Merge pull request #1386 from glennpj/r-car

New package r-car

var/spack/repos/builtin/packages/r-car/package.py

@@ -0,0 +1,48 @@
+##############################################################################
+# 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 RCar(Package):
+    """Functions and Datasets to Accompany J. Fox and S. Weisberg, An R
+    Companion to Applied Regression, Second Edition, Sage, 2011."""
+
+    homepage = "https://r-forge.r-project.org/projects/car/"
+    url      = "https://cran.r-project.org/src/contrib/car_2.1-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/car"
+
+    version('2.1-2', '0f78ad74ef7130126d319acec23951a0')
+
+    extends('R')
+
+    depends_on('r-mass', type=nolink)
+    depends_on('r-mgcv', type=nolink)
+    depends_on('r-nnet', type=nolink)
+    depends_on('r-pbkrtest', type=nolink)
+    depends_on('r-quantreg', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-lme4/package.py

@@ -0,0 +1,53 @@
+##############################################################################
+# 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 RLme4(Package):
+    """Fit linear and generalized linear mixed-effects models. The models and
+    their components are represented using S4 classes and methods. The core
+    computational algorithms are implemented using the 'Eigen' C++ library for
+    numerical linear algebra and 'RcppEigen' "glue"."""
+
+    homepage = "https://github.com/lme4/lme4/"
+    url      = "https://cran.r-project.org/src/contrib/lme4_1.1-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lme4"
+
+    version('1.1-12', 'da8aaebb67477ecb5631851c46207804')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-mass', type=nolink)
+    depends_on('r-lattice', type=nolink)
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-minqa', type=nolink)
+    depends_on('r-nloptr', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+    depends_on('r-rcppeigen', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-matrixmodels/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 RMatrixmodels(Package):
+    """Modelling with sparse and dense 'Matrix' matrices, using modular
+    prediction and response module classes."""
+
+    homepage = "http://matrix.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/MatrixModels"
+
+    version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-mgcv/package.py

@@ -0,0 +1,47 @@
+##############################################################################
+# 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 RMgcv(Package):
+    """GAMs, GAMMs and other generalized ridge regression with multiple
+    smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam()
+    function, a wide variety of smoothers, JAGS support and distributions
+    beyond the exponential family."""
+
+    homepage = "https://cran.r-project.org/package=mgcv"
+    url      = "https://cran.r-project.org/src/contrib/mgcv_1.8-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv"
+
+    version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984')
+
+    extends('R')
+
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-minqa/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 RMinqa(Package):
+    """Derivative-free optimization by quadratic approximation based on an
+    interface to Fortran implementations by M. J. D. Powell."""
+
+    homepage = "http://optimizer.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/minqa_1.2.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/minqa"
+
+    version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105')
+
+    extends('R')
+
+    depends_on('r-rcpp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-nlme/package.py

@@ -0,0 +1,43 @@
+##############################################################################
+# 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 RNlme(Package):
+    """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"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nlme"
+
+    version('3.1-128', '3d75ae7380bf123761b95a073eb55008')
+
+    extends('R')
+
+    depends_on('r-lattice', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-nloptr/package.py

@@ -0,0 +1,47 @@
+##############################################################################
+# 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 RNloptr(Package):
+    """nloptr is an R interface to NLopt. NLopt is a free/open-source library
+    for nonlinear optimization, providing a common interface for a number of
+    different free optimization routines available online as well as original
+    implementations of various other algorithms. See
+    http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
+    information on the available algorithms. During installation on Unix the
+    NLopt code is downloaded and compiled from the NLopt website."""
+
+    homepage = "https://cran.r-project.org/package=nloptr"
+    url      = "https://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nloptr"
+
+    version('1.0.4', '9af69a613349b236fd377d0a107f484c')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-nnet/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 RNnet(Package):
+    """Software for feed-forward neural networks with a single hidden layer,
+    and for multinomial log-linear models."""
+
+    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
+    url      = "https://cran.r-project.org/src/contrib/nnet_7.3-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nnet"
+
+    version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-pbkrtest/package.py

@@ -0,0 +1,49 @@
+##############################################################################
+# 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 RPbkrtest(Package):
+    """Test in mixed effects models. Attention is on mixed effects models as
+    implemented in the 'lme4' package. This package implements a parametric
+    bootstrap test and a Kenward Roger modification of F-tests for linear mixed
+    effects models and a parametric bootstrap test for generalized linear mixed
+    models."""
+
+    homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/"
+    url      = "https://cran.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest"
+
+    version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9')
+
+    extends('R')
+
+    depends_on('r-lme4', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-mass', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-quantreg/package.py

@@ -0,0 +1,50 @@
+##############################################################################
+# 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 RQuantreg(Package):
+    """Estimation and inference methods for models of conditional quantiles:
+        Linear and nonlinear parametric and non-parametric (total variation
+        penalized) models for conditional quantiles of a univariate response
+        and several methods for handling censored survival data. Portfolio
+        selection methods based on expected shortfall risk are also
+        included."""
+
+    homepage = "https://cran.r-project.org/package=quantreg"
+    url      = "https://cran.r-project.org/src/contrib/quantreg_5.26.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg"
+
+    version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f')
+
+    extends('R')
+
+    depends_on('r-sparsem', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-matrixmodels', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-sparsem/package.py

@@ -0,0 +1,43 @@
+##############################################################################
+# 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 RSparsem(Package):
+    """Some basic linear algebra functionality for sparse matrices is provided:
+        including Cholesky decomposition and backsolving as well as standard R
+        subsetting and Kronecker products."""
+
+    homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html"
+    url      = "https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM"
+
+    version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)