Merge pull request #1351 from glennpj/r_htmlwidgets

New packages - R htmlwidgets

var/spack/repos/builtin/packages/r-base64enc/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 RBase64enc(Package):
+    """This package provides tools for handling base64 encoding. It is more
+    flexible than the orphaned base64 package."""
+
+    homepage = "http://www.rforge.net/base64enc"
+    url      = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc"
+
+    version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190')
+
+    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-cluster/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 RCluster(Package):
+    """Methods for Cluster analysis. Much extended the original from Peter
+    Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw
+    (1990) "Finding Groups in Data"."""
+
+    homepage = "https://cran.r-project.org/web/packages/cluster/index.html"
+    url      = "https://cran.r-project.org/src/contrib/cluster_2.0.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cluster"
+
+    version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59')
+
+    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-codetools/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 RCodetools(Package):
+    """Code analysis tools for R."""
+
+    homepage = "https://cran.r-project.org/web/packages/codetools/index.html"
+    url      = "https://cran.r-project.org/src/contrib/codetools_0.2-14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/codetools"
+
+    version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d')
+
+    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-diagrammer/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 RDiagrammer(Package):
+    """Create graph diagrams and flowcharts using R."""
+
+    homepage = "https://github.com/rich-iannone/DiagrammeR"
+    url      = "https://cran.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/DiagrammeR"
+
+    version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-igraph', type=nolink)
+    depends_on('r-influencer', type=nolink)
+    depends_on('r-rstudioapi@0.6:', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-visnetwork', type=nolink)
+    depends_on('r-scales', 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-doparallel/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 RDoparallel(Package):
+    """Provides a parallel backend for the %dopar% function using the parallel
+    package."""
+
+    homepage = "https://cran.r-project.org/web/packages/doParallel/index.html"
+    url      = "https://cran.r-project.org/src/contrib/doParallel_1.0.10.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/doParallel"
+
+    version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43')
+
+    extends('R')
+
+    depends_on('r-foreach', type=nolink)
+    depends_on('r-iterators', 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-dt/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 RDt(Package):
+    """Data objects in R can be rendered as HTML tables using the JavaScript
+    library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables'
+    library has been included in this R package. The package name 'DT' is an
+    abbreviation of 'DataTables'."""
+
+    homepage = "http://rstudio.github.io/DT"
+    url      = "https://cran.r-project.org/src/contrib/DT_0.1.tar.gz"
+
+    version('0.1', '5c8df984921fa484784ec4b8a4fb6f3c')
+
+    extends('R')
+
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-magrittr', 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-dygraphs/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 RDygraphs(Package):
+    """An R interface to the 'dygraphs' JavaScript charting library (a copy of
+    which is included in the package). Provides rich facilities for charting
+    time-series data in R, including highly configurable series- and
+    axis-display and interactive features like zoom/pan and series/point
+    highlighting."""
+
+    homepage = "https://cran.r-project.org/web/packages/dygraphs/index.html"
+    url      = "https://cran.r-project.org/src/contrib/dygraphs_0.9.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dygraphs"
+
+    version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833')
+
+    extends('R')
+
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-zoo', type=nolink)
+    depends_on('r-xts', 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-foreach/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 RForeach(Package):
+    """Support for the foreach looping construct. Foreach is an idiom that
+    allows for iterating over elements in a collection, without the use of an
+    explicit loop counter. This package in particular is intended to be used
+    for its return value, rather than for its side effects. In that sense, it
+    is similar to the standard lapply function, but doesn't require the
+    evaluation of a function. Using foreach without side effects also
+    facilitates executing the loop in parallel."""
+
+    homepage = "https://cran.r-project.org/web/packages/foreach/index.html"
+    url      = "https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/foreach"
+
+    version('1.4.3', 'ef45768126661b259f9b8994462c49a0')
+
+    extends('R')
+
+    depends_on('r-codetools', type=nolink)
+    depends_on('r-iterators', 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-gridbase/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 RGridbase(Package):
+    """Integration of base and grid graphics."""
+
+    homepage = "https://cran.r-project.org/web/packages/gridBase/index.html"
+    url      = "https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gridBase"
+
+    version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f')
+
+    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-htmlwidgets/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 RHtmlwidgets(Package):
+    """A framework for creating HTML widgets that render in various contexts
+    including the R console, 'R Markdown' documents, and 'Shiny' web
+    applications."""
+
+    homepage = "https://github.com/ramnathv/htmlwidgets"
+    url      = "https://cran.r-project.org/src/contrib/htmlwidgets_0.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/htmlwidgets"
+
+    version('0.6', '7fa522d2eda97593978021bda9670c0e')
+
+    extends('R')
+
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-yaml', 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-igraph/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 RIgraph(Package):
+    """Routines for simple graphs and network analysis. It can handle large
+    graphs very well and provides functions for generating random and regular
+    graphs, graph visualization, centrality methods and much more."""
+
+    homepage = "http://igraph.org/"
+    url      = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/igraph"
+
+    version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-nmf', type=nolink)
+    depends_on('r-irlba', type=nolink)
+    depends_on('gmp')
+    depends_on('libxml2')
+
+    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-influencer/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 RInfluencer(Package):
+    """Provides functionality to compute various node centrality measures on
+    networks. Included are functions to compute betweenness centrality (by
+    utilizing Madduri and Bader's SNAP library), implementations of Burt's
+    constraint and effective network size (ENS) metrics, Borgatti's algorithm
+    to identify key players, and Valente's bridging metric. On Unix systems,
+    the betweenness, Key Players, and bridging implementations are parallelized
+    with OpenMP, which may run faster on systems which have OpenMP
+    configured."""
+
+    homepage = "https://github.com/rcc-uchicago/influenceR"
+    url      = "https://cran.r-project.org/src/contrib/influenceR_0.1.0.tar.gz"
+
+    version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5')
+
+    extends('R')
+
+    depends_on('r-igraph', 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-irlba/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 RIrlba(Package):
+    """Fast and memory efficient methods for truncated singular and eigenvalue
+    decompositions and principal component analysis of large sparse or dense
+    matrices."""
+
+    homepage = "https://cran.r-project.org/web/packages/irlba/index.html"
+    url      = "https://cran.r-project.org/src/contrib/irlba_2.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/irlba"
+
+    version('2.0.0', '557674cf8b68fea5b9f231058c324d26')
+
+    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-iterators/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 RIterators(Package):
+    """Support for iterators, which allow a programmer to traverse through all
+    the elements of a vector, list, or other collection of data."""
+
+    homepage = "https://cran.r-project.org/web/packages/iterators/index.html"
+    url      = "https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/iterators"
+
+    version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee')
+
+    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-leaflet/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 RLeaflet(Package):
+    """Create and customize interactive maps using the 'Leaflet' JavaScript
+    library and the 'htmlwidgets' package. These maps can be used directly from
+    the R console, from 'RStudio', in Shiny apps and R Markdown documents."""
+
+    homepage = "http://rstudio.github.io/leaflet/"
+    url      = "https://cran.r-project.org/src/contrib/leaflet_1.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/leaflet"
+
+    version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df')
+
+    extends('R')
+
+    depends_on('r-base64enc', type=nolink)
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-markdown', type=nolink)
+    depends_on('r-png', type=nolink)
+    depends_on('r-rcolorbrewer', type=nolink)
+    depends_on('r-raster', type=nolink)
+    depends_on('r-scales', type=nolink)
+    depends_on('r-sp', 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-markdown/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 RMarkdown(Package):
+    """Provides R bindings to the 'Sundown' 'Markdown' rendering library
+    (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting
+    syntax that can be converted to 'XHTML' or other formats. See
+    http://en.wikipedia.org/wiki/Markdown for more information about
+    'Markdown'."""
+
+    homepage = "https://github.com/rstudio/markdown"
+    url      = "https://cran.r-project.org/src/contrib/markdown_0.7.7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/markdown"
+
+    version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff')
+
+    extends('R')
+
+    depends_on('r-mime', 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-networkd3/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 RNetworkd3(Package):
+    """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs
+    from 'R'."""
+
+    homepage = "http://cran.r-project.org/package=networkD3"
+    url      = "https://cran.r-project.org/src/contrib/networkD3_0.2.12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/networkD3"
+
+    version('0.2.12', '356fe4be59698e6fb052644bd9659d84')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-igraph', type=nolink)
+    depends_on('r-magrittr', 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-nmf/package.py

