diff options
66 files changed, 1584 insertions, 137 deletions
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index 2c440096d1..da74ceb2f6 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -96,8 +96,7 @@ class ${class_name}(Package): ${versions} - # FIXME: Add additional dependencies if required. - ${dependencies} +${dependencies} def install(self, spec, prefix): ${install} @@ -105,13 +104,39 @@ ${install} # Build dependencies and extensions dependencies_dict = { - 'autotools': "# depends_on('foo')", - 'cmake': "depends_on('cmake')", - 'scons': "depends_on('scons')", - 'python': "extends('python')", - 'R': "extends('R')", - 'octave': "extends('octave')", - 'unknown': "# depends_on('foo')" + 'autotools': """\ + # FIXME: Add dependencies if required. + # depends_on('foo')""", + + 'cmake': """\ + # FIXME: Add additional dependencies if required. + depends_on('cmake', type='build')""", + + 'scons': """\ + # FIXME: Add additional dependencies if required. + depends_on('scons', type='build')""", + + 'python': """\ + extends('python') + + # FIXME: Add additional dependencies if required. + # depends_on('py-foo', type=nolink)""", + + 'R': """\ + extends('R') + + # FIXME: Add additional dependencies if required. + # depends_on('r-foo', type=nolink)""", + + 'octave': """\ + extends('octave') + + # FIXME: Add additional dependencies if required. + # depends_on('octave-foo', type=nolink)""", + + 'unknown': """\ + # FIXME: Add dependencies if required. + # depends_on('foo')""" } # Default installation instructions diff --git a/share/spack/csh/convert-pyext.sh b/share/spack/csh/convert-pyext.sh new file mode 100644 index 0000000000..a48bcdbcca --- /dev/null +++ b/share/spack/csh/convert-pyext.sh @@ -0,0 +1,5 @@ +#!/bin/bash --noprofile +PYEXT_REGEX=".*/.*/package.py" + +find var/spack/repos/builtin/packages/ -type f -regextype sed -regex ${PYEXT_REGEX} -exec \ + sed -i 's/python('\''setup.py'\'', /setup_py(/' {} \; diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 68032cb68d..08d5e5d552 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -24,8 +24,11 @@ ############################################################################## from spack import * + class PySetuptools(Package): - """Easily download, build, install, upgrade, and uninstall Python packages.""" + """A Python utility that aids in the process of downloading, building, + upgrading, installing, and uninstalling Python packages.""" + homepage = "https://pypi.python.org/pypi/setuptools" url = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz" @@ -40,4 +43,4 @@ class PySetuptools(Package): extends('python') def install(self, spec, prefix): - python('setup.py', 'install', '--prefix=%s' % prefix) + setup_py('install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index bbb1e9c13a..f755527607 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -27,6 +27,7 @@ import re from contextlib import closing import spack +import llnl.util.tty as tty from llnl.util.lang import match_predicate from spack import * from spack.util.environment import * @@ -72,40 +73,41 @@ class Python(Package): depends_on("tk", when="+tk") depends_on("tcl", when="+tk") + @when('@2.7,3.4:') + def patch(self): + # NOTE: Python's default installation procedure makes it possible for a + # user's local configurations to change the Spack installation. In + # order to prevent this behavior for a full installation, we must + # modify the installation script so that it ignores user files. + ff = FileFilter('Makefile.pre.in') + ff.filter( + r'^(.*)setup\.py(.*)((build)|(install))(.*)$', + r'\1setup.py\2 --no-user-cfg \3\6' + ) + def install(self, spec, prefix): + # TODO: The '--no-user-cfg' option for Python installation is only in + # Python v2.7 and v3.4+ (see https://bugs.python.org/issue1180) and + # adding support for ignoring user configuration will require + # significant changes to this package for other Python versions. + if not spec.satisfies('@2.7,3.4:'): + tty.warn(('Python v{0} may not install properly if Python ' + 'user configurations are present.').format(self.version)) + # Need this to allow python build to find the Python installation. - env['PYTHONHOME'] = prefix + env['PYTHONHOME'], env['PYTHONPATH'] = prefix, prefix env['MACOSX_DEPLOYMENT_TARGET'] = '10.6' # Rest of install is pretty standard except setup.py needs to # be able to read the CPPFLAGS and LDFLAGS as it scans for the # library and headers to build - include_dirs = [ - spec['openssl'].prefix.include, spec['bzip2'].prefix.include, - spec['readline'].prefix.include, spec['ncurses'].prefix.include, - spec['sqlite'].prefix.include, spec['zlib'].prefix.include - ] - - library_dirs = [ - spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib, - spec['readline'].prefix.lib, spec['ncurses'].prefix.lib, - spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib - ] - - if '+tk' in spec: - include_dirs.extend([ - spec['tk'].prefix.include, spec['tcl'].prefix.include - ]) - library_dirs.extend([ - spec['tk'].prefix.lib, spec['tcl'].prefix.lib - ]) - + dep_pfxs = [dspec.prefix for dspec in spec.dependencies('link')] config_args = [ - "--prefix={0}".format(prefix), - "--with-threads", - "--enable-shared", - "CPPFLAGS=-I{0}".format(" -I".join(include_dirs)), - "LDFLAGS=-L{0}".format(" -L".join(library_dirs)) + '--prefix={0}'.format(prefix), + '--with-threads', + '--enable-shared', + 'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)), + 'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)), ] if '+ucs4' in spec: @@ -121,9 +123,8 @@ class Python(Package): config_args.append('--without-ensurepip') configure(*config_args) - make() - make("install") + make('install') self.filter_compilers(spec, prefix) @@ -193,6 +194,8 @@ class Python(Package): def setup_dependent_environment(self, spack_env, run_env, extension_spec): """Set PYTHONPATH to include site-packages dir for the extension and any other python extensions it depends on.""" + pythonhome = self.prefix + spack_env.set('PYTHONHOME', pythonhome) python_paths = [] for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): @@ -214,15 +217,14 @@ class Python(Package): In most cases, extensions will only need to have one line:: - python('setup.py', 'install', '--prefix={0}'.format(prefix))""" + setup_py('install', '--prefix={0}'.format(prefix))""" + python_path = join_path( + self.spec.prefix.bin, + 'python{0}'.format('3' if self.spec.satisfies('@3') else '') + ) - # Python extension builds can have a global python executable function - if Version("3.0.0") <= self.version < Version("4.0.0"): - module.python = Executable(join_path(self.spec.prefix.bin, - 'python3')) - else: - module.python = Executable(join_path(self.spec.prefix.bin, - 'python')) + module.python = Executable(python_path) + module.setup_py = Executable(python_path + ' setup.py --no-user-cfg') # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. module.python_lib_dir = join_path(ext_spec.prefix, diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py new file mode 100644 index 0000000000..4c5d14a90f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 RBase64enc(Package): + """This package provides tools for handling base64 encoding. It is more + flexible than the orphaned base64 package.""" + + homepage = "http://www.rforge.net/base64enc" + url = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc" + + version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py new file mode 100644 index 0000000000..0fdf2ce5de --- /dev/null +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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 RCluster(Package): + """Methods for Cluster analysis. Much extended the original from Peter + Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw + (1990) "Finding Groups in Data".""" + + homepage = "https://cran.r-project.org/web/packages/cluster/index.html" + url = "https://cran.r-project.org/src/contrib/cluster_2.0.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/cluster" + + version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py new file mode 100644 index 0000000000..bea2f78c82 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 RCodetools(Package): + """Code analysis tools for R.""" + + homepage = "https://cran.r-project.org/web/packages/codetools/index.html" + url = "https://cran.r-project.org/src/contrib/codetools_0.2-14.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/codetools" + + version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 5f0b7b8779..75506dd257 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -36,14 +36,14 @@ class RDevtools(Package): extends('R') - depends_on('r-httr') - depends_on('r-memoise') - depends_on('r-whisker') - depends_on('r-digest') - depends_on('r-rstudioapi') - depends_on('r-jsonlite') - depends_on('r-git2r') - depends_on('r-withr') + depends_on('r-httr', type=nolink) + depends_on('r-memoise', type=nolink) + depends_on('r-whisker', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-rstudioapi', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-git2r', type=nolink) + depends_on('r-withr', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py new file mode 100644 index 0000000000..7ff3b8548b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -0,0 +1,49 @@ +############################################################################## +# 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 RDiagrammer(Package): + """Create graph diagrams and flowcharts using R.""" + + homepage = "https://github.com/rich-iannone/DiagrammeR" + url = "https://cran.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/DiagrammeR" + + version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-igraph', type=nolink) + depends_on('r-influencer', type=nolink) + depends_on('r-rstudioapi@0.6:', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-visnetwork', type=nolink) + depends_on('r-scales', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py new file mode 100644 index 0000000000..7cebfd9e58 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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 RDoparallel(Package): + """Provides a parallel backend for the %dopar% function using the parallel + package.""" + + homepage = "https://cran.r-project.org/web/packages/doParallel/index.html" + url = "https://cran.r-project.org/src/contrib/doParallel_1.0.10.