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authorAdam J. Stewart <ajstewart426@gmail.com>2017-01-31 08:54:34 -0600
committerTodd Gamblin <tgamblin@llnl.gov>2017-01-31 09:54:34 -0500
commit0c0a1fdedc036c1a7bbd420780d48215a9488819 (patch)
tree325ebd78e2d27c3021a7328f97e6bf423932413c /var
parent19cf7a2833ba2ffcff46bd4543ed93fd80c1d8ea (diff)
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Add several new R packages (#2952)
* Add several new R packages * Add a few more R packages * Update more versions * Convert Package to RPackage * Add a few more packages * Add missing dependencies
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/r-adabag/package.py39
-rw-r--r--var/spack/repos/builtin/packages/r-assertthat/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-biocinstaller/package.py37
-rw-r--r--var/spack/repos/builtin/packages/r-car/package.py13
-rw-r--r--var/spack/repos/builtin/packages/r-caret/package.py20
-rw-r--r--var/spack/repos/builtin/packages/r-checkpoint/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-cluster/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-codetools/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-coin/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-colorspace/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-corrplot/package.py36
-rw-r--r--var/spack/repos/builtin/packages/r-cubist/package.py38
-rw-r--r--var/spack/repos/builtin/packages/r-curl/package.py6
-rw-r--r--var/spack/repos/builtin/packages/r-data-table/package.py (renamed from var/spack/repos/builtin/packages/r-datatable/package.py)9
-rw-r--r--var/spack/repos/builtin/packages/r-devtools/package.py13
-rw-r--r--var/spack/repos/builtin/packages/r-digest/package.py8
-rw-r--r--var/spack/repos/builtin/packages/r-domc/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-ellipse/package.py38
-rw-r--r--var/spack/repos/builtin/packages/r-evaluate/package.py7
-rw-r--r--var/spack/repos/builtin/packages/r-ggplot2/package.py13
-rw-r--r--var/spack/repos/builtin/packages/r-git2r/package.py5
-rw-r--r--var/spack/repos/builtin/packages/r-httpuv/package.py4
-rw-r--r--var/spack/repos/builtin/packages/r-httr/package.py7
-rw-r--r--var/spack/repos/builtin/packages/r-ipred/package.py46
-rw-r--r--var/spack/repos/builtin/packages/r-irlba/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-jsonlite/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-kernlab/package.py40
-rw-r--r--var/spack/repos/builtin/packages/r-kernsmooth/package.py37
-rw-r--r--var/spack/repos/builtin/packages/r-kknn/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-lava/package.py40
-rw-r--r--var/spack/repos/builtin/packages/r-matrix/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-mda/package.py40
-rw-r--r--var/spack/repos/builtin/packages/r-mgcv/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-mlbench/package.py40
-rw-r--r--var/spack/repos/builtin/packages/r-modelmetrics/package.py40
-rw-r--r--var/spack/repos/builtin/packages/r-modeltools/package.py35
-rw-r--r--var/spack/repos/builtin/packages/r-multcomp/package.py8
-rw-r--r--var/spack/repos/builtin/packages/r-nlme/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-numderiv/package.py38
-rw-r--r--var/spack/repos/builtin/packages/r-openssl/package.py5
-rw-r--r--var/spack/repos/builtin/packages/r-pacman/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-party/package.py45
-rw-r--r--var/spack/repos/builtin/packages/r-pbkrtest/package.py7
-rw-r--r--var/spack/repos/builtin/packages/r-plotrix/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-pls/package.py39
-rw-r--r--var/spack/repos/builtin/packages/r-prodlim/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-quantreg/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-r6/package.py5
-rw-r--r--var/spack/repos/builtin/packages/r-rcpp/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-rcppeigen/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-reshape2/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-rminer/package.py54
-rw-r--r--var/spack/repos/builtin/packages/r-rpart-plot/package.py38
-rw-r--r--var/spack/repos/builtin/packages/r-rpart/package.py38
-rw-r--r--var/spack/repos/builtin/packages/r-sandwich/package.py2
-rw-r--r--var/spack/repos/builtin/packages/r-scales/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-sparsem/package.py5
-rw-r--r--var/spack/repos/builtin/packages/r-stringi/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-stringr/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-strucchange/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-survival/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-th-data/package.py (renamed from var/spack/repos/builtin/packages/r-thdata/package.py)5
-rw-r--r--var/spack/repos/builtin/packages/r-tibble/package.py7
-rw-r--r--var/spack/repos/builtin/packages/r-withr/package.py5
-rw-r--r--var/spack/repos/builtin/packages/r-xgboost/package.py15
-rw-r--r--var/spack/repos/builtin/packages/r-zoo/package.py3
66 files changed, 1202 insertions, 76 deletions
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'))