r-biobase: new package (#5398)

Add r-biobase package. Remove explicit R dependency from r-biocgenerics
package (since it is an instance of RPackage). Update version for
r-biocgenerics and remove github versions.

2 files changed, 43 insertions, 11 deletions

diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py
new file mode 100644
index 0000000000..25d7ee79f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biobase/package.py
@@ -0,0 +1,38 @@
+##############################################################################
+# 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 RBiobase(RPackage):
+    """Functions that are needed by many other packages
+ or which replace R functions."""
+
+    homepage = "https://www.bioconductor.org/packages/Biobase/"
+    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.36.2.tar.gz"
+    list_url = homepage
+    version('2.36.2', '8854eb70acabb07b55d2953fb1ecff31')
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index 7b91598ca1..76ca3a43f5 100644
--- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
@@ -22,19 +22,13 @@
 # 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 RBiocgenerics(RPackage):
     """S4 generic functions needed by many Bioconductor packages."""
-
-    homepage = 'https://bioconductor.org/packages/BiocGenerics/'
-    version('3.3',
-            git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
-            branch='release-3.3')
-    version('3.2',
-            git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
-            branch='release-3.2')
-
-    depends_on('r@3.3.0:3.3.9', when='@3.3')
-    depends_on('r@3.2.0:3.2.9', when='@3.2')
+    homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
+    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.22.0.tar.gz"
+    list_url = homepage
+    version('0.22.0', 'ef910f2011c0652e1f5fdf3b14219490')