diff options
Diffstat (limited to 'var')
164 files changed, 5729 insertions, 236 deletions
diff --git a/var/spack/repos/builtin.mock/packages/mpileaks/package.py b/var/spack/repos/builtin.mock/packages/mpileaks/package.py index bc26f539ba..10fbf3845e 100644 --- a/var/spack/repos/builtin.mock/packages/mpileaks/package.py +++ b/var/spack/repos/builtin.mock/packages/mpileaks/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Mpileaks(Package): homepage = "http://www.llnl.gov" url = "http://www.llnl.gov/mpileaks-1.0.tar.gz" @@ -35,6 +36,8 @@ class Mpileaks(Package): variant('debug', default=False, description='Debug variant') variant('opt', default=False, description='Optimized variant') + variant('shared', default=True, description='Build shared library') + variant('static', default=True, description='Build static library') depends_on("mpi") depends_on("callpath") diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index ad06c2ca48..e880a3aa66 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -22,10 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os - from spack import * from spack.util.environment import * +import shutil class R(Package): @@ -74,6 +73,10 @@ class R(Package): depends_on('pcre') depends_on('jdk') + @property + def etcdir(self): + return join_path(prefix, 'rlib', 'R', 'etc') + def install(self, spec, prefix): rlibdir = join_path(prefix, 'rlib') configure_args = ['--prefix=%s' % prefix, @@ -88,6 +91,12 @@ class R(Package): make() make('install') + # Make a copy of Makeconf because it will be needed to properly build R + # dependencies in Spack. + src_makeconf = join_path(self.etcdir, 'Makeconf') + dst_makeconf = join_path(self.etcdir, 'Makeconf.spack') + shutil.copy(src_makeconf, dst_makeconf) + self.filter_compilers(spec, prefix) def filter_compilers(self, spec, prefix): @@ -98,18 +107,16 @@ class R(Package): cc and c++. We want them to be bound to whatever compiler they were built with.""" - etcdir = join_path(prefix, 'rlib', 'R', 'etc') - kwargs = {'ignore_absent': True, 'backup': False, 'string': True} - filter_file(env['CC'], self.compiler.cc, - join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['CC'], self.compiler.cc, + join_path(self.etcdir, 'Makeconf'), **kwargs) filter_file(env['CXX'], self.compiler.cxx, - join_path(etcdir, 'Makeconf'), **kwargs) + join_path(self.etcdir, 'Makeconf'), **kwargs) filter_file(env['F77'], self.compiler.f77, - join_path(etcdir, 'Makeconf'), **kwargs) + join_path(self.etcdir, 'Makeconf'), **kwargs) filter_file(env['FC'], self.compiler.fc, - join_path(etcdir, 'Makeconf'), **kwargs) + join_path(self.etcdir, 'Makeconf'), **kwargs) # ======================================================================== # Set up environment to make install easy for R extensions. @@ -117,7 +124,7 @@ class R(Package): @property def r_lib_dir(self): - return os.path.join('rlib', 'R', 'library') + return join_path('rlib', 'R', 'library') def setup_dependent_environment(self, spack_env, run_env, extension_spec): # Set R_LIBS to include the library dir for the @@ -125,15 +132,21 @@ class R(Package): r_libs_path = [] for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): if d.package.extends(self.spec): - r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir)) + r_libs_path.append(join_path(d.prefix, self.r_lib_dir)) r_libs_path = ':'.join(r_libs_path) spack_env.set('R_LIBS', r_libs_path) + spack_env.set('R_MAKEVARS_SITE', + join_path(self.etcdir, 'Makeconf.spack')) + + # Use the number of make_jobs set in spack. The make program will + # determine how many jobs can actually be started. + spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) # For run time environment set only the path for extension_spec and # prepend it to R_LIBS if extension_spec.package.extends(self.spec): - run_env.prepend_path('R_LIBS', os.path.join( + run_env.prepend_path('R_LIBS', join_path( extension_spec.prefix, self.r_lib_dir)) def setup_environment(self, spack_env, run_env): @@ -147,13 +160,14 @@ class R(Package): def setup_dependent_package(self, module, ext_spec): """Called before R modules' install() methods. In most cases, extensions will only need to have one line: - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % - self.stage.source_path)""" + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path)""" + # R extension builds can have a global R executable function module.R = Executable(join_path(self.spec.prefix.bin, 'R')) # Add variable for library directry - module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir) + module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir) # Make the site packages directory for extensions, if it does not exist # already. diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py new file mode 100644 index 0000000000..70249aebac --- /dev/null +++ b/var/spack/repos/builtin/packages/ack/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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 Ack(Package): + """ack 2.14 is a tool like grep, optimized for programmers. + + Designed for programmers with large heterogeneous trees of + source code, ack is written purely in portable Perl 5 and takes + advantage of the power of Perl's regular expressions.""" + + homepage = "http://beyondgrep.com/" + url = "http://beyondgrep.com/ack-2.14-single-file" + + version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False) + + depends_on('perl') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + ack = 'ack-{0}-single-file'.format(self.version) + + # rewrite the script's #! line to call the perl dependency + shbang = '#!' + join_path(spec['perl'].prefix.bin, 'perl') + filter_file(r'^#!/usr/bin/env perl', shbang, ack) + + install(ack, join_path(prefix.bin, "ack")) + set_executable(join_path(prefix.bin, "ack")) diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index d5dc703c06..2874930cdd 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -86,10 +86,19 @@ class ArpackNg(Package): options.extend(std_cmake_args) options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) - # TODO: - # Arpack calls directly find_package(BLAS REQUIRED) and - # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are - # picked up. + # Make sure we use Spack's blas/lapack: + options.extend([ + '-DLAPACK_FOUND=true', + '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include, + '-DLAPACK_LIBRARIES=%s' % ( + spec['lapack'].lapack_shared_lib if '+shared' in spec else + spec['lapack'].lapack_static_lib), + '-DBLAS_FOUND=true', + '-DBLAS_INCLUDE_DIRS=%s' % spec['blas'].prefix.include, + '-DBLAS_LIBRARIES=%s' % ( + spec['blas'].blas_shared_lib if '+shared' in spec else + spec['blas'].blas_static_lib) + ]) if '+mpi' in spec: options.append('-DMPI=ON') @@ -101,9 +110,8 @@ class ArpackNg(Package): cmake('.', *options) make() - # TODO: make test does not work - # make('test') - + if self.run_tests: + make('test') make('install') @when('@3.3.0') @@ -120,10 +128,23 @@ class ArpackNg(Package): 'F77=%s' % spec['mpi'].mpif77 ]) - if '~shared' in spec: - options.append('--enable-shared=no') + if '+shared' in spec: + options.extend([ + '--with-blas=%s' % to_link_flags( + spec['blas'].blas_shared_lib), + '--with-lapack=%s' % to_link_flags( + spec['lapack'].lapack_shared_lib) + ]) + else: + options.extend([ + '--with-blas=%s' % spec['blas'].blas_static_lib, + '--with-lapack=%s' % spec['lapack'].lapack_static_lib, + '--enable-shared=no' + ]) bootstrap() configure(*options) make() + if self.run_tests: + make('check') make('install') diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index c43d92c34f..f9d5da6166 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -23,20 +23,24 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +from spack.package_test import * from spack.util.executable import Executable import os.path + class Atlas(Package): - """ - Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and - optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear - algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines - in the LAPACK library. + """Automatically Tuned Linear Algebra Software, generic shared ATLAS is an + approach for the automatic generation and optimization of numerical + software. Currently ATLAS supplies optimized versions for the complete set + of linear algebra kernels known as the Basic Linear Algebra Subroutines + (BLAS), and a subset of the linear algebra routines in the LAPACK library. """ homepage = "http://math-atlas.sourceforge.net/" version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', - url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + url='https://sourceforge.net/projects/math-atlas/files/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + # not all packages (e.g. Trilinos@12.6.3) stopped using deprecated in 3.6.0 + # Lapack routines. Stick with 3.5.0 until this is fixed. resource(name='lapack', url='http://www.netlib.org/lapack/lapack-3.5.0.tgz', md5='b1d3e3e425b2e44a06760ff173104bdf', @@ -44,7 +48,7 @@ class Atlas(Package): when='@3:') version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', - url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') + url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2') variant('shared', default=True, description='Builds shared library') @@ -66,9 +70,24 @@ class Atlas(Package): options = [] if '+shared' in spec: - options.append('--shared') + options.extend([ + '--shared' + ]) + # TODO: for non GNU add '-Fa', 'alg', '-fPIC' ? + + # configure for 64-bit build + options.extend([ + '-b', '64' + ]) - # Lapack resource + # set compilers: + options.extend([ + '-C', 'ic', spack_cc, + '-C', 'if', spack_f77 + ]) + + # Lapack resource to provide full lapack build. Note that + # ATLAS only provides a few LAPACK routines natively. lapack_stage = self.stage[1] lapack_tarfile = os.path.basename(lapack_stage.fetcher.url) lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile) @@ -81,4 +100,35 @@ class Atlas(Package): make('check') make('ptcheck') make('time') + if '+shared' in spec: + with working_dir('lib'): + make('shared_all') + make("install") + self.install_test() + + def setup_dependent_package(self, module, dspec): + # libsatlas.[so,dylib,dll ] contains all serial APIs (serial lapack, + # serial BLAS), and all ATLAS symbols needed to support them. Whereas + # libtatlas.[so,dylib,dll ] is parallel (multithreaded) version. + name = 'libsatlas.%s' % dso_suffix + libdir = find_library_path(name, + self.prefix.lib64, + self.prefix.lib) + + if '+shared' in self.spec: + self.spec.blas_shared_lib = join_path(libdir, name) + self.spec.lapack_shared_lib = self.spec.blas_shared_lib + + def install_test(self): + source_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.c') + blessed_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.output') + + include_flags = ["-I%s" % join_path(self.spec.prefix, "include")] + link_flags = ["-L%s" % join_path(self.spec.prefix, "lib"), + "-lsatlas"] + + output = compile_c_and_execute(source_file, include_flags, link_flags) + compare_output_file(output, blessed_file) diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c new file mode 100644 index 0000000000..2cb90fb883 --- /dev/null +++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c @@ -0,0 +1,49 @@ +#include <cblas.h> +#include <stdio.h> + +double m[] = { + 3, 1, 3, + 1, 5, 9, + 2, 6, 5 +}; + +double x[] = { + -1, 3, -3 +}; + +#ifdef __cplusplus +extern "C" { +#endif + + void dgesv_(int *n, int *nrhs, double *a, int *lda, + int *ipivot, double *b, int *ldb, int *info); + +#ifdef __cplusplus +} +#endif + +int main(void) { + int i; + // blas: + double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; + double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; + double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; + cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, + 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); + for (i = 0; i < 9; i++) + printf("%f\n", C[i]); + + // lapack: + int ipiv[3]; + int j; + int info; + int n = 1; + int nrhs = 1; + int lda = 3; + int ldb = 3; + dgesv_(&n,&nrhs, &m[0], &lda, ipiv, &x[0], &ldb, &info); + for (i=0; i<3; ++i) + printf("%5.1f\n", x[i]); + + return 0; +} diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output new file mode 100644 index 0000000000..01404462c4 --- /dev/null +++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output @@ -0,0 +1,12 @@ +11.000000 +-9.000000 +5.000000 +-9.000000 +21.000000 +-1.000000 +5.000000 +-1.000000 +3.000000 + -0.3 + 3.0 + -3.0 diff --git a/var/spack/repos/builtin/packages/bdw-gc/package.py b/var/spack/repos/builtin/packages/bdw-gc/package.py new file mode 100644 index 0000000000..2c61c21b43 --- /dev/null +++ b/var/spack/repos/builtin/packages/bdw-gc/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 BdwGc(Package): + """The Boehm-Demers-Weiser conservative garbage collector is a garbage + collecting replacement for C malloc or C++ new.""" + + homepage = "http://www.hboehm.info/gc/" + url = "http://www.hboehm.info/gc/gc_source/gc-7.4.4.tar.gz" + + version('7.4.4', '96d18b0448a841c88d56e4ab3d180297') + + variant('libatomic-ops', default=True, description='Use external libatomic-ops') + + depends_on('libatomic-ops', when='+libatomic-ops') + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--with-libatomic-ops={0}'.format( + 'yes' if '+libatomic-ops' in spec else 'no') + ] + + configure(*config_args) + + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/cask/package.py b/var/spack/repos/builtin/packages/cask/package.py new file mode 100644 index 0000000000..67cc48ab2a --- /dev/null +++ b/var/spack/repos/builtin/packages/cask/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 +############################################################################## +# +# Based on Homebrew's formula: +# https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb +# +from spack import * +from glob import glob + + +class Cask(Package): + """Cask is a project management tool for Emacs Lisp to automate the package + development cycle; development, dependencies, testing, building, + packaging and more.""" + homepage = "http://cask.readthedocs.io/en/latest/" + url = "https://github.com/cask/cask/archive/v0.7.4.tar.gz" + + version('0.7.4', 'c973a7db43bc980dd83759a5864a1260') + + depends_on('emacs', type=nolink) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('bin/cask', prefix.bin) + install_tree('templates', join_path(prefix, 'templates')) + for el_file in glob("*.el"): + install(el_file, prefix) + for misc_file in ['COPYING', 'cask.png', 'README.md']: + install(misc_file, prefix) + # disable cask's automatic upgrading feature + touch(join_path(prefix, ".no-upgrade")) diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py new file mode 100644 index 0000000000..8fdd1e0ca3 --- /dev/null +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -0,0 +1,161 @@ +############################################################################## +# 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 +############################################################################## +import os +import shutil +import copy + +from spack import * + + +class Cp2k(Package): + """CP2K is a quantum chemistry and solid state physics software package + that can perform atomistic simulations of solid state, liquid, molecular, + periodic, material, crystal, and biological systems + """ + homepage = 'https://www.cp2k.org' + url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2' + + version('3.0', 'c05bc47335f68597a310b1ed75601d35') + + variant('mpi', default=True, description='Enable MPI support') + + depends_on('python') # Build dependency + + depends_on('lapack') + depends_on('blas') + depends_on('fftw') + + depends_on('mpi', when='+mpi') + depends_on('scalapack', when='+mpi') + + # TODO : add dependency on libint + # TODO : add dependency on libsmm, libxsmm + # TODO : add dependency on elpa + # TODO : add dependency on CUDA + # TODO : add dependency on PEXSI + # TODO : add dependency on QUIP + # TODO : add dependency on plumed + # TODO : add dependency on libwannier90 + + parallel = False + + def install(self, spec, prefix): + # Construct a proper filename for the architecture file + cp2k_architecture = '{0.architecture}-{0.compiler.name}'.format(spec) + cp2k_version = 'sopt' if '~mpi' in spec else 'popt' + makefile_basename = '.'