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authorYifan Zhu <ifanzhu@foxmail.com>2018-04-12 12:55:10 -0500
committerAdam J. Stewart <ajstewart426@gmail.com>2018-04-12 12:55:10 -0500
commit8a4268837e1475c5986a119ce66a8ffa8a9ae5d2 (patch)
tree9129fa174bc0ec5651f1674e832ba9d0ddb05d67
parent61875784df490bd7ed3acb1dfc82c7725a04f227 (diff)
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New package r-spem (#7657)
* r-truncnorm: new package added * r-solnp: new package added * r-spem: new package added * r-truncnorm: removed dependency r-testthat
-rw-r--r--var/spack/repos/builtin/packages/r-rsolnp/package.py38
-rw-r--r--var/spack/repos/builtin/packages/r-spem/package.py40
-rw-r--r--var/spack/repos/builtin/packages/r-truncnorm/package.py36
3 files changed, 114 insertions, 0 deletions
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')