diff options
579 files changed, 4618 insertions, 1835 deletions
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 0000000000..c0efc2cb8c --- /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 62f948a4e2..0174733ccf 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 01eb083a7f..f10d79caba 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 @@ from spack import * 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 83d4ec8d94..ef015df04e 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 a0c3f8583b..ce7a675430 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 @@ from spack import * 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 86ef54bbe1..ef6ff1a84c 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 a3f9d73df9..563ed378a6 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 3a8749dfa9..c31dc05fcc 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 6314a09564..685fbf5f62 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 b22d6ff6fb..36cdc693f3 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 dc39191fff..69426a1cd7 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 1d5aaabddb..c028e56842 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 902a17aa4d..25c05ebcf8 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 0000000000..ea3bcd0572 --- /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 1bef74953c..2e88e9525e 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 045ae66022..6aef403750 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 69d69f8c14..9aa2ae0864 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 081dba4745..5c1fcc9979 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 cc30692af2..10dc0cc7f1 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 @@ from spack import * 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 8bc2144b94..400b7c8972 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 e23094434f..db560b5772 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 49a92cb972..54b07e9e61 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 @@ from spack import * 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 f25c167b71..68f87952ed 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 @@ from spack import * 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 1ee6eb483e..23d2909ddd 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 35224e3679..429ed842a9 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 8f91f3b945..8fd9a0154e 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 68183e8ddd..a3556e3b88 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 fc2e541f18..f20e62f729 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 e20580db69..7377db73a1 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 8a618951ac..ceb1975d7d 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 @@ from spack import * 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 141f3be1c8..5155c6a196 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 25dce86116..1d1cde59fd 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 @@ from spack import * 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 89b1ccc225..3a979ba384 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 fcc0eedc2a..f1333ba7c0 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 6757a11bab..1cbe28a120 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 a2fc84c4c9..3f7632f13d 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 e2d4271bd8..c6e882e825 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 3ec5b42779..5130507109 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 c81646f77e..0ca78a69be 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 @@ from spack import * 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 0240b9d159..e0004484e4 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 21ce4194d0..1cce105259 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 b44421ea2d..fbd5266bfe 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 0000000000..6e9c430d7f --- /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 f37b5099ae..fcbf54004b 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 152edc7cfc..a72a4977db 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 5cbdcea39b..9898ab68b3 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 e1a2e4770c..fa99d27ca9 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 8a9e55430c..4f8205d51f 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 10e69d62c6..df1abd2b6b 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 f841bc8c9c..258a7ee767 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 93fd4f5253..d2854903d1 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 71c1575577..3defd1653b 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 @@ from spack import * 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 89148b74f7..31dd662d76 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 aa31dfe6ef..472c8dbd4a 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 3a9f11c66d..fb859c3e7c 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 883a34e8eb..e841226979 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 fe2f21736a..bd6a07923c 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 0000000000..057fa67b9b --- /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 <https://github.com/sindresorhus/figures>).""" + + homepage = "https://github.com/gaborcsardi/clisymbols" + url = "https://cloud.r-project.org/src/contrib/clisymbols_1.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/clisymbols" + + 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 be9fdccdde..44a36e5b00 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 4dbcc13bb6..ccae368dde 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 @@ from spack import * 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 8c83b9d5da..bc06676d85 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 e7c7c8c11b..b69c0f5a80 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 4e451ba839..5ccaa4914c 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 @@ from spack import * 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 81a8bf45d4..b52fff5e77 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 ebe83745cc..9aaec8933e 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 98d89fffbd..7adf666972 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 @@ from spack import * 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 6cbafa742f..27afc8cfea 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 @@ from spack import * 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 1b5e22f4bd..112af5a1e5 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 @@ from spack import * 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 03f026dc2d..1ec973752f 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 ea8d4595ec..398e905016 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 @@ from spack import * 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 7d1632d5ac..41043b8a1c 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 bbebf81c22..3690284809 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 @@ from spack import * 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 702fe40fab..71ded1da62 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 404543baa1..1f62a54c17 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 150844ec43..3d3bd5549b 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 843851a592..4a5cd95145 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 39119c3e26..ad17c33aa6 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 6ce56a5584..e2d4410ebc 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 @@ from spack import * 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 0b5a475b81..7ed968d5bc 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 @@ from spack import * 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 1a89f3c21f..a41928e663 