diff options
Diffstat (limited to 'var')
137 files changed, 4592 insertions, 247 deletions
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/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 224105ea0f..72a5cb22f8 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -15,6 +15,7 @@ class Gcc(Package): list_depth = 2 version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1') + version('5.4.0', '4c626ac2a83ef30dfb9260e6f59c2b30') version('5.3.0', 'c9616fd448f980259c31de613e575719') version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467') version('4.9.3', '6f831b4d251872736e8e9cc09746f327') 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/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py index 493ca16417..fb98b2473c 100644 --- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py +++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py @@ -42,15 +42,27 @@ class IntelParallelStudio(IntelInstaller): variant('daal', default=True, description="Install the Intel DAAL libraries") variant('ipp', default=True, description="Install the Intel IPP libraries") - variant('tools', default=True, description="""Install the Intel Advisor,\ -VTune Amplifier, and Inspector tools""") + variant('tools', default=True, description="Install the Intel Advisor, " + "VTune Amplifier, and Inspector tools") provides('mpi', when='@cluster:+mpi') provides('mkl', when='+mkl') provides('daal', when='+daal') provides('ipp', when='+ipp') + def check_variants(self, spec): + error_message = '\t{variant} can not be turned off if "+all" is set' + + if self.spec.satisfies('+all'): + errors = [error_message.format(variant=x) + for x in ('mpi', 'mkl', 'daal', 'ipp', 'tools') + if ('~' + x) in self.spec] + if errors: + errors = ['incompatible variants given'] + errors + raise InstallError('\n'.join(errors)) + def install(self, spec, prefix): + self.check_variants(spec) base_components = "ALL" # when in doubt, install everything mpi_components = "" @@ -58,9 +70,7 @@ VTune Amplifier, and Inspector tools""") daal_components = "" ipp_components = "" - if spec.satisfies('+all'): - base_components = "ALL" - else: + if not spec.satisfies('+all'): all_components = get_all_components() regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)' base_components = \ @@ -77,10 +87,10 @@ VTune Amplifier, and Inspector tools""") regex = '(gdb|vtune|inspector|advisor)' tool_components = \ filter_pick(all_components, re.compile(regex).search) + components = base_components - components = base_components if not spec.satisfies('+all'): - if spec.satisfies('+mpi') and 'cluster' in str(spec.version): + if spec.satisfies('+mpi'): components += mpi_components if spec.satisfies('+mkl'): components += mkl_components @@ -92,7 +102,10 @@ VTune Amplifier, and Inspector tools""") spec.satisfies('@professional')): components += tool_components - self.intel_components = ';'.join(components) + if spec.satisfies('+all'): + self.intel_components = 'ALL' + else: + self.intel_components = ';'.join(components) IntelInstaller.install(self, spec, prefix) absbindir = os.path.dirname(os.path.realpath(os.path.join( @@ -116,8 +129,11 @@ VTune Amplifier, and Inspector tools""") if (spec.satisfies('+all') or spec.satisfies('+mpi')) and \ spec.satisfies('@cluster'): - os.symlink(self.global_license_file, os.path.join( - self.prefix, "itac_latest", "license.lic")) + for ifile in os.listdir(os.path.join(self.prefix, "itac")): + if os.path.isdir(os.path.join(self.prefix, "itac", ifile)): + os.symlink(self.global_license_file, + os.path.join(self.prefix, "itac", ifile, + "license.lic")) if spec.satisfies('~newdtags'): wrappers = ["mpif77", "mpif77", "mpif90", "mpif90", "mpigcc", "mpigcc", "mpigxx", "mpigxx", @@ -142,3 +158,110 @@ VTune Amplifier, and Inspector tools""") os.symlink(os.path.join(self.prefix.man, "common", "man1"), os.path.join(self.prefix.man, "man1")) + + def setup_environment(self, spack_env, run_env): + # TODO: Determine variables needed for the professional edition. + + major_ver = self.version[1] + + # Remove paths that were guessed but are incorrect for this package. + run_env.remove_path('LIBRARY_PATH', + join_path(self.prefix, 'lib')) + run_env.remove_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'lib')) + run_env.remove_path('CPATH', + join_path(self.prefix, 'include')) + + # Add the default set of variables + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'lib', 'intel64')) + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'lib', 'intel64')) + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', + 'intel64', 'gcc4.4')) + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', + 'intel64', 'gcc4.4')) + run_env.prepend_path('CPATH', + join_path(self.prefix, 