diff options
Diffstat (limited to 'var')
53 files changed, 1682 insertions, 98 deletions
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index a0899084d0..000e337ce0 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -50,6 +50,8 @@ class R(Package): variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK') + variant('X', default=True, + description='Enable X11 support (call configure --with-x)') # Virtual dependencies depends_on('blas', when='+external-lapack') @@ -65,10 +67,16 @@ class R(Package): depends_on('libtiff') depends_on('jpeg') depends_on('cairo') + depends_on('cairo+X', when='+X') + depends_on('cairo~X', when='~X') depends_on('pango') depends_on('freetype') depends_on('tcl') depends_on('tk') + depends_on('tk+X', when='+X') + depends_on('tk~X', when='~X') + depends_on('libx11', when='+X') + depends_on('libxt', when='+X') depends_on('curl') depends_on('pcre') depends_on('jdk') diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index b6aba8c03f..d812350ae8 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -27,6 +27,7 @@ from spack import * class Autoconf(AutotoolsPackage): """Autoconf -- system configuration part of autotools""" + homepage = 'https://www.gnu.org/software/autoconf/' url = 'http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz' @@ -35,7 +36,7 @@ class Autoconf(AutotoolsPackage): version('2.59', 'd4d45eaa1769d45e59dcb131a4af17a0') version('2.13', '9de56d4a161a723228220b0f425dc711') - depends_on('m4', type='build') + depends_on('m4@1.4.6:', type='build') def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py index 78b0a5b34f..6c0a47ff95 100644 --- a/var/spack/repos/builtin/packages/automake/package.py +++ b/var/spack/repos/builtin/packages/automake/package.py @@ -25,10 +25,9 @@ from spack import * -class Automake(Package): - """ - Automake -- make file builder part of autotools - """ +class Automake(AutotoolsPackage): + """Automake -- make file builder part of autotools""" + homepage = 'http://www.gnu.org/software/automake/' url = 'http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz' @@ -36,7 +35,7 @@ class Automake(Package): version('1.14.1', 'd052a3e884631b9c7892f2efce542d75') version('1.11.6', '0286dc30295b62985ca51919202ecfcc') - depends_on('autoconf') + depends_on('autoconf', type='build') def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) @@ -47,8 +46,3 @@ class Automake(Package): executables = ['aclocal', 'automake'] for name in executables: setattr(module, name, self._make_executable(name)) - - def install(self, spec, prefix): - configure("--prefix=%s" % prefix) - make() - make("install") diff --git a/var/spack/repos/builtin/packages/cairo/package.py b/var/spack/repos/builtin/packages/cairo/package.py index 12c7838f63..fce7da3f17 100644 --- a/var/spack/repos/builtin/packages/cairo/package.py +++ b/var/spack/repos/builtin/packages/cairo/package.py @@ -33,6 +33,12 @@ class Cairo(AutotoolsPackage): version('1.14.0', 'fc3a5edeba703f906f2241b394f0cced') + variant('X', default=True, description="Build with X11 support") + + depends_on('libx11', when='+X') + depends_on('libxext', when='+X') + depends_on('libxrender', when='+X') + depends_on('libxcb', when='+X') depends_on("libpng") depends_on("glib") depends_on("pixman") diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index 9b173bb0dd..a2e0c85903 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -25,20 +25,44 @@ from spack import * -class Flex(Package): +class Flex(AutotoolsPackage): """Flex is a tool for generating scanners.""" - homepage = "http://flex.sourceforge.net/" - url = "http://download.sourceforge.net/flex/flex-2.5.39.tar.gz" + homepage = "https://github.com/westes/flex" + url = "https://github.com/westes/flex/releases/download/v2.6.2/flex-2.6.2.tar.gz" - version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec') - version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde') + version('2.6.2', 'cc6d76c333db7653d5caf423a3335239') + version('2.6.1', '05bcd8fb629e0ae130311e8a6106fa82') + version('2.6.0', '760be2ee9433e822b6eb65318311c19d') + version('2.5.39', '5865e76ac69c05699f476515592750d7') - depends_on("bison", type='build') - depends_on("m4", type='build') + depends_on('bison', type='build') + depends_on('gettext@0.19:', type='build') + depends_on('help2man', type='build') - def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + # Older tarballs don't come with a configure script + depends_on('m4', type='build', when='@:2.6.0') + depends_on('autoconf', type='build', when='@:2.6.0') + depends_on('automake', type='build', when='@:2.6.0') + depends_on('libtool', type='build', when='@:2.6.0') - make() - make("install") + def url_for_version(self, version): + url = "https://github.com/westes/flex" + if version >= Version('2.6.1'): + url += "/releases/download/v{0}/flex-{0}.tar.gz".format(version) + elif version == Version('2.6.0'): + url += "/archive/v{0}.tar.gz".format(version) + elif version >= Version('2.5.37'): + url += "/archive/flex-{0}.tar.gz".format(version) + else: + url += "/archive/flex-{0}.tar.gz".format(version.dashed) + + return url + + def autoreconf(self, spec, prefix): + pass + + @when('@:2.6.0') + def autoreconf(self, spec, prefix): + libtoolize('--install', '--force') + autoreconf('--install', '--force') diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py index d48c7c9756..77a074e809 100644 --- a/var/spack/repos/builtin/packages/go-bootstrap/package.py +++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py @@ -41,14 +41,17 @@ class GoBootstrap(Package): extendable = True - # NOTE: Go@1.4.2 is the only supported bootstrapping compiler because all + # NOTE: Go@1.4.x is the only supported bootstrapping compiler because all # later versions require a Go compiler to build. - # See: https://golang.org/doc/install/source - version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2') + # See: https://golang.org/doc/install/source#go14 and + # https://github.com/golang/go/issues/17545 and + # https://github.com/golang/go/issues/16352 + version('1.4-bootstrap-20161024', '76e42c8152e8560ded880a6d1d1f53cb', + url='https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz') variant('test', default=True, description='Build and run tests as part of the build.') - provides('golang@:1.4.2') + provides('golang@:1.4-bootstrap-20161024') depends_on('git', type='alldeps') @@ -69,6 +72,7 @@ class GoBootstrap(Package): pass def install(self, spec, prefix): + env['CGO_ENABLED'] = '0' bash = which('bash') with working_dir('src'): bash('{0}.bash'.format('all' if '+test' in spec else 'make')) diff --git a/var/spack/repos/builtin/packages/go/misc-cgo-testcshared.patch b/var/spack/repos/builtin/packages/go/misc-cgo-testcshared.patch new file mode 100644 index 0000000000..17751df816 --- /dev/null +++ b/var/spack/repos/builtin/packages/go/misc-cgo-testcshared.patch @@ -0,0 +1,11 @@ +--- misc/cgo/testcshared/test.bash.orig 2016-11-19 00:00:11.917000000 +0000 ++++ misc/cgo/testcshared/test.bash 2016-11-19 00:00:22.081000000 +0000 +@@ -107,7 +107,7 @@ + + # test0: exported symbols in shared lib are accessible. + # TODO(iant): using _shared here shouldn't really be necessary. +-$(go env CC) ${GOGCCFLAGS} -I ${installdir} -o testp main0.c libgo.