From 23235cf3e33d8b16a6e9882724134ba681893c4f Mon Sep 17 00:00:00 2001 From: lingnanyuan <1297162327@qq.com> Date: Mon, 25 Sep 2017 17:37:31 -0500 Subject: r-annotationdbi: new package (#5408) * 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. --- .../builtin/packages/r-annotationdbi/package.py | 43 ++++++++++++++++++++ .../repos/builtin/packages/r-iranges/package.py | 46 ++++++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-annotationdbi/package.py create mode 100644 var/spack/repos/builtin/packages/r-iranges/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py new file mode 100644 index 0000000000..aaac979029 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py new file mode 100644 index 0000000000..1669c05bfe --- /dev/null +++ b/var/spack/repos/builtin/packages/r-iranges/package.py @@ -0,0 +1,46 @@ +############################################################################## +# 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')) -- cgit v1.2.3-70-g09d2