@@ -0,0 +1,60 @@
+##############################################################################
+# 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 RNmf(Package):
+    """Provides a framework to perform Non-negative Matrix Factorization (NMF).
+    The package implements a set of already published algorithms and seeding
+    methods, and provides a framework to test, develop and plug new/custom
+    algorithms. Most of the built-in algorithms have been optimized in C++, and
+    the main interface function provides an easy way of performing parallel
+    computations on multicore machines.."""
+
+    homepage = "http://renozao.github.io/NMF"
+    url      = "https://cran.r-project.org/src/contrib/NMF_0.20.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/NMF"
+
+    version('0.20.6', '81df07b3bf710a611db5af24730ff3d0')
+
+    extends('R')
+
+    depends_on('r-pkgmaker', type=nolink)
+    depends_on('r-registry', type=nolink)
+    depends_on('r-rngtools', type=nolink)
+    depends_on('r-cluster', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-gridbase', type=nolink)
+    depends_on('r-colorspace', type=nolink)
+    depends_on('r-rcolorbrewer', type=nolink)
+    depends_on('r-foreach', type=nolink)
+    depends_on('r-doparallel', type=nolink)
+    depends_on('r-ggplot2', type=nolink)
+    depends_on('r-reshape2', 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-pkgmaker/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 RPkgmaker(Package):
+    """This package provides some low-level utilities to use for package
+    development. It currently provides managers for multiple package specific
+    options and registries, vignette, unit test and bibtex related utilities.
+    It serves as a base package for packages like NMF, RcppOctave, doRNG, and
+    as an incubator package for other general purposes utilities, that will
+    eventually be packaged separately. It is still under heavy development and
+    changes in the interface(s) are more than likely to happen."""
+
+    homepage = "https://renozao.github.io/pkgmaker"
+    url      = "https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pkgmaker"
+
+    version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4')
+
+    extends('R')
+
+    depends_on('r-registry', type=nolink)
+    depends_on('r-codetools', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-xtable', 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-png/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 RPng(Package):
+    """This package provides an easy and simple way to read, write and display
+    bitmap images stored in the PNG format. It can read and write both files
+    and in-memory raw vectors."""
+
+    homepage = "http://www.rforge.net/png/"
+    url      = "https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/png"
+
+    version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f')
+
+    extends('R')
+
+    depends_on('libpng')
+
+    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-raster/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 RRaster(Package):
+    """Reading, writing, manipulating, analyzing and modeling of gridded
+    spatial data. The package implements basic and high-level functions.
+    Processing of very large files is supported."""
+
+    homepage = "http://cran.r-project.org/package=raster"
+    url      = "https://cran.r-project.org/src/contrib/raster_2.5-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/raster"
+
+    version('2.5-8', '2a7db931c74d50516e82d04687c0a577')
+
+    extends('R')
+
+    depends_on('r-sp', type=nolink)
+    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-registry/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 RRegistry(Package):
+    """Provides a generic infrastructure for creating and using registries."""
+
+    homepage = "https://cran.r-project.org/web/packages/registry/index.html"
+    url      = "https://cran.r-project.org/src/contrib/registry_0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/registry"
+
+    version('0.3', '85345b334ec81eb3da6edcbb27c5f421')
+
+    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-rngtools/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 RRngtools(Package):
+    """This package contains a set of functions for working with Random Number
+    Generators (RNGs). In particular, it defines a generic S4 framework for
+    getting/setting the current RNG, or RNG data that are embedded into objects
+    for reproducibility. Notably, convenient default methods greatly facilitate
+    the way current RNG settings can be changed."""
+
+    homepage = "https://renozao.github.io/rngtools"
+    url      = "https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rngtools"
+
+    version('1.2.4', '715967f8b3af2848a76593a7c718c1cd')
+
+    extends('R')
+
+    depends_on('r-pkgmaker', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-digest', 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-rstudioapi/package.py

