Merge branch 'develop' into eschnett/petsc-python-2

# Conflicts:
#	var/spack/packages/petsc/package.py
This commit is contained in:
Erik Schnetter 2016-01-12 14:36:37 -05:00
commit 8eb16ba02d
18 changed files with 335 additions and 77 deletions

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@ -0,0 +1,73 @@
##############################################################################
# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written 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 General Public License (as published by
# the Free Software Foundation) version 2.1 dated 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 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 Cgal(Package):
"""
CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of
a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems,
computer aided design, molecular biology, medical imaging, computer graphics, and robotics.
"""
homepage = 'http://www.cgal.org/'
url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz'
version('4.7', '4826714810f3b4c65cac96b90fb03b67')
version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d')
# Installation instructions : http://doc.cgal.org/latest/Manual/installation.html
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds a debug version of the libraries')
depends_on('boost')
depends_on('mpfr')
depends_on('gmp')
depends_on('zlib')
# FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
# FIXME : Optional third party libraries missing
def install(self, spec, prefix):
options = []
options.extend(std_cmake_args)
# CGAL supports only Release and Debug build type. Any other build type will raise an error at configure time
if '+debug' in spec:
options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
else:
options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
if '+shared' in spec:
options.append('-DBUILD_SHARED_LIBS:BOOL=ON')
else:
options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
build_directory = join_path(self.stage.path, 'spack-build')
source_directory = self.stage.source_path
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")

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@ -38,8 +38,9 @@ class Cmake(Package):
version('3.4.0', 'cd3034e0a44256a0917e254167217fc8',
url = 'https://cmake.org/files/v3.4/cmake-3.4.0.tar.gz')
# version('3.0.1', 'e2e05d84cb44a42f1371d9995631dcf5')
# version('3.0.0', '21a1c85e1a3b803c4b48e7ff915a863e')
variant('ncurses', default=True, description='Enables the build of the ncurses gui')
depends_on('ncurses', when='+ncurses')
def install(self, spec, prefix):
configure('--prefix=' + prefix,

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@ -32,13 +32,13 @@ class Gdb(Package):
-- or what another program was doing at the moment it crashed.
"""
homepage = "https://www.gnu.org/software/gdb"
url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.xz"
url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz"
version('7.10.1', '39e654460c9cdd80200a29ac020cfe11')
version('7.10', '2a35bac41fa8e10bf04f3a0dd7f7f363')
version('7.9.1', '35374c77a70884eb430c97061053a36e')
version('7.9', 'e6279f26559d839f0b4218a482bcb43e')
version('7.8.2', 'a80cf252ed2e775d4e4533341bbf2459')
version('7.10.1', 'b93a2721393e5fa226375b42d567d90b')
version('7.10', 'fa6827ad0fd2be1daa418abb11a54d86')
version('7.9.1', 'f3b97de919a9dba84490b2e076ec4cb0')
version('7.9', '8f8ced422fe462a00e0135a643544f17')
version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc')
depends_on('texinfo')

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@ -5,14 +5,14 @@ class Git(Package):
system designed to handle everything from small to very large
projects with speed and efficiency."""
homepage = "http://git-scm.com"
url = "https://www.kernel.org/pub/software/scm/git/git-2.2.1.tar.xz"
url = "https://www.kernel.org/pub/software/scm/git/git-2.2.1.tar.gz"
version('2.6.3', '5a6375349c3f13c8dbbabfc327bae429')
version('2.6.2', '32ae5ad29763fc927bfcaeab55385fd9')
version('2.6.1', 'dd4a3a7fe96598c553edd39d40c9c290')
version('2.6.0', '6b7d43d615fb3f0dfecf4d131e23f438')
version('2.5.4', 'ec118fcd1cf984edc17eb6588b78e81b')
version('2.2.1', '43e01f9d96ba8c11611e0eef0d9f9f28')
version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423')
version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8')
version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd')
version('2.6.0', 'eb76a07148d94802a1745d759716a57e')
version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
# Git compiles with curl support by default on but if your system