.join([cp2k_architecture, cp2k_version]) + makefile = join_path('arch', makefile_basename) + + # Write the custom makefile + with open(makefile, 'w') as mkf: + mkf.write('CC = {0.compiler.cc}\n'.format(self)) + if '%intel' in self.spec: + # CPP is a commented command in Intel arch of CP2K + # This is the hack through which cp2k developers avoid doing : + # + # ${CPP} <file>.F > <file>.f90 + # + # and use `-fpp` instead + mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self)) + mkf.write('AR = xiar -r\n') + else: + mkf.write('CPP = {0.compiler.cc} -E\n'.format(self)) + mkf.write('AR = ar -r\n') + fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc + mkf.write('FC = {0}\n'.format(fc)) + mkf.write('LD = {0}\n'.format(fc)) + # Optimization flags + optflags = { + 'gcc': ['-O2', + '-ffast-math', + '-ffree-form', + '-ffree-line-length-none', + '-ftree-vectorize', + '-funroll-loops', + '-mtune=native'], + 'intel': ['-O2', + '-pc64', + '-unroll', + '-heap-arrays 64'] + } + cppflags = [ + '-D__FFTW3', + '-I' + spec['fftw'].prefix.include + ] + fcflags = copy.deepcopy(optflags[self.spec.compiler.name]) + fcflags.extend([ + '-I' + spec['fftw'].prefix.include + ]) + ldflags = ['-L' + spec['fftw'].prefix.lib] + libs = [] + # Intel + if '%intel' in self.spec: + cppflags.extend([ + '-D__INTEL_COMPILER', + '-D__MKL' + ]) + fcflags.extend([ + '-diag-disable 8290,8291,10010,10212,11060', + '-free', + '-fpp' + ]) + # MPI + if '+mpi' in self.spec: + cppflags.extend([ + '-D__parallel', + '-D__SCALAPACK' + ]) + ldflags.extend([ + '-L' + spec['scalapack'].prefix.lib + ]) + libs.extend(spec['scalapack'].scalapack_shared_libs) + + # LAPACK / BLAS + ldflags.extend([ + '-L' + spec['lapack'].prefix.lib, + '-L' + spec['blas'].prefix.lib + ]) + libs.extend([ + join_path(spec['fftw'].prefix.lib, 'libfftw3.so'), + spec['lapack'].lapack_shared_lib, + spec['blas'].blas_shared_lib + ]) + + # Write compiler flags to file + mkf.write('CPPFLAGS = {0}\n'.format(' '.join(cppflags))) + mkf.write('FCFLAGS = {0}\n'.format(' '.join(fcflags))) + mkf.write('LDFLAGS = {0}\n'.format(' '.join(ldflags))) + mkf.write('LIBS = {0}\n'.format(' '.join(libs))) + + with working_dir('makefiles'): + # Apparently the Makefile bases its paths on PWD + # so we need to set PWD = os.getcwd() + pwd_backup = env['PWD'] + env['PWD'] = os.getcwd() + make('ARCH={0}'.format(cp2k_architecture), + 'VERSION={0}'.format(cp2k_version)) + env['PWD'] = pwd_backup + exe_dir = join_path('exe', cp2k_architecture) + shutil.copytree(exe_dir, self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py index df301aea3c..0a0b163a74 100644 --- a/var/spack/repos/builtin/packages/gettext/package.py +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -24,31 +24,84 @@ ############################################################################## from spack import * + class Gettext(Package): """GNU internationalization (i18n) and localization (l10n) library.""" homepage = "https://www.gnu.org/software/gettext/" url = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz" - version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + version('0.19.8.1', 'df3f5690eaa30fd228537b00cb7b7590') + version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + + # Recommended variants + variant('curses', default=True, description='Use libncurses') + variant('libxml2', default=True, description='Use libxml2') + variant('git', default=True, description='Enable git support') + variant('tar', default=True, description='Enable tar support') + variant('bzip2', default=True, description='Enable bzip2 support') + variant('xz', default=True, description='Enable xz support') + + # Optional variants + variant('libunistring', default=False, description='Use libunistring') + + # Recommended dependencies + depends_on('ncurses', when='+curses') + depends_on('libxml2', when='+libxml2') + # Java runtime and compiler (e.g. GNU gcj or kaffe) + # C# runtime and compiler (e.g. pnet or mono) + depends_on('git@1.6:', when='+git') + depends_on('tar', when='+tar') + # depends_on('gzip', when='+gzip') + depends_on('bzip2', when='+bzip2') + depends_on('xz', when='+xz') + + # Optional dependencies + # depends_on('glib') # circular dependency? + # depends_on('libcroco@0.6.1:') + depends_on('libunistring', when='+libunistring') + # depends_on('cvs') def install(self, spec, prefix): - options = ['--disable-dependency-tracking', - '--disable-silent-rules', - '--disable-debug', - '--prefix=%s' % prefix, - '--with-included-gettext', - '--with-included-glib', - '--with-included-libcroco', - '--with-included-libunistring', - '--with-emacs', - '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share, - '--disable-java', - '--disable-csharp', - '--without-git', # Don't use VCS systems to create these archives - '--without-cvs', - '--without-xz'] - - configure(*options) + config_args = [ + '--prefix={0}'.format(prefix), + '--disable-java', + '--disable-csharp', + '--with-included-glib', + '--with-included-gettext', + '--with-included-libcroco', + '--without-emacs', + '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share, + '--without-cvs' + ] + + if '+curses' in spec: + config_args.append('--with-ncurses-prefix={0}'.format( + spec['ncurses'].prefix)) + else: + config_args.append('--disable-curses') + + if '+libxml2' in spec: + config_args.append('--with-libxml2-prefix={0}'.format( + spec['libxml2'].prefix)) + else: + config_args.append('--with-included-libxml') + + if '+git' not in spec: + config_args.append('--without-git') + + if '+bzip2' not in spec: + config_args.append('--without-bzip2') + + if '+xz' not in spec: + config_args.append('--without-xz') + + if '+libunistring' in spec: + config_args.append('--with-libunistring-prefix={0}'.format( + spec['libunistring'].prefix)) + else: + config_args.append('--with-included-libunistring') + + configure(*config_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 4cbbaac342..01364580a0 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Git(Package): """Git is a free and open source distributed version control system designed to handle everything from small to very large @@ -36,31 +37,27 @@ class Git(Package): version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6') version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060') - # See here for info on vulnerable Git versions: # http://www.theregister.co.uk/2016/03/16/git_server_client_patch_now/ # All the following are vulnerable - #version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') - #version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') - #version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') - #version('2.6.0', 'eb76a07148d94802a1745d759716a57e') - #version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') - #version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') - + # version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') + # version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') + # version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') + # version('2.6.0', 'eb76a07148d94802a1745d759716a57e') + # version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') + # version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') depends_on("openssl") depends_on("autoconf", type='build') depends_on("curl") depends_on("expat") - - # Also depends_on gettext: apt-get install gettext (Ubuntu) + depends_on("gettext") + depends_on("zlib") # Use system perl for now. # depends_on("perl") # depends_on("pcre") - depends_on("zlib") - def install(self, spec, prefix): configure_args = [ "--prefix=%s" % prefix, @@ -68,8 +65,8 @@ class Git(Package): "--with-openssl=%s" % spec['openssl'].prefix, "--with-zlib=%s" % spec['zlib'].prefix, "--with-curl=%s" % spec['curl'].prefix, - "--with-expat=%s" % spec['expat'].prefix, - ] + "--with-expat=%s" % spec['expat'].prefix + ] which('autoreconf')('-i') configure(*configure_args) diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index e2c2892f18..d85330dd6e 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -24,16 +24,18 @@ ############################################################################## from spack import * + class Gmp(Package): - """GMP is a free library for arbitrary precision arithmetic, - operating on signed integers, rational numbers, and - floating-point numbers.""" + """GMP is a free library for arbitrary precision arithmetic, operating + on signed integers, rational numbers, and floating-point numbers.""" + homepage = "https://gmplib.org" url = "https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2" - version('6.1.0' , '86ee6e54ebfc4a90b643a65e402c4048') + version('6.1.1', '4c175f86e11eb32d8bf9872ca3a8e11d') + version('6.1.0', '86ee6e54ebfc4a90b643a65e402c4048') version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470') - version('6.0.0' , '6ef5869ae735db9995619135bd856b84') + version('6.0.0', '6ef5869ae735db9995619135bd856b84') depends_on("m4", type='build') diff --git a/var/spack/repos/builtin/packages/guile/package.py b/var/spack/repos/builtin/packages/guile/package.py new file mode 100644 index 0000000000..22aff1bddf --- /dev/null +++ b/var/spack/repos/builtin/packages/guile/package.py @@ -0,0 +1,68 @@ +############################################################################## +# 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 Guile(Package): + """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + + homepage = "https://www.gnu.org/software/guile/" + url = "ftp://ftp.gnu.org/gnu/guile/guile-2.0.11.tar.gz" + + version('2.0.11', 'e532c68c6f17822561e3001136635ddd') + + variant('readline', default=True, description='Use the readline library') + + depends_on('gmp@4.2:') + depends_on('gettext') + depends_on('libtool@1.5.6:') + depends_on('libunistring@0.9.3:') + depends_on('bdw-gc@7.0:') + depends_on('libffi') + depends_on('readline', when='+readline') + depends_on('pkg-config', type='build') + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--with-libunistring-prefix={0}'.format( + spec['libunistring'].prefix), + '--with-libltdl-prefix={0}'.format(spec['libtool'].prefix), + '--with-libgmp-prefix={0}'.format(spec['gmp'].prefix), + '--with-libintl-prefix={0}'.format(spec['gettext'].prefix) + ] + + if '+readline' in spec: + config_args.append('--with-libreadline-prefix={0}'.format( + spec['readline'].prefix)) + else: + config_args.append('--without-libreadline-prefix') + + configure(*config_args) + + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py new file mode 100644 index 0000000000..184535ebb0 --- /dev/null +++ b/var/spack/repos/builtin/packages/harminv/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 Harminv(Package): + """Harminv is a free program (and accompanying library) to solve the + problem of harmonic inversion - given a discrete-time, finite-length + signal that consists of a sum of finitely-many sinusoids (possibly + exponentially decaying) in a given bandwidth, it determines the + frequencies, decay constants, amplitudes, and phases of those sinusoids.""" + + homepage = "http://ab-initio.mit.edu/wiki/index.php/Harminv" + url = "http://ab-initio.mit.edu/harminv/harminv-1.4.tar.gz" + + version('1.4', 'b95e24a9bc7e07d3d2202d1605e9e86f') + + depends_on('blas') + depends_on('lapack') + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--with-blas={0}'.format(spec['blas'].prefix.lib), + '--with-lapack={0}'.format(spec['lapack'].prefix.lib), + '--enable-shared' + ] + + configure(*config_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 65fef57559..b339e068bf 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -62,10 +62,10 @@ class Hypre(Package): '--prefix=%s' % prefix, '--with-lapack-libs=%s' % to_lib_name( spec['lapack'].lapack_shared_lib), - '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix, + '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib, '--with-blas-libs=%s' % to_lib_name( spec['blas'].blas_shared_lib), - '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix + '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib ] if '+shared' in self.spec: diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index 593a6d8340..794966f1c3 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -25,7 +25,7 @@ # # Author: Justin Too <too1@llnl.gov> # -import distutils +import distutils.dir_util import spack from spack import * diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py new file mode 100644 index 0000000000..48f4b9c379 --- /dev/null +++ b/var/spack/repos/builtin/packages/kdiff3/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 Kdiff3(Package): + """Compare and merge 2 or 3 files or directories.""" + homepage = "http://kdiff3.sourceforge.net/" + url = "https://downloads.sourceforge.net/project/kdiff3/kdiff3/0.9.98/kdiff3-0.9.98.tar.gz" + + version('0.9.98', 'b52f99f2cf2ea75ed5719315cbf77446') + + depends_on("qt@5.2.0:") + + def install(self, spec, prefix): + # make is done inside + configure('qt4') + + # there is no make install, bummer... + mkdirp(self.prefix.bin) + install(join_path(self.stage.source_path, 'releaseQt', 'kdiff3'), + self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/libatomic-ops/package.py b/var/spack/repos/builtin/packages/libatomic-ops/package.py new file mode 100644 index 0000000000..0167fbcb33 --- /dev/null +++ b/var/spack/repos/builtin/packages/libatomic-ops/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 LibatomicOps(Package): + """This package provides semi-portable access to hardware-provided + atomic memory update operations on a number architectures.""" + + homepage = "https://github.com/ivmai/libatomic_ops" + url = "http://www.hboehm.info/gc/gc_source/libatomic_ops-7.4.4.tar.gz" + + version('7.4.4', '426d804baae12c372967a6d183e25af2') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), + '--enable-shared') + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/libctl/package.py b/var/spack/repos/builtin/packages/libctl/package.py new file mode 100644 index 0000000000..53d30ce5c3 --- /dev/null +++ b/var/spack/repos/builtin/packages/libctl/package.py @@ -0,0 +1,48 @@ +############################################################################## +# 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 Libctl(Package): + """libctl is a free Guile-based library implementing flexible + control files for scientific simulations.""" + + homepage = "http://ab-initio.mit.edu/wiki/index.php/Libctl" + url = "http://ab-initio.mit.edu/libctl/libctl-3.2.2.tar.gz" + + version('3.2.2', '5fd7634dc9ae8e7fa70a68473b9cbb68') + + depends_on('guile') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), + '--enable-shared', + 'GUILE={0}'.format(join_path( + spec['guile'].prefix.bin, 'guile')), + 'GUILE_CONFIG={0}'.format(join_path( + spec['guile'].prefix.bin, 'guile-config'))) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/libhio/package.py b/var/spack/repos/builtin/packages/libhio/package.py new file mode 100644 index 0000000000..17bd86d310 --- /dev/null +++ b/var/spack/repos/builtin/packages/libhio/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 Libhio(Package): + """ + A library for writing to hierarchical data store systems. + """ + + homepage = "https://github.com/hpc/libhio/" + url = "https://github.com/hpc/libhio/releases/download/hio.1.3.0.1/libhio-1.3.0.1.tar.gz" + + version('1.3.0.1', 'c073541de8dd70aeb8878bd00d6d877f') + + depends_on("libjson-c") + depends_on("bzip2") + depends_on("pkg-config", type="build") + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py new file mode 100644 index 0000000000..f2eeb07b26 --- /dev/null +++ b/var/spack/repos/builtin/packages/libiconv/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 Libiconv(Package): + """GNU libiconv provides an implementation of the iconv() function + and the iconv program for character set conversion.""" + + homepage = "https://www.gnu.org/software/libiconv/" + url = "http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz" + + version('1.14', 'e34509b1623cec449dfeb73d7ce9c6c6') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), + '--enable-extra-encodings') + + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py new file mode 100644 index 0000000000..5b8837e72b --- /dev/null +++ b/var/spack/repos/builtin/packages/libunistring/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 Libunistring(Package): + """This library provides functions for manipulating Unicode strings + and for manipulating C strings according to the Unicode standard.""" + + homepage = "https://www.gnu.org/software/libunistring/" + url = "http://ftp.gnu.org/gnu/libunistring/libunistring-0.9.6.tar.xz" + + version('0.9.6', 'cb09c398020c27edac10ca590e9e9ef3') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + # make('check') # test-verify fails for me, contacted developers + make('install') diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py index 55816ecdbd..b9215bc601 100644 --- a/var/spack/repos/builtin/packages/libxau/package.py +++ b/var/spack/repos/builtin/packages/libxau/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libxau(Package): """The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client @@ -34,11 +35,10 @@ class Libxau(Package): version('1.0.8', '685f8abbffa6d145c0f930f00703b21b') depends_on('xproto') + depends_on('pkg-config', type='build') def install(self, spec, prefix): - # FIXME: Modify the configure line to suit your build system here. configure('--prefix=%s' % prefix) - # FIXME: Add logic to build and install here make() make("install") diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py new file mode 100644 index 0000000000..a736490600 --- /dev/null +++ b/var/spack/repos/builtin/packages/libxsmm/package.py @@ -0,0 +1,66 @@ +############################################################################## +# 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 Libxsmm(Package): + '''LIBXSMM is a library for small dense and small sparse matrix-matrix + multiplications targeting Intel Architecture (x86).''' + + homepage = 'https://github.com/hfp/libxsmm' + url = 'https://github.com/hfp/libxsmm/archive/1.4.3.tar.gz' + + version('1.4.3', '9839bf0fb8be7badf1e97ce4c817149b') + version('1.4.2', 'ea025761437f3b5c936821b9ca21ec31') + version('1.4.1', '71648500ea4510529845d329091917df') + version('1.4', 'b42f91bf5285e7ad0463446e55ebdc2b') + + def patch(self): + kwargs = {'ignore_absent': False, 'backup': False, 'string': True} + makefile = FileFilter('Makefile.inc') + + # Spack sets CC, CXX, and FC to point to the compiler wrappers + # Don't let Makefile.inc overwrite these + makefile.filter('CC = icc', 'CC ?= icc', **kwargs) + makefile.filter('CC = gcc', 'CC ?= gcc', **kwargs) + makefile.filter('CXX = icpc', 'CXX ?= icpc', **kwargs) + makefile.filter('CXX = g++', 'CXX ?= g++', **kwargs) + makefile.filter('FC = ifort', 'FC ?= ifort', **kwargs) + makefile.filter('FC = gfortran', 'FC ?= gfortran', **kwargs) + + def manual_install(self, prefix): + install_tree('include', prefix.include) + install_tree('lib', prefix.lib) + install_tree('documentation', prefix.share + '/libxsmm/doc') + + def install(self, spec, prefix): + make_args = [ + 'ROW_MAJOR=0', + 'INDICES_M={0}'.format(' '.join(str(i) for i in range(1, 25))), + 'INDICES_N={0}'.format(' '.join(str(i) for i in range(1, 25))), + 'INDICES_K={0}'.format(' '.join(str(i) for i in range(1, 25))) + ] + make(*make_args) + self.manual_install(prefix) diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py new file mode 100644 index 0000000000..2c1018e711 --- /dev/null +++ b/var/spack/repos/builtin/packages/meep/package.py @@ -0,0 +1,109 @@ +############################################################################## +# 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 Meep(Package): + """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation + software package developed at MIT to model electromagnetic systems.""" + + homepage = "http://ab-initio.mit.edu/wiki/index.php/Meep" + + version('1.3', '18a5b9e18008627a0411087e0bb60db5') + version('1.2.1', '9be2e743c3a832ae922de9d955d016c5') + version('1.1.1', '415e0cd312b6caa22b5dd612490e1ccf') + + variant('blas', default=True, description='Enable BLAS support') + variant('lapack', default=True, description='Enable LAPACK support') + variant('harminv', default=True, description='Enable Harminv support') + variant('guile', default=True, description='Enable Guilde support') + variant('libctl', default=True, description='Enable libctl support') + variant('mpi', default=True, description='Enable MPI support') + variant('hdf5', default=True, description='Enable HDF5 support') + variant('gsl', default=True, description='Enable GSL support') + + depends_on('blas', when='+blas') + depends_on('lapack', when='+lapack') + depends_on('harminv', when='+harminv') + depends_on('guile', when='+guile') + depends_on('libctl@3.2:', when='+libctl') + depends_on('mpi', when='+mpi') + depends_on('hdf5~mpi', when='+hdf5~mpi') + depends_on('hdf5+mpi', when='+hdf5+mpi') + depends_on('gsl', when='+gsl') + + def url_for_version(self, version): + base_url = "http://ab-initio.mit.edu/meep" + if version > Version('1.1.1'): + return "{0}/meep-{1}.tar.gz".format(base_url, version) + else: + return "{0}/old/meep-{1}.tar.gz".format(base_url, version) + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--enable-shared' + ] + + if '+blas' in spec: + config_args.append('--with-blas={0}'.format( + spec['blas'].prefix.lib)) + else: + config_args.append('--without-blas') + + if '+lapack' in spec: + config_args.append('--with-lapack={0}'.format( + spec['lapack'].prefix.lib)) + else: + config_args.append('--without-lapack') + + if '+libctl' in spec: + config_args.append('--with-libctl={0}'.format( + join_path(spec['libctl'].prefix.share, 'libctl'))) + else: + config_args.append('--without-libctl') + + if '+mpi' in spec: + config_args.append('--with-mpi') + else: + config_args.append('--without-mpi') + + if '+hdf5' in spec: + config_args.append('--with-hdf5') + else: + config_args.append('--without-hdf5') + + configure(*config_args) + + make() + + # aniso_disp test fails unless installed with harminv + # near2far test fails unless installed with gsl + if self.run_tests and '+harminv' in spec and '+gsl' in spec: + # Most tests fail when run in parallel + # 2D_convergence tests still fails to converge for unknown reasons + make('check', parallel=False) + + make('install') diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py index 6ea64f5313..71a233ff3e 100644 --- a/var/spack/repos/builtin/packages/mkl/package.py +++ b/var/spack/repos/builtin/packages/mkl/package.py @@ -12,9 +12,9 @@ class Mkl(IntelInstaller): mirror, see http://software.llnl.gov/spack/mirrors.html. To set the threading layer at run time set MKL_THREADING_LAYER - variable to one of the following values: INTEL, SEQUENTIAL, PGI. + variable to one of the following values: INTEL (default), SEQUENTIAL, PGI. To set interface layer at run time, use set the MKL_INTERFACE_LAYER - variable to LP64 or ILP64. + variable to LP64 (default) or ILP64. """ homepage = "https://software.intel.com/en-us/intel-mkl" @@ -38,6 +38,13 @@ class Mkl(IntelInstaller): for f in os.listdir(mkl_dir): os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f)) + # Unfortunately MKL libs are natively distrubted in prefix/lib/intel64. + # To make MKL play nice with Spack, symlink all files to prefix/lib: + mkl_lib_dir = os.path.join(prefix, "lib", "intel64") + for f in os.listdir(mkl_lib_dir): + os.symlink(os.path.join(mkl_lib_dir, f), + os.path.join(self.prefix, "lib", f)) + def setup_dependent_package(self, module, dspec): # For now use Single Dynamic Library: # To set the threading layer at run time, use the @@ -53,6 +60,7 @@ class Mkl(IntelInstaller): name = 'libmkl_rt.%s' % dso_suffix libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib) + # Now set blas/lapack libs: self.spec.blas_shared_lib = join_path(libdir, name) self.spec.lapack_shared_lib = self.spec.blas_shared_lib diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index da386445bb..0fa5821b08 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -76,6 +76,7 @@ class Mvapich2(Package): ########## # FIXME : CUDA support is missing + depends_on('libpciaccess') def url_for_version(self, version): base_url = "http://mvapich.cse.ohio-state.edu/download" diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py new file mode 100644 index 0000000000..54f3dbf915 --- /dev/null +++ b/var/spack/repos/builtin/packages/nextflow/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 Nextflow(Package): + """Data-driven computational pipelines""" + + homepage = "http://www.nextflow.io" + + version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a', + url='https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow', + expand=False) + + depends_on('jdk') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install("nextflow", join_path(prefix.bin, "nextflow")) + set_executable(join_path(prefix.bin, "nextflow")) diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py index ff551d0b92..8f592342b0 100644 --- a/var/spack/repos/builtin/packages/opencv/package.py +++ b/var/spack/repos/builtin/packages/opencv/package.py @@ -23,51 +23,186 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +from glob import glob class Opencv(Package): + """OpenCV is released under a BSD license and hence it's free for both + academic and commercial use. It has C++, C, Python and Java interfaces and + supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for + computational efficiency and with a strong focus on real-time applications. + Written in optimized C/C++, the library can take advantage of multi-core + processing. Enabled with OpenCL, it can take advantage of the hardware + acceleration of the underlying heterogeneous compute platform. Adopted all + around the world, OpenCV has more than 47 thousand people of user community + and estimated number of downloads exceeding 9 million. Usage ranges from + interactive art, to mines inspection, stitching maps on the web or through + advanced robotics. """ - OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C, - Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for - computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library - can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware - acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than - 47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from - interactive art, to mines inspection, stitching maps on the web or through advanced robotics. - """ + homepage = 'http://opencv.org/' url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz' version('3.1.0', '70e1dd07f0aa06606f1bc0e3fa15abd3') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds a debug version of the libraries') variant('eigen', default=True, description='Activates support for eigen') variant('ipp', default=True, description='Activates support for IPP') + variant('jasper', default=True, description='Activates support for JasPer') + variant('cuda', default=False, description='Activates support for CUDA') + variant('gtk', default=False, description='Activates support for GTK') + variant('vtk', default=False, description='Activates support for VTK') + variant('qt', default=False, description='Activates support for QT') + variant('python', default=False, + description='Enables the build of Python extensions') + variant('java', default=False, + description='Activates support for Java') + + depends_on('cmake', type='build') + depends_on('eigen', when='+eigen', type='build') depends_on('zlib') depends_on('libpng') depends_on('libjpeg-turbo') depends_on('libtiff') - depends_on('python') - depends_on('py-numpy') + depends_on('jasper', when='+jasper') + depends_on('cuda', when='+cuda') + depends_on('gtkplus', when='+gtk') + depends_on('vtk', when='+vtk') + depends_on('qt', when='+qt') + depends_on('jdk', when='+java') + depends_on('py-numpy', when='+python') - depends_on('eigen', when='+eigen', type='build') - depends_on('cmake', type='build') - - # FIXME : GUI extensions missing - # FIXME : CUDA extensions still missing + extends('python', when='+python') def install(self, spec, prefix): cmake_options = [] cmake_options.extend(std_cmake_args) - cmake_options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), - '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), - '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF', - '-DWITH_IPP:BOOL=%s' % ('ON' if '+ipp' in spec else 'OFF')]) + cmake_options.extend([ + '-DCMAKE_BUILD_TYPE:STRING={0}'.format(( + 'Debug' if '+debug' in spec else 'Release')), + '-DBUILD_SHARED_LIBS:BOOL={0}'.format(( + 'ON' if '+shared' in spec else 'OFF')), + '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF', + '-DWITH_IPP:BOOL={0}'.format(( + 'ON' if '+ipp' in spec else 'OFF')), + '-DWITH_CUDA:BOOL={0}'.format(( + 'ON' if '+cuda' in spec else 'OFF')), + '-DWITH_QT:BOOL={0}'.format(( + 'ON' if '+qt' in spec else 'OFF')), + '-DWITH_VTK:BOOL={0}'.format(( + 'ON' if '+vtk' in spec else 'OFF')), + '-DBUILD_opencv_java:BOOL={0}'.format(( + 'ON' if '+java' in spec else 'OFF')), + ]) + + # Media I/O + zlib = spec['zlib'] + cmake_options.extend([ + '-DZLIB_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(zlib.prefix.lib, + 'libz.