From f8b90d50defb8a8b9bf39a799c7637af57e894c6 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 25 Oct 2017 04:17:37 -0500 Subject: r-geiger and dependencies (#5933) --- .../repos/builtin/packages/r-desolve/package.py | 37 ++++++++++++++++++ .../repos/builtin/packages/r-geiger/package.py | 45 ++++++++++++++++++++++ .../repos/builtin/packages/r-ncbit/package.py | 35 +++++++++++++++++ .../repos/builtin/packages/r-subplex/package.py | 34 ++++++++++++++++ 4 files changed, 151 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-desolve/package.py create mode 100644 var/spack/repos/builtin/packages/r-geiger/package.py create mode 100644 var/spack/repos/builtin/packages/r-ncbit/package.py create mode 100644 var/spack/repos/builtin/packages/r-subplex/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py new file mode 100644 index 0000000000..5603598767 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-desolve/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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') diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py new file mode 100644 index 0000000000..4be8638503 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-geiger/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py new file mode 100644 index 0000000000..8fbdd44214 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ncbit/package.py @@ -0,0 +1,35 @@ +############################################################################## +# 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') diff --git a/var/spack/repos/builtin/packages/r-subplex/package.py b/var/spack/repos/builtin/packages/r-subplex/package.py new file mode 100644 index 0000000000..e4067ab952 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-subplex/package.py @@ -0,0 +1,34 @@ +############################################################################## +# 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') -- cgit v1.2.3-70-g09d2