From 519b760222d953b9c79793e7803526846a814607 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Mon, 4 Jul 2016 17:30:05 -0500
Subject: [PATCH 1/2] New package - RStan

This PR creates the RStan package and its dependencies.
---
 .../repos/builtin/packages/r-bh/package.py    | 54 ++++++++++++++++++
 .../builtin/packages/r-colorspace/package.py  | 44 ++++++++++++++
 .../builtin/packages/r-dichromat/package.py   | 42 ++++++++++++++
 .../builtin/packages/r-ggplot2/package.py     | 54 ++++++++++++++++++
 .../builtin/packages/r-gridextra/package.py   | 44 ++++++++++++++
 .../builtin/packages/r-gtable/package.py      | 41 +++++++++++++
 .../builtin/packages/r-inline/package.py      | 42 ++++++++++++++
 .../builtin/packages/r-labeling/package.py    | 41 +++++++++++++
 .../builtin/packages/r-lattice/package.py     | 44 ++++++++++++++
 .../builtin/packages/r-magrittr/package.py    | 45 +++++++++++++++
 .../repos/builtin/packages/r-mass/package.py  | 42 ++++++++++++++
 .../builtin/packages/r-matrix/package.py      | 44 ++++++++++++++
 .../builtin/packages/r-munsell/package.py     | 47 +++++++++++++++
 .../repos/builtin/packages/r-plyr/package.py  | 48 ++++++++++++++++
 .../packages/r-rcolorbrewer/package.py        | 42 ++++++++++++++
 .../repos/builtin/packages/r-rcpp/package.py  | 49 ++++++++++++++++
 .../builtin/packages/r-rcppeigen/package.py   | 56 ++++++++++++++++++
 .../builtin/packages/r-reshape2/package.py    | 46 +++++++++++++++
 .../repos/builtin/packages/r-rstan/package.py | 57 +++++++++++++++++++
 .../builtin/packages/r-scales/package.py      | 49 ++++++++++++++++
 .../builtin/packages/r-stanheaders/package.py | 55 ++++++++++++++++++
 .../builtin/packages/r-stringi/package.py     | 51 +++++++++++++++++
 .../builtin/packages/r-stringr/package.py     | 48 ++++++++++++++++
 23 files changed, 1085 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-bh/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-colorspace/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-dichromat/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-ggplot2/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-gridextra/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-gtable/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-inline/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-labeling/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-lattice/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-magrittr/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-mass/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-matrix/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-munsell/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-plyr/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-rcpp/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-rcppeigen/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-reshape2/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-rstan/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-scales/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-stanheaders/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-stringi/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-stringr/package.py

diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py
new file mode 100644
index 0000000000..a0f30b779f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bh/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 RBh(Package):
+    """Boost provides free peer-reviewed portable C++ source libraries. A large
+    part of Boost is provided as C++ template code which is resolved entirely
+    at compile-time without linking. This package aims to provide the most
+    useful subset of Boost libraries for template use among CRAN package. By
+    placing these libraries in this package, we offer a more efficient
+    distribution system for CRAN as replication of this code in the sources of
+    other packages is avoided. As of release 1.60.0-2, the following Boost
+    libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer'
+    'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset'
+    'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion'
+    'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io'
+    'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric'
+    'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit'
+    'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'."""
+
+    homepage = "https://cran.r-project.org/web/packages/BH/index.html"
+    url      = "https://cran.r-project.org/src/contrib/BH_1.60.0-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/BH"
+
+    version('1.60.0-2', 'b50fdc85285da05add4e9da664a2d551')
+
+    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-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py
new file mode 100644
index 0000000000..a7622cad95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-colorspace/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 RColorspace(Package):
+    """Carries out mapping between assorted color spaces including RGB, HSV,
+    HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB.
+    Qualitative, sequential, and diverging color palettes based on HCL colors
+    are provided."""
+
+    homepage = "https://cran.r-project.org/web/packages/colorspace/index.html"
+    url      = "https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace"
+
+    version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1')
+
+    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-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py
new file mode 100644
index 0000000000..663e5295af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dichromat/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 RDichromat(Package):
+    """Collapse red-green or green-blue distinctions to simulate the effects of
+    different types of color-blindness."""
+
+    homepage = "https://cran.r-project.org/web/packages/dichromat/index.html"
+    url      = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat"
+
+    version('2.0-0', '84e194ac95a69763d740947a7ee346a6')
+
+    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-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py
new file mode 100644
index 0000000000..2d1f53af26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggplot2/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 RGgplot2(Package):
+    """An implementation of the grammar of graphics in R. It combines the
+    advantages of both base and lattice graphics: conditioning and shared axes
+    are handled automatically, and you can still build up a plot step by step
+    from multiple data sources. It also implements a sophisticated
+    multidimensional conditioning system and a consistent interface to map data
+    to aesthetic attributes. See http://ggplot2.org for more information,
+    documentation and examples."""
+
+    homepage = "http://ggplot2.org/"
+    url      = "https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ggplot2"
+
+    version('2.1.0', '771928cfb97c649c720423deb3ec7fd3')
+
+    extends('R')
+
+    depends_on('r-digest')
+    depends_on('r-gtable')
+    depends_on('r-mass')
+    depends_on('r-plyr')
+    depends_on('r-reshape2')
+    depends_on('r-scales')
+
+    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-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py
new file mode 100644
index 0000000000..d215d10678
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gridextra/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 RGridextra(Package):
+    """Provides a number of user-level functions to work with "grid" graphics,
+    notably to arrange multiple grid-based plots on a page, and draw tables."""
+
+    homepage = "https://github.com/baptiste/gridextra"
+    url      = "https://cran.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gridExtra"
+
+    version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2')
+
+    extends('R')
+
+    depends_on('r-gtable')
+
+    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-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py
new file mode 100644
index 0000000000..74dee0b3d5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gtable/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 RGtable(Package):
+    """Tools to make it easier to work with "tables" of 'grobs'."""
+
+    homepage = "https://cran.r-project.org/web/packages/gtable/index.html"
+    url      = "https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gtable"
+
+    version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab')
+
+    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-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py
new file mode 100644
index 0000000000..c972fe0ff0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-inline/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 RInline(Package):
+    """Functionality to dynamically define R functions and S4 methods with
+    inlined C, C++ or Fortran code supporting .C and .Call calling conventions."""
+
+    homepage = "https://cran.r-project.org/web/packages/inline/index.html"
+    url      = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/inline"
+
+    version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca')
+
+    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-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py
new file mode 100644
index 0000000000..02e5da9d85
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-labeling/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 RLabeling(Package):
+    """Provides a range of axis labeling algorithms."""
+
+    homepage = "https://cran.r-project.org/web/packages/labeling/index.html"
+    url      = "https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/labeling"
+
+    version('0.3', 'ccd7082ec0b211aba8a89d85176bb534')
+
+    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-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py
new file mode 100644
index 0000000000..ba29feefc4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lattice/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 RLattice(Package):
+    """A powerful and elegant high-level data visualization system inspired by
+    Trellis graphics, with an emphasis on multivariate data. Lattice is
+    sufficient for typical graphics needs, and is also flexible enough to
+    handle most nonstandard requirements. See ?Lattice for an introduction."""
+
+    homepage = "http://lattice.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lattice"
+
+    version('0.20-33', 'd487c94db1bfe00a27270f4c71baf53e')
+
+    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-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py
new file mode 100644
index 0000000000..11476c3d1e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-magrittr/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 RMagrittr(Package):
+    """Provides a mechanism for chaining commands with a new forward-pipe
+    operator, %>%. This operator will forward a value, or the result of an
+    expression, into the next function call/expression. There is flexible
+    support for the type of right-hand side expressions. For more information,
+    see package vignette."""
+
+    homepage = "https://cran.r-project.org/web/packages/magrittr/index.html"
+    url      = "https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/magrittr"
+
+    version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a')
+
+    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-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py
new file mode 100644
index 0000000000..1ab01d2256
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mass/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 RMass(Package):
+    """Functions and datasets to support Venables and Ripley, "Modern Applied
+    Statistics with S" (4th edition, 2002)."""
+
+    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
+    url      = "https://cran.r-project.org/src/contrib/MASS_7.3-45.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/MASS"
+
+    version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b')
+
+    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-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py
new file mode 100644
index 0000000000..fbd8a7b4df
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-matrix/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 RMatrix(Package):
+    """Classes and methods for dense and sparse matrices and operations on them
+    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"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix"
+
+    version('1.2-6', 'f545307fb1284861e9266c4e9712c55e')
+
+    extends('R')
+
+    depends_on('r-lattice')
+
+    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-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py
new file mode 100644
index 0000000000..3216c95e00
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-munsell/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 RMunsell(Package):
+    """Provides easy access to, and manipulation of, the Munsell colours.
+    Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and
+    hexadecimal strings suitable for use directly in R graphics. Also provides
+    utilities to explore slices through the Munsell colour tree, to transform
+    Munsell colours and display colour palettes."""
+
+    homepage = "https://cran.r-project.org/web/packages/munsell/index.html"
+    url      = "https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/munsell"
+
+    version('0.4.3', 'ebd205323dc37c948f499ee08be9c476')
+
+    extends('R')
+
+    depends_on('r-colorspace')
+
+    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-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py
new file mode 100644
index 0000000000..e071050f4a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-plyr/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 RPlyr(Package):