{0}'.format(dso_suffix))), + '-DZLIB_INCLUDE_DIR:PATH={0}'.format(zlib.prefix.include) + ]) + + libpng = spec['libpng'] + cmake_options.extend([ + '-DPNG_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(libpng.prefix.lib, + 'libpng.{0}'.format(dso_suffix))), + '-DPNG_INCLUDE_DIR:PATH={0}'.format(libpng.prefix.include) + ]) + + libjpeg = spec['libjpeg-turbo'] + cmake_options.extend([ + '-DJPEG_LIBRARY:FILEPATH={0}'.format( + join_path(libjpeg.prefix.lib, + 'libjpeg.{0}'.format(dso_suffix))), + '-DJPEG_INCLUDE_DIR:PATH={0}'.format(libjpeg.prefix.include) + ]) + + libtiff = spec['libtiff'] + cmake_options.extend([ + '-DTIFF_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(libtiff.prefix.lib, + 'libtiff.{0}'.format(dso_suffix))), + '-DTIFF_INCLUDE_DIR:PATH={0}'.format(libtiff.prefix.include) + ]) + + jasper = spec['jasper'] + cmake_options.extend([ + '-DJASPER_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(jasper.prefix.lib, + 'libjasper.{0}'.format(dso_suffix))), + '-DJASPER_INCLUDE_DIR:PATH={0}'.format(jasper.prefix.include) + ]) + + # GUI + if '+gtk' not in spec: + cmake_options.extend([ + '-DWITH_GTK:BOOL=OFF', + '-DWITH_GTK_2_X:BOOL=OFF' + ]) + elif '^gtkplus@3:' in spec: + cmake_options.extend([ + '-DWITH_GTK:BOOL=ON', + '-DWITH_GTK_2_X:BOOL=OFF' + ]) + elif '^gtkplus@2:3' in spec: + cmake_options.extend([ + '-DWITH_GTK:BOOL=OFF', + '-DWITH_GTK_2_X:BOOL=ON' + ]) + + # Python + if '+python' in spec: + python = spec['python'] + + try: + python_lib = glob(join_path( + python.prefix.lib, 'libpython*.{0}'.format(dso_suffix)))[0] + except KeyError: + raise InstallError('Cannot find libpython') + + try: + python_include_dir = glob(join_path(python.prefix.include, + 'python*'))[0] + except KeyError: + raise InstallError('Cannot find python include directory') + + if '^python@3:' in spec: + python_exe = join_path(python.prefix.bin, 'python3') + cmake_options.extend([ + '-DBUILD_opencv_python3=ON', + '-DPYTHON3_EXECUTABLE={0}'.format(python_exe), + '-DPYTHON3_LIBRARY={0}'.format(python_lib), + '-DPYTHON3_INCLUDE_DIR={0}'.format(python_include_dir), + '-DBUILD_opencv_python2=OFF', + ]) + elif '^python@2:3' in spec: + python_exe = join_path(python.prefix.bin, 'python2') + cmake_options.extend([ + '-DBUILD_opencv_python2=ON', + '-DPYTHON2_EXECUTABLE={0}'.format(python_exe), + '-DPYTHON2_LIBRARY={0}'.format(python_lib), + '-DPYTHON2_INCLUDE_DIR={0}'.format(python_include_dir), + '-DBUILD_opencv_python3=OFF', + ]) + else: + cmake_options.extend([ + '-DBUILD_opencv_python2=OFF', + '-DBUILD_opencv_python3=OFF' + ]) with working_dir('spack_build', create=True): cmake('..', *cmake_options) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index b9eada9e83..78bdd88d9c 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -52,7 +52,7 @@ class Openssl(Package): if '@system' in self.spec: return '@system (reserved version for system openssl)' else: - return super(Openssl, self).url_for_version(self.spec) + return super(Openssl, self).url_for_version(self.version) def handle_fetch_error(self, error): tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has " diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index 4bbf0c1311..114fd00011 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -24,46 +24,42 @@ ############################################################################## from spack import * + class P4est(Package): - """Dynamic management of a collection (a forest) of adaptive octrees in parallel""" + """Dynamic management of a collection (a forest) of adaptive octrees in + parallel""" homepage = "http://www.p4est.org" url = "http://p4est.github.io/release/p4est-1.1.tar.gz" version('1.1', '37ba7f4410958cfb38a2140339dbf64f') - variant('tests', default=True, description='Run small tests') - # build dependencies depends_on('automake', type='build') depends_on('autoconf', type='build') depends_on('libtool@2.4.2:', type='build') # other dependencies - depends_on('lua') # Needed for the submodule sc + depends_on('lua') # Needed for the submodule sc depends_on('mpi') depends_on('zlib') def install(self, spec, prefix): - options = ['--enable-mpi', - '--enable-shared', - '--disable-vtk-binary', - '--without-blas', - 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', - 'CFLAGS=-O2', - 'CC=%s' % self.spec['mpi'].mpicc, - 'CXX=%s' % self.spec['mpi'].mpicxx, - 'FC=%s' % self.spec['mpi'].mpifc, - 'F77=%s' % self.spec['mpi'].mpif77 - ] + options = [ + '--enable-mpi', + '--enable-shared', + '--disable-vtk-binary', + '--without-blas', + 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', + 'CFLAGS=-O2', + 'CC=%s' % self.spec['mpi'].mpicc, + 'CXX=%s' % self.spec['mpi'].mpicxx, + 'FC=%s' % self.spec['mpi'].mpifc, + 'F77=%s' % self.spec['mpi'].mpif77 + ] configure('--prefix=%s' % prefix, *options) make() - # Make tests optional as sometimes mpiexec can't be run with an error: - # mpiexec has detected an attempt to run as root. - # Running at root is *strongly* discouraged as any mistake (e.g., in - # defining TMPDIR) or bug can result in catastrophic damage to the OS - # file system, leaving your system in an unusable state. - if '+tests' in self.spec: - make("check") + if self.run_tests: + make("check") make("install") diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py new file mode 100644 index 0000000000..d71a7492ba --- /dev/null +++ b/var/spack/repos/builtin/packages/perl/package.py @@ -0,0 +1,75 @@ +############################################################################## +# 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 +############################################################################## +# +# Author: George Hartzell <hartzell@alerce.com> +# Date: July 21, 2016 +# Author: Justin Too <justin@doubleotoo.com> +# Date: September 6, 2015 +# +from spack import * + + +class Perl(Package): + """Perl 5 is a highly capable, feature-rich programming language with over + 27 years of development.""" + homepage = "http://www.perl.org" + url = "http://www.cpan.org/src/5.0/perl-5.22.2.tar.gz" + + version('5.24.0', 'c5bf7f3285439a2d3b6a488e14503701') + version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b') + version('5.20.3', 'd647d0ea5a7a8194c34759ab9f2610cd') + # 5.18.4 fails with gcc-5 + # https://rt.perl.org/Public/Bug/Display.html?id=123784 + # version('5.18.4' , '1f9334ff730adc05acd3dd7130d295db') + + # Installing cpanm alongside the core makes it safe and simple for + # people/projects to install their own sets of perl modules. Not + # having it in core increases the "energy of activation" for doing + # things cleanly. + variant('cpanm', default=True, + description='Optionally install cpanm with the core packages.') + + resource( + name="cpanm", + url="http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7042.tar.gz", + md5="e87f55fbcb3c13a4754500c18e89219f", + destination="cpanm", + placement="cpanm" + ) + + def install(self, spec, prefix): + configure = Executable('./Configure') + configure("-des", "-Dprefix=" + prefix) + make() + if self.run_tests: + make("test") + make("install") + + if '+cpanm' in spec: + with working_dir(join_path('cpanm', 'cpanm')): + perl = Executable(join_path(prefix.bin, 'perl')) + perl('Makefile.PL') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py index 7170c65303..c58d563682 100644 --- a/var/spack/repos/builtin/packages/pgi/package.py +++ b/var/spack/repos/builtin/packages/pgi/package.py @@ -41,6 +41,7 @@ class Pgi(Package): homepage = "http://www.pgroup.com/" url = "file://%s/pgi-16.3.tar.gz" % os.getcwd() + version('16.5', 'a40e8852071b5d600cb42f31631b3de1') version('16.3', '618cb7ddbc57d4e4ed1f21a0ab25f427') variant('network', default=True, diff --git a/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch new file mode 100644 index 0000000000..578cbf4d7c --- /dev/null +++ b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch @@ -0,0 +1,33 @@ +From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001 +From: coypu <coypu@sdf.org> +Date: Wed, 2 Mar 2016 19:43:10 +0200 +Subject: [PATCH 2/2] gdate: Suppress string format literal warning + +Newer versions of GCC emit an error here, but we know it's safe. +https://bugzilla.gnome.org/761550 +--- + glib/glib/gdate.c | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/glib/glib/gdate.c b/glib/glib/gdate.c +index 4aece02..92c34d2 100644 +--- a/glib/glib/gdate.c ++++ b/glib/glib/gdate.c +@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate *d, + * + * Returns: number of characters written to the buffer, or 0 the buffer was too small + */ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wformat-nonliteral" ++ + gsize + g_date_strftime (gchar *s, + gsize slen, +@@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s, + return retval; + #endif + } ++ ++#pragma GCC diagnostic pop +-- +2.7.1 diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py index ddbc151767..45e8e8b74e 100644 --- a/var/spack/repos/builtin/packages/pkg-config/package.py +++ b/var/spack/repos/builtin/packages/pkg-config/package.py @@ -24,23 +24,29 @@ ############################################################################## from spack import * + class PkgConfig(Package): - """pkg-config is a helper tool used when compiling applications and libraries""" + """pkg-config is a helper tool used when compiling applications + and libraries""" + homepage = "http://www.freedesktop.org/wiki/Software/pkg-config/" url = "http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz" - version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d') + version('0.29.1', 'f739a28cae4e0ca291f82d1d41ef107d') + version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d') parallel = False + # The following patch is needed for gcc-6.1 + patch('g_date_strftime.patch') + def install(self, spec, prefix): - configure("--prefix=%s" %prefix, - "--enable-shared", - "--with-internal-glib") # There's a bootstrapping problem here; - # glib uses pkg-config as well, so - # break the cycle by using the internal - # glib. + configure("--prefix={0}".format(prefix), + "--enable-shared", + # There's a bootstrapping problem here; + # glib uses pkg-config as well, so break + # the cycle by using the internal glib. + "--with-internal-glib") make() make("install") - diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py new file mode 100644 index 0000000000..32571455eb --- /dev/null +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -0,0 +1,84 @@ +############################################################################## +# 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 Plumed(Package): + """PLUMED is an open source library for free energy calculations in + molecular systems which works together with some of the most popular + molecular dynamics engines. + + Free energy calculations can be performed as a function of many order + parameters with a particular focus on biological problems, using state + of the art methods such as metadynamics, umbrella sampling and + Jarzynski-equation based steered MD. + + The software, written in C++, can be easily interfaced with both fortran + and C/C++ codes. + """ + homepage = 'http://www.plumed.org/' + url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz' + + version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8') + + variant('shared', default=True, description='Builds shared libraries') + variant('mpi', default=True, description='Activates MPI support') + variant('gsl', default=True, description='Activates GSL support') + + depends_on('zlib') + depends_on('blas') + depends_on('lapack') + + depends_on('mpi', when='+mpi') + depends_on('gsl', when='+gsl') + + def setup_dependent_package(self, module, ext_spec): + # Make plumed visible from dependent packages + module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed')) + + def install(self, spec, prefix): + # From plumed docs : + # Also consider that this is different with respect to what some other + # configure script does in that variables such as MPICXX are + # completely ignored here. In case you work on a machine where CXX is + # set to a serial compiler and MPICXX to a MPI compiler, to compile + # with MPI you should use: + # + # > ./configure CXX="$MPICXX" + configure_opts = [ + 'CXX={0}'.format(spec['mpi'].mpicxx) + ] if '+mpi' in self.spec else [] + + configure_opts.extend([ + '--prefix={0}'.format(prefix), + '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'), # NOQA: ignore=E501 + '--enable-mpi={0}'.format('yes' if '+mpi' in spec else 