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Packages/r ergm (#4314)

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* Add mpi support to R

* Add multiple precision math routines to R

* Add packages for r-ergm and it's dependents

* Fixed depends-on types

* Correct flake8 errors
This commit is contained in:
Tom Merrick 2017-05-23 10:05:05 -05:00 committed by Adam J. Stewart
parent e89c699c06
commit 1469cfd0e7
10 changed files with 384 additions and 0 deletions
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var/spack/repos/builtin/packages/r-coda/package.py Normal file
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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 RCoda(RPackage):
"""Provides functions for summarizing and plotting the output from
Markov Chain Monte Carlo (MCMC) simulations, as well as
diagnostic tests of convergence to the equilibrium distribution
of the Markov chain."""
homepage = "https://cran.r-project.org/web/packages/coda/index.html"
url = "https://cran.r-project.org/src/contrib/coda_0.19-1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/coda"
version('0.19-1', '0d2aca6a5a3bdae9542708817c1ec001')
depends_on('r-lattice', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-deoptimr/package.py Normal file
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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 RDeoptimr(RPackage):
"""An implementation of a bespoke jDE variant of the Differential
Evolution stochastic algorithm for global optimization of
nonlinear programming problems."""
homepage = "https://cran.r-project.org/web/packages/DEoptimR/index.html"
url = "https://cran.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz"
version('1.0-8', 'c85836a504fbe4166e3c8eba0efe705d')

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var/spack/repos/builtin/packages/r-ergm/package.py Normal file
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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 RErgm(RPackage):
"""An integrated set of tools to analyze and simulate networks based
on exponential-family random graph models (ERGM). "ergm" is a
part of the "statnet" suite of packages for network analysis."""
homepage = "http://statnet.org"
url = "https://cran.r-project.org/src/contrib/ergm_3.7.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ergm"
version('3.7.1', '431ae430c76b2408988f469831d80126')
depends_on('r-robustbase@0.9-10:', type=('build', 'run'))
depends_on('r-coda@0.18-1:', type=('build', 'run'))
depends_on('r-trust', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-lpsolve', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-statnet-common@3.3:', type=('build', 'run'))
depends_on('r-network@1.13:', type=('build', 'run'))

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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 RLaplacesdemon(RPackage):
"""Provides a complete environment for Bayesian inference using a variety
of different samplers (see ?LaplacesDemon for an overview). The README
describes the history of the package development process."""
homepage = "https://github.com/LaplacesDemonR/LaplacesDemon"
url = "https://cran.r-project.org/src/contrib/LaplacesDemon_16.0.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/LaplacesDemon"
version('16.0.1', '1e4dab2dd0e27251734d68b0bfdbe911')

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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 RLpsolve(RPackage):
"""Lp_solve is freely available (under LGPL 2) software for solving
linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems, assignment
problems, and transportation problems. This version calls
lp_solve"""
homepage = "https://cran.r-project.org/web/packages/lpSolve/index.html"
url = "https://cran.r-project.org/src/contrib/lpSolve_5.6.13.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/lpSolve"
version('5.6.13', '8471654d9ae76e0f85ff3449433d4bc1')

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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 RNetwork(RPackage):
"""Tools to create and modify network objects. The network class can
represent a range of relational data types, and supports
arbitrary vertex/edge/graph attributes."""
homepage = "https://statnet.org"
url = "https://cran.r-project.org/src/contrib/network_1.13.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/network"
version('1.13.0', 'd0b967d6f1aad43b6479d72f29b705de')

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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 RQuadprog(RPackage):
"""This package contains routines and documentation for solving
quadratic programming problems."""
homepage = "https://cran.r-project.org/web/packages/quadprog/index.html"
url = "https://cran.r-project.org/src/contrib/quadprog_1.5-5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/quadprog"
version('1.5-5', '8442f37afd8d0b19b12e77d63e6515ad')

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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 RRobustbase(RPackage):
""""Essential" Robust Statistics. Tools allowing to analyze data
with robust methods. This includes regression methodology
including model selections and multivariate statistics where we
strive to cover the book "Robust Statistics, Theory and Methods"
by 'Maronna, Martin and Yohai'; Wiley 2006."""
homepage = "https://robustbase.r-forge.r-project.org"
url = "https://cran.r-project.org/src/contrib/robustbase_0.92-7.tar.gz"
version('0.92-7', 'db3c8d12f9729b35bad17abf09e80b72')
depends_on('r-deoptimr', type=('build', 'run'))

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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 RStatnetCommon(RPackage):
"""Non-statistical utilities used by the software developed by the
Statnet Project. They may also be of use to others."""
homepage = "http://www.statnet.org"
url = "https://cran.r-project.org/src/contrib/statnet.common_3.3.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/statnet.common"
version('3.3.0', '36bc11098dcd3652a4beb05c156ad6c8')

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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 RTrust(RPackage):
"""Does local optimization using two derivatives and trust regions.
Guaranteed to converge to local minimum of objective function."""
homepage = "http://www.stat.umn.edu/geyer/trust"
url = "https://cran.r-project.org/src/contrib/trust_0.1-7.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/trust"
version('0.1-7', '7e218b3a6b33bd77bd7e86dc6360418d')