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r-geiger and dependencies (#5933)

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Audrey Thoma 2017-10-25 04:17:37 -05:00 committed by Todd Gamblin
parent cc51cc0b06
commit f8b90d50de
4 changed files with 151 additions and 0 deletions
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37
var/spack/repos/builtin/packages/r-desolve/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 RDesolve(RPackage):
"""Functions that solve initial value problems of a system of first-order
ordinary differential equations ('ODE'), of partial differential
equations ('PDE'), of differential algebraic equations ('DAE'), and of
delay differential equations."""
homepage = "https://cran.r-project.org/package=deSolve"
url = "https://cran.r-project.org/src/contrib/deSolve_1.20.tar.gz"
version('1.20', '85c6a2d8568944ae8eef27ac7c35fb25')

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var/spack/repos/builtin/packages/r-geiger/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 RGeiger(RPackage):
"""Methods for fitting macroevolutionary models to phylogenetic trees."""
homepage = "https://cran.r-project.org/package=geiger"
url = "https://cran.r-project.org/src/contrib/geiger_2.0.6.tar.gz"
version('2.0.6', 'e5e1a407ea56805227d0f91bf6d95afc')
depends_on('r-ape@3.0:', type=('build', 'run'))
depends_on('r-mvtnorm', type=('build', 'run'))
depends_on('r-subplex', type=('build', 'run'))
depends_on('r-desolve@1.7:', type=('build', 'run'))
depends_on('r-digest', type=('build', 'run'))
depends_on('r-rcpp@0.9.0:', type=('build', 'run'))
depends_on('r-coda', type=('build', 'run'))
depends_on('r-ncbit', type=('build', 'run'))
depends_on('r-colorspace', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-ncbit/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 RNcbit(RPackage):
"""Making NCBI taxonomic data locally available and searchable as an R
object."""
homepage = "https://cran.r-project.org/package=ncbit"
url = "https://cran.r-project.org/src/contrib/ncbit_2013.03.29.tar.gz"
version('2013.03.29', '29582d7e5c8bbf9683c57c4f6ac3e891')

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var/spack/repos/builtin/packages/r-subplex/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 RSubplex(RPackage):
"""Unconstrained Optimization using the Subplex Algorithm"""
homepage = "https://cran.r-project.org/package=subplex"
url = "https://cran.r-project.org/src/contrib/subplex_1.4-1.tar.gz"
version('1.4-1', '2ed963dbbb1dbef47ebec7003f39a117')