$libext ++$(go env CC) ${GOGCCFLAGS} -I ${installdir} -o testp main0.c ./libgo.$libext + binpush testp + + output=$(run LD_LIBRARY_PATH=. ./testp) diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 5fa3017ab5..7f4d509466 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -32,13 +32,12 @@ from spack import * class Go(Package): """The golang compiler and build environment""" homepage = "https://golang.org" - url = "https://go.googlesource.com/go" + url='https://storage.googleapis.com/golang/go1.7.3.src.tar.gz' extendable = True - version('1.6.2', git='https://go.googlesource.com/go', tag='go1.6.2') - version('1.5.4', git='https://go.googlesource.com/go', tag='go1.5.4') - version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2') + version('1.7.3', '83d1b7bd4281479ab7d153e5152c9fc9') + version('1.6.2', 'd1b50fa98d9a71eeee829051411e6207') variant('test', default=True, description='Build and run tests as part of the build.') @@ -49,6 +48,12 @@ class Go(Package): # should be a dep on external go compiler depends_on('go-bootstrap', type='build') + # https://github.com/golang/go/issues/17545 + patch('time_test.patch', when='@1.6.2:1.7.3') + + # https://github.com/golang/go/issues/17986 + patch('misc-cgo-testcshared.patch', level=0, when='@1.6.2:1.7.3') + # NOTE: Older versions of Go attempt to download external files that have # since been moved while running the test suite. This patch modifies the # test files so that these tests don't cause false failures. @@ -65,6 +70,9 @@ class Go(Package): def patch(self): pass + def url_for_version(self, version): + return "https://storage.googleapis.com/golang/go{0}.src.tar.gz".format(version) + def install(self, spec, prefix): bash = which('bash') with working_dir('src'): diff --git a/var/spack/repos/builtin/packages/go/time_test.patch b/var/spack/repos/builtin/packages/go/time_test.patch new file mode 100644 index 0000000000..c3e0697c91 --- /dev/null +++ b/var/spack/repos/builtin/packages/go/time_test.patch @@ -0,0 +1,18 @@ +diff --git a/src/time/time_test.go b/src/time/time_test.go +index 68236fd..2e47d08 100644 +--- a/src/time/time_test.go ++++ b/src/time/time_test.go +@@ -943,8 +943,11 @@ func TestLoadFixed(t *testing.T) { + // but Go and most other systems use "east is positive". + // So GMT+1 corresponds to -3600 in the Go zone, not +3600. + name, offset := Now().In(loc).Zone() +- if name != "GMT+1" || offset != -1*60*60 { +- t.Errorf("Now().In(loc).Zone() = %q, %d, want %q, %d", name, offset, "GMT+1", -1*60*60) ++ // The zone abbreviation is "-01" since tzdata-2016g, and "GMT+1" ++ // on earlier versions; we accept both. (Issue #17276). ++ if !(name == "GMT+1" || name == "-01") || offset != -1*60*60 { ++ t.Errorf("Now().In(loc).Zone() = %q, %d, want %q or %q, %d", ++ name, offset, "GMT+1", "-01", -1*60*60) + } + } + diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 2820a3a304..75aa239be3 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -175,7 +175,9 @@ HDF5 version {version} {version} # TODO: Automate these path and library settings cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c") cc('-o', "check", "check.o", - "-L%s" % join_path(spec.prefix, "lib"), "-lhdf5", + "-L%s" % join_path(spec.prefix, "lib"), + "-L%s" % join_path(spec.prefix, "lib64"), + "-lhdf5", "-lz") try: check = Executable('./check') diff --git a/var/spack/repos/builtin/packages/help2man/package.py b/var/spack/repos/builtin/packages/help2man/package.py new file mode 100644 index 0000000000..506b1c1465 --- /dev/null +++ b/var/spack/repos/builtin/packages/help2man/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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 Help2man(AutotoolsPackage): + """help2man produces simple manual pages from the '--help' and '--version' + output of other commands.""" + + homepage = "https://www.gnu.org/software/help2man/" + url = "http://gnu.askapache.com/help2man/help2man-1.47.4.tar.xz" + + version('1.47.4', '544aca496a7d89de3e5d99e56a2f03d3') + + depends_on('gettext', type='build') diff --git a/var/spack/repos/builtin/packages/icet/package.py b/var/spack/repos/builtin/packages/icet/package.py new file mode 100644 index 0000000000..cdace1481f --- /dev/null +++ b/var/spack/repos/builtin/packages/icet/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 Icet(CMakePackage): + """The Image Composition Engine for Tiles (IceT) is a high-performance + sort-last parallel rendering library.""" + + homepage = "http://icet.sandia.gov" + url = "https://example.com/icet-1.2.3.tar.gz" + + version('develop', branch='master', + git='https://gitlab.kitware.com/icet/icet.git') + version('2.1.1', '4f971c51105a64937460d482adca2a6c') + + depends_on('cmake', type='build') + depends_on('mpi') + + def url_for_version(self, version): + return ("https://gitlab.kitware.com/icet/icet/repository/" + "archive.tar.bz2?ref=IceT-{0}".format(version.dotted)) + + def cmake_args(self): + return ['-DICET_USE_OPENGL:BOOL=OFF'] diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py index e13d4292f8..839251f47b 100644 --- a/var/spack/repos/builtin/packages/jemalloc/package.py +++ b/var/spack/repos/builtin/packages/jemalloc/package.py @@ -31,6 +31,7 @@ class Jemalloc(Package): homepage = "http://www.canonware.com/jemalloc/" url = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2" + version('4.3.1', 'f204c0ea1aef92fbb339dc640de338a6') version('4.2.1', '094b0a7b8c77c464d0dc8f0643fd3901') version('4.2.0', 'e6b5d5a1ea93a04207528d274efdd144') version('4.1.0', 'c4e53c947905a533d5899e5cc3da1f94') diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py index 6c8b27478a..a5a3e8eb5f 100644 --- a/var/spack/repos/builtin/packages/libsigsegv/package.py +++ b/var/spack/repos/builtin/packages/libsigsegv/package.py @@ -25,8 +25,9 @@ from spack import * -class Libsigsegv(Package): +class Libsigsegv(AutotoolsPackage): """GNU libsigsegv is a library for handling