Standardize package names: lower-case, not Mixed_CASE (#2475)
* Rename packages
* Upcasing depends_on() in packages.
* Downcased extends('r')
* Fixed erroneously changed URL that had slipped through.
* Fixed typo
* Fixed link from documentation into package source code.
* Fixed another doc problem.
* Changed underscores to dashes in package names.
* Added test to enforce lowercase, no-underscore naming convention.
* Fix r-xgboost
* Downcase more instances of 'R' in package auto-creation.
* Fix test.
* Converted unit test packages to use dashes not underscores
* Downcase `r` in the docs.
* Update module_file_support.rst
Fix r->R for class R.
This commit is contained in:
Elizabeth Fischer
committed by
Todd Gamblin
Todd Gamblin
parent
4e653254c5
commit
3dd4a01a5e
184
var/spack/repos/builtin/packages/r/package.py
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184
var/spack/repos/builtin/packages/r/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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from spack.util.environment import *
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import shutil
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class R(Package):
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"""R is 'GNU S', a freely available language and environment for
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statistical computing and graphics which provides a wide variety of
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statistical and graphical techniques: linear and nonlinear modelling,
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statistical tests, time series analysis, classification, clustering, etc.
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Please consult the R project homepage for further information."""
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homepage = "https://www.r-project.org"
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url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
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extendable = True
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version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
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version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
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version('3.2.3', '1ba3dac113efab69e706902810cc2970')
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version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
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version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
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version('3.2.0', '66fa17ad457d7e618191aa0f52fc402e')
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version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
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version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
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variant('external-lapack', default=False,
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description='Links to externally installed BLAS/LAPACK')
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variant('X', default=False,
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description='Enable X11 support (call configure --with-x)')
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# Virtual dependencies
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depends_on('blas', when='+external-lapack')
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depends_on('lapack', when='+external-lapack')
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# Concrete dependencies
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depends_on('readline')
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depends_on('ncurses')
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depends_on('icu4c')
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depends_on('glib')
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depends_on('zlib')
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depends_on('zlib@:1.2.8', when='@:3.3.1')
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depends_on('bzip2')
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depends_on('libtiff')
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depends_on('jpeg')
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depends_on('cairo')
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depends_on('cairo+X', when='+X')
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depends_on('cairo~X', when='~X')
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depends_on('pango')
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depends_on('freetype')
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depends_on('tcl')
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depends_on('tk')
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depends_on('tk+X', when='+X')
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depends_on('tk~X', when='~X')
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depends_on('libx11', when='+X')
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depends_on('libxt', when='+X')
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depends_on('curl')
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depends_on('pcre')
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depends_on('jdk')
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@property
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def etcdir(self):
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return join_path(prefix, 'rlib', 'R', 'etc')
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def install(self, spec, prefix):
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rlibdir = join_path(prefix, 'rlib')
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configure_args = ['--prefix=%s' % prefix,
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'--libdir=%s' % rlibdir,
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'--enable-R-shlib',
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'--enable-BLAS-shlib',
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'--enable-R-framework=no']
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if '+external-lapack' in spec:
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configure_args.extend(['--with-blas', '--with-lapack'])
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configure(*configure_args)
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make()
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make('install')
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# Make a copy of Makeconf because it will be needed to properly build R
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# dependencies in Spack.
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src_makeconf = join_path(self.etcdir, 'Makeconf')
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dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
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shutil.copy(src_makeconf, dst_makeconf)
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self.filter_compilers(spec, prefix)
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def filter_compilers(self, spec, prefix):
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"""Run after install to tell the configuration files and Makefiles
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to use the compilers that Spack built the package with.
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If this isn't done, they'll have CC and CXX set to Spack's generic
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cc and c++. We want them to be bound to whatever compiler
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they were built with."""
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kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
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filter_file(env['CC'], self.compiler.cc,
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join_path(self.etcdir, 'Makeconf'), **kwargs)
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filter_file(env['CXX'], self.compiler.cxx,
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join_path(self.etcdir, 'Makeconf'), **kwargs)
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filter_file(env['F77'], self.compiler.f77,
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join_path(self.etcdir, 'Makeconf'), **kwargs)
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filter_file(env['FC'], self.compiler.fc,
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join_path(self.etcdir, 'Makeconf'), **kwargs)
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# ========================================================================
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# Set up environment to make install easy for R extensions.
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# ========================================================================
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@property
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def r_lib_dir(self):
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return join_path('rlib', 'R', 'library')
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def setup_dependent_environment(self, spack_env, run_env, extension_spec):
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# Set R_LIBS to include the library dir for the
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# extension and any other R extensions it depends on.
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r_libs_path = []
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for d in extension_spec.traverse(deptype=nolink, deptype_query='run'):
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if d.package.extends(self.spec):
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r_libs_path.append(join_path(d.prefix, self.r_lib_dir))
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r_libs_path = ':'.join(r_libs_path)
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spack_env.set('R_LIBS', r_libs_path)
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spack_env.set('R_MAKEVARS_SITE',
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join_path(self.etcdir, 'Makeconf.spack'))
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# Use the number of make_jobs set in spack. The make program will
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# determine how many jobs can actually be started.
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spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
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# For run time environment set only the path for extension_spec and
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# prepend it to R_LIBS
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if extension_spec.package.extends(self.spec):
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run_env.prepend_path('R_LIBS', join_path(
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extension_spec.prefix, self.r_lib_dir))
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('LIBRARY_PATH',
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join_path(self.prefix, 'rlib', 'R', 'lib'))
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run_env.prepend_path('LD_LIBRARY_PATH',
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join_path(self.prefix, 'rlib', 'R', 'lib'))
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run_env.prepend_path('CPATH',
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join_path(self.prefix, 'rlib', 'R', 'include'))
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def setup_dependent_package(self, module, ext_spec):
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"""Called before R modules' install() methods. In most cases,
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extensions will only need to have one line:
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R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
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self.stage.source_path)"""
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# R extension builds can have a global R executable function
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module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
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# Add variable for library directry
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module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir)
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# Make the site packages directory for extensions, if it does not exist
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# already.
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if ext_spec.package.is_extension:
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mkdirp(module.r_lib_dir)
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