diff options
Diffstat (limited to 'var')
12 files changed, 425 insertions, 115 deletions
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 001dde5329..07bb6b6b03 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -40,6 +40,7 @@ class R(Package): extendable = True + version('3.3.1', 'f50a659738b73036e2f5635adbd229c5') version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') version('3.2.3', '1ba3dac113efab69e706902810cc2970') version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') @@ -87,6 +88,29 @@ class R(Package): make() make('install') + self.filter_compilers(spec, prefix) + + def filter_compilers(self, spec, prefix): + """Run after install to tell the configuration files and Makefiles + to use the compilers that Spack built the package with. + + If this isn't done, they'll have CC and CXX set to Spack's generic + cc and c++. We want them to be bound to whatever compiler + they were built with.""" + + etcdir = join_path(prefix, 'rlib', 'R', 'etc') + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + + filter_file(env['CC'], self.compiler.cc, + join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['CXX'], self.compiler.cxx, + join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['F77'], self.compiler.f77, + join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['FC'], self.compiler.fc, + join_path(etcdir, 'Makeconf'), **kwargs) + # ======================================================================== # Set up environment to make install easy for R extensions. # ======================================================================== diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 068dbec10a..e7984466ba 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -37,7 +37,7 @@ class Dealii(Package): version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa') version('8.2.1', '71c728dbec14f371297cd405776ccf08') version('8.1.0', 'aa8fadc2ce5eb674f44f997461bf668d') - version('dev', git='https://github.com/dealii/dealii.git') + version('develop', git='https://github.com/dealii/dealii.git') variant('mpi', default=True, description='Compile with MPI') variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') @@ -73,20 +73,21 @@ class Dealii(Package): depends_on("doxygen+graphviz", when='+doc') depends_on("graphviz", when='+doc') depends_on("gsl", when='@8.5.0:+gsl') - depends_on("gsl", when='@dev+gsl') depends_on("hdf5+mpi", when='+hdf5+mpi') depends_on("metis@5:", when='+metis') depends_on("netcdf+mpi", when="+netcdf+mpi") depends_on("netcdf-cxx", when='+netcdf+mpi') depends_on("oce", when='+oce') depends_on("p4est", when='+p4est+mpi') - depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi') # FIXME: update after 3.7 is supported upstream. # NOQA: ignore=E501 - depends_on("slepc@:3.6.3", when='+slepc+petsc+mpi') + depends_on("petsc+mpi", when='@8.5.0:+petsc+mpi') + depends_on("slepc", when='@8.5.0:+slepc+petsc+mpi') + depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi') + depends_on("slepc@:3.6.3", when='@:8.4.1+slepc+petsc+mpi') depends_on("trilinos", when='+trilinos+mpi') # developer dependnecies - depends_on("numdiff", when='@dev') - depends_on("astyle@2.04", when='@dev') + depends_on("numdiff", when='@develop') + depends_on("astyle@2.04", when='@develop') def install(self, spec, prefix): options = [] @@ -119,6 +120,16 @@ class Dealii(Package): '-DZLIB_DIR=%s' % spec['zlib'].prefix ]) + # Set directory structure: + if spec.satisfies('@:8.2.1'): + options.extend(['-DDEAL_II_COMPONENT_COMPAT_FILES=OFF']) + else: + options.extend([ + '-DDEAL_II_EXAMPLES_RELDIR=share/deal.II/examples', + '-DDEAL_II_DOCREADME_RELDIR=share/deal.II/', + '-DDEAL_II_DOCHTML_RELDIR=share/deal.II/doc' + ]) + # MPI if '+mpi' in spec: options.extend([ @@ -193,115 +204,118 @@ class Dealii(Package): ]) cmake('.', *options) - make() - make("test") + if self.run_tests: + make("test") make("install") # run some MPI examples with different solvers from PETSc and Trilinos - env['DEAL_II_DIR'] = prefix - print('=====================================') - print('============ EXAMPLES ===============') - print('=====================================') - # take bare-bones step-3 - print('=====================================') - print('============ Step-3 =================') - print('=====================================') - with working_dir('examples/step-3'): - cmake('.') - make('release') - make('run', parallel=False) - - # An example which uses Metis + PETSc - # FIXME: switch step-18 to MPI - with working_dir('examples/step-18'): + if self.run_tests: + env['DEAL_II_DIR'] = prefix print('=====================================') - print('============= Step-18 ===============') + print('============ EXAMPLES ===============') print('=====================================') - # list the number of cycles to speed up - filter_file(r'(end_time = 10;)', ('end_time = 3;'), 'step-18.cc') - if '^petsc' in spec and '^metis' in spec: - cmake('.') - make('release') - make('run', parallel=False) - - # take step-40 which can use both PETSc and Trilinos - # FIXME: switch step-40 to MPI run - with working_dir('examples/step-40'): + # take bare-bones step-3 print('=====================================') - print('========== Step-40 PETSc ============') + print('============ Step-3 =================') print('=====================================') - # list the number of cycles to speed up - filter_file(r'(const unsigned int n_cycles = 8;)', - ('const unsigned int n_cycles = 2;'), 'step-40.cc') - cmake('.') - if '^petsc' in spec: + with working_dir('examples/step-3'): + cmake('.') make('release') make('run', parallel=False) - print('=====================================') - print('========= Step-40 Trilinos ==========') - print('=====================================') - # change Linear Algebra to Trilinos - # The below filter_file should be different for versions - # before and after 8.4.0 - if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): - filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', - ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc') - else: - filter_file(r'(#define USE_PETSC_LA.*)', - ('// #define USE_PETSC_LA'), 'step-40.cc') - if '^trilinos+hypre' in spec: - make('release') - make('run', parallel=False) + # An example which uses Metis + PETSc + # FIXME: switch step-18 to MPI + with working_dir('examples/step-18'): + print('=====================================') + print('============= Step-18 ===============') + print('=====================================') + # list the number of cycles to speed up + filter_file(r'(end_time = 10;)', ('end_time = 3;'), + 'step-18.cc') + if '^petsc' in spec and '^metis' in spec: + cmake('.') + make('release') + make('run', parallel=False) - # the rest of the tests on step 40 only works for - # dealii version 8.4.0 and after - if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): + # take step-40 which can use both PETSc and Trilinos + # FIXME: switch step-40 to MPI run + with working_dir('examples/step-40'): print('=====================================') - print('=== Step-40 Trilinos SuperluDist ====') + print('========== Step-40 PETSc ============') print('=====================================') - # change to direct solvers - filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 - filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', - (''), 'step-40.cc') - filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 - (''), 'step-40.cc') - filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501 - (''), 'step-40.cc') - filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501 - filter_file(r'(preconditioner\);)', (''), 'step-40.cc') - if '^trilinos+superlu-dist' in spec: + # list the number of cycles to speed up + filter_file(r'(const unsigned int n_cycles = 8;)', + ('const unsigned int n_cycles = 2;'), 'step-40.cc') + cmake('.') + if '^petsc' in spec: make('release') - make('run', paralle=False) + make('run', parallel=False) print('=====================================') - print('====== Step-40 Trilinos MUMPS =======') + print('========= Step-40 Trilinos ==========') print('=====================================') - # switch to Mumps - filter_file(r'(Amesos_Superludist)', - ('Amesos_Mumps'), 'step-40.cc') - if '^trilinos+mumps' in spec: + # change Linear Algebra to Trilinos + # The below filter_file should be different for versions + # before and after 8.4.0 + if spec.satisfies('@8.4.0:'): + filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', + ('#define FORCE_USE_OF_TRILINOS'), + 'step-40.cc') + else: + filter_file(r'(#define USE_PETSC_LA.*)', + ('// #define USE_PETSC_LA'), 'step-40.cc') + if '^trilinos+hypre' in spec: make('release') make('run', parallel=False) - print('=====================================') - print('============ Step-36 ================') - print('=====================================') - with working_dir('examples/step-36'): - if 'slepc' in spec: - cmake('.') - make('release') - make('run', parallel=False) + # the rest of the tests on step 40 only works for + # dealii version 8.4.0 and after + if spec.satisfies('@8.4.0:'): + print('=====================================') + print('=== Step-40 Trilinos SuperluDist ====') + print('=====================================') + # change to direct solvers + filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 + filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', + (''), 'step-40.cc') + filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 + (''), 'step-40.cc') + filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501 + (''), 'step-40.cc') + filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501 + filter_file(r'(preconditioner\);)', (''), 'step-40.cc') + if '^trilinos+superlu-dist' in spec: + make('release') + make('run', paralle=False) - print('=====================================') - print('============ Step-54 ================') - print('=====================================') - with working_dir('examples/step-54'): - if 'oce' in spec: - cmake('.') - make('release') - make('run', parallel=False) + print('=====================================') + print('====== Step-40 Trilinos MUMPS =======') + print('=====================================') + # switch to Mumps + filter_file(r'(Amesos_Superludist)', + ('Amesos_Mumps'), 'step-40.cc') + if '^trilinos+mumps' in spec: + make('release') + make('run', parallel=False) + + print('=====================================') + print('============ Step-36 ================') + print('=====================================') + with working_dir('examples/step-36'): + if 'slepc' in spec: + cmake('.') + make('release') + make('run', parallel=False) + + print('=====================================') + print('============ Step-54 ================') + print('=====================================') + with working_dir('examples/step-54'): + if 'oce' in spec: + cmake('.') + make('release') + make('run', parallel=False) def setup_environment(self, spack_env, env): env.set('DEAL_II_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py index baaa2fc83d..360386669a 100644 --- a/var/spack/repos/builtin/packages/libxml2/package.py +++ b/var/spack/repos/builtin/packages/libxml2/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Libxml2(Package): """Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free @@ -42,8 +43,11 @@ class Libxml2(Package): def install(self, spec, prefix): if '+python' in spec: - site_packages_dir = os.path.join(prefix, 'lib/python%s.%s/site-packages' %(spec['python'].version[:2])) - python_args = ["--with-python=%s" % spec['python'].prefix, "--with-python-install-dir=%s" % site_packages_dir] + site_packages_dir = os.path.join(prefix, + 'lib/python%s/site-packages' % + (spec['python'].version.up_to(2))) + python_args = ["--with-python=%s" % spec['python'].prefix, + "--with-python-install-dir=%s" % site_packages_dir] else: python_args = ["--without-python"] diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index f97bfc7d12..6535f528ee 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -61,7 +61,7 @@ class Octave(Package): variant('qrupdate', default=False) variant('qscintilla', default=False) variant('qt', default=False) - variant('suiteparse', default=False) + variant('suitesparse', default=False) variant('zlib', default=False) # Required dependencies diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 6a7bee9788..11f5c36c22 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -149,20 +149,22 @@ class Petsc(Package): make("install") # solve Poisson equation in 2D to make sure nothing is broken: - with working_dir('src/ksp/ksp/examples/tutorials'): - cc = os.environ['CC'] if '~mpi' in self.spec else self.spec['mpi'].mpicc # NOQA: ignore=E501 - os.system('%s ex50.c -I%s -L%s -lpetsc -o ex50' % ( - cc, prefix.include, prefix.lib)) - ex50 = Executable('./ex50') - ex50('-da_grid_x', '4', '-da_grid_y', '4') - if 'superlu-dist' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 - - if 'mumps' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 - - if 'hypre' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 + if ('mpi' in spec) and self.run_tests: + with working_dir('src/ksp/ksp/examples/tutorials'): + env['PETSC_DIR'] = self.prefix + cc = Executable(spec['mpi'].mpicc) + cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib, + '-lpetsc', '-lm', '-o', 'ex50') + run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun')) + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4') + if 'superlu-dist' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 + + if 'mumps' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 + + if 'hypre' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # set up PETSC_DIR for everyone using PETSc package diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py new file mode 100644 index 0000000000..4070b6fe8d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-assertthat/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 RAssertthat(Package): + """assertthat is an extension to stopifnot() that makes it easy to declare + the pre and post conditions that you code should satisfy, while also + producing friendly error messages so that your users know what they've done + wrong.""" + + homepage = "https://cran.r-project.org/web/packages/assertthat/index.html" + url = "https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz" + + version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') + + 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-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py new file mode 100644 index 0000000000..b065e0b817 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dplyr/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 RDplyr(Package): + """A fast, consistent tool for working with data frame like objects, both + in memory and out of memory.""" + + homepage = "https://github.com/hadley/dplyr" + url = "https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/dplyr" + + 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') + + 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-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py new file mode 100644 index 0000000000..f80fb4d272 