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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import inspect
from spack.directives import extends
from spack.package import PackageBase, run_after
class RPackage(PackageBase):
"""Specialized class for packages that are built using R.
For more information on the R build system, see:
https://stat.ethz.ch/R-manual/R-devel/library/utils/html/INSTALL.html
This class provides a single phase that can be overridden:
1. :py:meth:`~.RPackage.install`
It has sensible defaults, and for many packages the only thing
necessary will be to add dependencies
"""
phases = ['install']
# package attributes that can be expanded to set the homepage, url,
# list_url, and git values
# For CRAN packages
cran = None
# For Bioconductor packages
bioc = None
maintainers = ['glennpj']
#: This attribute is used in UI queries that need to know the build
#: system base class
build_system_class = 'RPackage'
extends('r')
@property
def homepage(self):
if self.cran:
return 'https://cloud.r-project.org/package=' + self.cran
elif self.bioc:
return 'https://bioconductor.org/packages/' + self.bioc
@property
def url(self):
if self.cran:
return (
'https://cloud.r-project.org/src/contrib/'
+ self.cran + '_' + str(list(self.versions)[0]) + '.tar.gz'
)
@property
def list_url(self):
if self.cran:
return (
'https://cloud.r-project.org/src/contrib/Archive/'
+ self.cran + '/'
)
@property
def git(self):
if self.bioc:
return 'https://git.bioconductor.org/packages/' + self.bioc
def configure_args(self):
"""Arguments to pass to install via ``--configure-args``."""
return []
def configure_vars(self):
"""Arguments to pass to install via ``--configure-vars``."""
return []
def install(self, spec, prefix):
"""Installs an R package."""
config_args = self.configure_args()
config_vars = self.configure_vars()
args = [
'--vanilla',
'CMD',
'INSTALL'
]
if config_args:
args.append('--configure-args={0}'.format(' '.join(config_args)))
if config_vars:
args.append('--configure-vars={0}'.format(' '.join(config_vars)))
args.extend([
'--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path
])
inspect.getmodule(self).R(*args)
# Check that self.prefix is there after installation
run_after('install')(PackageBase.sanity_check_prefix)
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