+    """A set of tools that solves a common set of problems: you need to break a
+    big problem down into manageable pieces, operate on each piece and then put
+    all the pieces back together. For example, you might want to fit a model to
+    each spatial location or time point in your study, summarise data by panels
+    or collapse high-dimensional arrays to simpler summary statistics. The
+    development of 'plyr' has been generously supported by 'Becton Dickinson'."""
+
+    homepage = "http://had.co.nz/plyr"
+    url      = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/plyr"
+
+    version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b')
+
+    extends('R')
+
+    depends_on('r-rcpp')
+
+    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-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
new file mode 100644
index 0000000000..b81ec2561c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/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 RRcolorbrewer(Package):
+    """Provides color schemes for maps (and other graphics) designed by Cynthia
+    Brewer as described at http://colorbrewer2.org"""
+
+    homepage = "http://colorbrewer2.org"
+    url      = "https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RColorBrewer"
+
+    version('1.1-2', '66054d83eade4dff8a43ad4732691182')
+
+    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-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py
new file mode 100644
index 0000000000..2428f4af3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcpp/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 RRcpp(Package):
+    """The 'Rcpp' package provides R functions as well as C++ classes which
+    offer a seamless integration of R and C++. Many R data types and objects
+    can be mapped back and forth to C++ equivalents which facilitates both
+    writing of new code as well as easier integration of third-party libraries.
+    Documentation about 'Rcpp' is provided by several vignettes included in
+    this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the
+    paper by Eddelbuettel and Francois (2011, JSS), and the book by
+    Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these
+    last two."""
+
+    homepage = "http://dirk.eddelbuettel.com/code/rcpp.html"
+    url      = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp"
+
+    version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2')
+
+    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-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
new file mode 100644
index 0000000000..3175628a73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
@@ -0,0 +1,56 @@
+##############################################################################
+# 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 RRcppeigen(Package):
+    """R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template
+    library for linear algebra: matrices, vectors, numerical solvers and
+    related algorithms. It supports dense and sparse matrices on integer,
+    floating point and complex numbers, decompositions of such matrices, and
+    solutions of linear systems. Its performance on many algorithms is
+    comparable with some of the best implementations based on 'Lapack' and
+    level-3 'BLAS'. The 'RcppEigen' package includes the header files from the
+    'Eigen' C++ template library (currently version 3.2.8). Thus users do not
+    need to install 'Eigen' itself in order to use 'RcppEigen'. Since version
+    3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2);
+    earlier version were licensed under the GNU LGPL version 3 or later.
+    'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the
+    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"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen"
+
+    version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f')
+
+    extends('R')
+
+    depends_on('r-matrix')
+    depends_on('r-rcpp')
+
+    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-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py
new file mode 100644
index 0000000000..a96a314008
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-reshape2/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 RReshape2(Package):
+    """Flexibly restructure and aggregate data using just two functions: melt
+    and dcast (or acast)."""
+
+    homepage = "https://github.com/hadley/reshape"
+    url      = "https://cran.r-project.org/src/contrib/reshape2_1.4.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/reshape2"
+
+    version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00')
+
+    extends('R')
+
+    depends_on('r-plyr')
+    depends_on('r-stringr')
+    depends_on('r-rcpp')
+
+    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-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py
new file mode 100644
index 0000000000..00fd5116d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rstan/package.py
@@ -0,0 +1,57 @@
+##############################################################################
+# 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 RRstan(Package):
+    """User-facing R functions are provided to parse, compile, test, estimate,
+    and analyze Stan models by accessing the header-only Stan library provided
+    by the 'StanHeaders' package. The Stan project develops a probabilistic
+    programming language that implements full Bayesian statistical inference
+    via Markov Chain Monte Carlo, rough Bayesian inference via variational
+    approximation, and (optionally penalized) maximum likelihood estimation via
+    optimization. In all three cases, automatic differentiation is used to
+    quickly and accurately evaluate gradients without burdening the user with
+    the need to derive the partial derivatives."""
+
+    homepage = "http://mc-stan.org/"
+    url      = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rstan"
+
+    version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a')
+
+    extends('R')
+
+    depends_on('r-ggplot2')
+    depends_on('r-stanheaders')
+    depends_on('r-inline')
+    depends_on('r-gridextra')
+    depends_on('r-rcpp')
+    depends_on('r-rcppeigen')
+    depends_on('r-bh')
+
+    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-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py
new file mode 100644
index 0000000000..046a05d48e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-scales/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 RScales(Package):
+    """Graphical scales map data to aesthetics, and provide methods for
+    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"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/scales"
+
+    version('0.4.0', '7b5602d9c55595901192248bca25c099')
+
+    extends('R')
+
+    depends_on('r-rcolorbrewer')
+    depends_on('r-dichromat')
+    depends_on('r-plyr')
+    depends_on('r-munsell')
+    depends_on('r-labeling')
+    depends_on('r-rcpp')
+
+    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-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py
new file mode 100644
index 0000000000..c77b5aa8b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# 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 RStanheaders(Package):
+    """The C++ header files of the Stan project are provided by this package,
+    but it contains no R code, vignettes, or function documentation. There is a
+    shared object containing part of the CVODES library, but it is not
+    accessible from R. StanHeaders is only useful for developers who want to
+    utilize the LinkingTo directive of their package's DESCRIPTION file to
+    build on the Stan library without incurring unnecessary dependencies. The
+    Stan project develops a probabilistic programming language that implements
+    full or approximate Bayesian statistical inference via Markov Chain Monte
+    Carlo or variational methods and implements (optionally penalized) maximum
+    likelihood estimation via optimization. The Stan library includes an
+    advanced automatic differentiation scheme, templated statistical and linear
+    algebra functions that can handle the automatically differentiable scalar
+    types (and doubles, ints, etc.), and a parser for the Stan language. The
+    'rstan' package provides user-facing R functions to parse, compile, test,
+    estimate, and analyze Stan models."""
+
+    homepage = "http://mc-stan.org/"
+    url      = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders"
+
+    version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57')
+
+    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-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py
new file mode 100644
index 0000000000..22774dedec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-stringi/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 RStringi(Package):
+    """Allows for fast, correct, consistent, portable, as well as convenient
+    character string/text processing in every locale and any native encoding.
+    Owing to the use of the ICU library, the package provides R users with
+    platform-independent functions known to Java, Perl, Python, PHP, and Ruby
+    programmers. Among available features there are: pattern searching (e.g.,
+    with ICU Java-like regular expressions or the Unicode Collation Algorithm),
+    random string generation, case mapping, string transliteration,
+    concatenation, Unicode normalization, date-time formatting and parsing,
+    etc."""
+
+    homepage = "http://www.gagolewski.com/software/stringi/"
+    url      = "https://cran.r-project.org/src/contrib/stringi_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/stringi"
+
+    version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9')
+
+    extends('R')
+
+    depends_on('icu')
+
+    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-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py
new file mode 100644
index 0000000000..01fd969522
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-stringr/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 RStringr(Package):
+    """A consistent, simple and easy to use set of wrappers around the
+    fantastic 'stringi' package. All function and argument names (and
+    positions) are consistent, all functions deal with "NA"'s and zero length
+    vectors in the same way, and the output from one function is easy to feed
+    into the input of another."""
+
+    homepage = "https://cran.r-project.org/web/packages/stringr/index.html"
+    url      = "https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/stringr"
+
+    version('1.0.0', '5ca977c90351f78b1b888b379114a7b4')
+
+    extends('R')
+
+    depends_on('r-stringi')
+    depends_on('r-magrittr')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

