r-geiger and dependencies (#5933)

4 files changed, 151 insertions, 0 deletions

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')