'no'), + '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no') + ]) + + configure(*configure_opts) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index f96cb9b4cd..90a67c51bd 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -43,6 +43,7 @@ class PyH5py(Package): # Build dependencies depends_on('py-cython@0.19:', type='build') depends_on('pkg-config', type='build') + depends_on('py-setuptools', type='build') depends_on('hdf5@1.8.4:') depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-meep/package.py new file mode 100644 index 0000000000..269ac55c67 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-meep/package.py @@ -0,0 +1,75 @@ +############################################################################## +# 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 PyMeep(Package): + """Python-meep is a wrapper around libmeep. It allows the scripting of + Meep-simulations with Python""" + + homepage = "https://launchpad.net/python-meep" + url = "https://launchpad.net/python-meep/1.4/1.4/+download/python-meep-1.4.2.tar" + + version('1.4.2', 'f8913542d18b0dda92ebc64f0a10ce56') + + variant('mpi', default=True, description='Enable MPI support') + + extends('python') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-matplotlib', type=nolink) + + depends_on('mpi', when='+mpi') + depends_on('meep~mpi', when='~mpi') + depends_on('meep+mpi', when='+mpi') + + # As of SWIG 3.0.3, Python-style comments are now treated as + # pre-processor directives. Use older SWIG. But not too old, + # or else it can't handle newer C++ compilers and flags. + depends_on('swig@1.3.39:3.0.2') + + def install(self, spec, prefix): + setup = 'setup-mpi.py' if '+mpi' in spec else 'setup.py' + + include_dirs = [ + spec['meep'].prefix.include, + spec['py-numpy'].include + ] + + library_dirs = [ + spec['meep'].prefix.lib + ] + + if '+mpi' in spec: + include_dirs.append(spec['mpi'].prefix.include) + library_dirs.append(spec['mpi'].prefix.lib) + + include_flags = '-I{0}'.format(','.join(include_dirs)) + library_flags = '-L{0}'.format(','.join(library_dirs)) + + python(setup, 'clean', '--all') + python(setup, 'build_ext', include_flags, library_flags) + python(setup, 'install', '--prefix={0}'.format(prefix)) + python(setup, 'bdist', include_flags, library_flags) diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index d545717628..79ad420f8f 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyNetworkx(Package): - """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.""" + """NetworkX is a Python package for the creation, manipulation, and study + of the structure, dynamics, and functions of complex networks.""" homepage = "http://networkx.github.io/" url = "https://pypi.python.org/packages/source/n/networkx/networkx-1.11.tar.gz" @@ -34,6 +36,7 @@ class PyNetworkx(Package): extends('python') depends_on('py-decorator', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index d15a1784d1..eb3dd77219 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -36,7 +36,7 @@ class PyNose(Package): version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') - extends('python', ignore=r'bin/nosetests.*$') + extends('python') depends_on('py-setuptools', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 2febdac658..f800b5e834 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import platform class PyNumpy(Package): @@ -48,6 +49,18 @@ class PyNumpy(Package): depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') + def setup_dependent_package(self, module, dep_spec): + python_version = self.spec['python'].version.up_to(2) + arch = '{0}-{1}'.format(platform.system().lower(), platform.machine()) + + self.spec.include = join_path( + self.prefix.lib, + 'python{0}'.format(python_version), + 'site-packages', + 'numpy-{0}-py{1}-{2}.egg'.format( + self.spec.version, python_version, arch), + 'numpy/core/include') + def install(self, spec, prefix): libraries = [] library_dirs = [] diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py index 58ed067b21..f87e74211f 100644 --- a/var/spack/repos/builtin/packages/py-pytables/package.py +++ b/var/spack/repos/builtin/packages/py-pytables/package.py @@ -23,10 +23,11 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import re + class PyPytables(Package): - """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.""" + """PyTables is a package for managing hierarchical datasets and designed to + efficiently and easily cope with extremely large amounts of data.""" homepage = "http://www.pytables.org/" url = "https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz" @@ -37,6 +38,7 @@ class PyPytables(Package): depends_on('py-numpy', type=nolink) depends_on('py-numexpr', type=nolink) depends_on('py-cython', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): env["HDF5_DIR"] = spec['hdf5'].prefix diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 26c286e4be..fbeb5c95ca 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -42,6 +42,7 @@ class PyScikitImage(Package): depends_on('py-six', type=nolink) depends_on('py-scipy', type=nolink) depends_on('py-matplotlib', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % 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-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py new file mode 100644 index 0000000000..1f2f541fec --- /dev/null +++ b/var/spack/repos/builtin/packages/r-boot/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 RBoot(Package): + """Functions and datasets for bootstrapping from the book "Bootstrap + Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, + CUP), originally written by Angelo Canty for S.""" + + homepage = "https://cran.r-project.org/package=boot" + url = "https://cran.r-project.org/src/contrib/boot_1.3-18.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/boot" + + version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f') + + 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-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py new file mode 100644 index 0000000000..111606d576 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-brew/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 RBrew(Package): + """brew implements a templating framework for mixing text and R code for + report generation. brew template syntax is similar to PHP, Ruby's erb + module, Java Server Pages, and Python's psp module.""" + + homepage = "https://cran.r-project.org/package=brew" + url = "https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/brew" + + version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806') + + 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-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py new file mode 100644 index 0000000000..f4a3824983 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -0,0 +1,48 @@ +############################################################################## +# 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 RCar(Package): + """Functions and Datasets to Accompany J. Fox and S. Weisberg, An R + Companion to Applied Regression, Second Edition, Sage, 2011.""" + + homepage = "https://r-forge.r-project.org/projects/car/" + url = "https://cran.r-project.org/src/contrib/car_2.1-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/car" + + version('2.1-2', '0f78ad74ef7130126d319acec23951a0') + + extends('R') + + depends_on('r-mass', type=nolink) + depends_on('r-mgcv', type=nolink) + depends_on('r-nnet', type=nolink) + depends_on('r-pbkrtest', type=nolink) + depends_on('r-quantreg', 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-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py new file mode 100644 index 0000000000..460526c7d3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-caret/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 RCaret(Package): + """Misc functions for training and plotting classification and regression + models.""" + + homepage = "https://github.com/topepo/caret/" + url = "https://cran.r-project.org/src/contrib/caret_6.0-70.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/caret" + + version('6.0-70', '202d7abb6a679af716ea69fb2573f108') + + extends('R') + + depends_on('r-lattice', type=nolink) + depends_on('r-ggplot2', type=nolink) + depends_on('r-car', type=nolink) + depends_on('r-foreach', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-nlme', 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-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py new file mode 100644 index 0000000000..9cd9d76e9e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-chron/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 RChron(Package): + """Chronological objects which can handle dates and times.""" + + homepage = "https://cran.r-project.org/package=chron" + url = "https://cran.r-project.org/src/contrib/chron_2.3-47.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/chron" + + version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f') + + 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-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py new file mode 100644 index 0000000000..f541ea3611 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 RClass(Package): + """Various functions for classification, including k-nearest neighbour, + Learning Vector Quantization and Self-Organizing Maps.""" + + homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" + url = "https://cran.r-project.org/src/contrib/class_7.3-14.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/class" + + version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') + + extends('R') + + depends_on('r-mass', 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-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-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py new file mode 100644 index 0000000000..1e0befbca9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-crayon/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 RCrayon(Package): + """Colored terminal output on terminals that support 'ANSI' color and + highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is + automatically detected. Colors and highlighting can be combined and nested. + New styles can also be created easily. This package was inspired by the + 'chalk' 'JavaScript' project.""" + + homepage = "https://github.com/gaborcsardi/crayon" + url = "https://cran.r-project.org/src/contrib/crayon_1.3.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/crayon" + + version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9') + + 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-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py new file mode 100644 index 0000000000..1d8f837922 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-cubature/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 RCubature(Package): + """Adaptive multivariate integration over hypercubes""" + + homepage = "https://cran.r-project.org/package=cubature" + url = "https://cran.r-project.org/src/contrib/cubature_1.1-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/cubature" + + version('1.1-2', '5617e1d82baa803a3814d92461da45c9') + + 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-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index c6e8f22a94..24c0eadb2d 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -38,8 +38,9 @@ class RCurl(Package): homepage = "https://github.com/jeroenooms/curl" url = "https://cran.r-project.org/src/contrib/curl_0.9.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl" + list_url = "https://cran.r-project.org/src/contrib/Archive/curl" + version('1.0', '93d34926d6071e1fba7e728b482f0dd9') version('0.9.7', 'a101f7de948cb828fef571c730f39217') extends('R') diff --git a/var/spack/repos/builtin/packages/r-datatable/package.py b/var/spack/repos/builtin/packages/r-datatable/package.py new file mode 100644 index 0000000000..8b50643341 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-datatable/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 RDatatable(Package): + """Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, + fast add/modify/delete of columns by group using no copies at all, list + columns and a fast file reader (fread). Offers a natural and flexible + syntax, for faster development.""" + + homepage = "https://github.com/Rdatatable/data.table/wiki" + url = "https://cran.r-project.org/src/contrib/data.table_1.9.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/data.table" + + version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372') + + extends('R') + + depends_on('r-chron') + + 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-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py new file mode 100644 index 0000000000..c2e7166403 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-e1071/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 RE1071(Package): + """Functions for latent class analysis, short time Fourier transform, fuzzy + clustering, support vector machines, shortest path computation, bagged + clustering, naive Bayes classifier, ...""" + + homepage = "https://cran.r-project.org/package=e1071" + url = "https://cran.r-project.org/src/contrib/e1071_1.6-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/e1071" + + version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') + + extends('R') + + depends_on('r-class', 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-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py new file mode 100644 index 0000000000..0a09a1145b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -0,0 +1,59 @@ +############################################################################## +# 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 RGdata(Package): + """Various R programming tools for data manipulation, including: - medical + unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects + ('bindData', 'cbindX', 'combine', 'interleave'), - character vector + operations ('centerText', 'startsWith', 'trim'), - factor manipulation + ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R + objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', + 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel + formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', + 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - + extricating components of date & time objects ('getYear', 'getMonth', + 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data + frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', + 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', + 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames + ('frameApply', 'wideByFactor'), - value of last evaluated expression + ('ans'), and - wrapper for 'sample' that ensures consistent behavior for + both scalar and vector arguments ('resample').""" + + homepage = "https://cran.r-project.org/package=gdata" + url = "https://cran.r-project.org/src/contrib/gdata_2.17.