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@ -30,8 +30,11 @@ class Gperftools(Package):
homepage = "https://code.google.com/p/gperftools"
url = "https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz"
version('2.4', '2171cea3bbe053036fb5d5d25176a160', url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz")
version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90', url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz")
depends_on("libunwind")
def install(self, spec, prefix):
configure("--prefix=" + prefix)
make()

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@ -0,0 +1,11 @@
--- julia/src/gc.c
+++ julia/src/gc.c
@@ -162,7 +162,7 @@
// A region is contiguous storage for up to REGION_PG_COUNT naturally aligned GC_PAGE_SZ pages
// It uses a very naive allocator (see malloc_page & free_page)
#if defined(_P64) && !defined(_COMPILER_MICROSOFT_)
-#define REGION_PG_COUNT 16*8*4096 // 8G because virtual memory is cheap
+#define REGION_PG_COUNT 8*4096 // 512M
#else
#define REGION_PG_COUNT 8*4096 // 512M
#endif

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@ -8,11 +8,14 @@ class Julia(Package):
version('0.4.2', 'ccfeb4f4090c8b31083f5e1ccb03eb06')
patch('gc.patch')
# Build-time dependencies
# depends_on("cmake")
depends_on("cmake @2.8:")
# depends_on("awk")
# depends_on("m4")
# depends_on("pkg-config")
depends_on("python @2.6:2.9")
# I think that Julia requires the dependencies above, but it builds find (on
# my system) without these. We should enable them as necessary.

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@ -5,12 +5,10 @@ class Libpciaccess(Package):
"""Generic PCI access library."""
homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
url = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
url = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.4.tar.bz2"
version('0.13.4', git='http://anongit.freedesktop.org/git/xorg/lib/libpciaccess.git',
tag='libpciaccess-0.13.4')
version('0.13.4', 'ace78aec799b1cf6dfaea55d3879ed9f')
depends_on('autoconf')
depends_on('libtool')
def install(self, spec, prefix):
@ -20,9 +18,6 @@ def install(self, spec, prefix):
mkdir(prefix.lib)
return
from subprocess import call
call(["./autogen.sh"])
configure("--prefix=%s" % prefix)
make()
make("install")

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@ -6,6 +6,7 @@ class Lua(Package):
homepage = "http://www.lua.org"
url = "http://www.lua.org/ftp/lua-5.1.5.tar.gz"
version('5.3.2', '33278c2ab5ee3c1a875be8d55c1ca2a1')
version('5.3.1', '797adacada8d85761c079390ff1d9961')
version('5.3.0', 'a1b0a7e92d0c85bbff7a8d27bf29f8af')
version('5.2.4', '913fdb32207046b273fdb17aad70be13')
@ -18,11 +19,16 @@ class Lua(Package):
version('5.1.3', 'a70a8dfaa150e047866dc01a46272599')
depends_on('ncurses')
depends_on('readline')
def install(self, spec, prefix):
if spec.satisfies("=darwin-i686") or spec.satisfies("=darwin-x86_64"):
target = 'macosx'
else:
target = 'linux'
make('INSTALL_TOP=%s' % prefix,
'MYLDFLAGS="-L%s/lib -Wl,-rpath,%s"' % (spec['ncurses'].prefix,spec['ncurses'].prefix),
'linux')
'MYLDFLAGS=-L%s -lncurses' % spec['ncurses'].prefix.lib,
target)
make('INSTALL_TOP=%s' % prefix,
'MYLDFLAGS="-L%s/lib -Wl,-rpath,%s"' % (spec['ncurses'].prefix,spec['ncurses'].prefix),
'MYLDFLAGS=-L%s -lncurses' % spec['ncurses'].prefix.lib,
'install')

