diff options
Diffstat (limited to 'var')
13 files changed, 430 insertions, 23 deletions
diff --git a/var/spack/repos/builtin/packages/gts/package.py b/var/spack/repos/builtin/packages/gts/package.py new file mode 100644 index 0000000000..2b3d4dd4f8 --- /dev/null +++ b/var/spack/repos/builtin/packages/gts/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 Gts(Package): + """GTS stands for the GNU Triangulated Surface Library. + + It is an Open Source Free Software Library intended to provide a set of + useful functions to deal with 3D surfaces meshed with interconnected + triangles. The source code is available free of charge under the Free + Software LGPL license. + + The code is written entirely in C with an object-oriented approach + based mostly on the design of GTK+. Careful attention is paid to + performance related issues as the initial goal of GTS is to provide a + simple and efficient library to scientists dealing with 3D computational + surface meshes. + """ + + homepage = "http://gts.sourceforge.net/index.html" + url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz" + + version('121130', '023ebb6b13b8707534182a3ef0d12908') + + depends_on('glib') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py new file mode 100644 index 0000000000..6a236e9fc9 --- /dev/null +++ b/var/spack/repos/builtin/packages/hmmer/package.py @@ -0,0 +1,76 @@ +############################################################################## +# 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 Hmmer(Package): + """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments. It implements methods using + probabilistic models called profile hidden Markov models (profile HMMs). + """ + homepage = 'http://www.hmmer.org' + url = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz' + + version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f') + version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588') + version('2.4i', 'dab234c87e026ac1de942450750acd20') + version('2.3.2', '5f073340c0cf761288f961a73821228a') + version('2.3.1', 'c724413e5761c630892506698a4716e2') + + variant('mpi', default=True, description='Compile with MPI') + variant('gsl', default=False, description='Compile with GSL') + + depends_on('mpi', when='+mpi') + depends_on('gsl', when='+gsl') + + def url_for_version(self, version): + base_url = 'http://eddylab.org/software' + + if version >= Version('3.0'): + return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version) + else: + return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version) + + def install(self, spec, prefix): + configure_args = [ + '--prefix={0}'.format(prefix) + ] + + if '+gsl' in self.spec: + configure_args.extend([ + '--with-gsl', + 'LIBS=-lgsl -lgslcblas' + ]) + + if '+mpi' in self.spec: + configure_args.append('--enable-mpi') + + configure(*configure_args) + make() + + if self.run_tests: + make('check') + + make('install') diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index f87dae9f4e..65fef57559 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -23,7 +23,9 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os, sys +import os +import sys + class Hypre(Package): """Hypre is a library of high performance preconditioners that @@ -37,7 +39,7 @@ class Hypre(Package): version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') # hypre does not know how to build shared libraries on Darwin - variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)") + variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)") # SuperluDist have conflicting headers with those in Hypre variant('internal-superlu', default=True, description="Use internal Superlu routines") @@ -46,21 +48,26 @@ class Hypre(Package): depends_on("lapack") def install(self, spec, prefix): - blas_dir = spec['blas'].prefix - lapack_dir = spec['lapack'].prefix - mpi_dir = spec['mpi'].prefix - - os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc') - os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx') - os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77') - + os.environ['CC'] = spec['mpi'].mpicc + os.environ['CXX'] = spec['mpi'].mpicxx + os.environ['F77'] = spec['mpi'].mpif77 + # Since +shared does not build on macOS and also Atlas does not have + # a single static lib to build against, link against shared libs with + # a hope that --whole-archive linker option (or alike) was used + # to command the linker to include whole static libs' content into the + # shared lib + # Note: --with-(lapack|blas)_libs= needs space separated list of names configure_args = [ - "--prefix=%s" % prefix, - "--with-lapack-libs=lapack", - "--with-lapack-lib-dirs=%s/lib" % lapack_dir, - "--with-blas-libs=blas", - "--with-blas-lib-dirs=%s/lib" % blas_dir] + '--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-blas-libs=%s' % to_lib_name( + spec['blas'].blas_shared_lib), + '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix + ] + if '+shared' in self.spec: configure_args.append("--enable-shared") @@ -76,4 +83,12 @@ class Hypre(Package): configure(*configure_args) make() + if self.run_tests: + make("check") + make("test") + Executable(join_path('test', 'ij'))() + sstruct = Executable(join_path('test', 'struct')) + sstruct() + sstruct('-in', 'test/sstruct.in.default', '-solver', '40', + '-rhsone') make("install") diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 15c8eefe96..3fcf942f05 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -63,6 +63,7 @@ class Openmpi(Package): list_url = "http://www.open-mpi.org/software/ompi/" list_depth = 3 + version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674') version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b') version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c') version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e') @@ -101,6 +102,7 @@ class Openmpi(Package): provides('mpi@:2.2', when='@1.6.5') provides('mpi@:3.0', when='@1.7.5:') + provides('mpi@:3.1', when='@2.0.0:') depends_on('hwloc') depends_on('sqlite', when='+sqlite3') @@ -169,7 +171,8 @@ class Openmpi(Package): '--with-psm2' if '+psm2' in spec else '--without-psm2', '--with-mxm' if '+mxm' in spec else '--without-mxm', # Other options - '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple', # NOQA: ignore=E501 + ('--enable-mpi-thread-multiple' if '+thread_multiple' in spec + else '--disable-mpi-thread-multiple'), '--with-pmi' if '+pmi' in spec else '--without-pmi', '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3', '--enable-vt' if '+vt' in spec else '--disable-vt' diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 273f5bfd8d..6bc11a5e48 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyNumpy(Package): """NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, @@ -38,7 +39,6 @@ class PyNumpy(Package): version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') version('1.9.1', '78842b73560ec378142665e712ae4ad9') - variant('blas', default=True) variant('lapack', default=True) @@ -63,6 +63,6 @@ class PyNumpy(Package): f.write('[DEFAULT]\n') f.write('libraries=%s\n' % ','.join(libraries)) f.write('library_dirs=%s\n' % ':'.join(library_dirs)) + f.write('rpath=%s\n' % ':'.join(library_dirs)) python('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 dafafabb05..516b5c6cfe 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -38,16 +38,29 @@ class Python(Package): homepage = "http://www.python.org" url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz" + version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72') version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') - version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True) + version('3.4.3', '4281ff86778db65892c05151d5de738d') + version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9') + version('3.2.6', '23815d82ae706e9b781ca65865353d39') + version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab') + version('2.7.12', '88d61f82e3616a4be952828b3694109d', preferred=True) + version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b') version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521') version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') extendable = True - variant('ucs4', default=False, description='Enable UCS4 unicode strings') + variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings') + # From https://docs.python.org/2/c-api/unicode.html: Python's default + # builds use a 16-bit type for Py_UNICODE and store Unicode values + # internally as UCS2. It is also possible to build a UCS4 version of Python + # (most recent Linux distributions come with UCS4 builds of Python). These + # builds then use a 32-bit type for Py_UNICODE and store Unicode data + # internally as UCS4. Note that UCS2 and UCS4 Python builds are not binary + # compatible. depends_on("openssl") depends_on("bzip2") @@ -85,7 +98,13 @@ class Python(Package): ] if '+ucs4' in spec: - config_args.append('--enable-unicode=ucs4') + if spec.satisfies('@:2.7'): + config_args.append('--enable-unicode=ucs4') + elif spec.satisfies('@3.0:3.2'): + config_args.append('--with-wide-unicode') + elif spec.satisfies('@3.3:'): + # https://docs.python.org/3.3/whatsnew/3.3.html + raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond') # NOQA: ignore=E501 if spec.satisfies('@3:'): config_args.append('--without-ensurepip') diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py new file mode 100644 index 0000000000..8fc1f397c8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggvis/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 RGgvis(Package): + """An implementation of an interactive grammar of graphics, taking the best + parts of 'ggplot2', combining them with the reactive framework from 'shiny' + and web graphics from 'vega'.""" + + homepage = "http://ggvis.rstudio.com/" + url = "https://cran.r-project.org/src/contrib/ggvis_0.4.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis" + + version('0.4.2', '039f45e5c7f1e0652779163d7d99f922') + + 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') + + 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 new file mode 100644 index 0000000000..0aea564372 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-htmltools/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 RHtmltools(Package): + """Tools for HTML generation and output.""" + + homepage = "https://github.com/rstudio/htmltools" + url = "https://cran.r-project.org/src/contrib/htmltools_0.3.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools" + + version('0.3.5', '5f001aff4a39e329f7342dcec5139724') + + extends('R') + + depends_on('r-digest') + 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/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py new file mode 100644 index 0000000000..6ab12bcf9d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-httpuv/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 RHttpuv(Package): + """Provides low-level socket and protocol support for handling HTTP and + WebSocket requests directly from within R. It is primarily intended as a + building block for other packages, rather than making it particularly easy + to create complete web applications using httpuv alone. httpuv is built on + top of the libuv and http-parser C libraries, both of which were developed + by Joyent, Inc. (See LICENSE file for libuv and http-parser license + information.)""" + + homepage = "https://github.com/rstudio/httpuv" + url = "https://cran.r-project.org/src/contrib/httpuv_1.3.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/httpuv" + + version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') + + extends('R') + + 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/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py new file mode 100644 index 0000000000..a9a9532910 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -0,0 +1,52 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RShiny(Package): + """Makes it incredibly easy to build interactive web applications with R. + Automatic "reactive" binding between inputs and outputs and extensive + pre-built widgets make it possible to build beautiful, responsive, and + powerful applications with minimal effort.""" + + homepage = "http://shiny.rstudio.com/" + url = "https://cran.r-project.org/src/contrib/shiny_0.13.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/shiny" + + version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611') + + 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') + + 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-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py new file mode 100644 index 0000000000..46434b4842 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xtable/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 RXtable(Package): + """Coerce data to LaTeX and HTML tables.""" + + homepage = "http://xtable.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/xtable" + + version('1.8-2', '239e4825cd046156a67efae3aac01d86') + + 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/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index 37862a73a9..620d658a10 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -71,6 +71,7 @@ class Swiftsim(Package): # Configure and install options = ['--prefix=%s' % prefix, '--enable-mpi' if '+mpi' in spec else '--disable-mpi', + '--with-metis={0}'.format(spec['metis'].prefix), '--enable-optimization'] configure(*options) make() diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 56499af8d9..77589bb8f9 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -118,6 +118,7 @@ class Trilinos(Package): options.extend(std_cmake_args) mpi_bin = spec['mpi'].prefix.bin + # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names options.extend([ '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON', @@ -131,10 +132,12 @@ class Trilinos(Package): '-DTPL_ENABLE_MPI:BOOL=ON', '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, '-DTPL_ENABLE_BLAS=ON', - '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names + '-DBLAS_LIBRARY_NAMES=%s' % to_lib_name( + spec['blas'].blas_shared_lib), '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib, '-DTPL_ENABLE_LAPACK=ON', - '-DLAPACK_LIBRARY_NAMES=lapack', + '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name( + spec['lapack'].lapack_shared_lib), '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix, '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', |