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gdata" + + version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f') + + extends('R') + + depends_on('r-gtools', 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-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py new file mode 100644 index 0000000000..21ae07fd41 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-geosphere/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 RGeosphere(Package): + """Spherical trigonometry for geographic applications. That is, compute + distances and related measures for angular (longitude/latitude) + locations.""" + + homepage = "https://cran.r-project.org/package=geosphere" + url = "https://cran.r-project.org/src/contrib/geosphere_1.5-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/geosphere" + + version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e') + + extends('R') + + 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-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py new file mode 100644 index 0000000000..2dfca19b51 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -0,0 +1,57 @@ +############################################################################## +# 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 RGgmap(Package): + """A collection of functions to visualize spatial data and models on top of + static maps from various online sources (e.g Google Maps and Stamen Maps). + It includes tools common to those tasks, including functions for + geolocation and routing.""" + + homepage = "https://github.com/dkahle/ggmap" + url = "https://cran.r-project.org/src/contrib/ggmap_2.6.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggmap" + + version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a') + + extends('R') + + depends_on('r-ggplot2', type=nolink) + depends_on('r-proto', type=nolink) + depends_on('r-rgooglemaps', type=nolink) + depends_on('r-png', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-reshape2', type=nolink) + depends_on('r-rjson', type=nolink) + depends_on('r-mapproj', type=nolink) + depends_on('r-jpeg', type=nolink) + depends_on('r-geosphere', type=nolink) + depends_on('r-digest', 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-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-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py new file mode 100644 index 0000000000..af6e1d1b63 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-glmnet/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 RGlmnet(Package): + """Extremely efficient procedures for fitting the entire lasso or + elastic-net regularization path for linear regression, logistic and + multinomial regression models, Poisson regression and the Cox model. Two + recent additions are the multiple-response Gaussian, and the grouped + multinomial. The algorithm uses cyclical coordinate descent in a path-wise + fashion, as described in the paper linked to via the URL below.""" + + homepage = "http://www.jstatsoft.org/v33/i01/" + url = "https://cran.r-project.org/src/contrib/glmnet_2.0-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/glmnet" + + version('2.0-5', '049b18caa29529614cd684db3beaec2a') + + extends('R') + + depends_on('r-matrix', type=nolink) + depends_on('r-foreach', 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-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-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py new file mode 100644 index 0000000000..367bb30f87 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gtools/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 RGtools(Package): + """Functions to assist in R programming, including: - assist in developing, + updating, and maintaining R and R packages ('ask', 'checkRVersion', + 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse + logit transformations ('logit', 'inv.logit'), - test if a value is missing, + empty or contains only NA and NULL values ('invalid'), - manipulate R's + .Last function ('addLast'), - define macros ('defmacro'), - detect odd and + even integers ('odd', 'even'), - convert strings containing non-ASCII + characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a + binary search ('binsearch'), - sort strings containing both numeric and + character components ('mixedsort'), - create a factor variable from the + quantiles of a continuous variable ('quantcut'), - enumerate permutations + and combinations ('combinations', 'permutation'), - calculate and convert + between fold-change and log-ratio ('foldchange', 'logratio2foldchange', + 'foldchange2logratio'), - calculate probabilities and generate random + numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply + a function over adjacent subsets of a vector ('running'), - modify the + TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of + data frames, even if the column names don't match ('smartbind'), - generate + significance stars from p-values ('stars.pval'), - convert characters + to/from ASCII codes.""" + + homepage = "https://cran.r-project.org/package=gtools" + url = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gtools" + + version('3.5.0', '45f8800c0336d35046641fbacc56bdbb') + + 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-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-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py new file mode 100644 index 0000000000..ef940720f8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-jpeg/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 RJpeg(Package): + """This package provides an easy and simple way to read, write and display + bitmap images stored in the JPEG format. It can read and write both files + and in-memory raw vectors.""" + + homepage = "http://www.rforge.net/jpeg/" + url = "https://cran.r-project.org/src/contrib/jpeg_0.1-8.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/jpeg" + + version('0.1-8', '696007451d14395b1ed1d0e9af667a57') + + extends('R') + + depends_on('jpeg') + + 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-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 6e231ed345..d1cb4b52c1 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -38,9 +38,10 @@ class RJsonlite(Package): use with dynamic data in systems and applications.""" homepage = "https://github.com/jeroenooms/jsonlite" - url = "https://cran.r-project.org/src/contrib/jsonlite_0.9.21.tar.gz" + url = "https://cran.r-project.org/src/contrib/jsonlite_1.0.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite" + version('1.0', 'c8524e086de22ab39b8ac8000220cc87') version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') extends('R') 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-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py new file mode 100644 index 0000000000..c52d9d0e27 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lme4/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 RLme4(Package): + """Fit linear and generalized linear mixed-effects models. The models and + their components are represented using S4 classes and methods. The core + computational algorithms are implemented using the 'Eigen' C++ library for + numerical linear algebra and 'RcppEigen' "glue".""" + + homepage = "https://github.com/lme4/lme4/" + url = "https://cran.r-project.org/src/contrib/lme4_1.1-12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lme4" + + version('1.1-12', 'da8aaebb67477ecb5631851c46207804') + + extends('R') + + depends_on('r-matrix', type=nolink) + depends_on('r-mass', type=nolink) + depends_on('r-lattice', type=nolink) + depends_on('r-nlme', type=nolink) + depends_on('r-minqa', type=nolink) + depends_on('r-nloptr', type=nolink) + depends_on('r-rcpp', type=nolink) + depends_on('r-rcppeigen', 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-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py new file mode 100644 index 0000000000..31a36f1f7e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lmtest/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 RLmtest(Package): + """A collection of tests, data sets, and examples for diagnostic checking + in linear regression models. Furthermore, some generic tools for inference + in parametric models are provided.""" + + homepage = "https://cran.r-project.org/package=lmtest" + url = "https://cran.r-project.org/src/contrib/lmtest_0.9-34.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lmtest" + + version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe') + + 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-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-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py new file mode 100644 index 0000000000..0f8bbe199b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mapproj/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 RMapproj(Package): + """Converts latitude/longitude into projected coordinates.""" + + homepage = "https://cran.r-project.org/package=mapproj" + url = "https://cran.r-project.org/src/contrib/mapproj_1.2-4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mapproj" + + version('1.2-4', '10e22bde1c790e1540672f15ddcaee71') + + extends('R') + + depends_on('r-maps', 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-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py new file mode 100644 index 0000000000..1e0bfd2d43 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-maps/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 RMaps(Package): + """Display of maps. Projection code and larger maps are in separate + packages ('mapproj' and 'mapdata').""" + + homepage = "https://cran.r-project.org/" + url = "https://cran.r-project.org/src/contrib/maps_3.1.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/maps" + + version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764') + + 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-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py new file mode 100644 index 0000000000..8d045a4ed4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-maptools/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 RMaptools(Package): + """Set of tools for manipulating and reading geographic data, in particular + ESRI shapefiles; C code used from shapelib. It includes binary access to + GSHHG shoreline files. The package also provides interface wrappers for + exchanging spatial objects with packages such as PBSmapping, spatstat, + maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.""" + + homepage = "http://r-forge.r-project.org/projects/maptools/" + url = "https://cran.r-project.org/src/contrib/maptools_0.8-39.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/maptools" + + version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836') + + extends('R') + + depends_on('r-sp', type=nolink) + depends_on('r-foreign', type=nolink) + 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-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-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py new file mode 100644 index 0000000000..3cdce6fea6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 RMatrixmodels(Package): + """Modelling with sparse and dense 'Matrix' matrices, using modular + prediction and response module classes.""" + + homepage = "http://matrix.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/MatrixModels" + + version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') + + 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-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-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py new file mode 100644 index 0000000000..4c49462ba2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mgcv/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 RMgcv(Package): + """GAMs, GAMMs and other generalized ridge regression with multiple + smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam() + function, a wide variety of smoothers, JAGS support and distributions + beyond the exponential family.""" + + homepage = "https://cran.r-project.org/package=mgcv" + url = "https://cran.r-project.org/src/contrib/mgcv_1.8-13.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv" + + version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') + + extends('R') + + depends_on('r-nlme', 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-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index fb079f44c5..5e78889a76 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -30,9 +30,10 @@ class RMime(Package): from /etc/mime.types in UNIX-type systems.""" homepage = "https://github.com/yihui/mime" - url = "https://cran.r-project.org/src/contrib/mime_0.4.tar.gz" + url = "https://cran.r-project.org/src/contrib/mime_0.5.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/mime" + version('0.5', '87e00b6d57b581465c19ae869a723c4d') version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') extends('R') diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py new file mode 100644 index 0000000000..16cff20b41 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 RMinqa(Package): + """Derivative-free optimization by quadratic approximation based on an + interface to Fortran implementations by M. J. D. Powell.""" + + homepage = "http://optimizer.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/minqa_1.2.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/minqa" + + version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105') + + extends('R') + + 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-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py new file mode 100644 index 0000000000..54416502d9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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 RMultcomp(Package): + """Simultaneous tests and confidence intervals for general linear + hypotheses in parametric models, including linear, generalized linear, + linear mixed effects, and survival models. The package includes demos + reproducing analyzes presented in the book "Multiple Comparisons Using R" + (Bretz, Hothorn, Westfall, 2010, CRC Press).""" + + homepage = "http://multcomp.