From d5abcc5c88a1aef31cba571a03966efded19c4ae Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Mon, 4 Jul 2016 17:55:10 -0500
Subject: [PATCH 2/2] Fix flake errors

---
 var/spack/repos/builtin/packages/r-inline/package.py | 3 ++-
 var/spack/repos/builtin/packages/r-plyr/package.py   | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py
index c972fe0ff0..35eb8ca76f 100644
--- a/var/spack/repos/builtin/packages/r-inline/package.py
+++ b/var/spack/repos/builtin/packages/r-inline/package.py
@@ -27,7 +27,8 @@
 
 class RInline(Package):
     """Functionality to dynamically define R functions and S4 methods with
-    inlined C, C++ or Fortran code supporting .C and .Call calling conventions."""
+    inlined C, C++ or Fortran code supporting .C and .Call calling
+    conventions."""
 
     homepage = "https://cran.r-project.org/web/packages/inline/index.html"
     url      = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz"
diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py
index e071050f4a..192e7e8b18 100644
--- a/var/spack/repos/builtin/packages/r-plyr/package.py
+++ b/var/spack/repos/builtin/packages/r-plyr/package.py
@@ -31,7 +31,8 @@ class RPlyr(Package):
     all the pieces back together. For example, you might want to fit a model to
     each spatial location or time point in your study, summarise data by panels
     or collapse high-dimensional arrays to simpler summary statistics. The
-    development of 'plyr' has been generously supported by 'Becton Dickinson'."""
+    development of 'plyr' has been generously supported by 'Becton
+    Dickinson'."""
 
     homepage = "http://had.co.nz/plyr"
     url      = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz"