From 5382279fa6f9277d80333533a9afa60c8aeb5e81 Mon Sep 17 00:00:00 2001
From: lingnanyuan <1297162327@qq.com>
Date: Thu, 30 Nov 2017 02:14:12 -0600
Subject: [PATCH] r-biomformat: Create new package. (#6517)

---
 .../builtin/packages/r-biomformat/package.py  | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-biomformat/package.py

diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py
new file mode 100644
index 0000000000..fe290c1fd9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biomformat/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# 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 RBiomformat(RPackage):
+    """This is an R package for interfacing with the BIOM format. This
+    package includes basic tools for reading biom-format files, accessing
+    and subsetting data tables from a biom object (which is more complex
+    than a single table), as well as limited support for writing a
+    biom-object back to a biom-format file. The design of this API is
+    intended to match the python API and other tools included with the
+    biom-format project, but with a decidedly "R flavor" that should be
+    familiar to R users. This includes S4 classes and methods, as well
+    as extensions of common core functions/methods."""
+
+    homepage = "https://www.bioconductor.org/packages/biomformat/"
+    url      = "https://git.bioconductor.org/packages/biomformat"
+
+    version('1.4.0', git='https://git.bioconductor.org/packages/biomformat', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a')
+
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-rhdf5', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.4.0')