page faults in user mode.""" + homepage = "https://www.gnu.org/software/libsigsegv/" url = "ftp://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.10.tar.gz" @@ -34,9 +35,5 @@ class Libsigsegv(Package): version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f') - def install(self, spec, prefix): - configure('--prefix=%s' % prefix, - '--enable-shared') - - make() - make("install") + def configure_args(self): + return ['--enable-shared'] diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index a0070d72d0..cd12503681 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -25,17 +25,16 @@ from spack import * -class Libtool(Package): - """ - libtool -- library building part of autotools - """ +class Libtool(AutotoolsPackage): + """libtool -- library building part of autotools.""" + homepage = 'https://www.gnu.org/software/libtool/' url = 'http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz' version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e') version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50') - depends_on('m4', type='build') + depends_on('m4@1.4.6:', type='build') def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) @@ -46,8 +45,3 @@ class Libtool(Package): executables = ['libtoolize', 'libtool'] for name in executables: setattr(module, name, self._make_executable(name)) - - def install(self, spec, prefix): - configure("--prefix=%s" % prefix) - make() - make("install") diff --git a/var/spack/repos/builtin/packages/llvm-lld/package.py b/var/spack/repos/builtin/packages/llvm-lld/package.py index 1dcf88e3c0..6a167cca33 100644 --- a/var/spack/repos/builtin/packages/llvm-lld/package.py +++ b/var/spack/repos/builtin/packages/llvm-lld/package.py @@ -38,7 +38,7 @@ class LlvmLld(Package): depends_on('cmake', type='build') def install(self, spec, prefix): - env['CXXFLAGS'] = self.compier.cxx11_flag + env['CXXFLAGS'] = self.compiler.cxx11_flag with working_dir('spack-build', create=True): cmake('..', diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py index f7150727fe..15dbf4793b 100644 --- a/var/spack/repos/builtin/packages/m4/package.py +++ b/var/spack/repos/builtin/packages/m4/package.py @@ -26,8 +26,9 @@ from spack import * import sys -class M4(Package): +class M4(AutotoolsPackage): """GNU M4 is an implementation of the traditional Unix macro processor.""" + homepage = "https://www.gnu.org/software/m4/m4.html" url = "ftp://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz" @@ -40,19 +41,19 @@ class M4(Package): depends_on('libsigsegv', when='+sigsegv') - def install(self, spec, prefix): - configure_args = [] - if 'libsigsegv' in spec: - configure_args.append('--with-libsigsegv-prefix=%s' % - spec['libsigsegv'].prefix) + def configure_args(self): + spec = self.spec + args = ['--enable-c++'] + + if '+sigsegv' in spec: + args.append('--with-libsigsegv-prefix={0}'.format( + spec['libsigsegv'].prefix)) else: - configure_args.append('--without-libsigsegv-prefix') + args.append('--without-libsigsegv-prefix') # http://lists.gnu.org/archive/html/bug-m4/2016-09/msg00002.html - if (sys.platform == "darwin") and (spec.satisfies('%gcc')) and \ - (spec.architecture.platform_os.version == "10.12"): - configure_args.append('ac_cv_type_struct_sched_param=yes') + if (sys.platform == 'darwin') and (spec.satisfies('%gcc')) and \ + (spec.architecture.platform_os.version == '10.12'): + args.append('ac_cv_type_struct_sched_param=yes') - configure("--prefix=%s" % prefix, *configure_args) - make() - make("install") + return args diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index b1e406157b..38bbc4e5ba 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -39,8 +39,12 @@ class Netcdf(Package): version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e') version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') - variant('mpi', default=True, description='Enables MPI parallelism') - variant('hdf4', default=False, description='Enable HDF4 support') + variant('mpi', default=True, description='Enables MPI parallelism') + variant('hdf4', default=False, description='Enable HDF4 support') + variant('shared', default=True, description='Enable shared library') + variant('parallel-netcdf', default=False, description='Enable PnetCDF support') + variant('dap', default=False, description='Enable DAP support') + variant('cdmremote', default=False, description='Enable CDM Remote support') # These variants control the number of dimensions (i.e. coordinates and # attributes) and variables (e.g. time, entity ID, number of coordinates) # that can be used in any particular NetCDF file. @@ -51,9 +55,9 @@ class Netcdf(Package): depends_on("m4", type='build') depends_on("hdf", when='+hdf4') - - # Required for DAP support - depends_on("curl@7.18.0:") + depends_on("curl@7.18.0:", when='+dap') + depends_on("curl@7.18.0:", when='+cdmremote') + depends_on('parallel-netcdf', when='@4.2.1.1:+parallel-netcdf') # Required for NetCDF-4 support depends_on("zlib@1.2.5:") @@ -84,6 +88,7 @@ class Netcdf(Package): 'hdf5+mpi, but spec asked for hdf5~mpi.') # Environment variables + CFLAGS = [] CPPFLAGS = [] LDFLAGS = [] LIBS = [] @@ -93,23 +98,38 @@ class Netcdf(Package): "--enable-fsync", "--enable-v2", "--enable-utilities", - "--enable-shared", "--enable-static", "--enable-largefile", # necessary for HDF5 support "--enable-netcdf-4", "--enable-dynamic-loading", - # necessary for DAP support - "--enable-dap" ] - # Make sure Netcdf links against Spack's curl, otherwise - # otherwise it may pick up system's curl, which can give link - # errors, e.g.: - # undefined reference to `SSL_CTX_use_certificate_chain_file` - LIBS.append("-lcurl") - CPPFLAGS.append("-I%s" % spec['curl'].prefix.include) - LDFLAGS.append("-L%s" % spec['curl'].prefix.lib) + if '+shared' in spec: + config_args.append('--enable-shared') + else: + config_args.append('--disable-shared') + # We don't have shared libraries but we still want it to be + # possible to use this library in shared builds + CFLAGS.append('-fPIC') + + if '+dap' in spec: + config_args.append('--enable-dap') + else: + config_args.append('--disable-dap') + + if '+cdmremote' in spec: + config_args.append('--enable-cdmremote') + else: + config_args.append('--disable-cdmremote') + + if '+dap' in spec or '+cdmremote' in spec: + # Make sure Netcdf links against Spack's curl, otherwise it may + # pick up system's curl, which can give link errors, e.g.: + # undefined reference to `SSL_CTX_use_certificate_chain_file` + LIBS.append("-lcurl") + CPPFLAGS.append("-I%s" % spec['curl'].prefix.include) + LDFLAGS.append("-L%s" % spec['curl'].prefix.lib) if '+mpi' in spec: config_args.append('--enable-parallel4') @@ -131,10 +151,18 @@ class Netcdf(Package): LDFLAGS.append("-L%s/lib" % spec['szip'].prefix) LIBS.append("-l%s" % "sz") + # PnetCDF support + if '+parallel-netcdf' in spec: + config_args.append('--enable-pnetcdf') + config_args.append('CC=%s' % spec['mpi'].mpicc) + CPPFLAGS.append("-I%s/include" % spec['parallel-netcdf'].prefix) + LDFLAGS.append("-L%s/lib" % spec['parallel-netcdf'].prefix) + # Fortran support # In version 4.2+, NetCDF-C and NetCDF-Fortran have split. # Use the netcdf-fortran package to install Fortran support. + config_args.append('CFLAGS=%s' % ' '.join(CFLAGS)) config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS)) config_args.append('LDFLAGS=%s' % ' '.join(LDFLAGS)) config_args.append('LIBS=%s' % ' '.join(LIBS)) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 4ac96b8127..276237a536 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -37,6 +37,7 @@ class Petsc(Package): homepage = "http://www.mcs.anl.gov/petsc/index.html" url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz" + version('develop', git='https://bitbucket.org/petsc/petsc.git', tag='master') version('3.7.4', 'aaf94fa54ef83022c14091f10866eedf') version('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34') version('3.6.4', '7632da2375a3df35b8891c9526dbdde7') @@ -67,6 +68,9 @@ class Petsc(Package): description='Activates support for SuperluDist (only parallel)') # Virtual dependencies + # Git repository needs sowing to build Fortran interface + depends_on('sowing', when='@develop') + depends_on('blas') depends_on('lapack') depends_on('mpi', when='+mpi') @@ -127,6 +131,7 @@ class Petsc(Package): def install(self, spec, prefix): options = ['--with-ssl=0', '--download-c2html=0', + '--download-sowing=0', '--download-hwloc=0'] options.extend(self.mpi_dependent_options()) options.extend([ diff --git a/var/spack/repos/builtin/packages/py-pyqt/package.py b/var/spack/repos/builtin/packages/py-pyqt/package.py index de68bfaa90..43f2e2630b 100644 --- a/var/spack/repos/builtin/packages/py-pyqt/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt/package.py @@ -39,7 +39,7 @@ class PyPyqt(Package): # TODO: allow qt5 when conditional deps are supported. # TODO: Fix version matching so that @4 works like @:4 - depends_on('qt@:4') + depends_on('qt@:4+phonon+dbus') def install(self, spec, prefix): python('configure.py', diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 6447d7d6d4..1db651c02b 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -51,6 +51,7 @@ class Qt(Package): variant('webkit', default=False, description="Build the Webkit extension") variant('examples', default=False, description="Build examples.") variant('dbus', default=False, description="Build with D-Bus support.") + variant('phonon', default=False, description="Build with phonon support.") patch('qt3krell.patch', when='@3.3.8b+krellpatch') @@ -179,7 +180,7 @@ class Qt(Package): if '~examples' in self.spec: config_args.extend(['-nomake', 'examples']) - if '@4' in self.spec: + if '@4' in self.spec and '~phonon' in self.spec: config_args.append('-no-phonon') if '+dbus' in self.spec: diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py new file mode 100644 index 0000000000..6399202aba --- /dev/null +++ b/var/spack/repos/builtin/packages/r-bitops/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 RBitops(Package): + """Functions for bitwise operations on integer vectors.""" + + homepage = "https://cran.r-project.org/package=bitops" + url = "https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/bitops" + + version('1.0-6', 'fba16485a51b1ccd354abde5816b6bdd') + + 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-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py new file mode 100644 index 0000000000..e9b582b52f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-c50/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 RC50(Package): + """C5.0 decision trees and rule-based models for pattern recognition.""" + + homepage = "https://cran.r-project.org/package=C50" + url = "https://cran.r-project.org/src/contrib/C50_0.1.0-24.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/C50" + + version('0.1.0-24', '42631e65c5c579532cc6edf5ea175949') + + extends('R') + + depends_on('r-partykit', 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-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py new file mode 100644 index 0000000000..adc64e269c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-catools/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 RCatools(Package): + """Contains several basic utility functions including: moving (rolling, + running) window statistic functions, read/write for GIF and ENVI binary + files, fast calculation of AUC, LogitBoost classifier, base64 + encoder/decoder, round-off-error-free sum and cumsum, etc.""" + + homepage = "https://cran.r-project.org/package=caTools" + url = "https://cran.r-project.org/src/contrib/caTools_1.17.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/caTools" + + version('1.17.1', '5c872bbc78b177b306f36709deb44498') + + extends('R') + + depends_on('r-bitops', 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-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py new file mode 100644 index 0000000000..16aacccd0e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-deoptim/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 RDeoptim(Package): + """Implements the differential evolution algorithm for global optimization + of a real-valued function of a real-valued parameter vector.""" + + homepage = "https://cran.r-project.org/package=DEoptim" + url = "https://cran.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptim" + + version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326') + + 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-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py new file mode 100644 index 0000000000..5583c0ed68 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-evaluate/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 REvaluate(Package): + """Parsing and evaluation tools that make it easy to recreate the command + line behaviour of R.""" + + homepage = "https://github.com/hadley/evaluate" + url = "https://cran.rstudio.com/src/contrib/evaluate_0.9.