'tbb', 'include')) + run_env.prepend_path('MIC_LIBRARY_PATH', + join_path(self.prefix, 'lib', 'mic')) + run_env.prepend_path('MIC_LD_LIBRARY_PATH', + join_path(self.prefix, 'lib', 'mic')) + run_env.prepend_path('MIC_LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', 'mic')) + run_env.prepend_path('MIC_LD_LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', 'mic')) + + if self.spec.satisfies('+all'): + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, + 'debugger_{0}'.format(major_ver), + 'libipt', 'intel64', 'lib')) + run_env.set('GDBSERVER_MIC', + join_path(self.prefix, + 'debugger_{0}'.format(major_ver), 'gdb', + 'targets', 'mic', 'bin', 'gdbserver')) + run_env.set('GDB_CROSS', + join_path(self.prefix, + 'debugger_{0}'.format(major_ver), + 'gdb', 'intel64_mic', 'bin', 'gdb-mic')) + run_env.set('MPM_LAUNCHER', + join_path(self.prefix, + 'debugger_{0}'.format(major_ver), 'mpm', + 'mic', + 'bin', 'start_mpm.sh')) + run_env.set('INTEL_PYTHONHOME', + join_path(self.prefix, + 'debugger_{0}'.format(major_ver), 'python', + 'intel64')) + + if (self.spec.satisfies('+all') or self.spec.satisfies('+mpi')): + # Only I_MPI_ROOT is set here because setting the various PATH + # variables will potentially be in conflict with other MPI + # environment modules. The I_MPI_ROOT environment variable can be + # used as a base to set necessary PATH variables for using Intel + # MPI. It is also possible to set the variables in the modules.yaml + # file if Intel MPI is the dominant, or only, MPI on a system. + run_env.set('I_MPI_ROOT', join_path(self.prefix, 'impi')) + + if self.spec.satisfies('+all') or self.spec.satisfies('+mkl'): + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'mkl', 'lib', + 'intel64')) + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'mkl', 'lib', + 'intel64')) + run_env.prepend_path('CPATH', + join_path(self.prefix, 'mkl', 'include')) + run_env.prepend_path('MIC_LD_LIBRARY_PATH', + join_path(self.prefix, 'mkl', 'lib', 'mic')) + run_env.set('MKLROOT', join_path(self.prefix, 'mkl')) + + if self.spec.satisfies('+all') or self.spec.satisfies('+daal'): + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'daal', 'lib', + 'intel64_lin')) + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'daal', 'lib', + 'intel64_lin')) + run_env.prepend_path('CPATH', + join_path(self.prefix, 'daal', 'include')) + run_env.prepend_path('CLASSPATH', + join_path(self.prefix, 'daal', 'lib', + 'daal.jar')) + run_env.set('DAALROOT', join_path(self.prefix, 'daal')) + + if self.spec.satisfies('+all') or self.spec.satisfies('+ipp'): + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'ipp', 'lib', + 'intel64')) + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'ipp', 'lib', + 'intel64')) + run_env.prepend_path('CPATH', + join_path(self.prefix, 'ipp', 'include')) + run_env.prepend_path('MIC_LD_LIBRARY_PATH', + join_path(self.prefix, 'ipp', 'lib', 'mic')) + run_env.set('IPPROOT', join_path(self.prefix, 'ipp')) diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py index 56d9fabddf..d171411946 100644 --- a/var/spack/repos/builtin/packages/intel/package.py +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -49,13 +49,6 @@ class IntelInstaller(Package): def install(self, spec, prefix): - # Remove the installation DB, otherwise it will try to install into - # location of other Intel builds - if os.path.exists(os.path.join(os.environ["HOME"], "intel", - "intel_sdp_products.db")): - os.remove(os.path.join(os.environ["HOME"], "intel", - "intel_sdp_products.db")) - if not hasattr(self, "intel_prefix"): self.intel_prefix = self.prefix @@ -66,12 +59,14 @@ ACCEPT_EULA=accept PSET_MODE=install CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes PSET_INSTALL_DIR=%s +NONRPM_DB_DIR=%s ACTIVATION_LICENSE_FILE=%s ACTIVATION_TYPE=license_file PHONEHOME_SEND_USAGE_DATA=no CONTINUE_WITH_OPTIONAL_ERROR=yes COMPONENTS=%s -""" % (self.intel_prefix, self.global_license_file, self.intel_components)) +""" % (self.intel_prefix, self.intel_prefix, self.global_license_file, + self.intel_components)) install_script = Executable("./install.sh") install_script('--silent', silent_config_filename) @@ -111,8 +106,8 @@ class Intel(IntelInstaller): self.prefix.lib, "intel64", "libimf.a")))[0] # symlink or copy? - os.symlink(self.global_license_file, os.path.join(absbindir, - "license.lic")) + os.symlink(self.global_license_file, + os.path.join(absbindir, "license.lic")) if spec.satisfies('+rpath'): for compiler_command in ["icc", "icpc", "ifort"]: @@ -123,3 +118,35 @@ class Intel(IntelInstaller): os.symlink(os.path.join(self.prefix.man, "common", "man1"), os.path.join(self.prefix.man, "man1")) + + def setup_environment(self, spack_env, run_env): + + # Remove