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

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')