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/evaluate" + + version('0.9', '877d89ce8a9ef7f403b1089ca1021775') + + extends('R') + + depends_on('r-stringr', 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-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py new file mode 100644 index 0000000000..4c92e1f34b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-formatr/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 RFormatr(Package): + """Provides a function tidy_source() to format R source code. Spaces and + indent will be added to the code automatically, and comments will be + preserved under certain conditions, so that R code will be more + human-readable and tidy. There is also a Shiny app as a user interface in + this package.""" + + homepage = "http://yihui.name/formatR" + url = "https://cran.r-project.org/src/contrib/formatR_1.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/formatR" + + version('1.4', '98b9b64b2785b35f9df403e1aab6c73c') + + extends('R') + + depends_on('r-codetools', type=nolink) + depends_on('r-shiny', type=nolink) + depends_on('r-testit', type=nolink) + # depends_on('r-knitr', type=nolink) - mutual dependency + + 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-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py new file mode 100644 index 0000000000..3c4347ee50 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-formula/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 RFormula(Package): + """Infrastructure for extended formulas with multiple parts on the right-hand + side and/or multiple responses on the left-hand side.""" + + homepage = "https://cran.r-project.org/package=Formula" + url = "https://cran.r-project.org/src/contrib/Formula_1.2-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/Formula" + + version('1.2-1', '2afb31e637cecd0c1106317aca1e4849') + + 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-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py new file mode 100644 index 0000000000..646299b97b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gistr/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 RGistr(Package): + """Work with 'GitHub' 'gists' from 'R'. This package allows the user to + create new 'gists', update 'gists' with new files, rename files, delete + files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', + open a 'gist' in your default browser, get embed code for a 'gist', list + 'gist' 'commits', and get rate limit information when 'authenticated'. Some + requests require authentication and some do not.""" + + homepage = "https://github.com/ropensci/gistr" + url = "https://cran.r-project.org/src/contrib/gistr_0.3.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gistr" + + version('0.3.6', '49d548cb3eca0e66711aece37757a2c0') + + extends('R') + + depends_on('r-jsonlite', type=nolink) + depends_on('r-httr', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-assertthat', type=nolink) + depends_on('r-knitr', type=nolink) + depends_on('r-rmarkdown', type=nolink) + depends_on('r-dplyr', 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-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py new file mode 100644 index 0000000000..5d2972ff96 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-hexbin/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 RHexbin(Package): + """Binning and plotting functions for hexagonal bins. Now uses and relies + on grid graphics and formal (S4) classes and methods.""" + + homepage = "http://github.com/edzer/hexbin" + url = "https://cran.r-project.org/src/contrib/hexbin_1.27.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/hexbin" + + version('1.27.1', '7f380390c6511e97df10a810a3b3bb7c') + + 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-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py new file mode 100644 index 0000000000..f977a7302f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-highr/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 RHighr(Package): + """Provides syntax highlighting for R source code. Currently it supports + LaTeX and HTML output. Source code of other languages is supported via + Andre Simon's highlight package.""" + + homepage = "https://github.com/yihui/highr" + url = "https://cran.r-project.org/src/contrib/highr_0.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/highr" + + version('0.6', 'bf47388c5f57dc61962362fb7e1d8b16') + + 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-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py new file mode 100644 index 0000000000..a3c49feb93 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-irdisplay/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 RIrdisplay(Package): + """An interface to the rich display capabilities of Jupyter front-ends + (e.g. 'Jupyter Notebook') Designed to be used from a running IRkernel + session""" + + homepage = "https://irkernel.github.io" + url = "https://cran.rstudio.com/src/contrib/IRdisplay_0.4.4.tar.gz" + + version('0.4.4', '5be672fb82185b90f23bd99ac1e1cdb6') + + extends('R') + + depends_on('r-repr', 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-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py new file mode 100644 index 0000000000..34b5c3c363 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-irkernel/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 RIrkernel(Package): + """R kernel for Jupyter""" + + homepage = "https://irkernel.github.io/" + + # Git repository + version('master', git='https://github.com/IRkernel/IRkernel.git', + tag='0.7') + + extends('R') + + depends_on('r-repr', type=nolink) + depends_on('r-irdisplay', type=nolink) + depends_on('r-evaluate', type=nolink) + depends_on('r-crayon', type=nolink) + depends_on('r-pbdzmq', type=nolink) + depends_on('r-devtools', type=nolink) + depends_on('r-uuid', 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-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py new file mode 100644 index 0000000000..4976e12b45 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-knitr/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 RKnitr(Package): + """Provides a general-purpose tool for dynamic report generation in R using + Literate Programming techniques.""" + + homepage = "http://yihui.name/knitr/" + url = "https://cran.rstudio.com/src/contrib/knitr_1.14.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/knitr" + + version('1.14', 'ef0fbeaa9372f99ffbc57212a7781511') + version('0.6' , 'c67d6db84cd55594a9e870c90651a3db') + + extends('R') + + depends_on('r-evaluate', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-formatr', type=nolink) + depends_on('r-highr', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-markdown', 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-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index ba29feefc4..a798b1ce65 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -32,10 +32,10 @@ class RLattice(Package): handle most nonstandard requirements. See ?Lattice for an introduction.""" homepage = "http://lattice.