r-vsn: new package (#6210)

* r-hexbin: updated md5

* r-vsn: created new package

2 files changed, 54 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py
index db51d68538..179914fca3 100644
--- a/var/spack/repos/builtin/packages/r-hexbin/package.py
+++ b/var/spack/repos/builtin/packages/r-hexbin/package.py
@@ -34,6 +34,6 @@ class RHexbin(RPackage):
     url      = "https://cran.r-project.org/src/contrib/hexbin_1.27.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/hexbin"
 
-    version('1.27.1', '7f380390c6511e97df10a810a3b3bb7c')
+    version('1.27.1', '7590ed158f8a57a71901bf6ca26f81be')
 
     depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py
new file mode 100644
index 0000000000..649f42ea5d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-vsn/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# 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 RVsn(RPackage):
+    """The package implements a method for normalising microarray intensities,
+       and works for single- and multiple-color arrays. It can also be used
+       for data from other technologies, as long as they have similar format.
+       The method uses a robust variant of the maximum-likelihood estimator
+       for an additive-multiplicative error model and affine calibration. The
+       model incorporates data calibration step (a.k.a. normalization), a
+       model for the dependence of the variance on the mean intensity and a
+       variance stabilizing data transformation. Differences between
+       transformed intensities are analogous to "normalized log-ratios".
+       However, in contrast to the latter, their variance is independent of
+       the mean, and they are usually more sensitive and specific in detecting
+       differential transcription."""
+
+    homepage = "https://www.bioconductor.org/packages/vsn/"
+    url      = "https://git.bioconductor.org/packages/vsn"
+
+    version('3.44.0', git='https://git.bioconductor.org/packages/vsn', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
+
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-affy', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-hexbin', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@3.44.0')