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r-biobase: new package (#5398)

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Add r-biobase package. Remove explicit R dependency from r-biocgenerics
package (since it is an instance of RPackage). Update version for
r-biocgenerics and remove github versions.
This commit is contained in:
Levi Baber 2017-09-20 21:00:56 -05:00 committed by scheibelp
parent 1d5f1576a5
commit 04489d6dfa
2 changed files with 43 additions and 11 deletions
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var/spack/repos/builtin/packages/r-biobase/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 RBiobase(RPackage):
"""Functions that are needed by many other packages
or which replace R functions."""
homepage = "https://www.bioconductor.org/packages/Biobase/"
url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.36.2.tar.gz"
list_url = homepage
version('2.36.2', '8854eb70acabb07b55d2953fb1ecff31')
depends_on('r-biocgenerics', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-biocgenerics/package.py
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@ -22,19 +22,13 @@
# 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
############################################################################## ##############################################################################
#
from spack import * from spack import *
class RBiocgenerics(RPackage): class RBiocgenerics(RPackage):
"""S4 generic functions needed by many Bioconductor packages.""" """S4 generic functions needed by many Bioconductor packages."""
homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
homepage = 'https://bioconductor.org/packages/BiocGenerics/' url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.22.0.tar.gz"
version('3.3', list_url = homepage
git='https://github.com/Bioconductor-mirror/BiocGenerics.git', version('0.22.0', 'ef910f2011c0652e1f5fdf3b14219490')
branch='release-3.3')
version('3.2',
git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
branch='release-3.2')
depends_on('r@3.3.0:3.3.9', when='@3.3')
depends_on('r@3.2.0:3.2.9', when='@3.2')