paths that were guessed but are incorrect for this package. + run_env.remove_path('LIBRARY_PATH', + join_path(self.prefix, 'lib')) + run_env.remove_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'lib')) + run_env.remove_path('CPATH', + join_path(self.prefix, 'include')) + + # Add the default set of variables + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'lib', 'intel64')) + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'lib', 'intel64')) + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', + 'intel64', 'gcc4.4')) + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', + 'intel64', 'gcc4.4')) + run_env.prepend_path('CPATH', + join_path(self.prefix, 'tbb', 'include')) + run_env.prepend_path('MIC_LIBRARY_PATH', + join_path(self.prefix, 'lib', 'mic')) + run_env.prepend_path('MIC_LD_LIBRARY_PATH', + join_path(self.prefix, 'lib', 'mic')) + run_env.prepend_path('MIC_LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', 'mic')) + run_env.prepend_path('MIC_LD_LIBRARY_PATH', + join_path(self.prefix, 'tbb', 'lib', 'mic')) diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index 2ec86f05e3..794966f1c3 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -22,34 +22,35 @@ # 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: Justin Too <too1@llnl.gov> -#------------------------------------------------------------------------------ -import distutils -from distutils import dir_util -from subprocess import call +# +import distutils.dir_util import spack from spack import * import llnl.util.tty as tty + class Jdk(Package): """The Java Development Kit (JDK) released by Oracle Corporation in the form of a binary product aimed at Java developers.""" - homepage = "http://www.oracle.com/technetwork/java/javase/downloads/index.html" + homepage = "http://www.oracle.com/technetwork/java/javase/downloads/index.html" # noqa: E501 version('8u66-linux-x64', '88f31f3d642c3287134297b8c10e61bf', url="http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz") + version('8u92-linux-x64', '65a1cc17ea362453a6e0eb4f13be76e4', + url="http://download.oracle.com/otn-pub/java/jdk/8u92-b14/jdk-8u92-linux-x64.tar.gz") # Oracle requires that you accept their License Agreement in order # to access the Java packages in download.oracle.com. In order to # automate this process, we need to utilize these additional curl # commandline options. # - # See http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux - curl_options=[ - '-j', # junk cookies - '-H', # specify required License Agreement cookie + # See http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux # noqa: E501 + curl_options = [ + '-j', # junk cookies + '-H', # specify required License Agreement cookie 'Cookie: oraclelicense=accept-securebackup-cookie'] def do_fetch(self, mirror_only=False): @@ -65,6 +66,5 @@ class Jdk(Package): # Now perform the actual fetch super(Jdk, self).do_fetch(mirror_only) - def install(self, spec, prefix): distutils.dir_util.copy_tree(".", prefix) 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/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/lmod/fix_tclsh_paths.patch b/var/spack/repos/builtin/packages/lmod/fix_tclsh_paths.patch new file mode 100644 index 0000000000..70f0d47925 --- /dev/null +++ b/var/spack/repos/builtin/packages/lmod/fix_tclsh_paths.patch @@ -0,0 +1,10 @@ +--- a/Makefile.in 2016-07-21 13:03:27.861000000 -0400 ++++ b/Makefile.in 2016-07-21 13:03:58.416000000 -0400 +@@ -197,6 +197,7 @@ + -e 's|@colorize@|$(COLORIZE)|g' \ + -e 's|@duplicate_paths@|$(DUPLICATE_PATHS)|g' \ + -e 's|@allow_tcl_mfiles@|$(ALLOW_TCL_MFILES)|g' \ ++ -e 's|@path_to_tclsh@|$(PATH_TO_TCLSH)|g' \ + -e 's|@mpath_avail@|$(MPATH_AVAIL)|g' \ + -e 's|@short_time@|$(SHORT_TIME)|g' \ + -e 's|@cacheDirs@|$(SPIDER_CACHE_DIRS)|g' \ diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index efa235f646..01911c1a30 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +from glob import glob class Lmod(Package): @@ -44,6 +45,7 @@ class Lmod(Package): depends_on('lua@5.2:') depends_on('lua-luaposix', type=nolink) depends_on('lua-luafilesystem', type=nolink) + depends_on('tcl', type=nolink) parallel = False @@ -53,6 +55,16 @@ class Lmod(Package): spack_env.append_path('LUA_PATH', stage_lua_path.format( version=self.version), separator=';') + patch('fix_tclsh_paths.patch') + + def patch(self): + """The tcl scripts should use the tclsh that was discovered + by the configure script. Touch up their #! lines so that the + sed in the Makefile's install step has something to work on. + Requires the change in the associated patch file.fg""" + for tclscript in glob('src/*.tcl'): + filter_file(r'^#!.*tclsh', '#!