r-gdsfmt: new package (#7035)

1 files changed, 47 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# 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/spack/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 RGdsfmt(RPackage):
+    """This package provides a high-level R interface to CoreArray Genomic
+       Data Structure (GDS) data files, which are portable across platforms
+       with hierarchical structure to store multiple scalable array-oriented
+       data sets with metadata information. It is suited for large-scale
+       datasets, especially for data which are much larger than the available
+       random-access memory. The gdsfmt package offers the efficient
+       operations specifically designed for integers of less than 8 bits,
+       since a diploid genotype, like single-nucleotide polymorphism (SNP),
+       usually occupies fewer bits than a byte. Data compression and
+       decompression are available with relatively efficient random access.
+       It is also allowed to read a GDS file in parallel with multiple R
+       processes supported by the package parallel."""
+
+    homepage = "http://bioconductor.org/packages/gdsfmt/"
+    url      = "https://git.bioconductor.org/packages/gdsfmt"
+
+    version('1.14.1', git='https://git.bioconductor.org/packages/gdsfmt', commit='15743647b7eea5b82d3284858b4591fb6e59959d')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.14.1')