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lazyeval/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 RLazyeval(Package): + """An alternative approach to non-standard evaluation using formulas. + Provides a full implementation of LISP style 'quasiquotation', making it + easier to generate code with other code.""" + + homepage = "https://cran.r-project.org/web/packages/lazyeval/index.html" + url = "https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lazyeval" + + version('0.2.0', 'df1daac908dcf02ae7e12f4335b1b13b') + + 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-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py new file mode 100644 index 0000000000..88576911f0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lubridate/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 RLubridate(Package): + """Functions to work with date-times and timespans: fast and user friendly + parsing of date-time data, extraction and updating of components of a + date-time (years, months, days, hours, minutes, and seconds), algebraic + manipulation on date-time and timespan objects. The 'lubridate' package has + a consistent and memorable syntax that makes working with dates easy and + fun.""" + + homepage = "https://cran.r-project.org/web/packages/lubridate/index.html" + url = "https://cran.r-project.org/src/contrib/lubridate_1.5.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lubridate" + + version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') + + extends('R') + depends_on('r-stringr') + + 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 new file mode 100644 index 0000000000..837c3df603 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tibble/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 RTibble(Package): + """Provides a 'tbl_df' class that offers better checking and printing + capabilities than traditional data frames.""" + + homepage = "https://github.com/hadley/tibble" + url = "https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/tibble" + + version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') + + extends('R') + + depends_on('r-assertthat') + depends_on('r-lazyeval') + depends_on('r-rcpp') + + 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/slepc/install_name_371.patch b/var/spack/repos/builtin/packages/slepc/install_name_371.patch new file mode 100644 index 0000000000..d02ca88657 --- /dev/null +++ b/var/spack/repos/builtin/packages/slepc/install_name_371.patch @@ -0,0 +1,32 @@ +From 7489a3f3d569e2fbf5513ac9dcd769017d9f7eb7 Mon Sep 17 00:00:00 2001 +From: Lisandro Dalcin <dalcinl@gmail.com> +Date: Thu, 2 Jun 2016 21:57:38 +0300 +Subject: [PATCH] OS X: Fix library path in invocation of install_name_tool + +--- + config/install.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/config/install.py b/config/install.py +index 09acd03..6ce98ae 100755 +--- a/config/install.py ++++ b/config/install.py +@@ -25,6 +25,7 @@ class Installer: + + def setupDirectories(self): + self.installDir = self.destDir ++ self.archDir = os.path.join(self.rootDir, self.arch) + self.rootIncludeDir = os.path.join(self.rootDir, 'include') + self.archIncludeDir = os.path.join(self.rootDir, self.arch, 'include') + self.rootConfDir = os.path.join(self.rootDir, 'lib','slepc','conf') +@@ -220,7 +221,7 @@ for dir in dirs: + if os.path.splitext(dst)[1] == '.dylib' and os.path.isfile('/usr/bin/install_name_tool'): + (result, output) = commands.getstatusoutput('otool -D '+src) + oldname = output[output.find("\n")+1:] +- installName = oldname.replace(self.destDir, self.installDir) ++ installName = oldname.replace(self.archDir, self.installDir) + (result, output) = commands.getstatusoutput('/usr/bin/install_name_tool -id ' + installName + ' ' + dst) + # preserve the original timestamps - so that the .a vs .so time order is preserved + shutil.copystat(src,dst) +-- +2.7.4.1.g5468f9e diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index d3739bf6a6..fd6c42d9fc 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -28,7 +28,7 @@ from spack import * class Slepc(Package): """ - Scalable Library for Eigenvalue Computations. + Scalable Library for Eigenvalue Problem Computations. """ homepage = "http://www.grycap.upv.es/slepc" @@ -45,9 +45,13 @@ class Slepc(Package): depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi') depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi') + patch('install_name_371.patch', when='@3.7.1') + def install(self, spec, prefix): # set SLEPC_DIR for installation - os.environ['SLEPC_DIR'] = self.stage.source_path + # Note that one should set the current (temporary) directory instead + # its symlink in spack/stage/ ! + os.environ['SLEPC_DIR'] = os.getcwd() options = [] @@ -67,9 +71,10 @@ class Slepc(Package): configure('--prefix=%s' % prefix, *options) make('MAKE_NP=%s' % make_jobs, parallel=False) - # FIXME: - # make('test') - make('install') + if self.run_tests: + make('test', parallel=False) + + make('install', parallel=False) def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # set up SLEPC_DIR for everyone using SLEPc package |