diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py new file mode 100644 index 0000000000..0fa1caa755 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2018, 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 RRsolnp(RPackage): + """General Non-linear Optimization Using Augmented Lagrange Multiplier + Method.""" + + homepage = "https://cran.r-project.org/package=Rsolnp" + url = "https://cran.rstudio.com/src/contrib/Rsolnp_1.16.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/Rsolnp" + + version('1.16', '507e1e1a64f5f1d32b7e4e12ed19599f') + + depends_on('r-truncnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py new file mode 100644 index 0000000000..bcc7e4716e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spem/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2018, 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 RSpem(RPackage): + """This package can optimize the parameter in S-system models given time + series data""" + + homepage = "https://bioconductor.org/packages/SPEM/" + url = "https://git.bioconductor.org/packages/SPEM" + + version('1.18.0', git='https://git.bioconductor.org/packages/SPEM', + commit='3ab425dd9889885eac328d26b73366a875cd250b') + + depends_on('r-rsolnp', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r@3.4.3:3.4.9', when='@1.18.0') diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py new file mode 100644 index 0000000000..579ee65130 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py @@ -0,0 +1,36 @@ +############################################################################## +# Copyright (c) 2013-2018, 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 RTruncnorm(RPackage): + """Density, probability, quantile and random number generation functions + for the truncated normal distribution.""" + + homepage = "https://cran.r-project.org/package=truncnorm" + url = "https://cran.rstudio.com/src/contrib/truncnorm_1.0-8.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/truncnorm" + + version('1.0-8', 'c60cd6555be0dd2ea91e61757439282d')