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@ -1,27 +1,83 @@
##############################################################################
# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written 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 General Public License (as published by
# the Free Software Foundation) version 2.1 dated 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 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 Metis(Package):
"""METIS is a set of serial programs for partitioning graphs,
partitioning finite element meshes, and producing fill reducing
orderings for sparse matrices. The algorithms implemented in
METIS are based on the multilevel recursive-bisection,
multilevel k-way, and multi-constraint partitioning schemes."""
homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
class Metis(Package):
"""
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill
reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel
recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
"""
homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
version('5.1.0', '5465e67079419a69e0116de24fce58fe')
depends_on('mpi')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds the library in debug mode')
variant('gdb', default=False, description='Enables gdb support')
variant('idx64', default=False, description='Use int64_t as default index type')
variant('double', default=False, description='Use double precision floating point types')
depends_on('cmake @2.8:') # build-time dependency
depends_on('gdb', when='+gdb')
def install(self, spec, prefix):
cmake(".",
'-DGKLIB_PATH=%s/GKlib' % pwd(),
'-DSHARED=1',
'-DCMAKE_C_COMPILER=mpicc',
'-DCMAKE_CXX_COMPILER=mpicxx',
'-DSHARED=1',
*std_cmake_args)
make()
make("install")
options = []
options.extend(std_cmake_args)
build_directory = join_path(self.stage.path, 'spack-build')
source_directory = self.stage.source_path
options.append('-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=source_directory))
if '+shared' in spec:
options.append('-DSHARED:BOOL=ON')
if '+debug' in spec:
options.extend(['-DDEBUG:BOOL=ON',
'-DCMAKE_BUILD_TYPE:STRING=Debug'])
if '+gdb' in spec:
options.append('-DGDB:BOOL=ON')
metis_header = join_path(source_directory, 'include', 'metis.h')
if '+idx64' in spec:
filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
if '+double' in spec:
filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")

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@ -17,6 +17,10 @@ class Openssl(Package):
parallel = False
def install(self, spec, prefix):
# OpenSSL uses a variable APPS in its Makefile. If it happens to be set
# in the environment, then this will override what is set in the
# Makefile, leading to build errors.
env.pop('APPS', None)
if spec.satisfies("=darwin-x86_64") or spec.satisfies("=ppc64"):
# This needs to be done for all 64-bit architectures (except Linux,
# where it happens automatically?)

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@ -1,26 +1,95 @@
##############################################################################
# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written 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 General Public License (as published by
# the Free Software Foundation) version 2.1 dated 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 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 *
# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce
# FIXME : the installation rules to just a few lines
class Parmetis(Package):
"""ParMETIS is an MPI-based parallel library that implements a
variety of algorithms for partitioning unstructured graphs,
meshes, and for computing fill-reducing orderings of sparse
matrices."""
homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview"
url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz"
"""
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured
graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
"""
homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz'
version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds the library in debug mode')
variant('gdb', default=False, description='Enables gdb support')
variant('idx64', default=False, description='Use int64_t as default index type')
variant('double', default=False, description='Use double precision floating point types')
depends_on('cmake @2.8:') # build dependency
depends_on('mpi')
def install(self, spec, prefix):
cmake(".",
'-DGKLIB_PATH=%s/metis/GKlib' % pwd(),
'-DMETIS_PATH=%s/metis' % pwd(),
'-DSHARED=1',
'-DCMAKE_C_COMPILER=mpicc',
'-DCMAKE_CXX_COMPILER=mpicxx',
'-DSHARED=1',
*std_cmake_args)
# FIXME : this should conflict with metis as it builds its own version internally
make()
make("install")
depends_on('gdb', when='+gdb')
def install(self, spec, prefix):
options = []
options.extend(std_cmake_args)
build_directory = join_path(self.stage.path, 'spack-build')
source_directory = self.stage.source_path
metis_source = join_path(source_directory, 'metis')
# FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
# FIXME : they use a non-standard name
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source),
'-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source),
'-DCMAKE_C_COMPILER:STRING=mpicc',
'-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
if '+shared' in spec:
options.append('-DSHARED:BOOL=ON')
if '+debug' in spec:
options.extend(['-DDEBUG:BOOL=ON',
'-DCMAKE_BUILD_TYPE:STRING=Debug'])
if '+gdb' in spec:
options.append('-DGDB:BOOL=ON')
metis_header = join_path(metis_source, 'include', 'metis.h')
if '+idx64' in spec:
filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
if '+double' in spec:
filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")
# Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required
# metis header either
install(metis_header, self.prefix.include)

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@ -0,0 +1,16 @@
from spack import *
class Patchelf(Package):
"""PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables."""
homepage = "https://nixos.org/patchelf.html"
url = "http://nixos.org/releases/patchelf/patchelf-0.8/patchelf-0.8.tar.gz"
list_url = "http://nixos.org/releases/patchelf/"
list_depth = 2
version('0.8', '407b229e6a681ffb0e2cdd5915cb2d01')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

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@ -25,9 +25,6 @@ class Petsc(Package):
def install(self, spec, prefix):
configure("--prefix=%s" % prefix,
"CC=cc",
"CXX=c++",
"FC=f90",
"--with-blas-lib=%s/libblas.a" % spec['blas'].prefix.lib,
"--with-lapack-lib=%s/liblapack.a" % spec['lapack'].prefix.lib,
"--with-boost-dir=%s" % spec['boost'].prefix,
@ -35,6 +32,7 @@ def install(self, spec, prefix):
"--with-parmetis-dir=%s" % spec['parmetis'].prefix,
"--with-metis-dir=%s" % spec['metis'].prefix,
"--with-hdf5-dir=%s" % spec['hdf5'].prefix,
"--with-mpi-dir=%s" % spec['mpi'].prefix,
"--with-shared-libraries=0")
# PETSc has its own way of doing parallel make.

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@ -11,15 +11,16 @@
class Python(Package):
"""The Python programming language."""
homepage = "http://www.python.org"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tar.xz"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
extendable = True
version('2.7.8', 'd235bdfa75b8396942e360a70487ee00')
version('2.7.10', 'c685ef0b8e9f27b5e3db5db12b268ac6')
version('2.7.11', '1dbcc848b4cd8399a8199d000f9f823c', preferred=True)
version('3.5.0', 'd149d2812f10cbe04c042232e7964171')
version('3.5.1', 'e9ea6f2623fffcdd871b7b19113fde80')
version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
depends_on("openssl")
depends_on("bzip2")

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@ -0,0 +1,21 @@
from spack import *
class Szip(Package):
"""Szip is an implementation of the extended-Rice lossless compression algorithm.
It provides lossless compression of scientific data, and is provided with HDF
software products."""
homepage = "https://www.hdfgroup.org/doc_resource/SZIP/"
url = "http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz"
version('2.1', '902f831bcefb69c6b635374424acbead')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix,
'--enable-production',
'--enable-shared',
'--enable-static',
'--enable-encoding')
make()
make("install")

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@ -33,12 +33,12 @@ class Texinfo(Package):
used by many non-GNU projects as well.FIXME: put a proper description of your package here.
"""
homepage = "https://www.gnu.org/software/texinfo/"
url = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.xz"
url = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.gz"
version('6.0', '02818e62a5b8ae0213a7ff572991bb50')
version('5.2', 'cb489df8a7ee9d10a236197aefdb32c5')
version('5.1', '52ee905a3b705020d2a1b6ec36d53ca6')
version('5.0', 'ef2fad34c71ddc95b20c7d6a08c0d7a6')
version('6.0', 'e1a2ef5dce5018b53f0f6eed45b247a7')
version('5.2', '1b8f98b80a8e6c50422125e07522e8db')
version('5.1', '54e250014fe698fb4832016158747c03')
version('5.0', '918432285abe6fe96c98355594c5656a')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)

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@ -8,9 +8,10 @@ class Wget(Package):
etc."""
homepage = "http://www.gnu.org/software/wget/"
url = "http://ftp.gnu.org/gnu/wget/wget-1.16.tar.xz"
url = "http://ftp.gnu.org/gnu/wget/wget-1.16.tar.gz"
version('1.16', 'fe102975ab3a6c049777883f1bb9ad07')
version('1.17', 'c4c4727766f24ac716936275014a0536')
version('1.16', '293a37977c41b5522f781d3a3a078426')
depends_on("openssl")