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/doParallel" + + version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43') + + extends('R') + + depends_on('r-foreach', type=nolink) + depends_on('r-iterators', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index b065e0b817..ded7651278 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -36,14 +36,15 @@ class RDplyr(Package): version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef') extends('R') - depends_on('r-assertthat') - depends_on('r-R6') - depends_on('r-rcpp') - depends_on('r-tibble') - depends_on('r-magrittr') - depends_on('r-lazyeval') - depends_on('r-dbi') - depends_on('r-bh') + + depends_on('r-assertthat', type=nolink) + depends_on('r-R6', type=nolink) + depends_on('r-rcpp', type=nolink) + depends_on('r-tibble', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-dbi', type=nolink) + depends_on('r-bh', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py new file mode 100644 index 0000000000..f134ee8913 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RDt(Package): + """Data objects in R can be rendered as HTML tables using the JavaScript + library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' + library has been included in this R package. The package name 'DT' is an + abbreviation of 'DataTables'.""" + + homepage = "http://rstudio.github.io/DT" + url = "https://cran.r-project.org/src/contrib/DT_0.1.tar.gz" + + version('0.1', '5c8df984921fa484784ec4b8a4fb6f3c') + + extends('R') + + depends_on('r-htmltools', type=nolink) + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-magrittr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py new file mode 100644 index 0000000000..9b01d7aa18 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RDygraphs(Package): + """An R interface to the 'dygraphs' JavaScript charting library (a copy of + which is included in the package). Provides rich facilities for charting + time-series data in R, including highly configurable series- and + axis-display and interactive features like zoom/pan and series/point + highlighting.""" + + homepage = "https://cran.r-project.org/web/packages/dygraphs/index.html" + url = "https://cran.r-project.org/src/contrib/dygraphs_0.9.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/dygraphs" + + version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833') + + extends('R') + + depends_on('r-magrittr', type=nolink) + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-zoo', type=nolink) + depends_on('r-xts', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py new file mode 100644 index 0000000000..2a7324ae99 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RForeach(Package): + """Support for the foreach looping construct. Foreach is an idiom that + allows for iterating over elements in a collection, without the use of an + explicit loop counter. This package in particular is intended to be used + for its return value, rather than for its side effects. In that sense, it + is similar to the standard lapply function, but doesn't require the + evaluation of a function. Using foreach without side effects also + facilitates executing the loop in parallel.""" + + homepage = "https://cran.r-project.org/web/packages/foreach/index.html" + url = "https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/foreach" + + version('1.4.3', 'ef45768126661b259f9b8994462c49a0') + + extends('R') + + depends_on('r-codetools', type=nolink) + depends_on('r-iterators', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index 2d1f53af26..a8cf21930f 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -42,12 +42,12 @@ class RGgplot2(Package): extends('R') - depends_on('r-digest') - depends_on('r-gtable') - depends_on('r-mass') - depends_on('r-plyr') - depends_on('r-reshape2') - depends_on('r-scales') + depends_on('r-digest', type=nolink) + depends_on('r-gtable', type=nolink) + depends_on('r-mass', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-reshape2', type=nolink) + depends_on('r-scales', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 8fc1f397c8..29b2069ae9 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -38,13 +38,13 @@ class RGgvis(Package): extends('R') - depends_on('r-assertthat') - depends_on('r-jsonlite') - depends_on('r-shiny') - depends_on('r-magrittr') - depends_on('r-dplyr') - depends_on('r-lazyeval') - depends_on('r-htmltools') + depends_on('r-assertthat', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-shiny', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-dplyr', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-htmltools', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py new file mode 100644 index 0000000000..bcb7caa0fb --- /dev/null +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RGooglevis(Package): + """R interface to Google Charts API, allowing users to create interactive + charts based on data frames. Charts are displayed locally via the R HTTP + help server. A modern browser with an Internet connection is required and + for some charts a Flash player. The data remains local and is not uploaded + to Google.""" + + homepage = "https://github.com/mages/googleVis#googlevis" + url = "https://cran.r-project.org/src/contrib/googleVis_0.6.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/googleVis" + + version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468') + + extends('R') + + depends_on('r-jsonlite', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py new file mode 100644 index 0000000000..a2f55b4470 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 RGridbase(Package): + """Integration of base and grid graphics.""" + + homepage = "https://cran.r-project.org/web/packages/gridBase/index.html" + url = "https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gridBase" + + version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index d215d10678..537426d42f 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -37,7 +37,7 @@ class RGridextra(Package): extends('R') - depends_on('r-gtable') + depends_on('r-gtable', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 0aea564372..21cdbe9184 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -36,8 +36,8 @@ class RHtmltools(Package): extends('R') - depends_on('r-digest') - depends_on('r-rcpp') + depends_on('r-digest', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py new file mode 100644 index 0000000000..8090776f06 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RHtmlwidgets(Package): + """A framework for creating HTML widgets that render in various contexts + including the R console, 'R Markdown' documents, and 'Shiny' web + applications.""" + + homepage = "https://github.com/ramnathv/htmlwidgets" + url = "https://cran.r-project.org/src/contrib/htmlwidgets_0.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/htmlwidgets" + + version('0.6', '7fa522d2eda97593978021bda9670c0e') + + extends('R') + + depends_on('r-htmltools', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-yaml', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index 6ab12bcf9d..57025d3a3c 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -42,7 +42,7 @@ class RHttpuv(Package): extends('R') - depends_on('r-rcpp') + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index 77ec34ab03..227594fc0d 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -38,11 +38,11 @@ class RHttr(Package): extends('R') - depends_on('r-jsonlite') - depends_on('r-mime') - depends_on('r-curl') - depends_on('r-openssl') - depends_on('r-R6') + depends_on('r-jsonlite', type=nolink) + depends_on('r-mime', type=nolink) + depends_on('r-curl', type=nolink) + depends_on('r-openssl', type=nolink) + depends_on('r-R6', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py new file mode 100644 index 0000000000..37925d4e02 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RIgraph(Package): + """Routines for simple graphs and network analysis. It can handle large + graphs very well and provides functions for generating random and regular + graphs, graph visualization, centrality methods and much more.""" + + homepage = "http://igraph.org/" + url = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/igraph" + + version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065') + + extends('R') + + depends_on('r-matrix', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-nmf', type=nolink) + depends_on('r-irlba', type=nolink) + depends_on('gmp') + depends_on('libxml2') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py new file mode 100644 index 0000000000..dd525daf2b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RInfluencer(Package): + """Provides functionality to compute various node centrality measures on + networks. Included are functions to compute betweenness centrality (by + utilizing Madduri and Bader's SNAP library), implementations of Burt's + constraint and effective network size (ENS) metrics, Borgatti's algorithm + to identify key players, and Valente's bridging metric. On Unix systems, + the betweenness, Key Players, and bridging implementations are parallelized + with OpenMP, which may run faster on systems which have OpenMP + configured.""" + + homepage = "https://github.com/rcc-uchicago/influenceR" + url = "https://cran.r-project.org/src/contrib/influenceR_0.1.0.tar.gz" + + version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5') + + extends('R') + + depends_on('r-igraph', type=nolink) + depends_on('r-matrix', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py new file mode 100644 index 0000000000..42cc142e8a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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 RIrlba(Package): + """Fast and memory efficient methods for truncated singular and eigenvalue + decompositions and principal component analysis of large sparse or dense + matrices.""" + + homepage = "https://cran.r-project.org/web/packages/irlba/index.html" + url = "https://cran.r-project.org/src/contrib/irlba_2.0.