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 @@ from spack import * 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 785b4487c5..2a720b2a99 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 4b669b8a76..e9e2bc0440 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 866b19dd4c..bd8e4289e3 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 5950fb4a02..2f88bb3fc8 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 0000000000..590fe5f23a --- /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 299ef640ac..f206bc6a6b 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 3fe9677f90..b1e578164c 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 @@ from spack import * 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 4a993a7185..a17bd18179 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 5c24834833..a48e98af48 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 3aa442852f..9504ed5052 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 @@ from spack import * 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 f26872629c..466c8107ed 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 8a4ed3db3c..b5a1151702 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 713740f1b0..23ad11daf8 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 4372047e89..0f00d6ea5a 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 aced519038..cda6906901 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 eac9587155..84fb7c2084 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 d69645f7ee..feb608e7f4 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 b7b25d8215..0e5edc21ef 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 @@ from spack import * 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 3876f1aa85..4fb5e5e321 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 9578bbb4ec..bb2c27dac6 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 8228866515..9488d31952 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 5db870b699..250e396dfb 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 9e8baa6a77..a493805a36 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 0000000000..7ad841b431 --- /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 9a410e7972..7b59089be6 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 b2aed2c626..a7ed7868d7 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 0000000000..ebb82b942c --- /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 + <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as Xoroshiro128+ + and Xoshiro256+ by Blackman and Vigna (2018 <arXiv:1805.01407>). In + 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, <doi:10.18637/jss.v005.i08>). 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 + <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.""" + + homepage = "https://www.daqana.org/dqrng" + url = "https://cloud.r-project.org/src/contrib/dqrng_0.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dqrng" + + 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 b419985173..141b40006b 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 bb82035897..f963965161 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 ce17c9dd6d..f286e5363f 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 39e3dde227..856e6efb89 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 c09473fe79..41ada9809e 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 5dd67a3415..abd9783b0f 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 0000000000..8945722068 --- /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 249f3c3f6d..974bb81c8b 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 897e96a8ad..ab2ef621de 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 @@ from spack import * 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 36c251cfa0..9fedc0c078 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 4df731967b..c56425716d 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 39d01fe50d..4bce63d28a 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 @@ from spack import * 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 c576ec912f..f7e5588e4e 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 47e442cbc7..562dc81c95 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 71d6f34415..a5723eff14 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 41695ebc72..ff24e351bf 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 0ec80c7207..d08a5ddb66 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 0257a475de..88ef290d70 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 76056bca94..6b352a2008 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 9d0a427a3e..418347cd8e 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 e2c6b42ddc..8a44c29f70 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 736ff0cb4c..acfc903c33 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 c15c7701e7..3f1619d2e2 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 @@ from spack import * 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 0000000000..7a0cdfb107 --- /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 4b32218943..6564e50a2b 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 @@ from spack import * 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 b37f42e906..324839aa7d 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 6eb90aa44b..a8d3e03d9a 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 @@ from spack import * 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 4061e49108..02afb622d2 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 769bbe4797..e6cf5b73e2 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 091b970299..37baf00b4b 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 b1d32d5710..6b33bdd1eb 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 928d9df0ce..9bba9e81a0 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 8d55e6c96c..15914e209f 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 cbe9071086..38b50015d9 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 ddc3ea3fea..fd20c495dc 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 5f947244ed..8f902428ec 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 0000000000..59d581838e --- /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 88a9471526..d45418aa72 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 0325508c09..c493ac0ea6 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 @@ from spack import * 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 0000000000..a0fd59e473 --- /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 0000000000..d3778bb2c2 --- /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 186654cc17..25b9fde1a5 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 @@ from spack import * 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 4f08a15657..107dacdea6 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 0b04d2af53..0215a7fc19 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 @@ from spack import * 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 2c5b4e8f91..1846290c44 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 @@ from spack import * 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 0000000000..0dfe6081db --- /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 d8adeae443..96f5e2f59b 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 @@ from spack import * 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 f23f96165f..40f27d4e00 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 23453b776c..2225c7051e 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 @@ from spack import * 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 0000000000..0b9e1f681e --- /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 e8dc639494..e93e9ce9cb 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 3d33e64837..32049e61e3 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 1d138cfc16..c8de77d062 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 @@ from spack import * 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 daa827c939..2c499a19b8 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 58d3da5aea..689e2f3c1d 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 302f1f145c..08c8b97611 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 f7726bb23e..e6064611e5 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 16f54d4744..7ccb73a128 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 e429a319b8..87052809cc 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 df34c9513d..3262750b38 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 cc7e0a4e3d..a468f4b18c 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 1d0591e85b..59e9b46b35 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 4184d2e4e3..fcd2fc9e93 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 84f811e28b..aca5c2fee3 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 5968ced805..c63fc86b41 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 d7f263c38b..fa4fe4130f 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 0000000000..4a2e8cb544 --- /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 1543f23dd2..bf4b902e1d 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 0000000000..779e3e649e --- /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 a5769db25f..ca1d6127ca 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 2306bf9b08..0e6ce00871 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 21cb2a5986..0e98d4ff0d 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 d1b0d3d8a0..6831b436bf 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 0000000000..cb3eaad818 --- /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 7e60a323fb..c4886be7a4 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 3baa8c7358..6eee528156 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 c3c99c7676..0070a61fdf 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 8077403912..5ac11e6a7a 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 4e41bcc8c3..fb94c72f3e 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 0000000000..72393b714b --- /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 6b61f87f90..3ba000a5dd 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 @@ from spack import * 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 e1f00f410c..cb057aef3c 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 6c2acf087d..38d7b684a2 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 @@ from spack import * 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 8486e2c23d..3f26f2ef56 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 0000000000..aa27d7a228 --- /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 26018c242e..0c652099fc 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 1a7ecb919f..b5c9d95eff 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 fec5fdbb75..6df80edc58 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 @@ from spack import * 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 2103df512f..752dd44437 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 dfbcaf9b89..08e1cb9c1b 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 e825ac5f79..1ddb4e0bff 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, <https://github.com/WizardMac/ReadStat>.""" 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 0000000000..670d1acb63 --- /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 + <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> 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 2f2a39554d..adfec4c76b 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 9824c1e55d..fb600dc567 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 a7f4c5e4df..1ef0b1aa91 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 6e4b513799..b39d7f4ee5 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 2e00826bbe..cbc9806c3e 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 @@ from spack import * 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 09c77875bb..8693a8d8cc 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 0f23d8df4e..866f20fe56 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 f6a42ac733..aed9faa579 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 edbed0d232..ffd772eee7 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 ea9461773e..9bc6326d95 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 e1ba98698e..7f79836f9a 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 9fa89f91d6..de980bb2d5 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 ef882eb51e..aea4b44ead 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 69c1d161e1..2dbc16b173 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 b6f2c7eb62..5144761850 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 0000000000..67edc74e65 --- /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 88cb95a696..6083319dbd 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 3b384f772c..52ce3e8ccf 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 0000000000..7376f998ff --- /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 edd42b5645..43d9153092 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 f908fff778..c246abbae0 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 466e75ee45..46a5d712dc 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 83e9d92a84..bb5e038d04 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 4bbca3b0b6..9640af6cbf 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 397ba24644..da880c792f 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 a48d57f851..a754eb61ee 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 39eced1560..8fcbd881b2 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 ca83414049..53b986d6d6 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 81601f6dd6..6cbdf132a8 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 6c8694f3c8..3eedaac279 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 8910c12247..d39ea1e4ff 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 @@ from spack import * 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 4729ce905f..c63bbf2d6a 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 f6fcb80398..90f3cbb334 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 ceab1b8eb0..5ff34544a4 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 @@ from spack import * 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 061d10272c..49b481f61c 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 @@ from spack import * 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 bbc6b81ad4..459ac5a341 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 a07c84a32c..60bfe0ba76 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 82fbc6fd79..e2595d3c3a 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 0000000000..1a1f2fa679 --- /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 4c040d88e5..c47360d701 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 b82f7a9f25..7cf8b7da49 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 01739d205f..b9daaf2e3a 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 @@ from spack import * 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 ded81125a8..5650181c56 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 4c88c49712..3a436e009a 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 ae0e7f7909..b02ab2cfe4 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 @@ from spack import * 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 5a152d06ef..71644b853b 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 0000000000..3079ce3ba6 --- /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: + <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain + to Leiden: guaranteeing well-connected communities. + <arXiv:1810.08473>.""" + + homepage = "https://github.com/TomKellyGenetics/leiden" + url = "https://cloud.r-project.org/src/contrib/leiden_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/leiden" + + 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 a0b5a7f4df..da10bff658 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 0000000000..69e70f4c8f --- /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) + <http://epub.wu.ac.at/102/>. This package must not be used by end-users. + CRAN package 'coin' implements all user interfaces and is ready to be used + by anyone.""" + + homepage = "https://cloud.r-project.org/package=libcoin" + url = "https://cloud.r-project.org/src/contrib/libcoin_1.0-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/libcoin" + + 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 0000000000..ef931f2612 --- /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 0f6d6bbb0b..64a021616c 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 eebc165b3f..ad59ed29c7 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 141b25fbea..ce7536500f 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 @@ from spack import * 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 66ea6a38cd..82d73f3bf8 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 6135d41ade..9a41eec8bc 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 ef132bc632..c118b4ebfc 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 59e23c1e0e..e23f0e2033 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 <http://www.netlib.org/lawson-hanson>.""" - 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 34466be118..675cdaf098 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 d65fa443dc..c4a04edc8d 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 0000000000..66ae049615 --- /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 2020a11689..5f9cda54b4 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 5e2ea009c1..6e596d92b1 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 fa589df09b..0f04db37d9 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 65206ca7bc..a30907c055 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 @@ from spack import * 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 090fcfec37..4e98fbbff4 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 fd5e62a93a..131a57bf88 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 9629da7627..b90967ce5a 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 a5dd34ec2d..35356a6375 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 5277fdb7c4..47e2f782a6 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 c39e209d0f..c624e1c89e 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 de276c8c90..ced334ea4f 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 5d098bbc48..5918f8b8a5 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 4b748d22d1..aca88d788f 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 79a93688eb..4c952a3271 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 @@ from spack import * 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 4769f3a879..a6cee70aa3 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 fcdda3baa2..2568f2fc5b 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 ec039cc08f..627b4e1609 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 0000000000..2b9ee109a6 --- /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 5938192ddb..c4e2d98b7a 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 25eba17c7d..9aa0023095 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 c785631bc1..daaefe5a9c 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 41b42a18f7..8c99d8d720 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 1dc54ed86c..5b7de8ba85 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 bb54a7252a..f579dbdf57 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 e215a4fcb2..a4043961ae 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 @@ from spack import * 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 88e6784c4d..4980a9e157 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 0000000000..45a9f80c6e --- /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 5b2f9d912e..f818006754 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 c0bebc0672..f861d6a547 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 6994ace5d0..34a8f8f1fd 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 fcde2d6d8b..3caeec50dc 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 83799560ae..cb36d6e6fb 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 cdea6845c3..e322a43d12 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 106e90e330..47e925e4da 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 f693fd7b2e..b65d8ec323 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 bbcfc99671..16f2c63116 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 @@ from spack import * 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 ce0b0d0e35..ef159313d9 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 @@ from spack import * class RMpm(RPackage): """Exploratory graphical analysis of multivariate data, specifically - gene expression data with different projection methods: principal - component analysis, correspondence analysis, spectral map analysis.""" + 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 656b55a54d..db2bf15312 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 5d9548da2b..c4e322f678 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 @@ from spack import * 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 172c24dce5..8e31a39c39 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 20ba74f6f1..8a0678d5d4 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 db6ef6d65a..bd7b6eab46 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 40eb209c4d..8d0b6c7cc0 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 ad8c2b79cf..f01a2035dd 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 21ce037fba..a040454530 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 ef59109a02..03f728256f 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 4db5c88274..976f313fcd 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 97d29e4bfc..75dda5930d 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 @@ from spack import * 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 1356f73967..bd13d96c20 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 @@ from spack import * 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 13a8469e0e..f6f7502524 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 854aafd636..91c356d794 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 0000000000..ccd3061f12 --- /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 5f5c8cc759..dada76423e 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 548dc480c9..815f35b925 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 14543b4571..050252b7e3 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 5407eb9721..c93b8b79bb 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 f076e4d808..0a7e983535 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 0000000000..6ef60c6345 --- /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 16342ff5c5..d234dca538 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 a11bb4546a..72ef242667 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 0000000000..cd375247e5 --- /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 6bbe628b6b..be8c989605 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 0000000000..ad837a3411 --- /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 a871964a0e..427843d080 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 a65db10103..fef678b671 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 9a4f31c872..f14ea30f0c 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 c56459b865..f4697f4c17 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 @@ from spack import * 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 21c6155ba5..176104e3df 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 @@ from spack import * 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 b5911996c8..cc43793728 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 5898de58fe..2aa307b30d 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 73fc0c8233..db876b5faf 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 @@ from spack import * 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 d01292d307..1e914397a0 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 0a230ab759..cc481c277a 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 e0a8ef25ba..48625786c1 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 42cca11729..a696abf87a 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 4e49bd47aa..bcc1b7a472 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 @@ from spack import * 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 4798b844ef..a386df053b 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 b147d5c9f1..3b0c34fb7e 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 385e76ff36..718e54cb4b 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 e9e20b030f..6cfa91cfc2 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 @@ from spack import * 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 d23c6eb662..213a2658db 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 723180c333..2e4dedfa1b 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 @@ from spack import * 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 1f589b5b61..947d6f4ee5 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 e1a579adaf..fa6d0aa635 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 @@ from spack import * 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 29628b68e7..b89ec59b80 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 b85fdaf2b0..c35e0900e4 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 <plogr.h>' 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 b856601463..8e338d123b 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 7b7cc8999d..29d1ea37a5 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 6ef2607342..a03e77b93a 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 @@ from spack import * 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 706448e19d..d310c5d5fb 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 077c331b50..c5fc1bf68d 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 25936e929b..3097e0861f 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 80689773af..a9bdc3318b 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 0000000000..4244a2a4ea --- /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 de573b59f5..70ca45e3b4 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 c5398eb1bf..15e1c03645 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 f406a2f56a..0ee38127a0 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 124049d0ca..fd12aaddee 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 be0785716b..830b9cfc00 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 3a3a3bf029..00d903db5c 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 86a2a3e73c..d6661875b4 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 157fa3b832..e945333a1c 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 44955975ae..1d74872e34 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 0000000000..6b0f6bf679 --- /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 2b8aa7211a..d2f5012ccb 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 99ffc64571..94c954f821 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 d0d504a248..a3ba60d71e 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 dc10f7b1a0..6c75998ed5 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 b5fc1085ca..e98d427f3d 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 b0d8b89d50..a571c31e30 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 67ab921aec..5e80aec44e 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 fcacfb58af..010b95665c 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 4991cf03b7..d9ff67e804 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 972fe3e71d..9fb04ff133 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 deaffa31f3..65b538146e 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 index f52de95e12..e2887c572d 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 index cef0f76cd8..8dc62a1b16 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 0000000000..9318bdc1d9 --- /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 2e8209fd5e..983cabee2d 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 b8a6232842..815eba3557 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 cbd0199257..fa51ba6c9a 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 b2e9987393..b24defd121 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 47e513968d..817d6467b4 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 0a95a55635..a8cf0f0d0a 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 0000000000..bbe014ee45 --- /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 49e24bf0d5..5366f07494 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 e0cc4a9555..912f9c17e0 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 332de772ba..b0e8e510f7 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 0000000000..c64a59bc97 --- /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 287e846c7c..b2cb38aa1f 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 3ee436d104..e2abba3b83 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 0000000000..64ee9a72aa --- /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 + <https://github.com/spotify/annoy> 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 51ef1b3daf..55f412a45c 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 d2161ceaa2..e9af43aded 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 ad2b03965b..d4f48d3a5c 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): <https://github.com/google/cctz> 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 1344d5931f..dc517e9060 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 1f07972974..221a998383 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 0000000000..ad723a0de5 --- /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 5ef2b4ea1f..4680b00964 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 2c88de66fe..0af3d5275e 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 3dc929a13a..4cdbe65ac0 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 0000000000..2febe78186 --- /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 1b6753916b..586d0d9528 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 f01cc790ff..599534113d 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 0000000000..12c00f6613 --- /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 4c6acb2624..457908f4df 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 @@ from spack import * 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 00f5d75da5..2887630876 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 0000000000..9c4a790dcb --- /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 d1ed897d0e..5d63690aa8 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 eed19834ad..de4930c4c8 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 ca7f3a37e6..90da8713f6 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 c0c0393f73..7a0f506389 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 7e38c9fdc1..ed783c9def 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 cd2a9d59b3..0a04e1b4ed 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 0000000000..f1dc039491 --- /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 968f4a0959..54d124d84a 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 @@ from spack import * 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 1146e0ff58..39c95f3cb5 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 7b836f82fb..f5cc12720d 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 fb889dda96..fd982f9996 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 0000000000..3a98d90035 --- /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 372833f8ab..2195923a6e 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 5450d5dd8e..1c615f7e77 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 4fe328f739..23854fb2b1 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 @@ from spack import * 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 7ed751394e..5681e87113 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 0000000000..5b4934f429 --- /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 dc66dd0c39..0b86c0e8e6 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 8148ed2d74..cc6bb3cdfb 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 b6c928ad06..9c2c7a1409 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 @@ from spack import * 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 2f68f67596..b981fa80fe 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 2fada49290..f7a5344ba4 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 30c61e6770..aec117f37a 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 08b8ea7aa3..92b99dd9f7 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 54d9238265..840a4f3f20 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 614e7be67e..fe43add7b8 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 4e73352019..6739bdb104 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 4ab784813f..ea11d03f0f 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 0eabbc6585..7434fb58ba 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 3e83224ead..b49de8879f 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 @@ from spack import * 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 f8b96ddcf0..6b8c510639 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 02d3b7e367..4952136ac5 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 4eb0f0d017..a21269c1ef 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 @@ from spack import * 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 0000000000..4d3b1dbda9 --- /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 f85b27187c..3958ab1298 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 59a74efa90..4671e1078a 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 1679317b6d..4c309ba4ab 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 3aa969bed4..a5c9e11974 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 56ddb40aa0..b1ec14200d 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 882711f392..b165e2a527 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 78a0b65d46..7b1d3bd74a 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 @@ from spack import * 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 c20f200845..a2448a3636 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 4bde5a8680..1fdc932652 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 65ecf288ec..03c24b0b46 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 0000000000..460a649c25 --- /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 <https://spectralib.org/> 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 9afd523511..d9e018304d 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 9bebbc38a2..6e8bc94458 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 a50941c9d6..08f2e968bb 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 13f4d0c10c..9a7779f063 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 0000000000..554824aea5 --- /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) + <arXiv:1608.02148>.""" + + homepage = "https://github.com/erichson/rSVD" + url = "https://cloud.r-project.org/src/contrib/rsvd_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rsvd" + + 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 80909001a2..be053b293f 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 246c189cb2..03452d630e 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 @@ from spack import * 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 bd0fd37ed2..9adfd8d31d 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 18353fe750..1872315f77 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 fb6f0f5634..8b800c4b5f 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 79ae1762c7..5ebc81a468 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 @@ from spack import * 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 68feab8e3c..d303fe56cf 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 fbc6d69d81..0ea8442689 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 2c53d96745..e4bb9abbc6 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 @@ from spack import * 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 0000000000..7dd0b4e703 --- /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 + <doi:10.1101/576827> for more details.""" + + homepage = "https://github.com/ChristophH/sctransform" + url = "https://cloud.r-project.org/src/contrib/sctransform_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sctransform" + + 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 46acd8c8a6..e6dd23d74d 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 45bc7df141..748d8811ef 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 5b57993a85..628ee221f9 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): (<https://pythonhosted.org/cssselect/>).""" 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 a685f86a14..ab7685fc47 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 0000000000..f8770c7f19 --- /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 abb49e0628..c3e5de9dce 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 711915fc6f..bd79b7a4fd 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 8b9707d750..779d13959c 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 f5cdc61858..67851868f1 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 4d6a9d83b1..3c1c3bcb47 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 5c71ff533a..23733e9576 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 @@ from spack import * 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 0000000000..70b4864f40 --- /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 0000000000..eab70f5ac4 --- /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 89de1cb4e9..29a46acd05 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 839d5a1ce2..60520006b8 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 7b3fa2c3e9..61d84c1df2 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 0000000000..fddcd2c56c --- /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 ada2cfaefa..e7173b4c35 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 @@ from spack import * 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 880b8523d7..fbc86513af 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 a2de57deb0..f87b92c367 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 @@ from spack import * 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 6a107c9d8e..2df62d25d8 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 @@ from spack import * 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 373c373e87..2cdbaf6ffd 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 88037ed699..e12bd4cc0b 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 bd28089911..e5974e19af 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 6129cf5865..6673560c04 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 @@ from spack import * 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 e99f955be8..bcbadc07a1 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 @@ from spack import * 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 1a40030c36..0cfa061db6 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 1ae0a16f0e..2c0f9bc47b 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 cd7e69ef2a..2371b3090e 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 