@path_to_tclsh@', tclscript) + def install(self, spec, prefix): configure('--prefix=%s' % prefix) 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/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index e7c105d5f5..78bdd88d9c 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -22,7 +22,6 @@ # 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 urllib import llnl.util.tty as tty from spack import * @@ -50,61 +49,15 @@ class Openssl(Package): parallel = False def url_for_version(self, version): - # This URL is computed pinging the place where the latest version is - # stored. To avoid slowdown due to repeated pinging, we store the URL - # in a private class attribute to do the job only once per version - openssl_urls = getattr(Openssl, '_openssl_url', {}) - openssl_url = openssl_urls.get(version, None) - # Same idea, but just to avoid issuing the same message multiple times - warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) - if openssl_url is None: - if self.spec.satisfies('@system'): - # The version @system is reserved to system openssl. In that - # case return a fake url and exit - openssl_url = '@system (reserved version for system openssl)' - if not warnings_given_to_user.get(version, False): - tty.msg('Using openssl@system: ' - 'the version @system is reserved for system openssl') - warnings_given_to_user[version] = True - else: - openssl_url = self.check_for_outdated_release( - version, warnings_given_to_user) # Store the computed URL - openssl_urls[version] = openssl_url - # Store the updated dictionary of URLS - Openssl._openssl_url = openssl_urls - # Store the updated dictionary of warnings - Openssl._warnings_given = warnings_given_to_user - - return openssl_url - - def check_for_outdated_release(self, version, warnings_given_to_user): - latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz' - older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' # NOQA: ignore=E501 - # Try to use the url where the latest tarballs are stored. - # If the url does not exist (404), then return the url for - # older format - version_number = '.'.join([str(x) for x in version[:-1]]) - try: - openssl_url = latest.format(version=version) - urllib.urlopen(openssl_url) - except IOError: - openssl_url = older.format( - version_number=version_number, version_full=version) - # Checks if we already warned the user for this particular - # version of OpenSSL. If not we display a warning message - # and mark this version - if not warnings_given_to_user.get(version, False): - tty.warn( - 'This installation depends on an old version of OpenSSL, ' - 'which may have known security issues. ') - tty.warn( - 'Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format( - homepage=Openssl.homepage)) - warnings_given_to_user[version] = True - - return openssl_url - + if '@system' in self.spec: + return '@system (reserved version for system openssl)' + else: + 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 " + "been updated, and the version in your instance of Spack is " + "insecure. Consider updating to the latest OpenSSL version.") def install(self, spec, prefix): # OpenSSL uses a variable APPS in its Makefile. If it happens to be set 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/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/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-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 68032cb68d..08d5e5d552 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -24,8 +24,11 @@ ############################################################################## from spack import * + class PySetuptools(Package): - """Easily download, build, install, upgrade, and uninstall Python packages.""" + """A Python utility that aids in the process of downloading, building, + upgrading, installing, and uninstalling Python packages.""" + homepage = "https://pypi.python.org/pypi/setuptools" url = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz" @@ -40,4 +43,4 @@ class PySetuptools(Package): extends('python') def install(self, spec, prefix): - python('setup.py', 'install', '--prefix=%s' % prefix) + setup_py('install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index bbb1e9c13a..f755527607 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -27,6 +27,7 @@ import re from contextlib import closing import spack +import llnl.util.tty as tty from llnl.util.lang import match_predicate from spack import * from spack.util.environment import * @@ -72,40 +73,41 @@ class Python(Package): depends_on("tk", when="+tk") depends_on("tcl", when="+tk") + @when('@2.7,3.4:') + def patch(self): + # NOTE: Python's default installation procedure makes it possible for a + # user's local configurations to change the Spack installation. In + # order to prevent this behavior for a full installation, we must + # modify the installation script so that it ignores user files. + ff = FileFilter('Makefile.pre.in') + ff.filter( + r'^(.