From 1469cfd0e7b470704091ac0848bb8aebd1a23ccb Mon Sep 17 00:00:00 2001 From: Tom Merrick Date: Tue, 23 May 2017 10:05:05 -0500 Subject: 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 --- var/spack/repos/builtin/packages/r-coda/package.py | 40 +++++++++++++++++++ .../repos/builtin/packages/r-deoptimr/package.py | 36 +++++++++++++++++ var/spack/repos/builtin/packages/r-ergm/package.py | 46 ++++++++++++++++++++++ .../builtin/packages/r-laplacesdemon/package.py | 37 +++++++++++++++++ .../repos/builtin/packages/r-lpsolve/package.py | 40 +++++++++++++++++++ .../repos/builtin/packages/r-network/package.py | 37 +++++++++++++++++ .../repos/builtin/packages/r-quadprog/package.py | 36 +++++++++++++++++ .../repos/builtin/packages/r-robustbase/package.py | 40 +++++++++++++++++++ .../builtin/packages/r-statnet-common/package.py | 36 +++++++++++++++++ .../repos/builtin/packages/r-trust/package.py | 36 +++++++++++++++++ 10 files changed, 384 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-coda/package.py create mode 100644 var/spack/repos/builtin/packages/r-deoptimr/package.py create mode 100644 var/spack/repos/builtin/packages/r-ergm/package.py create mode 100644 var/spack/repos/builtin/packages/r-laplacesdemon/package.py create mode 100644 var/spack/repos/builtin/packages/r-lpsolve/package.py create mode 100644 var/spack/repos/builtin/packages/r-network/package.py create mode 100644 var/spack/repos/builtin/packages/r-quadprog/package.py create mode 100644 var/spack/repos/builtin/packages/r-robustbase/package.py create mode 100644 var/spack/repos/builtin/packages/r-statnet-common/package.py create mode 100644 var/spack/repos/builtin/packages/r-trust/package.py (limited to 'var') 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') -- cgit v1.2.3-60-g2f50