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New package r-phangorn and its dependencies (#7034)

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This commit is contained in:
Yifan Zhu 2018-03-08 01:30:02 -06:00 committed by Massimiliano Culpo
parent 98808196cb
commit 66c46ae655
4 changed files with 90 additions and 1 deletions
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4
var/spack/repos/builtin/packages/r-ape/package.py
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@ -46,6 +46,10 @@ class RApe(RPackage):
url = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
version('5.0', '82fd2786a502f070ca020797f7b19fa4')
version('4.1', 'a9ed416d6d172d4b9682556cf692d7c2')
depends_on('r@3.2:')
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))

38
var/spack/repos/builtin/packages/r-fastmatch/package.py Normal file
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@ -0,0 +1,38 @@
##############################################################################
# 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/spack/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 RFastmatch(RPackage):
"""Package providing a fast match() replacement for cases that require
repeated look-ups. It is slightly faster that R's built-in match()
function on first match against a table, but extremely fast on any
subsequent lookup as it keeps the hash table in memory."""
homepage = "http://www.rforge.net/fastmatch"
url = "https://cran.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/fastmatch"
version('1.1-0', '900c2363c15059ac9d63c4c71ea2d6b2')

3
var/spack/repos/builtin/packages/r-igraph/package.py
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@ -34,11 +34,12 @@ class RIgraph(RPackage):
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('1.1.2', 'ca1617aea272852d2856c4661ad1c7d8')
version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065')
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-nmf', type=('build', 'run'))
depends_on('r-pkgconfig', type=('build', 'run'))
depends_on('r-irlba', type=('build', 'run'))
depends_on('gmp')
depends_on('libxml2')

46
var/spack/repos/builtin/packages/r-phangorn/package.py Normal file
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@ -0,0 +1,46 @@
##############################################################################
# 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/spack/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 RPhangorn(RPackage):
"""Package contains methods for estimation of phylogenetic trees and
networks using Maximum Likelihood, Maximum Parsimony, distance methods
and Hadamard conjugation. Allows to compare trees, models selection and
offers visualizations for trees and split networks."""
homepage = "http://www.example.co://github.com/KlausVigo/phangorn"
url = "https://cran.r-project.org/src/contrib/phangorn_2.3.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/phangorn"
version('2.3.1', '85e7309900d061432508ab6f7e3e627e')
depends_on('r-ape@5.0:', type=('build', 'run'))
depends_on('r-quadprog', type=('build', 'run'))
depends_on('r-igraph@1.0:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-fastmatch', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-rcpp@0.12.0:', type=('build', 'run'))