From 35583f48f4dbc324b26cebca249fc28b8c5cfd91 Mon Sep 17 00:00:00 2001
From: lingnanyuan <1297162327@qq.com>
Date: Mon, 9 Oct 2017 18:10:29 -0500
Subject: [PATCH] r-adsplit: Create new package and update version for its
 dependencies. (#5640)

* r-adsplit: Create new package.

* r-rlang: Update version.

* r-s4vectors: Update version.
---
 .../builtin/packages/r-adsplit/package.py     | 44 +++++++++++++++++++
 .../repos/builtin/packages/r-rlang/package.py |  1 +
 .../builtin/packages/r-s4vectors/package.py   |  2 +
 3 files changed, 47 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-adsplit/package.py

diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py
new file mode 100644
index 0000000000..9419c69bae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-adsplit/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 RAdsplit(RPackage):
+    """This package implements clustering of microarray gene expression
+    profiles according to functional annotations. For each term genes
+    are annotated to, splits into two subclasses are computed and a
+    significance of the supporting gene set is determined."""
+
+    homepage = "https://www.bioconductor.org/packages/adSplit/"
+    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/adSplit_1.46.0.tar.gz"
+
+    version('1.46.0', '7638432c734c1fe458acbb9b29384f57')
+
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-kegg-db', type=('build', 'run'))
+    depends_on('r-multtest', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py
index 995bc11cec..675382e62b 100644
--- a/var/spack/repos/builtin/packages/r-rlang/package.py
+++ b/var/spack/repos/builtin/packages/r-rlang/package.py
@@ -33,4 +33,5 @@ class RRlang(RPackage):
     url      = "https://cran.r-project.org/src/contrib/rlang_0.1.2.tar.gz"
     list_url = homepage
 
+    version('0.1.2', '170f8cf7b61898040643515a1746a53a')
     version('0.1.1', '38a51a0b8f8487eb52b4f3d986313682')
diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py
index 1697895982..dba9d515f2 100644
--- a/var/spack/repos/builtin/packages/r-s4vectors/package.py
+++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py
@@ -37,7 +37,9 @@ class RS4vectors(RPackage):
 
     homepage = "https://bioconductor.org/packages/S4Vectors/"
     url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/S4Vectors_0.14.4.tar.gz"
+    list_url = homepage
 
+    version('0.14.6', 'e40ba5de581fc54d70bd5c049415973c')
     version('0.14.4', '08ccc46e6d39f3aa9091f868ecec1f70')
 
     depends_on('r-biocgenerics', type=('build', 'run'))