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r-annotationdbi: new package (#5408)

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* r-annotationdbi: Create New Package.

* r-iranges: Create new package.

* r-s4vectors: Create new package.

* r-annotationdbi: Create new package.

* r-s4vectors: Delete file.

* r-annotationdbi: Correct format.

* r-iranges: Correct format.
This commit is contained in:
lingnanyuan 2017-09-25 17:37:31 -05:00 committed by Christoph Junghans
parent f94b23a249
commit 23235cf3e3
2 changed files with 89 additions and 0 deletions
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var/spack/repos/builtin/packages/r-annotationdbi/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 RAnnotationdbi(RPackage):
"""Provides user interface and database connection code for
annotation data packages using SQLite data storage."""
homepage = "https://www.bioconductor.org/packages/AnnotationDbi/"
url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.38.2.tar.gz"
list_url = homepage
version('1.38.2', 'aea4a5cd1f752b59cb9f4a8dcca05734')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-iranges/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 RIranges(RPackage):
"""Provides efficient low-level and highly
reusable S4 classes for storing,
manipulating and aggregating over annotated ranges of
integers. Implements an
algebra of range operations, including efficient
algorithms for finding overlaps
and nearest neighbors. Defines efficient list-like
classes for storing, transforming
and aggregating large grouped data,
i.e., collections of atomic vectors and DataFrames."""
homepage = "https://www.bioconductor.org/packages/IRanges/"
url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.10.3.tar.gz"
list_url = homepage
version('2.10.3', '8fd2a39934de72affef35df8bdf53636')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))