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/irlba" + + version('2.0.0', '557674cf8b68fea5b9f231058c324d26') + + extends('R') + + depends_on('r-matrix', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py new file mode 100644 index 0000000000..f5a3489e7d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 RIterators(Package): + """Support for iterators, which allow a programmer to traverse through all + the elements of a vector, list, or other collection of data.""" + + homepage = "https://cran.r-project.org/web/packages/iterators/index.html" + url = "https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/iterators" + + version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py new file mode 100644 index 0000000000..2a91100c34 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -0,0 +1,54 @@ +############################################################################## +# 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 RLeaflet(Package): + """Create and customize interactive maps using the 'Leaflet' JavaScript + library and the 'htmlwidgets' package. These maps can be used directly from + the R console, from 'RStudio', in Shiny apps and R Markdown documents.""" + + homepage = "http://rstudio.github.io/leaflet/" + url = "https://cran.r-project.org/src/contrib/leaflet_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/leaflet" + + version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df') + + extends('R') + + depends_on('r-base64enc', type=nolink) + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-htmltools', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-markdown', type=nolink) + depends_on('r-png', type=nolink) + depends_on('r-rcolorbrewer', type=nolink) + depends_on('r-raster', type=nolink) + depends_on('r-scales', type=nolink) + depends_on('r-sp', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 88576911f0..2e5661fa4d 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -40,7 +40,8 @@ class RLubridate(Package): version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') extends('R') - depends_on('r-stringr') + + depends_on('r-stringr', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index f6ba97740b..2b8f95351a 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -39,7 +39,7 @@ class RMagic(Package): extends('R') - depends_on('r-abind') + depends_on('r-abind', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py new file mode 100644 index 0000000000..c34727d2b0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RMarkdown(Package): + """Provides R bindings to the 'Sundown' 'Markdown' rendering library + (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting + syntax that can be converted to 'XHTML' or other formats. See + http://en.wikipedia.org/wiki/Markdown for more information about + 'Markdown'.""" + + homepage = "https://github.com/rstudio/markdown" + url = "https://cran.r-project.org/src/contrib/markdown_0.7.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/markdown" + + version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff') + + extends('R') + + depends_on('r-mime', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index fbd8a7b4df..1b45dc55ca 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -37,7 +37,7 @@ class RMatrix(Package): extends('R') - depends_on('r-lattice') + depends_on('r-lattice', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index 6a0fb78650..81f3ff1dab 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -37,7 +37,7 @@ class RMemoise(Package): extends('R') - depends_on('r-digest') + depends_on('r-digest', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index 3216c95e00..b96b90f9c7 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -40,7 +40,7 @@ class RMunsell(Package): extends('R') - depends_on('r-colorspace') + depends_on('r-colorspace', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py new file mode 100644 index 0000000000..8884f7cf1b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-networkd3/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 RNetworkd3(Package): + """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs + from 'R'.""" + + homepage = "http://cran.r-project.org/package=networkD3" + url = "https://cran.r-project.org/src/contrib/networkD3_0.2.12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/networkD3" + + version('0.2.12', '356fe4be59698e6fb052644bd9659d84') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-igraph', type=nolink) + depends_on('r-magrittr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py new file mode 100644 index 0000000000..c30a1ac101 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -0,0 +1,60 @@ +############################################################################## +# 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 RNmf(Package): + """Provides a framework to perform Non-negative Matrix Factorization (NMF). + The package implements a set of already published algorithms and seeding + methods, and provides a framework to test, develop and plug new/custom + algorithms. Most of the built-in algorithms have been optimized in C++, and + the main interface function provides an easy way of performing parallel + computations on multicore machines..""" + + homepage = "http://renozao.github.io/NMF" + url = "https://cran.r-project.org/src/contrib/NMF_0.20.