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz" + url = "https://cran.r-project.org/src/contrib/lattice_0.20-34.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/lattice" - version('0.20-33', 'd487c94db1bfe00a27270f4c71baf53e') + version('0.20-34', 'c2a648b22d4206ae7526fb70b8e90fed') extends('R') diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py new file mode 100644 index 0000000000..dff9099c07 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-partykit/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 RPartykit(Package): + """A toolkit with infrastructure for representing, summarizing, and + visualizing tree-structured regression and classification models. This + unified infrastructure can be used for reading/coercing tree models from + different sources ('rpart', 'RWeka', 'PMML') yielding objects that share + functionality for print()/plot()/predict() methods. Furthermore, new and + improved reimplementations of conditional inference trees (ctree()) and + model-based recursive partitioning (mob()) from the 'party' package are + provided based on the new infrastructure.""" + + homepage = "http://partykit.r-forge.r-project.org/partykit" + url = "https://cran.r-project.org/src/contrib/partykit_1.1-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/partykit" + + version('1.1-1', '8fcb31d73ec1b8cd3bcd9789639a9277') + + extends('R') + + depends_on('r-survival', type=nolink) + depends_on('r-formula', 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-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py new file mode 100644 index 0000000000..b5a9546124 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pbdzmq/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 RPbdzmq(Package): + """'ZeroMQ' is a well-known library for high-performance asynchronous + messaging in scalable, distributed applications. This package provides + high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus + on interactive client/server programming frameworks. For convenience, a + minimal 'ZeroMQ' library (4.1.0 rc1) is shipped with 'pbdZMQ', which can + be used if no system installation of 'ZeroMQ' is available. A few wrapper + functions compatible with 'rzmq' are also provided.""" + + homepage = "http://r-pbd.org/" + url = "https://cran.r-project.org/src/contrib/pbdZMQ_0.2-4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/pbdZMQ" + + version('0.2-4', 'e5afb70199aa54d737ee7a0e26bde060') + + extends('R') + + depends_on('r-R6', type=nolink) + depends_on('zeromq') + + 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-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py new file mode 100644 index 0000000000..acd502b536 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pryr/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 RPryr(Package): + """Useful tools to pry back the covers of R and understand the language + at a deeper level.""" + + homepage = "https://github.com/hadley/pryr" + url = "https://cran.r-project.org/src/contrib/pryr_0.1.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/pryr" + + version('0.1.2', '66b597a762aa15a3b7037779522983b6') + + extends('R') + + 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), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py new file mode 100644 index 0000000000..074c545534 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rbokeh/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 RRbokeh(Package): + """R interface for creating plots in Bokeh. Bokeh by Continuum + Analytics.""" + + homepage = "https://hafen.github.io/rbokeh" + url = "https://cran.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rbokeh" + + version('0.5.0', '4e14778c3fbd9286460ca28c68f57d10') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-maps', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-hexbin', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-pryr', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-ggplot2', type=nolink) + depends_on('r-scales', type=nolink) + depends_on('r-gistr', 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-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py new file mode 100644 index 0000000000..2e1f6126f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-repr/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 RRepr(Package): + """String and binary representations of objects for several formats and + mime types.""" + + homepage = "https://github.com/IRkernel/repr" + url = "https://cran.r-project.org/src/contrib/repr_0.9.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/repr" + + version('0.9', 'db5ff74893063b492f684e42283070bd') + + 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-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py new file mode 100644 index 0000000000..41af3a4392 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rinside/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 RRinside(Package): + """C++ classes to embed R in C++ applications The 'RInside' packages makes + it easier to have "R inside" your C++ application by providing a C++ + wrapperclass providing the R interpreter. As R itself is embedded into + your application, a shared library build of R is required. This works on + Linux, OS X and even on Windows provided you use the same tools used to + build R itself. Numerous examples are provided in the eight subdirectories + of the examples/ directory of the installed package: standard, mpi (for + parallel computing) qt (showing how to embed 'RInside' inside a Qt GUI + application), wt (showing how to build a "web-application" using the Wt + toolkit), armadillo (for 'RInside' use with 'RcppArmadillo') and eigen (for + 'RInside' use with 'RcppEigen'). The example use GNUmakefile(s) with GNU + extensions, so a GNU make is required (and will use the GNUmakefile + automatically). Doxygen-generated documentation of the C++ classes is + available at the 'RInside' website as well.""" + + homepage = "http://dirk.eddelbuettel.com/code/rinside.html" + url = "https://cran.r-project.org/src/contrib/RInside_0.2.13.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RInside" + + version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88') + + 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-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py new file mode 100644 index 0000000000..c379388314 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rmarkdown/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 RRmarkdown(Package): + """Convert R Markdown documents into a variety of formats.""" + + homepage = "http://rmarkdown.rstudio.com/" + url = "https://cran.r-project.org/src/contrib/rmarkdown_1.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rmarkdown" + + version('1.0', '264aa6a59e9680109e38df8270e14c58') + + extends('R') + + depends_on('r-knitr', type=nolink) + depends_on('r-yaml', type=nolink) + depends_on('r-htmltools', type=nolink) + depends_on('r-catools', type=nolink) + depends_on('r-evaluate', type=nolink) + depends_on('r-base64enc', 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-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py new file mode 100644 index 0000000000..7684792ba1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rsnns/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 RRsnns(Package): + """The Stuttgart Neural Network Simulator (SNNS) is a library containing + many standard implementations of neural networks. This package wraps the + SNNS functionality to make it available from within R. Using the RSNNS + low-level interface, all of the algorithmic functionality and flexibility + of SNNS can be accessed. Furthermore, the package contains a convenient + high-level interface, so that the most common neural network topologies + and learning algorithms integrate seamlessly into R.""" + + homepage = "http://sci2s.ugr.es/dicits/software/RSNNS" + url = "https://cran.r-project.org/src/contrib/RSNNS_0.4-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RSNNS" + + version('0.4-7', 'ade7736611c456effb5f72e0ce0a1e6f') + + 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-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py new file mode 100644 index 0000000000..472e706e72 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rzmq/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 RRzmq(Package): + """Interface to the ZeroMQ lightweight messaging kernel.""" + + homepage = "http://github.com/armstrtw/rzmq" + url = "https://cran.r-project.org/src/contrib/rzmq_0.7.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rzmq" + + version('0.7.7', '8ba18fd1c222d1eb25bb622ccd2897e0') + + depends_on('zeromq') + + 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-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py new file mode 100644 index 0000000000..a10b55d66c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-testit/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 RTestit(Package): + """Provides two convenience functions assert() and test_pkg() to facilitate + testing R packages.""" + + homepage = "https://github.com/yihui/testit" + url = "https://cran.r-project.org/src/contrib/testit_0.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/testit" + + version('0.5', 'f206d3cbdc5174e353d2d05ba6a12e59') + + 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-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py new file mode 100644 index 0000000000..97541bc3b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-uuid/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 RUuid(Package): + """Tools for generating and handling of UUIDs (Universally Unique + Identifiers).""" + + homepage = "http://www.rforge.net/uuid" + url = "https://cran.rstudio.com/src/contrib/uuid_0.1-2.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/uuid" + + version('0.1-2', 'f97d000c0b16bca455fb5bf2cd668ddf') + + 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/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index 94a323ce90..58bbcd8383 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -85,16 +85,29 @@ class Scotch(Package): '-DIDXSIZE64' ] + if self.spec.satisfies('platform=darwin'): + cflags.extend([ + '-Drestrict=__restrict' + ]) + # Library Build Type # if '+shared' in self.spec: - makefile_inc.extend([ - # todo change for Darwin systems - 'LIB = .so', - 'CLIBFLAGS = -shared -fPIC', - 'RANLIB = echo', - 'AR = $(CC)', - 'ARFLAGS = -shared $(LDFLAGS) -o' - ]) + if self.spec.satisfies('platform=darwin'): + makefile_inc.extend([ + 'LIB = .dylib', + 'CLIBFLAGS = -dynamiclib -fPIC', + 'RANLIB = echo', + 'AR = $(CC)', + 'ARFLAGS = -dynamiclib $(LDFLAGS) -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % prefix.lib # noqa + ]) + else: + makefile_inc.extend([ + 'LIB = .so', + 'CLIBFLAGS = -shared -fPIC', + 'RANLIB = echo', + 'AR = $(CC)', + 'ARFLAGS = -shared $(LDFLAGS) -o' + ]) cflags.append('-fPIC') else: makefile_inc.extend([ @@ -126,7 +139,11 @@ class Scotch(Package): ldflags.append('-L%s -lz' % (self.spec['zlib'].prefix.lib)) cflags.append('-DCOMMON_PTHREAD') - ldflags.append('-lm -lrt -pthread') + if self.spec.satisfies('platform=darwin'): + cflags.append('-DCOMMON_PTHREAD_BARRIER') + ldflags.append('-lm -pthread') + else: + ldflags.append('-lm -lrt -pthread') makefile_inc.append('LDFLAGS = %s' % ' '.join(ldflags)) diff --git a/var/spack/repos/builtin/packages/sowing/package.py b/var/spack/repos/builtin/packages/sowing/package.py new file mode 100644 index 0000000000..f7f6297488 --- /dev/null +++ b/var/spack/repos/builtin/packages/sowing/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 Sowing(Package): + """Sowing generates Fortran interfaces and documentation for PETSc + and MPICH. + """ + + homepage = "http://www.mcs.anl.gov/petsc/index.html" + url = "http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz" + + version('1.1.23-p1', '65aaf3ae2a4c0f30d532fec291702e16') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make('ALL', parallel=False) + make("install") diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py index d9cff650b6..8e23a2a14e 100644 --- a/var/spack/repos/builtin/packages/superlu/package.py +++ b/var/spack/repos/builtin/packages/superlu/package.py @@ -23,6 +23,8 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import glob +import os class Superlu(Package): @@ -34,21 +36,90 @@ class Superlu(Package): url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_5.2.1.tar.gz" version('5.2.1', '3a1a9bff20cb06b7d97c46d337504447') + version('4.3', 'b72c6309f25e9660133007b82621ba7c') + variant('fpic', default=False, + description='Build with position independent code') + + depends_on('cmake', when='@5.2.1:', type='build') depends_on('blas') + # CMake installation method + @when('@5.2.1:') def install(self, spec, prefix): cmake_args = [ - '-DCMAKE_POSITION_INDEPENDENT_CODE=ON', - # BLAS support '-Denable_blaslib=OFF', '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_libs.joined()) ] + if '+fpic' in spec: + cmake_args.extend([ + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON' + ]) + cmake_args.extend(std_cmake_args) with working_dir('spack-build', create=True): cmake('..', *cmake_args) - make() make('install') + + # Pre-cmake installation method + @when('@4.3') + def install(self, spec, prefix): + config = [] + + # Define make.inc file + config.extend([ + 'PLAT = _x86_64', + 'SuperLUroot = %s' % self.stage.source_path, + # 'SUPERLULIB = $(SuperLUroot)/lib/libsuperlu$(PLAT).a', + 'SUPERLULIB = $(SuperLUroot)/lib/libsuperlu_{0}.a' \ + .format(self.spec.version), + 'BLASDEF = -DUSE_VENDOR_BLAS', + 'BLASLIB = {0}'.format(spec['blas'].blas_libs.ld_flags), + # or BLASLIB = -L/usr/lib64 -lblas + 'TMGLIB = libtmglib.a', + 'LIBS = $(SUPERLULIB) $(BLASLIB)', + 'ARCH = ar', + 'ARCHFLAGS = cr', + 'RANLIB = {0}'.format('ranlib' if which('ranlib') else 'echo'), + 'CC = {0}'.format(os.environ['CC']), + 'FORTRAN = {0}'.format(os.environ['FC']), + 'LOADER = {0}'.format(os.environ['CC']), + 'CDEFS = -DAdd_' + ]) + + if '+fpic' in spec: + config.extend([ + # Use these lines instead when pic_flag capability arrives + # 'CFLAGS = -O3 {0}'.format(self.compiler.pic_flag), + # 'NOOPTS = {0}'.format(self.compiler.pic_flag), + # 'FFLAGS = -O2 {0}'.format(self.compiler.pic_flag), + # 'LOADOPTS = {0}'.format(self.compiler.pic_flag) + 'CFLAGS = -O3 -fPIC', + 'NOOPTS = -fPIC', + 'FFLAGS = -O2 -fPIC', + 'LOADOPTS = -fPIC' + ]) + else: + config.extend([ + 'CFLAGS = -O3', + 'NOOPTS = ', + 'FFLAGS = -O2', + 'LOADOPTS = ' + ]) + + # Write configuration options to make.inc file + with open('make.inc', 'w') as inc: + for option in config: + inc.write('{0}\n'.format(option)) + + make(parallel=False) + + # Install manually + install_tree('lib', prefix.lib) + headers = glob.glob(join_path('SRC', '*.h')) + mkdir(prefix.include) + for h in headers: + install(h, prefix.include) diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py index 7ac55a6785..6e5ed79c36 100644 --- a/var/spack/repos/builtin/packages/tetgen/package.py +++ b/var/spack/repos/builtin/packages/tetgen/package.py @@ -22,7 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## + from spack import * +import glob class Tetgen(Package): @@ -33,13 +35,35 @@ class Tetgen(Package): """ homepage = "http://www.tetgen.org" - url = "http://www.tetgen.org/files/tetgen1.4.3.tar.gz" - version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18') - version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', - url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') + version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') + version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18', url='http://www.tetgen.org/files/tetgen1.4.3.tar.gz') + + variant('debug', default=False, description='Builds the library in debug mode.') + variant('except', default=False, description='Replaces asserts with exceptions for better C++ compatibility.') + + patch('tetgen-1.5.0-free.patch', when='@1.5.0') + + def patch(self): + cflags = '-g -O0' if '+debug' in self.spec else '-g0 -O3' + + mff = FileFilter('makefile') + mff.filter(r'^(C(XX)?FLAGS\s*=)(.*)$', r'\1 {0}'.format(cflags)) + + if '+except' in self.spec: + hff = FileFilter('tetgen.h') + hff.filter(r'(\b)(throw)(\b)(.*);', r'\1assert_throw(false);') + hff.filter(r'^(#define\s*tetgenH\s*)$', r'\1{0}'.format("""\n +#include <stdexcept> + +inline void assert_throw(bool assertion) +{ + if(!assertion) + throw std::runtime_error("Tetgen encountered a problem (assert failed)!"); +}\n""")) - depends_on('cmake@2.8.7:', when='@1.5.0:', type='build') + sff = FileFilter(*(glob.glob('*.cxx'))) + sff.filter(r'(\b)(assert)(\b)', r'\1assert_throw\3') def install(self, spec, prefix): make('tetgen', 'tetlib') diff --git a/var/spack/repos/builtin/packages/tetgen/tetgen-1.5.0-free.patch b/var/spack/repos/builtin/packages/tetgen/tetgen-1.5.0-free.patch new file mode 100644 index 0000000000..009ccd834f --- /dev/null +++ b/var/spack/repos/builtin/packages/tetgen/tetgen-1.5.0-free.patch @@ -0,0 +1,49 @@ +diff --git a/tetgen.h b/tetgen.h +index 3196e03..2ff3138 100644 +--- a/tetgen.h ++++ b/tetgen.h +@@ -2206,6 +2206,44 @@ public: + if (highordertable != NULL) { + delete [] highordertable; + } ++ ++ bgm = NULL; ++ ++ points = NULL; ++ dummypoint = NULL; ++ ++ tetrahedrons = NULL; ++ ++ subfaces = NULL; ++ subsegs = NULL; ++ ++ tet2segpool = NULL; ++ tet2subpool = NULL; ++ ++ flippool = NULL; ++ unflipqueue = NULL; ++ ++ cavetetlist = NULL; ++ cavebdrylist = NULL; ++ caveoldtetlist = NULL; ++ cavetetvertlist = NULL; ++ ++ caveshlist = NULL; ++ caveshbdlist = NULL; ++ cavesegshlist = NULL; ++ cavetetshlist = NULL; ++ cavetetseglist = NULL; ++ caveencshlist = NULL; ++ caveencseglist = NULL; ++ ++ subsegstack = NULL; ++ subfacstack = NULL; ++ subvertstack = NULL; ++ ++ idx2facetlist = NULL; ++ facetverticeslist = NULL; ++ segmentendpointslist = NULL; ++ highordertable = NULL; + } + + ~tetgenmesh() diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py index 894d3af6cc..12a7049e72 100644 --- a/var/spack/repos/builtin/packages/tk/package.py +++ b/var/spack/repos/builtin/packages/tk/package.py @@ -37,7 +37,10 @@ class Tk(Package): version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4') version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221') + variant('X', default=True, description='Enable X11 support') + depends_on("tcl") + depends_on("libx11", when='+X') def url_for_version(self, version): base_url = "http://prdownloads.sourceforge.net/tcl" diff --git a/var/spack/repos/builtin/packages/yaml-cpp/package.py b/var/spack/repos/builtin/packages/yaml-cpp/package.py new file mode 100644 index 0000000000..0ffedb30cd --- /dev/null +++ b/var/spack/repos/builtin/packages/yaml-cpp/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 YamlCpp(Package): + """A YAML parser and emitter in C++""" + + homepage = "https://github.com/jbeder/yaml-cpp" + url = \ + "https://github.com/jbeder/yaml-cpp/archive/yaml-cpp-0.5.3.tar.gz" + + version('0.5.3', '4e47733d98266e46a1a73ae0a72954eb') + + variant('fpic', default=False, + description='Build with position independent code') + + depends_on('cmake', type='build') + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + args = std_cmake_args + if '+fpic' in spec: + args += ['-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true'] + cmake('..', *args) + make() + make("install") |