*)setup\.py(.*)((build)|(install))(.*)$', + r'\1setup.py\2 --no-user-cfg \3\6' + ) + def install(self, spec, prefix): + # TODO: The '--no-user-cfg' option for Python installation is only in + # Python v2.7 and v3.4+ (see https://bugs.python.org/issue1180) and + # adding support for ignoring user configuration will require + # significant changes to this package for other Python versions. + if not spec.satisfies('@2.7,3.4:'): + tty.warn(('Python v{0} may not install properly if Python ' + 'user configurations are present.').format(self.version)) + # Need this to allow python build to find the Python installation. - env['PYTHONHOME'] = prefix + env['PYTHONHOME'], env['PYTHONPATH'] = prefix, prefix env['MACOSX_DEPLOYMENT_TARGET'] = '10.6' # Rest of install is pretty standard except setup.py needs to # be able to read the CPPFLAGS and LDFLAGS as it scans for the # library and headers to build - include_dirs = [ - spec['openssl'].prefix.include, spec['bzip2'].prefix.include, - spec['readline'].prefix.include, spec['ncurses'].prefix.include, - spec['sqlite'].prefix.include, spec['zlib'].prefix.include - ] - - library_dirs = [ - spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib, - spec['readline'].prefix.lib, spec['ncurses'].prefix.lib, - spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib - ] - - if '+tk' in spec: - include_dirs.extend([ - spec['tk'].prefix.include, spec['tcl'].prefix.include - ]) - library_dirs.extend([ - spec['tk'].prefix.lib, spec['tcl'].prefix.lib - ]) - + dep_pfxs = [dspec.prefix for dspec in spec.dependencies('link')] config_args = [ - "--prefix={0}".format(prefix), - "--with-threads", - "--enable-shared", - "CPPFLAGS=-I{0}".format(" -I".join(include_dirs)), - "LDFLAGS=-L{0}".format(" -L".join(library_dirs)) + '--prefix={0}'.format(prefix), + '--with-threads', + '--enable-shared', + 'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)), + 'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)), ] if '+ucs4' in spec: @@ -121,9 +123,8 @@ class Python(Package): config_args.append('--without-ensurepip') configure(*config_args) - make() - make("install") + make('install') self.filter_compilers(spec, prefix) @@ -193,6 +194,8 @@ class Python(Package): def setup_dependent_environment(self, spack_env, run_env, extension_spec): """Set PYTHONPATH to include site-packages dir for the extension and any other python extensions it depends on.""" + pythonhome = self.prefix + spack_env.set('PYTHONHOME', pythonhome) python_paths = [] for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): @@ -214,15 +217,14 @@ class Python(Package): In most cases, extensions will only need to have one line:: - python('setup.py', 'install', '--prefix={0}'.format(prefix))""" + setup_py('install', '--prefix={0}'.format(prefix))""" + python_path = join_path( + self.spec.prefix.bin, + 'python{0}'.format('3' if self.spec.satisfies('@3') else '') + ) - # Python extension builds can have a global python executable function - if Version("3.0.0") <= self.version < Version("4.0.0"): - module.python = Executable(join_path(self.spec.prefix.bin, - 'python3')) - else: - module.python = Executable(join_path(self.spec.prefix.bin, - 'python')) + module.python = Executable(python_path) + module.setup_py = Executable(python_path + ' setup.py --no-user-cfg') # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. module.python_lib_dir = join_path(ext_spec.prefix, diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py new file mode 100644 index 0000000000..4c5d14a90f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RBase64enc(Package): + """This package provides tools for handling base64 encoding. It is more + flexible than the orphaned base64 package.""" + + homepage = "http://www.rforge.net/base64enc" + url = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc" + + version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-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-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-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-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-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index 0ce0942602..47804bd7fc 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -37,6 +37,8 @@ class RRjava(Package): extends('R') + depends_on('jdk') + def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-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 774c166f8b..bc42c51ca9 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -36,7 +36,7 @@ class RRmysql(Package): extends('R') - depends_on('r-DBI') + depends_on('r-dbi', type=nolink) depends_on('mariadb') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py new file mode 100644 index 0000000000..2f33cd9f88 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRngtools(Package): + """This package contains a set of functions for working with Random Number + Generators (RNGs). In particular, it defines a generic S4 framework for + getting/setting the current RNG, or RNG data that are embedded into objects + for reproducibility. Notably, convenient default methods greatly facilitate + the way current RNG settings can be changed.""" + + homepage = "https://renozao.github.io/rngtools" + url = "https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rngtools" + + version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') + + extends('R') + + depends_on('r-pkgmaker', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-digest', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index 9cc9aebd9a..11fe0ace56 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -36,7 +36,7 @@ class RRodbc(Package): extends('R') - depends_on('unixODBC') + depends_on('unixodbc') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-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 83c9b85525..999fb4a1b9 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -44,7 +44,7 @@ class RRpostgresql(Package): extends('R') - depends_on('r-DBI') + depends_on('r-dbi', type=nolink) depends_on('postgresql') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index 9602f6d927..c7d41f0fb3 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -38,7 +38,7 @@ class RRsqlite(Package): extends('R') - depends_on('r-DBI') + depends_on('r-dbi', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 00fd5116d9..1d0052563b 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -44,13 +44,13 @@ class RRstan(Package): extends('R') - depends_on('r-ggplot2') - depends_on('r-stanheaders') - depends_on('r-inline') - depends_on('r-gridextra') - depends_on('r-rcpp') - depends_on('r-rcppeigen') - depends_on('r-bh') + depends_on('r-ggplot2', type=nolink) + depends_on('r-stanheaders', type=nolink) + depends_on('r-inline', type=nolink) + depends_on('r-gridextra', type=nolink) + depends_on('r-rcpp', type=nolink) + depends_on('r-rcppeigen', type=nolink) + depends_on('r-bh', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index 0ef2d9b987..bf9b35fe5b 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -33,6 +33,7 @@ class RRstudioapi(Package): url = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi" + version('0.6', 'fdb13bf46aab02421557e713fceab66b') version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') extends('R') diff --git a/var/spack/repos/builtin/packages/r-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 919291a023..332c80fb92 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -33,12 +33,13 @@ class RXlconnect(Package): url = "https://cran.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnect" + version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') version('0.2-11', '9d1769a103cda05665df399cc335017d') extends('R') - depends_on('r-XLConnectJars') - depends_on('r-rJava') + depends_on('r-xlconnectjars', type=nolink) + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index 15d08cc5af..26e822d2b7 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -32,11 +32,12 @@ class RXlconnectjars(Package): url = "https://cran.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnectJars" + version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') extends('R') - depends_on('r-rJava') + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index 0aac6cdd1f..6fed09296d 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -37,8 +37,8 @@ class RXlsx(Package): extends('R') - depends_on('r-rJava') - depends_on('r-xlsxjars') + depends_on('r-rjava', type=nolink) + depends_on('r-xlsxjars', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index cff6e7427e..19f0006ce9 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -37,7 +37,7 @@ class RXlsxjars(Package): extends('R') - depends_on('r-rJava') + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-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/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py index ef922314d8..16d896acc6 100644 --- a/var/spack/repos/builtin/packages/tcl/package.py +++ b/var/spack/repos/builtin/packages/tcl/package.py @@ -57,3 +57,5 @@ class Tcl(Package): configure("--prefix={0}".format(prefix)) make() make("install") + with working_dir(prefix.bin): + symlink('tclsh{0}'.format(self.version.up_to(2)), 'tclsh') 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', |