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Standardize package names: lower-case, not Mixed_CASE (#2475)

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* 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
2017-01-04 21:24:07 -05:00
committed by Todd Gamblin
parent 4e653254c5
commit 3dd4a01a5e
205 changed files with 215 additions and 204 deletions
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56
var/spack/repos/builtin/packages/r-biocgenerics/package.py Normal file
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##############################################################################
# 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 RBiocgenerics(Package):
"""S4 generic functions needed by many Bioconductor packages."""
homepage = 'https://bioconductor.org/packages/BiocGenerics/'
version('bioc-3.3',
git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
branch='release-3.3')
version('bioc-3.2',
git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
branch='release-3.2')
extends('r')
def validate(self, spec):
"""
Checks that the version of R is appropriate for the Bioconductor
version.
"""
if spec.satisfies('@bioc-3.3'):
if not spec.satisfies('^R@3.3.0:3.3.9'):
raise InstallError('Must use R-3.3 for Bioconductor-3.3')
elif spec.satisfies('@bioc-3.2'):
if not spec.satisfies('^R@3.2.0:3.2.9'):
raise InstallError('Must use R-3.2 for Bioconductor-3.2')
def install(self, spec, prefix):
self.validate(spec)
R('CMD', 'INSTALL', '--library=%s' %
self.module.r_lib_dir, '%s' % self.stage.source_path)