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/multcomp_1.4-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/multcomp" + + version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') + + extends('R') + + depends_on('r-mvtnorm', type=nolink) + depends_on('r-survival', type=nolink) + depends_on('r-thdata', type=nolink) + depends_on('r-sandwich', type=nolink) + depends_on('r-codetools', 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-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-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py new file mode 100644 index 0000000000..b3f7db60c6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mvtnorm/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 RMvtnorm(Package): + """Computes multivariate normal and t probabilities, quantiles, random + deviates and densities.""" + + homepage = "http://mvtnorm.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm" + + version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') + + 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-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py new file mode 100644 index 0000000000..11bf7abb38 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -0,0 +1,56 @@ +############################################################################## +# 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 RNcdf4(Package): + """Provides a high-level R interface to data files written using Unidata's + netCDF library (version 4 or earlier), which are binary data files that are + portable across platforms and include metadata information in addition to + the data sets. Using this package, netCDF files (either version 4 or + "classic" version 3) can be opened and data sets read in easily. It is also + easy to create new netCDF dimensions, variables, and files, in either + version 3 or 4 format, and manipulate existing netCDF files. This package + replaces the former ncdf package, which only worked with netcdf version 3 + files. For various reasons the names of the functions have had to be + changed from the names in the ncdf package. The old ncdf package is still + available at the URL given below, if you need to have backward + compatibility. It should be possible to have both the ncdf and ncdf4 + packages installed simultaneously without a problem. However, the ncdf + package does not provide an interface for netcdf version 4 files.""" + + homepage = "http://cirrus.ucsd.edu/~pierce/ncdf" + url = "https://cran.r-project.org/src/contrib/ncdf4_1.15.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ncdf4" + + version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a') + + extends('R') + + depends_on('netcdf') + + 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-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-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py new file mode 100644 index 0000000000..1b6bb114e1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nlme/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 RNlme(Package): + """Fit and compare Gaussian linear and nonlinear mixed-effects models.""" + + homepage = "https://cran.r-project.org/package=nlme" + url = "https://cran.r-project.org/src/contrib/nlme_3.1-128.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/nlme" + + version('3.1-128', '3d75ae7380bf123761b95a073eb55008') + + 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-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py new file mode 100644 index 0000000000..58cb585c49 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nloptr/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 RNloptr(Package): + """nloptr is an R interface to NLopt. NLopt is a free/open-source library + for nonlinear optimization, providing a common interface for a number of + different free optimization routines available online as well as original + implementations of various other algorithms. See + http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more + information on the available algorithms. During installation on Unix the + NLopt code is downloaded and compiled from the NLopt website.""" + + homepage = "https://cran.r-project.org/package=nloptr" + url = "https://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/nloptr" + + version('1.0.4', '9af69a613349b236fd377d0a107f484c') + + 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-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-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py new file mode 100644 index 0000000000..be048f5ad0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nnet/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 RNnet(Package): + """Software for feed-forward neural networks with a single hidden layer, + and for multinomial log-linear models.""" + + homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" + url = "https://cran.r-project.org/src/contrib/nnet_7.3-12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/nnet" + + version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e') + + 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-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py new file mode 100644 index 0000000000..bff7d0f195 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-np/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 RNp(Package): + """This package provides a variety of nonparametric (and semiparametric) + kernel methods that seamlessly handle a mix of continuous, unordered, and + ordered factor data types. We would like to gratefully acknowledge support + from the Natural Sciences and Engineering Research Council of Canada + (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council + of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic + Research Computing Network (SHARCNET:www.sharcnet.ca).""" + + homepage = "https://github.com/JeffreyRacine/R-Package-np/" + url = "https://cran.r-project.org/src/contrib/np_0.60-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/np" + + version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389') + + extends('R') + + depends_on('r-boot', type=nolink) + depends_on('r-cubature', 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-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py new file mode 100644 index 0000000000..40b6f96927 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pbkrtest/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 RPbkrtest(Package): + """Test in mixed effects models. Attention is on mixed effects models as + implemented in the 'lme4' package. This package implements a parametric + bootstrap test and a Kenward Roger modification of F-tests for linear mixed + effects models and a parametric bootstrap test for generalized linear mixed + models.""" + + homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/" + url = "https://cran.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest" + + version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') + + extends('R') + + depends_on('r-lme4', type=nolink) + depends_on('r-matrix', type=nolink) + depends_on('r-mass', 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-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py new file mode 100644 index 0000000000..d1d61dbc4d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-plotrix/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 RPlotrix(Package): + """Lots of plots, various labeling, axis and color scaling functions.""" + + homepage = "https://cran.r-project.org/package=plotrix" + url = "https://cran.r-project.org/src/contrib/plotrix_3.6-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/plotrix" + + version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') + + 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-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-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py new file mode 100644 index 0000000000..102d86d2fa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-praise/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 RPraise(Package): + """Build friendly R packages that praise their users if they have done + something good, or they just need it to feel better.""" + + homepage = "https://github.com/gaborcsardi/praise" + url = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz" + + version('1.0.0', '9318724cec0454884b5f762bee2da6a1') + + 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-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py new file mode 100644 index 0000000000..07ace3ad29 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-proto/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 RProto(Package): + """An object oriented system using object-based, also called + prototype-based, rather than class-based object oriented ideas.""" + + homepage = "http://r-proto.googlecode.com/" + url = "https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/proto" + + version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212') + + 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-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py new file mode 100644 index 0000000000..ecfbf49055 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-quantmod/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 RQuantmod(Package): + """Specify, build, trade, and analyse quantitative financial trading + strategies.""" + + homepage = "http://www.quantmod.com/" + url = "https://cran.r-project.org/src/contrib/quantmod_0.4-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/quantmod" + + version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631') + + extends('R') + + depends_on('r-xts', type=nolink) + depends_on('r-zoo', type=nolink) + depends_on('r-ttr', 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-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py new file mode 100644 index 0000000000..89a26070ba --- /dev/null +++ b/var/spack/repos/builtin/packages/r-quantreg/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 RQuantreg(Package): + """Estimation and inference methods for models of conditional quantiles: + Linear and nonlinear parametric and non-parametric (total variation + penalized) models for conditional quantiles of a univariate response + and several methods for handling censored survival data. Portfolio + selection methods based on expected shortfall risk are also + included.""" + + homepage = "https://cran.r-project.org/package=quantreg" + url = "https://cran.r-project.org/src/contrib/quantreg_5.26.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg" + + version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') + + extends('R') + + depends_on('r-sparsem', type=nolink) + depends_on('r-matrix', type=nolink) + depends_on('r-matrixmodels', 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-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py new file mode 100644 index 0000000000..1066c217f4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-randomforest/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 RRandomforest(Package): + """Classification and regression based on a forest of trees using random + inputs.""" + + homepage = "https://www.stat.berkeley.edu/~breiman/RandomForests/" + url = "https://cran.r-project.org/src/contrib/randomForest_4.6-12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/randomForest" + + version('4.6-12', '071c03af974198e861f1475c5bab9e7a') + + 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-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-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 2428f4af3b..94580a8700 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -37,9 +37,10 @@ class RRcpp(Package): last two.""" homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" - url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz" + url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.6.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp" + version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b') version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') extends('R') 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-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py new file mode 100644 index 0000000000..0d28b68b94 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/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 RRgooglemaps(Package): + """This package serves two purposes: (i) Provide a comfortable R interface + to query the Google server for static maps, and (ii) Use the map as a + background image to overlay plots within R. This requires proper coordinate + scaling.""" + + homepage = "https://cran.r-project.org/package=RgoogleMaps" + url = "https://cran.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RgoogleMaps" + + version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5') + + extends('R') + + depends_on('r-png', type=nolink) + depends_on('r-rjsonio', 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-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py new file mode 100644 index 0000000000..94ca45f485 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rjson/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 RRjson(Package): + """Converts R object into JSON objects and vice-versa.""" + + homepage = "https://cran.r-project.org/package=rjson" + url = "https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rjson" + + version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9') + + 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-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py new file mode 100644 index 0000000000..b56dfbe21d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -0,0 +1,55 @@ +############################################################################## +# 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 RRjsonio(Package): + """This is a package that allows conversion to and from data in Javascript + object notation (JSON) format. This allows R objects to be inserted into + Javascript/ECMAScript/ActionScript code and allows R programmers to read + and convert JSON content to R objects. This is an alternative to rjson + package. Originally, that was too slow for converting large R objects to + JSON and was not extensible. rjson's performance is now similar to this + package, and perhaps slightly faster in some cases. This package uses + methods and is readily extensible by defining methods for different + classes, vectorized operations, and C code and callbacks to R functions for + deserializing JSON objects to R. The two packages intentionally share the + same basic interface. This package (RJSONIO) has many additional options to + allow customizing the generation and processing of JSON content. This + package uses libjson rather than implementing yet another JSON parser. The + aim is to support other general projects by building on their work, + providing feedback and benefit from their ongoing development.""" + + homepage = "https://cran.r-project.org/package=RJSONIO" + url = "https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RJSONIO" + + version('1.3-0', '72c395622ba8d1435ec43849fd32c830') + + 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-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 086374df07..