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Merge pull request #1166 from glennpj/rstan

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New package - RStan
This commit is contained in:
Todd Gamblin 2016-07-04 21:23:10 -07:00 committed by GitHub
commit d166c04db5
23 changed files with 1087 additions and 0 deletions
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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)

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##############################################################################
# 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)