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/NMF" + + version('0.20.6', '81df07b3bf710a611db5af24730ff3d0') + + extends('R') + + depends_on('r-pkgmaker', type=nolink) + depends_on('r-registry', type=nolink) + depends_on('r-rngtools', type=nolink) + depends_on('r-cluster', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-gridbase', type=nolink) + depends_on('r-colorspace', type=nolink) + depends_on('r-rcolorbrewer', type=nolink) + depends_on('r-foreach', type=nolink) + depends_on('r-doparallel', type=nolink) + depends_on('r-ggplot2', type=nolink) + depends_on('r-reshape2', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py new file mode 100644 index 0000000000..87daec5ad0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -0,0 +1,53 @@ +############################################################################## +# 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 RPkgmaker(Package): + """This package provides some low-level utilities to use for package + development. It currently provides managers for multiple package specific + options and registries, vignette, unit test and bibtex related utilities. + It serves as a base package for packages like NMF, RcppOctave, doRNG, and + as an incubator package for other general purposes utilities, that will + eventually be packaged separately. It is still under heavy development and + changes in the interface(s) are more than likely to happen.""" + + homepage = "https://renozao.github.io/pkgmaker" + url = "https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/pkgmaker" + + version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4') + + extends('R') + + depends_on('r-registry', type=nolink) + depends_on('r-codetools', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-xtable', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index 192e7e8b18..fe4512347a 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -42,7 +42,7 @@ class RPlyr(Package): extends('R') - depends_on('r-rcpp') + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py new file mode 100644 index 0000000000..d3a80a4e16 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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 RPng(Package): + """This package provides an easy and simple way to read, write and display + bitmap images stored in the PNG format. It can read and write both files + and in-memory raw vectors.""" + + homepage = "http://www.rforge.net/png/" + url = "https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/png" + + version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f') + + extends('R') + + depends_on('libpng') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py new file mode 100644 index 0000000000..39f4256703 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-raster/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 RRaster(Package): + """Reading, writing, manipulating, analyzing and modeling of gridded + spatial data. The package implements basic and high-level functions. + Processing of very large files is supported.""" + + homepage = "http://cran.r-project.org/package=raster" + url = "https://cran.r-project.org/src/contrib/raster_2.5-8.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/raster" + + version('2.5-8', '2a7db931c74d50516e82d04687c0a577') + + extends('R') + + depends_on('r-sp', type=nolink) + depends_on('r-rcpp', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index 3175628a73..ecf9256ab3 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -48,8 +48,8 @@ class RRcppeigen(Package): extends('R') - depends_on('r-matrix') - depends_on('r-rcpp') + depends_on('r-matrix', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py new file mode 100644 index 0000000000..119a84718a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 RRegistry(Package): + """Provides a generic infrastructure for creating and using registries.""" + + homepage = "https://cran.r-project.org/web/packages/registry/index.html" + url = "https://cran.r-project.org/src/contrib/registry_0.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/registry" + + version('0.3', '85345b334ec81eb3da6edcbb27c5f421') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index a96a314008..769e82aff9 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -37,9 +37,9 @@ class RReshape2(Package): extends('R') - depends_on('r-plyr') - depends_on('r-stringr') - depends_on('r-rcpp') + depends_on('r-plyr', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index 0ce0942602..47804bd7fc 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -37,6 +37,8 @@ class RRjava(Package): extends('R') + depends_on('jdk') + def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 774c166f8b..bc42c51ca9 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -36,7 +36,7 @@ class RRmysql(Package): extends('R') - depends_on('r-DBI') + depends_on('r-dbi', type=nolink) depends_on('mariadb') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py new file mode 100644 index 0000000000..2f33cd9f88 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -0,0 +1,49 @@ +############################################################################## +# 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 RRngtools(Package): + """This package contains a set of functions for working with Random Number + Generators (RNGs). In particular, it defines a generic S4 framework for + getting/setting the current RNG, or RNG data that are embedded into objects + for reproducibility. Notably, convenient default methods greatly facilitate + the way current RNG settings can be changed.""" + + homepage = "https://renozao.github.io/rngtools" + url = "https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rngtools" + + version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') + + extends('R') + + depends_on('r-pkgmaker', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-digest', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index 9cc9aebd9a..11fe0ace56 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -36,7 +36,7 @@ class RRodbc(Package): extends('R') - depends_on('unixODBC') + depends_on('unixodbc') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 83c9b85525..999fb4a1b9 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -44,7 +44,7 @@ class RRpostgresql(Package): extends('R') - depends_on('r-DBI') + depends_on('r-dbi', type=nolink) depends_on('postgresql') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index 9602f6d927..c7d41f0fb3 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -38,7 +38,7 @@ class RRsqlite(Package): extends('R') - depends_on('r-DBI') + depends_on('r-dbi', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 00fd5116d9..1d0052563b 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -44,13 +44,13 @@ class RRstan(Package): extends('R') - depends_on('r-ggplot2') - depends_on('r-stanheaders') - depends_on('r-inline') - depends_on('r-gridextra') - depends_on('r-rcpp') - depends_on('r-rcppeigen') - depends_on('r-bh') + depends_on('r-ggplot2', type=nolink) + depends_on('r-stanheaders', type=nolink) + depends_on('r-inline', type=nolink) + depends_on('r-gridextra', type=nolink) + depends_on('r-rcpp', type=nolink) + depends_on('r-rcppeigen', type=nolink) + depends_on('r-bh', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index 0ef2d9b987..bf9b35fe5b 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -33,6 +33,7 @@ class RRstudioapi(Package): url = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi" + version('0.6', 'fdb13bf46aab02421557e713fceab66b') version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') extends('R') diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index 046a05d48e..44bd5a5a2a 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -37,12 +37,12 @@ class RScales(Package): extends('R') - depends_on('r-rcolorbrewer') - depends_on('r-dichromat') - depends_on('r-plyr') - depends_on('r-munsell') - depends_on('r-labeling') - depends_on('r-rcpp') + depends_on('r-rcolorbrewer', type=nolink) + depends_on('r-dichromat', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-munsell', type=nolink) + depends_on('r-labeling', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index a9a9532910..a80860f4a5 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -39,13 +39,13 @@ class RShiny(Package): extends('R') - depends_on('r-httpuv') - depends_on('r-mime') - depends_on('r-jsonlite') - depends_on('r-xtable') - depends_on('r-digest') - depends_on('r-htmltools') - depends_on('r-R6') + depends_on('r-httpuv', type=nolink) + depends_on('r-mime', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-xtable', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-htmltools', type=nolink) + depends_on('r-R6', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py new file mode 100644 index 0000000000..bb7589d490 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sp/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 RSp(Package): + """Classes and methods for spatial data; the classes document where the + spatial location information resides, for 2D or 3D data. Utility functions + are provided, e.g. for plotting data as maps, spatial selection, as well as + methods for retrieving coordinates, for subsetting, print, summary, etc.""" + + homepage = "https://github.com/edzer/sp/" + url = "https://cran.r-project.org/src/contrib/sp_1.2-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/sp" + + version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1') + + extends('R') + + depends_on('r-lattice', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index 01fd969522..08ded95833 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -40,8 +40,8 @@ class RStringr(Package): extends('R') - depends_on('r-stringi') - depends_on('r-magrittr') + depends_on('r-stringi', type=nolink) + depends_on('r-magrittr', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py new file mode 100644 index 0000000000..89ecce8bfc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RThreejs(Package): + """Create interactive 3D scatter plots, network plots, and globes using the + 'three.js' visualization library ("http://threejs.org").""" + + homepage = "http://bwlewis.github.io/rthreejs" + url = "https://cran.r-project.org/src/contrib/threejs_0.2.