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Clean up R package files

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- remove unused imports
- apply pep8
- reformat text strings
This commit is contained in:
Glenn Johnson 2016-05-28 20:19:45 -05:00
parent f351e011d1
commit 64acbbfcf0
1 changed files with 19 additions and 25 deletions
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44
var/spack/repos/builtin/packages/R/package.py
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@ -22,28 +22,22 @@
# License along with this program; if not, write to the Free Software # License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
import functools
import glob
import inspect
import os import os
import re
from contextlib import closing
import spack
from llnl.util.lang import match_predicate
from spack import * from spack import *
from spack.util.environment import * from spack.util.environment import *
class R(Package): class R(Package):
""" """R is 'GNU S', a freely available language and environment for
R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a statistical computing and graphics which provides a wide variety of
wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series statistical and graphical techniques: linear and nonlinear modelling,
analysis, classification, clustering, etc. Please consult the R project homepage for further information. statistical tests, time series analysis, classification, clustering, etc.
""" Please consult the R project homepage for further information."""
homepage = "https://www.r-project.org" homepage = "https://www.r-project.org"
url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz" url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
extendable = True extendable = True
version('3.2.3', '1ba3dac113efab69e706902810cc2970') version('3.2.3', '1ba3dac113efab69e706902810cc2970')
@ -53,7 +47,8 @@ class R(Package):
version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4') version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74') version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK') variant('external-lapack', default=False,
description='Links to externally installed BLAS/LAPACK')
# Virtual dependencies # Virtual dependencies
depends_on('blas', when='+external-lapack') depends_on('blas', when='+external-lapack')
@ -106,25 +101,24 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
r_libs_path = ':'.join(r_libs_path) r_libs_path = ':'.join(r_libs_path)
spack_env.set('R_LIBS', r_libs_path) spack_env.set('R_LIBS', r_libs_path)
# For run time environment set only the path for extension_spec and prepend it to R_LIBS # For run time environment set only the path for extension_spec and
# prepend it to R_LIBS
if extension_spec.package.extends(self.spec): if extension_spec.package.extends(self.spec):
run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir)) run_env.prepend_path('R_LIBS', os.path.join(
extension_spec.prefix, self.r_lib_dir))
def setup_dependent_package(self, module, ext_spec): def setup_dependent_package(self, module, ext_spec):
""" """Called before R modules' install() methods. In most cases,
Called before R modules' install() methods. extensions will only need to have one line:
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' %
In most cases, extensions will only need to have one line:: self.stage.archive_file)"""
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
"""
# R extension builds can have a global R executable function # R extension builds can have a global R executable function
module.R = Executable(join_path(self.spec.prefix.bin, 'R')) module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
# Add variable for library directry # Add variable for library directry
module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir) module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
# Make the site packages directory for extensions, if it does not exist already. # Make the site packages directory for extensions, if it does not exist
# already.
if ext_spec.package.is_extension: if ext_spec.package.is_extension:
mkdirp(module.r_lib_dir) mkdirp(module.r_lib_dir)