Packages/r ergm (#4314)

* Add mpi support to R

* Add multiple precision math routines to R

* Add packages for r-ergm and it's dependents

* Fixed depends-on types

* Correct flake8 errors

10 files changed, 384 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py
new file mode 100644
index 0000000000..08f0f10bb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-coda/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RCoda(RPackage):
+    """Provides functions for summarizing and plotting the output from
+       Markov Chain Monte Carlo (MCMC) simulations, as well as
+       diagnostic tests of convergence to the equilibrium distribution
+       of the Markov chain."""
+
+    homepage = "https://cran.r-project.org/web/packages/coda/index.html"
+    url      = "https://cran.r-project.org/src/contrib/coda_0.19-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/coda"
+
+    version('0.19-1', '0d2aca6a5a3bdae9542708817c1ec001')
+
+    depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py
new file mode 100644
index 0000000000..758b10f9e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RDeoptimr(RPackage):
+    """An implementation of a bespoke jDE variant of the Differential
+       Evolution stochastic algorithm for global optimization of
+       nonlinear programming problems."""
+
+    homepage = "https://cran.r-project.org/web/packages/DEoptimR/index.html"
+    url      = "https://cran.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz"
+
+    version('1.0-8', 'c85836a504fbe4166e3c8eba0efe705d')
diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py
new file mode 100644
index 0000000000..72663cc1f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ergm/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RErgm(RPackage):
+    """An integrated set of tools to analyze and simulate networks based
+       on exponential-family random graph models (ERGM). "ergm" is a
+       part of the "statnet" suite of packages for network analysis."""
+
+    homepage = "http://statnet.org"
+    url      = "https://cran.r-project.org/src/contrib/ergm_3.7.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ergm"
+
+    version('3.7.1', '431ae430c76b2408988f469831d80126')
+
+    depends_on('r-robustbase@0.9-10:', type=('build', 'run'))
+    depends_on('r-coda@0.18-1:', type=('build', 'run'))
+    depends_on('r-trust', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-lpsolve', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-statnet-common@3.3:', type=('build', 'run'))
+    depends_on('r-network@1.13:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
new file mode 100644
index 0000000000..1518b34bea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RLaplacesdemon(RPackage):
+    """Provides a complete environment for Bayesian inference using a variety
+       of different samplers (see ?LaplacesDemon for an overview). The README
+       describes the history of the package development process."""
+
+    homepage = "https://github.com/LaplacesDemonR/LaplacesDemon"
+    url      = "https://cran.r-project.org/src/contrib/LaplacesDemon_16.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/LaplacesDemon"
+
+    version('16.0.1', '1e4dab2dd0e27251734d68b0bfdbe911')
diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py
new file mode 100644
index 0000000000..1ef84eb672
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RLpsolve(RPackage):
+    """Lp_solve is freely available (under LGPL 2) software for solving
+       linear, integer and mixed integer programs. In this
+       implementation we supply a "wrapper" function in C and some R
+       functions that solve general linear/integer problems, assignment
+       problems, and transportation problems. This version calls
+       lp_solve"""
+
+    homepage = "https://cran.r-project.org/web/packages/lpSolve/index.html"
+    url      = "https://cran.r-project.org/src/contrib/lpSolve_5.6.13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lpSolve"
+
+    version('5.6.13', '8471654d9ae76e0f85ff3449433d4bc1')
diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py
new file mode 100644
index 0000000000..9fdc59c02b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-network/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RNetwork(RPackage):
+    """Tools to create and modify network objects. The network class can
+       represent a range of relational data types, and supports
+       arbitrary vertex/edge/graph attributes."""
+
+    homepage = "https://statnet.org"
+    url      = "https://cran.r-project.org/src/contrib/network_1.13.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/network"
+
+    version('1.13.0', 'd0b967d6f1aad43b6479d72f29b705de')
diff --git a/var/spack/repos/builtin/packages/r-quadprog/package.py b/var/spack/repos/builtin/packages/r-quadprog/package.py
new file mode 100644
index 0000000000..84e4624e16
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-quadprog/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RQuadprog(RPackage):
+    """This package contains routines and documentation for solving
+       quadratic programming problems."""
+
+    homepage = "https://cran.r-project.org/web/packages/quadprog/index.html"
+    url      = "https://cran.r-project.org/src/contrib/quadprog_1.5-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/quadprog"
+
+    version('1.5-5', '8442f37afd8d0b19b12e77d63e6515ad')
diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py
new file mode 100644
index 0000000000..1b7db70fbe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-robustbase/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RRobustbase(RPackage):
+    """"Essential" Robust Statistics. Tools allowing to analyze data
+       with robust methods. This includes regression methodology
+       including model selections and multivariate statistics where we
+       strive to cover the book "Robust Statistics, Theory and Methods"
+       by 'Maronna, Martin and Yohai'; Wiley 2006."""
+
+    homepage = "https://robustbase.r-forge.r-project.org"
+    url      = "https://cran.r-project.org/src/contrib/robustbase_0.92-7.tar.gz"
+
+    version('0.92-7', 'db3c8d12f9729b35bad17abf09e80b72')
+
+    depends_on('r-deoptimr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-statnet-common/package.py b/var/spack/repos/builtin/packages/r-statnet-common/package.py
new file mode 100644
index 0000000000..68bf2c4222
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RStatnetCommon(RPackage):
+    """Non-statistical utilities used by the software developed by the
+       Statnet Project. They may also be of use to others."""
+
+    homepage = "http://www.statnet.org"
+    url      = "https://cran.r-project.org/src/contrib/statnet.common_3.3.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/statnet.common"
+
+    version('3.3.0', '36bc11098dcd3652a4beb05c156ad6c8')
diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py
new file mode 100644
index 0000000000..622a0325a7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-trust/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 RTrust(RPackage):
+    """Does local optimization using two derivatives and trust regions.
+       Guaranteed to converge to local minimum of objective function."""
+
+    homepage = "http://www.stat.umn.edu/geyer/trust"
+    url      = "https://cran.r-project.org/src/contrib/trust_0.1-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/trust"
+
+    version('0.1-7', '7e218b3a6b33bd77bd7e86dc6360418d')