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/threejs" + + version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-base64enc', type=nolink) + depends_on('r-matrix', type=nolink) + depends_on('r-jsonlite', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 837c3df603..c601de3c88 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -37,9 +37,9 @@ class RTibble(Package): extends('R') - depends_on('r-assertthat') - depends_on('r-lazyeval') - depends_on('r-rcpp') + depends_on('r-assertthat', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index 2db7b174c2..d82ae278fe 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -37,12 +37,12 @@ class RTidyr(Package): version('0.5.1', '3cadc869510c054ed93d374ab44120bd') extends('R') - depends_on('r-tibble') - depends_on('r-dplyr') - depends_on('r-stringi') - depends_on('r-lazyeval') - depends_on('r-magrittr') - depends_on('r-rcpp') + depends_on('r-tibble', type=nolink) + depends_on('r-dplyr', type=nolink) + depends_on('r-stringi', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py new file mode 100644 index 0000000000..90d55bbb2f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RVisnetwork(Package): + """Provides an R interface to the 'vis.js' JavaScript charting library. It + allows an interactive visualization of networks.""" + + homepage = "https://github.com/datastorm-open/visNetwork" + url = "https://cran.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/visNetwork" + + version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-htmltools', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-magrittr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 919291a023..332c80fb92 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -33,12 +33,13 @@ class RXlconnect(Package): url = "https://cran.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnect" + version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') version('0.2-11', '9d1769a103cda05665df399cc335017d') extends('R') - depends_on('r-XLConnectJars') - depends_on('r-rJava') + depends_on('r-xlconnectjars', type=nolink) + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index 15d08cc5af..26e822d2b7 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -32,11 +32,12 @@ class RXlconnectjars(Package): url = "https://cran.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnectJars" + version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') extends('R') - depends_on('r-rJava') + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index 0aac6cdd1f..6fed09296d 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -37,8 +37,8 @@ class RXlsx(Package): extends('R') - depends_on('r-rJava') - depends_on('r-xlsxjars') + depends_on('r-rjava', type=nolink) + depends_on('r-xlsxjars', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index cff6e7427e..19f0006ce9 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -37,7 +37,7 @@ class RXlsxjars(Package): extends('R') - depends_on('r-rJava') + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py new file mode 100644 index 0000000000..d8a4b62d27 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xts/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 RXts(Package): + """Provide for uniform handling of R's different time-based data classes by + extending zoo, maximizing native format information preservation and + allowing for user level customization and extension, while simplifying + cross-class interoperability.""" + + homepage = "http://r-forge.r-project.org/projects/xts/" + url = "https://cran.r-project.org/src/contrib/xts_0.9-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/xts" + + version('0.9-7', 'a232e94aebfa654653a7d88a0503537b') + + extends('R') + + depends_on('r-zoo', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py new file mode 100644 index 0000000000..b68f26e9b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 RYaml(Package): + """This package implements the libyaml YAML 1.1 parser and emitter + (http://pyyaml.org/wiki/LibYAML) for R.""" + + homepage = "https://cran.r-project.org/web/packages/yaml/index.html" + url = "https://cran.r-project.org/src/contrib/yaml_2.1.13.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/yaml" + + version('2.1.13', 'f2203ea395adaff6bd09134666191d9a') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py new file mode 100644 index 0000000000..d889cacbee --- /dev/null +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RZoo(Package): + """An S3 class with methods for totally ordered indexed observations. It is + particularly aimed at irregular time series of numeric vectors/matrices and + factors. zoo's key design goals are independence of a particular + index/date/time class and consistency with ts and base R by providing + methods to extend standard generics.""" + + homepage = "http://zoo.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/zoo_1.7-13.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/zoo" + + version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') + + extends('R') + + depends_on('r-lattice', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) |