@@ -33,6 +33,7 @@ class RRstudioapi(Package):
     url      = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi"
 
+    version('0.6', 'fdb13bf46aab02421557e713fceab66b')
     version('0.5', '6ce1191da74e7bcbf06b61339486b3ba')
 
     extends('R')

var/spack/repos/builtin/packages/r-sp/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 RSp(Package):
+    """Classes and methods for spatial data; the classes document where the
+    spatial location information resides, for 2D or 3D data. Utility functions
+    are provided, e.g. for plotting data as maps, spatial selection, as well as
+    methods for retrieving coordinates, for subsetting, print, summary, etc."""
+
+    homepage = "https://github.com/edzer/sp/"
+    url      = "https://cran.r-project.org/src/contrib/sp_1.2-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sp"
+
+    version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1')
+
+    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-threejs/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 RThreejs(Package):
+    """Create interactive 3D scatter plots, network plots, and globes using the
+    'three.js' visualization library ("http://threejs.org")."""
+
+    homepage = "http://bwlewis.github.io/rthreejs"
+    url      = "https://cran.r-project.org/src/contrib/threejs_0.2.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/threejs"
+
+    version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-base64enc', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-jsonlite', 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-visnetwork/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 RVisnetwork(Package):
+    """Provides an R interface to the 'vis.js' JavaScript charting library. It
+    allows an interactive visualization of networks."""
+
+    homepage = "https://github.com/datastorm-open/visNetwork"
+    url      = "https://cran.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/visNetwork"
+
+    version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-magrittr', 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-xts/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 RXts(Package):
+    """Provide for uniform handling of R's different time-based data classes by
+    extending zoo, maximizing native format information preservation and
+    allowing for user level customization and extension, while simplifying
+    cross-class interoperability."""
+
+    homepage = "http://r-forge.r-project.org/projects/xts/"
+    url      = "https://cran.r-project.org/src/contrib/xts_0.9-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/xts"
+
+    version('0.9-7', 'a232e94aebfa654653a7d88a0503537b')
+
+    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)

var/spack/repos/builtin/packages/r-yaml/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 RYaml(Package):
+    """This package implements the libyaml YAML 1.1 parser and emitter
+    (http://pyyaml.org/wiki/LibYAML) for R."""
+
+    homepage = "https://cran.r-project.org/web/packages/yaml/index.html"
+    url      = "https://cran.r-project.org/src/contrib/yaml_2.1.13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/yaml"
+
+    version('2.1.13', 'f2203ea395adaff6bd09134666191d9a')
+
+    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-zoo/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 RZoo(Package):
+    """An S3 class with methods for totally ordered indexed observations. It is
+    particularly aimed at irregular time series of numeric vectors/matrices and
+    factors. zoo's key design goals are independence of a particular
+    index/date/time class and consistency with ts and base R by providing
+    methods to extend standard generics."""
+
+    homepage = "http://zoo.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/zoo_1.7-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/zoo"
+
+    version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30')
+
+    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)