Merge pull request #1388 from glennpj/r-multcomp

New package - r-multcomp

5 files changed, 226 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py
new file mode 100644
index 0000000000..54416502d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-multcomp/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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 RMultcomp(Package):
+    """Simultaneous tests and confidence intervals for general linear
+    hypotheses in parametric models, including linear, generalized linear,
+    linear mixed effects, and survival models. The package includes demos
+    reproducing analyzes presented in the book "Multiple Comparisons Using R"
+    (Bretz, Hothorn, Westfall, 2010, CRC Press)."""
+
+    homepage = "http://multcomp.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/multcomp_1.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/multcomp"
+
+    version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88')
+
+    extends('R')
+
+    depends_on('r-mvtnorm', type=nolink)
+    depends_on('r-survival', type=nolink)
+    depends_on('r-thdata', type=nolink)
+    depends_on('r-sandwich', type=nolink)
+    depends_on('r-codetools', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
new file mode 100644
index 0000000000..b3f7db60c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mvtnorm/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 RMvtnorm(Package):
+    """Computes multivariate normal and t probabilities, quantiles, random
+    deviates and densities."""
+
+    homepage = "http://mvtnorm.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm"
+
+    version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py
new file mode 100644
index 0000000000..ffd62b1b14
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sandwich/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 RSandwich(Package):
+    """Model-robust standard error estimators for cross-sectional, time series,
+    and longitudinal data."""
+
+    homepage = "https://cran.r-project.org/package=sandwich"
+    url      = "https://cran.r-project.org/src/contrib/sandwich_2.3-4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sandwich"
+
+    version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5')
+
+    extends('R')
+
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py
new file mode 100644
index 0000000000..cfba9298fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-survival/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 RSurvival(Package):
+    """Contains the core survival analysis routines, including definition of
+    Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox
+    models, and parametric accelerated failure time models."""
+
+    homepage = "https://cran.r-project.org/package=survival"
+    url      = "https://cran.r-project.org/src/contrib/survival_2.39-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/survival"
+
+    version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2')
+
+    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)
diff --git a/var/spack/repos/builtin/packages/r-thdata/package.py b/var/spack/repos/builtin/packages/r-thdata/package.py
new file mode 100644
index 0000000000..e1cf050181
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-thdata/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 RThdata(Package):
+    """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"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/TH.data"
+
+    version('1.0-7', '3e8b6b1a4699544f175215aed7039a94')
+
+    extends('R')
+
+    depends_on('r-survival', 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)