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-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py new file mode 100644 index 0000000000..4f4b8dcafa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -0,0 +1,48 @@ +############################################################################## +# 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 RRoxygen2(Package): + """A 'Doxygen'-like in-source documentation system for Rd, collation, and + 'NAMESPACE' files.""" + + homepage = "https://github.com/klutometis/roxygen" + url = "https://cran.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/roxygen2" + + version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7') + + extends('R') + + depends_on('r-stringr', type=nolink) + depends_on('r-stringi', type=nolink) + depends_on('r-brew', type=nolink) + 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), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 53e1978ffe..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 7c03ab8950..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-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py new file mode 100644 index 0000000000..ffd62b1b14 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 RSandwich(Package): + """Model-robust standard error estimators for cross-sectional, time series, + and longitudinal data.""" + + homepage = "https://cran.r-project.org/package=sandwich" + url = "https://cran.r-project.org/src/contrib/sandwich_2.3-4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/sandwich" + + version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') + + 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-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-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py new file mode 100644 index 0000000000..c4dabf5c15 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sparsem/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 RSparsem(Package): + """Some basic linear algebra functionality for sparse matrices is provided: + including Cholesky decomposition and backsolving as well as standard R + subsetting and Kronecker products.""" + + homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html" + url = "https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM" + + version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') + + 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-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-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py new file mode 100644 index 0000000000..646793f7a4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-survey/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 RSurvey(Package): + """Summary statistics, two-sample tests, rank tests, generalised linear + models, cumulative link models, Cox models, loglinear models, and general + maximum pseudolikelihood estimation for multistage stratified, + cluster-sampled, unequally weighted survey samples. Variances by Taylor + series linearisation or replicate weights. Post-stratification, + calibration, and raking. Two-phase subsampling designs. Graphics. PPS + sampling without replacement. Principal components, factor analysis.""" + + homepage = "http://r-survey.r-forge.r-project.org/survey/" + url = "https://cran.r-project.org/src/contrib/survey_3.30-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/survey" + + version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0') + + 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-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py new file mode 100644 index 0000000000..cfba9298fe --- /dev/null +++ b/var/spack/repos/builtin/packages/r-survival/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 RSurvival(Package): + """Contains the core survival analysis routines, including definition of + Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox + models, and parametric accelerated failure time models.""" + + homepage = "https://cran.r-project.org/package=survival" + url = "https://cran.r-project.org/src/contrib/survival_2.39-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/survival" + + version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') + + 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-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py new file mode 100644 index 0000000000..a85aa8baef --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 RTarifx(Package): + """A collection of various utility and convenience functions.""" + + homepage = "https://cran.r-project.org/package=taRifx" + url = "https://cran.r-project.org/src/contrib/taRifx_1.0.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/taRifx" + + version('1.0.6', '7e782e04bd69d929b29f91553382e6a2') + + extends('R') + + depends_on('r-reshape2', type=nolink) + depends_on('r-plyr', 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-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py new file mode 100644 index 0000000000..60dfd2afcd --- /dev/null +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -0,0 +1,48 @@ +############################################################################## +# 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 RTestthat(Package): + """A unit testing system designed to be fun, flexible and easy to set + up.""" + + homepage = "https://github.com/hadley/testthat" + url = "https://cran.r-project.org/src/contrib/testthat_1.0.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/testthat" + + version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc') + + extends('R') + + depends_on('r-digest', type=nolink) + depends_on('r-crayon', type=nolink) + depends_on('r-praise', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-R6', 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-thdata/package.py b/var/spack/repos/builtin/packages/r-thdata/package.py new file mode 100644 index 0000000000..e1cf050181 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-thdata/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 RThdata(Package): + """Contains data sets used in other packages Torsten Hothorn maintains.""" + + homepage = "https://cran.r-project.org/package=TH.data" + url = "https://cran.r-project.org/src/contrib/TH.data_1.0-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/TH.data" + + version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') + + extends('R') + + depends_on('r-survival', type=nolink) + depends_on('r-mass', 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-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-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py new file mode 100644 index 0000000000..c9b40a8262 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 RTtr(Package): + """Functions and data to construct technical trading rules with R.""" + + homepage = "https://github.com/joshuaulrich/TTR" + url = "https://cran.r-project.org/src/contrib/TTR_0.23-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/TTR" + + version('0.23-1', '35f693ac0d97e8ec742ebea2da222986') + + extends('R') + + depends_on('r-xts', type=nolink) + 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-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py new file mode 100644 index 0000000000..06e609b1ef --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vcd/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 RVcd(Package): + """Visualization techniques, data sets, summary and inference procedures + aimed particularly at categorical data. Special emphasis is given to highly + extensible grid graphics. The package was package was originally inspired + by the book "Visualizing Categorical Data" by Michael Friendly and is now + the main support package for a new book, "Discrete Data Analysis with R" by + Michael Friendly and David Meyer (2015).""" + + homepage = "https://cran.r-project.org/package=vcd" + url = "https://cran.r-project.org/src/contrib/vcd_1.4-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/vcd" + + version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02') + + extends('R') + + depends_on('r-mass', type=nolink) + depends_on('r-colorspace', type=nolink) + depends_on('r-lmtest', 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-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 4ee7163be1..332c80fb92 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -33,13 +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('0.2-11', '9d1769a103cda05665df399cc335017d', - url='https://cran.r-project.org/src/contrib/Archive/XLConnect/XLConnect_0.2-11.tar.gz') + 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 c1fb365883..26e822d2b7 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -32,12 +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('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb', - url='https://cran.r-project.org/src/contrib/Archive/XLConnectJars/XLConnectJars_0.2-9.tar.gz') + 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 99d41dbb94..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 80e86d0c73..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-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py new file mode 100644 index 0000000000..591c887f32 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xml/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 RXml(Package): + """Many approaches for both reading and creating XML (and HTML) documents + (including DTDs), both local and accessible via HTTP or FTP. Also offers + access to an 'XPath' "interpreter".""" + + homepage = "http://www.omegahat.net/RSXML" + url = "https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/XML" + + version('3.98-1', '1a7f3ce6f264eeb109bfa57bedb26c14') + + extends('R') + + 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-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) diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index f552621821..b43246dcee 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -22,9 +22,9 @@ # 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 Swig(Package): """SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, @@ -38,6 +38,7 @@ class Swig(Package): homepage = "http://www.swig.org" url = "http://prdownloads.sourceforge.net/swig/swig-3.0.8.tar.gz" + version('3.0.10', 'bb4ab8047159469add7d00910e203124') version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97') version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4') diff --git a/var/spack/repos/builtin/packages/texlive/package.py b/var/spack/repos/builtin/packages/texlive/package.py new file mode 100644 index 0000000000..d44a6e311e --- /dev/null +++ b/var/spack/repos/builtin/packages/texlive/package.py @@ -0,0 +1,57 @@ +############################################################################## +# 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 * +import os + + +class Texlive(Package): + """TeX Live is a free software distribution for the TeX typesetting + system""" + + homepage = "http://www.tug.org/texlive" + + version('live', 'e671eea7f142c438959493cc42a2a59b', url="http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz") + + # There does not seem to be a complete list of schemes. + # Examples include: + # full scheme (everything) + # medium scheme (small + more packages and languages) + # small scheme (basic + xetex, metapost, a few languages) + # basic scheme (plain and latex) + # minimal scheme (plain only) + # See: + # https://www.tug.org/texlive/doc/texlive-en/texlive-en.html#x1-25025r6 + variant('scheme', default="small", + description='Package subset to install (e.g. full, small, basic)') + + depends_on('perl') + + def install(self, spec, prefix): + env = os.environ + env['TEXLIVE_INSTALL_PREFIX'] = prefix + perl = which('perl') + scheme = spec.variants['scheme'].value + perl('./install-tl', '-scheme', scheme, + '-portable', '-profile', '/dev/null') diff --git a/var/spack/repos/builtin/packages/tree/package.py b/var/spack/repos/builtin/packages/tree/package.py new file mode 100644 index 0000000000..8e0e176c4c --- /dev/null +++ b/var/spack/repos/builtin/packages/tree/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 Tree(Package): + """Tree is a recursive directory listing command that produces a depth + indented listing of files, which is colorized ala dircolors if + the LS_COLORS environment variable is set and output is to + tty. Tree has been ported and reported to work under the + following operating systems: Linux, FreeBSD, OS X, Solaris, + HP/UX, Cygwin, HP Nonstop and OS/2.""" + + homepage = "http://mama.indstate.edu/users/ice/tree/" + url = "http://mama.indstate.edu/users/ice/tree/src/tree-1.7.0.tgz" + + version('1.7.0', 'abe3e03e469c542d8e157cdd93f4d8a6') + + def install(self, spec, prefix): + filter_file(r'^prefix =.*', 'prefix = %s' % prefix, 'Makefile') + filter_file(r'^CFLAGS', '# use spack settings instead... CFLAGS', + 'Makefile') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 77589bb8f9..4d1d27e74a 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -138,16 +138,23 @@ class Trilinos(Package): '-DTPL_ENABLE_LAPACK=ON', '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name( spec['lapack'].lapack_shared_lib), - '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix, + '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix.lib, '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', '-DTPL_ENABLE_Netcdf:BOOL=ON', '-DTPL_ENABLE_HYPRE:BOOL=%s' % ( - 'ON' if '+hypre' in spec else 'OFF'), - '-DTPL_ENABLE_HDF5:BOOL=%s' % ( - 'ON' if '+hdf5' in spec else 'OFF'), + 'ON' if '+hypre' in spec else 'OFF') ]) + if '+hdf5' in spec: + options.extend([ + '-DTPL_ENABLE_HDF5:BOOL=ON', + '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include, + '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib + ]) + else: + options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF']) + if '+boost' in spec: options.extend([ '-DTPL_ENABLE_Boost:BOOL=ON', |