev/null +++ b/var/spack/repos/builtin/packages/swftools/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2019 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 Swftools(AutotoolsPackage): + """SWFTools is a collection of utilities for working with Adobe Flash files + (SWF files). The tool collection includes programs for reading SWF files, + combining them, and creating them from other content (like images, sound + files, videos or sourcecode). SWFTools is released under the GPL. + """ + + homepage = "http://swftools.org" + url = "http://swftools.org/swftools-0.9.2.tar.gz" + + version('0.9.2', sha256='bf6891bfc6bf535a1a99a485478f7896ebacbe3bbf545ba551298080a26f01f1') + + patch('configure.patch') + patch('swfs_Makefile.in.patch') + patch('https://aur.archlinux.org/cgit/aur.git/plain/giflib-5.1.patch?h=swftools', + sha256='6a995dfd674c5954f5b967e3d45d6845a186872fcaa4223d725902fd4d679f1b', + level=0) + + depends_on('giflib') + depends_on('lame') + depends_on('poppler') + depends_on('freetype') + depends_on('jpeg') + depends_on('fftw') diff --git a/var/spack/repos/builtin/packages/swftools/swfs_Makefile.in.patch b/var/spack/repos/builtin/packages/swftools/swfs_Makefile.in.patch new file mode 100644 index 00000000000..c53f3dbfa32 --- /dev/null +++ b/var/spack/repos/builtin/packages/swftools/swfs_Makefile.in.patch @@ -0,0 +1,14 @@ +--- a/swfs/Makefile.ing 2019-08-07 21:53:26.077931626 -0500 ++++ b/swfs/Makefile.in 2019-08-07 21:54:18.845809017 -0500 +@@ -41,9 +41,9 @@ + $(INSTALL_DATA) ./PreLoaderTemplate.swf $(pkgdatadir)/swfs/PreLoaderTemplate.swf + $(INSTALL_DATA) ./tessel_loader.swf $(pkgdatadir)/swfs/tessel_loader.swf + $(INSTALL_DATA) ./swft_loader.swf $(pkgdatadir)/swfs/swft_loader.swf +- rm -f $(pkgdatadir)/swfs/default_viewer.swf -o -L $(pkgdatadir)/swfs/default_viewer.swf ++ #rm -f $(pkgdatadir)/swfs/default_viewer.swf -o -L $(pkgdatadir)/swfs/default_viewer.swf + $(LN_S) $(pkgdatadir)/swfs/simple_viewer.swf $(pkgdatadir)/swfs/default_viewer.swf +- rm -f $(pkgdatadir)/swfs/default_loader.swf -o -L $(pkgdatadir)/swfs/default_loader.swf ++ #rm -f $(pkgdatadir)/swfs/default_loader.swf -o -L $(pkgdatadir)/swfs/default_loader.swf + $(LN_S) $(pkgdatadir)/swfs/tessel_loader.swf $(pkgdatadir)/swfs/default_loader.swf + + uninstall: