diff options
67 files changed, 1203 insertions, 76 deletions
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index aa3f82a331..2901dcfa63 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -249,6 +249,7 @@ class PythonPackageTemplate(PackageTemplate): class RPackageTemplate(PackageTemplate): """Provides appropriate overrides for R extensions""" + base_class_name = 'RPackage' dependencies = """\ # FIXME: Add dependencies if required. diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py new file mode 100644 index 0000000000..aa16047856 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-adabag/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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" + + version('4.1', '2e019f053d49f62ebb3b1697bbb50afa') + + depends_on('r-rpart', type=('build', 'run')) + depends_on('r-mlbench', type=('build', 'run')) + depends_on('r-caret', 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 97c29b4a99..b8ab7d7a0c 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -31,7 +31,8 @@ class RAssertthat(RPackage): producing friendly error messages so that your users know what they've done wrong.""" - homepage = "https://cran.r-project.org/web/packages/assertthat/index.html" + 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" version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py new file mode 100644 index 0000000000..c145de688c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocinstaller/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RBiocinstaller(RPackage): + """This package is used to install and update Bioconductor, CRAN, + and (some) github packages.""" + + homepage = "http://bioconductor.org/packages/devel/bioc/html/BiocInstaller.html" + url = "http://bioconductor.org/packages/devel/bioc/src/contrib/BiocInstaller_1.25.3.tar.gz" + + version('1.25.3', '6214770455a5122dca5544861f52c91d') + + depends_on('r@3.4.0:') diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index 80a0206a8a..56c87c27a6 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -30,13 +30,14 @@ 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_2.1-2.tar.gz" + 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" + version('2.1-4', 'a66c307e8ccf0c336ed197c0f1799565') version('2.1-2', '0f78ad74ef7130126d319acec23951a0') - 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-quantreg', 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-quantreg', 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 d795cfa204..277fdc7143 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -30,15 +30,19 @@ class RCaret(RPackage): models.""" homepage = "https://github.com/topepo/caret/" - url = "https://cran.r-project.org/src/contrib/caret_6.0-70.tar.gz" + 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" + version('6.0-73', 'ca869e3357b5358f028fb926eb62eb70') version('6.0-70', '202d7abb6a679af716ea69fb2573f108') - depends_on('r-lattice', type=('build','run')) - depends_on('r-ggplot2', type=('build','run')) - depends_on('r-car', type=('build','run')) - depends_on('r-foreach', type=('build','run')) - depends_on('r-plyr', type=('build','run')) - depends_on('r-nlme', type=('build','run')) - depends_on('r-reshape2', type=('build','run')) + depends_on('r@2.10:') + + 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-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')) diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py new file mode 100644 index 0000000000..5fd862fa46 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCheckpoint(RPackage): + """The goal of checkpoint is to solve the problem of package + reproducibility in R. Specifically, checkpoint allows you to + 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" + + version('0.3.18', '021d7faeb72c36167951e103b2b065ea') + version('0.3.15', 'a4aa8320338f1434a330d984e97981ea') + + depends_on('r@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index 29e16c2271..caa96a380a 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -31,7 +31,8 @@ class RCluster(RPackage): (1990) "Finding Groups in Data".""" homepage = "https://cran.r-project.org/web/packages/cluster/index.html" - url = "https://cran.r-project.org/src/contrib/cluster_2.0.4.tar.gz" + url = "https://cran.r-project.org/src/contrib/cluster_2.0.5.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/cluster" + version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a') version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index 39186bf54a..60b8fc2cc8 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -29,7 +29,8 @@ 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_0.2-14.tar.gz" + 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" + version('0.2-15', '37419cbc3de81984cf6d9b207d4f62d4') version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py new file mode 100644 index 0000000000..51b61a6164 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-coin/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCoin(RPackage): + """Conditional inference procedures for the general independence problem + 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" + + version('1.1-3', '97d3d21f1e4a5762e36dd718dd2d0661') + + depends_on('r@2.14.0:') + + 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')) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index b7561ea360..af2895acbf 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -32,7 +32,8 @@ class RColorspace(RPackage): are provided.""" homepage = "https://cran.r-project.org/web/packages/colorspace/index.html" - url = "https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz" + 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" + version('1.3-2', '63000bab81d995ff167df76fb97b2984') version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1') diff --git a/var/spack/repos/builtin/packages/r-corrplot/package.py b/var/spack/repos/builtin/packages/r-corrplot/package.py new file mode 100644 index 0000000000..ccae3bf913 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-corrplot/package.py @@ -0,0 +1,36 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCorrplot(RPackage): + """A graphical display of a correlation matrix or general matrix. + It also contains some algorithms to do matrix reordering.""" + + 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" + + version('0.77', '2a5d54fd5c65618b9afba1a32f6b4542') diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py new file mode 100644 index 0000000000..acc0261383 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-cubist/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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" + + version('0.0.19', 'bf9364f655536ec03717fd2ad6223a47') + + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-reshape2', 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 7b62d1be60..ae9ccf3f5e 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -37,10 +37,12 @@ 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_0.9.7.tar.gz" + url = "https://cran.r-project.org/src/contrib/curl_2.3.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/curl" - version('1.0', '93d34926d6071e1fba7e728b482f0dd9') + version('2.3', '7250ee8caed98ba76906ab4d32da60f8') + version('1.0', '93d34926d6071e1fba7e728b482f0dd9') version('0.9.7', 'a101f7de948cb828fef571c730f39217') + depends_on('r@3.0.0:') depends_on('curl') diff --git a/var/spack/repos/builtin/packages/r-datatable/package.py b/var/spack/repos/builtin/packages/r-data-table/package.py index 23802524e8..4381d1e0f8 100644 --- a/var/spack/repos/builtin/packages/r-datatable/package.py +++ b/var/spack/repos/builtin/packages/r-data-table/package.py @@ -25,16 +25,17 @@ from spack import * -class RDatatable(RPackage): +class RDataTable(RPackage): """Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development.""" homepage = "https://github.com/Rdatatable/data.table/wiki" - url = "https://cran.r-project.org/src/contrib/data.table_1.9.6.tar.gz" + 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" - version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372') + version('1.10.0', 'f0e08dd5ba1b3f46c59dd1574fe497c1') + version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372') - depends_on('r-chron', type=('build', 'run')) + depends_on('r@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 9895a3b390..c994f557c8 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -29,16 +29,19 @@ class RDevtools(RPackage): """Collection of package development tools.""" homepage = "https://github.com/hadley/devtools" - url = "https://cran.r-project.org/src/contrib/devtools_1.11.1.tar.gz" + 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" + version('1.12.0', '73b46c446273566e5b21c9f5f72aeca3') version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') - depends_on('r-httr', type=('build', 'run')) - depends_on('r-memoise', type=('build', 'run')) + depends_on('r@3.0.2:') + + 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-digest', type=('build', 'run')) - depends_on('r-rstudioapi', type=('build', 'run')) + depends_on('r-rstudioapi@0.2.0:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-git2r', type=('build', 'run')) + depends_on('r-git2r@0.11.0:', type=('build', 'run')) depends_on('r-withr', 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 7e077442f9..08f5af0aca 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -44,7 +44,11 @@ class RDigest(RPackage): used.""" homepage = "http://dirk.eddelbuettel.com/code/digest.html" - url = "https://cran.r-project.org/src/contrib/digest_0.6.9.tar.gz" + 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" - version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') + version('0.6.12', '738efd4d9a37c5a4001ae66e954ce07e') + version('0.6.11', '52a864f55846b48b3cab0b5d0304a82a') + version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') + + depends_on('r@2.4.1:') diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py new file mode 100644 index 0000000000..1a44aa537d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-domc/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('1.3.4', 'f965b09add9056e84f99a831dc3af7d1') + + depends_on('r@2.14.0:') + + 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-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py new file mode 100644 index 0000000000..1f6144285e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ellipse/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('0.3-8', '385f5ec5e49bcda4317ca9dffd33f771') + + depends_on('r@2.0.0:') diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index cf6c72dc62..004048e985 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -35,6 +35,9 @@ class REvaluate(RPackage): url = "https://cran.rstudio.com/src/contrib/evaluate_0.9.tar.gz" list_url = "https://cran.rstudio.com/src/contrib/Archive/evaluate" - version('0.9', '877d89ce8a9ef7f403b1089ca1021775') + version('0.10', 'c49326babf984a8b36e7e276da370ad2') + version('0.9', '877d89ce8a9ef7f403b1089ca1021775') - depends_on('r-stringr', type=('build', 'run')) + depends_on('r@3.0.2:') + + depends_on('r-stringr@0.6.2:', 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 3b4c437f0c..e5c80e4b79 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -35,14 +35,19 @@ class RGgplot2(RPackage): documentation and examples.""" homepage = "http://ggplot2.org/" - url = "https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz" + 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" + version('2.2.1', '14c5a3507bc123c6e7e9ad3bef7cee5c') version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') + depends_on('r@3.1:') + depends_on('r-digest', type=('build', 'run')) - depends_on('r-gtable', type=('build', 'run')) + depends_on('r-gtable@0.1.1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) + depends_on('r-plyr@1.7.1:', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-scales', type=('build', 'run')) + depends_on('r-scales@0.4.1', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-lazyeval', 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 7c4ff3144b..a0df2d9b23 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -31,10 +31,13 @@ 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_0.15.0.tar.gz" + 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" + version('0.18.0', 'fb5741eb490c3d6e23a751a72336f24d') version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') + depends_on('r@3.0.2:') + depends_on('zlib') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index e4b60893b6..a81e3c3fb1 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -40,4 +40,6 @@ class RHttpuv(RPackage): version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@2.15.1:') + + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index 55a5b0efab..b27bee4fbb 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -31,13 +31,16 @@ 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_1.1.0.tar.gz" + 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" + version('1.2.1', 'c469948dedac9ab3926f23cf484b33d9') version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') + depends_on('r@3.0.0:') + depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-mime', type=('build', 'run')) - depends_on('r-curl', type=('build', 'run')) + depends_on('r-curl@0.9.1:', type=('build', 'run')) depends_on('r-openssl', type=('build', 'run')) depends_on('r-r6', 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 new file mode 100644 index 0000000000..37accb6ee2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ipred/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RIpred(RPackage): + """Improved predictive models by indirect classification and bagging for + classification, regression and survival problems as well as resampling + based estimators of prediction error.""" + + homepage = "https://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" + + version('0.9-5', 'ce8768547a7aa9554ad3650b18ea3cbd') + + depends_on('r@2.10:') + + depends_on('r-rpart@3.1-8:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) + depends_on('r-class', type=('build', 'run')) + depends_on('r-prodlim', 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 e0d1b32565..ad383492ff 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -31,9 +31,10 @@ class RIrlba(RPackage): matrices.""" homepage = "https://cran.r-project.org/web/packages/irlba/index.html" - url = "https://cran.r-project.org/src/contrib/irlba_2.0.0.tar.gz" + 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" + version('2.1.2', '290940abf6662ed10c0c5a8db1bc6e88') version('2.0.0', '557674cf8b68fea5b9f231058c324d26') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 7368187af5..4a690d475a 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -38,8 +38,9 @@ class RJsonlite(RPackage): use with dynamic data in systems and applications.""" homepage = "https://github.com/jeroenooms/jsonlite" - url = "https://cran.r-project.org/src/contrib/jsonlite_1.0.tar.gz" + url = "https://cran.r-project.org/src/contrib/jsonlite_1.2.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite" + version('1.2', '80cd2678ae77254be470f5931db71c51') version('1.0', 'c8524e086de22ab39b8ac8000220cc87') version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py new file mode 100644 index 0000000000..67159297ab --- /dev/null +++ b/var/spack/repos/builtin/packages/r-kernlab/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RKernlab(RPackage): + """Kernel-based machine learning methods for classification, regression, + clustering, novelty detection, quantile regression and dimensionality + reduction. Among other methods 'kernlab' includes Support Vector Machines, + Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.""" + + homepage = "https://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" + + version('0.9-25', '1182a2a336a79fd2cf70b4bc5a35353f') + + depends_on('r@2.10:') diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py new file mode 100644 index 0000000000..14e58072dc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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" + + version('2.23-15', '746cdf26dec72004cf19978e87dcc982') + + depends_on('r@2.5.0:') diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py new file mode 100644 index 0000000000..bd5d688b14 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-kknn/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('1.3.1', '372cd84f618cd5005f8c4c5721755117') + + depends_on('r@2.10:') + + 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-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py new file mode 100644 index 0000000000..c38f9003ea --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lava/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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_1.4.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lava" + + version('1.4.7', '28039248a7039ba9281d172e4dbf9543') + + depends_on('r@3.0:') + + depends_on('r-numderiv', type=('build', 'run')) + depends_on('r-survival', 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 07c2eaf9da..ba1323a737 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -30,9 +30,10 @@ class RMatrix(RPackage): using 'LAPACK' and 'SuiteSparse'.""" homepage = "http://matrix.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/Matrix_1.2-6.tar.gz" + url = "https://cran.r-project.org/src/contrib/Matrix_1.2-8.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix" + version('1.2-8', '4a6406666bf97d3ec6b698eea5d9c0f5') version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') depends_on('r-lattice', 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 new file mode 100644 index 0000000000..4a3325abec --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mda/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('0.4-9', '2ce1446c4a013e0ebcc1099a00269ad9') + + depends_on('r@1.9.0:') + + depends_on('r-class', 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 c8cb067275..611abfd47c 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -32,9 +32,10 @@ class RMgcv(RPackage): beyond the exponential family.""" homepage = "https://cran.r-project.org/package=mgcv" - url = "https://cran.r-project.org/src/contrib/mgcv_1.8-13.tar.gz" + 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" + version('1.8-16', '4c1d85e0f80b017bccb4b63395842911') version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') depends_on('r-nlme', 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 new file mode 100644 index 0000000000..ec7957d5f7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mlbench/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('2.1-1', '9f06848b8e137b8a37417c92d8e57f3b') + + depends_on('r@2.10:') + + depends_on('r-lattice', 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 new file mode 100644 index 0000000000..99644ef190 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('1.1.0', 'd43175001f0531b8810d2802d76b7b44') + + depends_on('r@3.2.2:') + + depends_on('r-rcpp', 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 new file mode 100644 index 0000000000..97c3cf0682 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-modeltools/package.py @@ -0,0 +1,35 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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" + + version('0.2-21', '3bf56b2e7bf78981444385d87eeccdd7') diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index 70704a9c61..0dbfb14ea0 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -38,8 +38,8 @@ class RMultcomp(RPackage): version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') - depends_on('r-mvtnorm', type=('build', 'run')) - depends_on('r-survival', type=('build', 'run')) - depends_on('r-thdata', type=('build', 'run')) - depends_on('r-sandwich', type=('build', 'run')) + depends_on('r-mvtnorm@1.0-3:', 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')) depends_on('r-codetools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index 869e03ab51..32fa484f60 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -29,9 +29,10 @@ 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_3.1-128.tar.gz" + 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" + version('3.1-130', '1935d6e308a8018ed8e45d25c8731288') version('3.1-128', '3d75ae7380bf123761b95a073eb55008') depends_on('r-lattice', 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 new file mode 100644 index 0000000000..135c4f4141 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-numderiv/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('2016.8-1', '30e486298d5126d86560095be8e8aac1') + + depends_on('r@2.11.1:') diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index bf9f38be72..8b20482c32 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -38,9 +38,10 @@ class ROpenssl(RPackage): calculations on large multibyte integers.""" homepage = "https://github.com/jeroenooms/openssl#readme" - url = "https://cran.r-project.org/src/contrib/openssl_0.9.4.tar.gz" + 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" + version('0.9.6', '7ef137929d9dd07db690d35db242ba4b') version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') - depends_on('openssl') + depends_on('openssl@1.0.1:') diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py new file mode 100644 index 0000000000..a51633fbb4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pacman/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPacman(RPackage): + """Tools to more conveniently perform tasks associated with add-on + packages. pacman conveniently wraps library and package related functions + and names them in an intuitive and consistent fashion. It seeks to combine + functionality from lower level functions which can speed up workflow.""" + + homepage = "https://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" + + version('0.4.1', 'bf18fe6d1407d31e00b337d9b07fb648') + + depends_on('r@3.0.2:') + + depends_on('r-devtools', 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 new file mode 100644 index 0000000000..23f66ca4a4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-party/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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" + + version('1.1-2', '40a00336cf8418042d2ab616675c8ddf') + + depends_on('r@2.14.0:') + + depends_on('r-mvtnorm@1.0-2:', type=('build', 'run')) + depends_on('r-modeltools@0.1-21:', 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')) + depends_on('r-zoo', type=('build', 'run')) + depends_on('r-sandwich@1.1-1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index 2d51d2b958..2a2edc50ce 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -37,7 +37,10 @@ class RPbkrtest(RPackage): list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest" version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') + version('0.4-4', '5e54b1b1b35413dd1d24ef15735ec645') - depends_on('r-lme4', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.2.3:') + + 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-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index 8a17c72f91..0cd3423f73 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -29,7 +29,8 @@ 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_3.6-3.tar.gz" + 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" + version('3.6-4', 'efe9b9b093d8903228a9b56c46d943fa') version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py new file mode 100644 index 0000000000..ddb18ff42e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pls/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPls(RPackage): + """Multivariate regression methods Partial Least Squares Regression (PLSR), + 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" + + version('2.6-0', '04e02e8e46d983c5ed53c1f952b329df') + + depends_on('r@2.10:') diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py new file mode 100644 index 0000000000..5219578d94 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-prodlim/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RProdlim(RPackage): + """Product-Limit Estimation for Censored Event History Analysis. Fast and + user friendly implementation of nonparametric estimators for censored event + history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.""" + + homepage = "https://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" + + version('1.5.9', 'e0843053c9270e41b657a733d6675dc9') + + depends_on('r@2.9.0:') + + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) + depends_on('r-kernsmooth', type=('build', 'run')) + depends_on('r-lava', 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 2d5091ccaf..c9bdaefa44 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -34,9 +34,10 @@ class RQuantreg(RPackage): included.""" homepage = "https://cran.r-project.org/package=quantreg" - url = "https://cran.r-project.org/src/contrib/quantreg_5.26.tar.gz" + url = "https://cran.r-project.org/src/contrib/quantreg_5.29.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg" + version('5.29', '643ca728200d13f8c2e62365204e9907') version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') depends_on('r-sparsem', 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 e64a8a6532..700771f40f 100644 --- a/var/spack/repos/builtin/packages/r-r6/package.py +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -34,7 +34,10 @@ class RR6(RPackage): classes are defined in different packages.""" homepage = "https://github.com/wch/R6/" - url = "https://cran.r-project.org/src/contrib/R6_2.1.2.tar.gz" + url = "https://cran.r-project.org/src/contrib/R6_2.2.0.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/R6" + version('2.2.0', '659d83b2d3f7a308a48332b4cfbdab49') version('2.1.2', 'b6afb9430e48707be87638675390e457') + + depends_on('r@3.0:') diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index b447dea8bd..5b89324970 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -37,8 +37,9 @@ class RRcpp(RPackage): last two.""" homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" - url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.6.tar.gz" + url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.9.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp" + version('0.12.9', '691c49b12794507288b728ede03668a5') version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b') version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index 23ec0bc27b..b33e938d5b 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -41,9 +41,10 @@ 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_0.3.2.8.1.tar.gz" + 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" + version('0.3.2.9.0', '14a7786882a5d9862d53c4b2217df318') version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') depends_on('r-matrix', 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 d27231e139..ca65e006dc 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -30,9 +30,10 @@ class RReshape2(RPackage): and dcast (or acast).""" homepage = "https://github.com/hadley/reshape" - url = "https://cran.r-project.org/src/contrib/reshape2_1.4.1.tar.gz" + 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" + version('1.4.2', 'c851a0312191b8c5bab956445df7cf5f') version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') depends_on('r-plyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py new file mode 100644 index 0000000000..b22612a238 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rminer/package.py @@ -0,0 +1,54 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRminer(RPackage): + """Facilitates the use of data mining algorithms in classification and + regression (including time series forecasting) tasks by presenting a short + 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" + + version('1.4.2', '7d5d90f4ae030cf647d67aa962412c05') + + depends_on('r-plotrix', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) + depends_on('r-kknn', type=('build', 'run')) + depends_on('r-pls', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-mda', type=('build', 'run')) + depends_on('r-rpart', type=('build', 'run')) + depends_on('r-randomforest', type=('build', 'run')) + depends_on('r-adabag', type=('build', 'run')) + depends_on('r-party', type=('build', 'run')) + depends_on('r-cubist', type=('build', 'run')) + depends_on('r-kernlab', type=('build', 'run')) + depends_on('r-e1071', type=('build', 'run')) + depends_on('r-glmnet', type=('build', 'run')) + depends_on('r-xgboost', 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 new file mode 100644 index 0000000000..d7d40f2154 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('2.1.0', 'fb0f8edfe22c464683ee82aa429136f9') + + depends_on('r-rpart@4.1-0:', 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 new file mode 100644 index 0000000000..a81c9d7d91 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rpart/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('4.1-10', '15873cded4feb3ef44d63580ba3ca46e') + + depends_on('r@2.15.0:') diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index 62bd2880e5..bae8e82d68 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -35,4 +35,6 @@ class RSandwich(RPackage): version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') + depends_on('r@2.0.0:') + 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 e3832f78e0..e88ef144cf 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -30,9 +30,10 @@ 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_0.4.0.tar.gz" + url = "https://cran.r-project.org/src/contrib/scales_0.4.1.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/scales" + version('0.4.1', '3fb2218866a7fe4c1f6e66790876f85a') version('0.4.0', '7b5602d9c55595901192248bca25c099') depends_on('r-rcolorbrewer', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index 370497e395..bcd11a5c1f 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -31,7 +31,8 @@ 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_1.7.tar.gz" + url = "https://cran.r-project.org/src/contrib/SparseM_1.74.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM" - version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') + version('1.74', 'a16c9b7db172dfd2b7b6508c48e81a5d') + version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index d89238f3d7..b116c328f5 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -37,9 +37,10 @@ class RStringi(RPackage): etc.""" homepage = "http://www.gagolewski.com/software/stringi/" - url = "https://cran.r-project.org/src/contrib/stringi_1.1.1.tar.gz" + 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" + version('1.1.2', '0ec2faa62643e1900734c0eaf5096648') version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') depends_on('icu4c') diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index de8d83b500..4accd04e51 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -33,9 +33,10 @@ class RStringr(RPackage): 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_1.0.0.tar.gz" + 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" + version('1.1.0', '47973a33944c6d5db9524b1e835b8a5d') version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') depends_on('r-stringi', 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 new file mode 100644 index 0000000000..6d00d31402 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-strucchange/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +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" + + version('1.5-1', 'fc751fc011df9c8df82d577298cb8395') + + depends_on('r@2.10.0:') + + depends_on('r-zoo', type=('build', 'run')) + depends_on('r-sandwich', 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 1df00f0c93..067cdcfd6b 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -31,9 +31,10 @@ class RSurvival(RPackage): models, and parametric accelerated failure time models.""" homepage = "https://cran.r-project.org/package=survival" - url = "https://cran.r-project.org/src/contrib/survival_2.39-5.tar.gz" + url = "https://cran.r-project.org/src/contrib/survival_2.40-1.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/survival" + version('2.40-1', 'a2474b656cd723791268e3114481b8a7') version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-thdata/package.py b/var/spack/repos/builtin/packages/r-th-data/package.py index cf2b01e6e8..b9c5fab0d0 100644 --- a/var/spack/repos/builtin/packages/r-thdata/package.py +++ b/var/spack/repos/builtin/packages/r-th-data/package.py @@ -25,13 +25,14 @@ from spack import * -class RThdata(RPackage): +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_1.0-7.tar.gz" + 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" + version('1.0-8', '2cc20acc8b470dff1202749b4bea55c4') version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') depends_on('r-survival', 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 39dfc3893b..a06b33e7f2 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -30,11 +30,14 @@ class RTibble(RPackage): capabilities than traditional data frames.""" homepage = "https://github.com/hadley/tibble" - url = "https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz" + url = "https://cran.r-project.org/src/contrib/tibble_1.2.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/tibble" + version('1.2', 'bdbc3d67aa16860741add6d6ec20ea13') version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') + depends_on('r@3.1.2:') + depends_on('r-assertthat', type=('build', 'run')) - depends_on('r-lazyeval', type=('build', 'run')) + depends_on('r-lazyeval@0.1.10:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index 785050ed87..082b94e2a6 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -32,7 +32,10 @@ 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_1.0.1.tar.gz" + 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" + version('1.0.2', 'ca52b729af9bbaa14fc8b7bafe38663c') version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') + + depends_on('r@3.0.2:') diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py index 766191dcc1..4246d73e49 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -37,12 +37,19 @@ 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_0.4-4.tar.gz" + 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" + version('0.6-4', '86e517e3ce39f8a01de796920f6b425e') version('0.4-4', 'c24d3076058101a71de4b8af8806697c') - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-datatable', type=('build', 'run')) - depends_on('r-magrittr', type=('build', 'run')) + depends_on('r@3.3.0:') + + depends_on('r-matrix@1.1-0:', type=('build', 'run')) + depends_on('r-data-table@1.9.6:', type=('build', 'run')) + depends_on('r-magrittr@1.5:', type=('build', 'run')) + depends_on('r-stringi@0.5.2:', type=('build', 'run')) + + # This is not listed as required, but installation fails without it + # ERROR: dependency 'stringr' is not available for package 'xgboost' depends_on('r-stringr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index 230c78a61a..7418d36a64 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -33,9 +33,10 @@ 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_1.7-13.tar.gz" + 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" + version('1.7-14', '8c577a7c1e535c899ab14177b1039c32') version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') depends_on('r-lattice', type=('build', 'run')) |