60cf5fa30e..4ef99ef42c 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 @@ from spack import * 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 8ceb1fe1b9..a314d22134 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 dd9289fe0f..da7d95aa31 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 0000000000..a4f0e9de36 --- /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 580255de98..f38963c8d0 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 @@ from spack import * 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 a1b2cb2e4c..2cac7d0963 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 b48e62a910..ceee29fceb 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 b1b68e6522..7ad4104329 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 5e10fff5f9..8c44256da8 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 54a43fe9b7..aa6bee349d 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 4cf073e9e1..8e111a58d7 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 cc9efbfb24..2ddbb19bf3 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 @@ from spack import * 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 d0729c9996..a3f2249521 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 fec334728b..34c23beca0 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 0000000000..af8fb3ebbd --- /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 a7ef6efd60..3637255bf1 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 @@ from spack import * 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 384e90f63b..973d75262b 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 @@ from spack import * 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 b2a0f2d5c6..e053432981 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 @@ from spack import * 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 6735fbb829..4330b8c965 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 f83669a9e8..e4a9ae9db7 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 6b7c048950..baf7fced96 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 1a305242a0..8631d5d726 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 7460b5d4ee..593cb7e6ae 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 @@ from spack import * 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 c32f33acf9..604bbb9c2a 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 29b2f614cd..9e2aa5cebb 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 c6e41da83d..c6c52e3bd1 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 e3a5ac05e5..456a6b7931 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 fbcad34264..89eba20d6d 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 1f8abb3d6f..83027d7ff2 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 596d058754..b74693ac46 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 93ace4a3ee..19c1cef79a 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 ab31d415b0..2025d4af64 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 0000000000..e8384c0285 --- /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' (<https://yihui.name/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 f2d04924da..a3521c9c1b 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 d918d31439..df73e3bf94 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 28929fa103..19d76beb06 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 2964eb6b7e..221be990b5 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 3055430340..e55c8c3b1a 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 @@ from spack import * 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 11247374a9..a65ae8cfa2 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 @@ from spack import * 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 8e81f13825..08583bb6db 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 0000000000..a0ddaaa7b1 --- /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 b72b7224ab..0adfcef4b3 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 0dcf8c35d9..49ae88dcba 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 0000000000..1dc5753a43 --- /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 6c1b78deb2..5187a31288 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 0000000000..4f7cfc743c --- /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 2e40f83bfa..8a00a26db6 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 45caeafb93..0000000000 --- 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 d161948c05..d68b08fc99 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 0000000000..092288646d --- /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) <arXiv:1802.03426>. 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) <arXiv:1602.00370> 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 + (<https://github.com/jlmelville/uwot>) for more documentation and + examples.""" + + homepage = "https://github.com/jlmelville/uwot" + url = "https://cloud.r-project.org/src/contrib/uwot_0.1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/uwot" + + 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 b187f4a542..03fedb632a 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 6980e5459a..f342ec5770 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 0000000000..0dc05227c5 --- /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 1410129e62..2248bfd9e1 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 0e5d8c0a72..d6c52c2c50 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 @@ from spack import * 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 236de33f3a..3039bbbd6c 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 354305221f..e4deb92f86 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 @@ from spack import * 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 5492e1451c..82f5578b1a 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 8b73a9f6c0..5ff479d2f4 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 80e254de0c..bbf78d7372 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 5821e2949c..987dd60c2c 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 14c6d8b8a6..7b21e756ed 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 @@ from spack import * 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 55b3a4f1ba..951e64faba 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 fffb8ee84a..f1e50a2ec4 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 0000000000..9ffb8f618e --- /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 581c442a05..13cc2d6139 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 0d2b658537..a6b1d4619d 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 ce529fe6be..57edc703ae 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 af4ec6f739..06f3b7e916 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 541028a873..ad383b3fef 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 1454226466..954c1c7633 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 80c748ef86..cf355c7f6f 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 348245d267..609340c966 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 0000000000..4365dff7e1 --- /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 0265a5e3f2..96eeedcaba 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 2e657117ea..d698110be7 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 a7d537e094..9454402e20 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 0000000000..7276bff255 --- /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 0000000000..13270d7b32 --- /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 50b38f8aa9..fe845adea5 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 0000000000..fdaff87aa4 --- /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 0000000000..779358df74 --- /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 0000000000..c53f3dbfa3 --- /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: |