r-affycoretools: Create new package and its dependency r-ff. (#6082)

* r-ff: Create new package

* r-affycoretools: Create new package.

* r-ff: update url.

2 files changed, 92 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py
new file mode 100644
index 0000000000..8228cbe5a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# 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 RAffycoretools(RPackage):
+    """Various wrapper functions that have been written to streamline
+    the more common analyses that a core Biostatistician might see."""
+
+    homepage = "https://www.bioconductor.org/packages/affycoretools/"
+    url      = "https://git.bioconductor.org/packages/affycoretools"
+
+    version('1.48.0', git='https://git.bioconductor.org/packages/affycoretools', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.48.0')
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-affy', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-gostats', type=('build', 'run'))
+    depends_on('r-gcrma', type=('build', 'run'))
+    depends_on('r-xtable', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-gplots', type=('build', 'run'))
+    depends_on('r-oligoclasses', type=('build', 'run'))
+    depends_on('r-reportingtools', type=('build', 'run'))
+    depends_on('r-hwriter', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-edger', type=('build', 'run'))
+    depends_on('r-rsqlite', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py
new file mode 100644
index 0000000000..d305ca34f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ff/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 RFf(RPackage):
+    """memory-efficient storage of large data on disk and
+    fast access functions."""
+
+    homepage = "http://ff.r-forge.r-project.org/"
+    url      = "https://cran.rstudio.com/src/contrib/ff_2.2-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ff"
+
+    version('2.2-13', '4adf8840d24cb6e2927a3ef885c86fcd')
+
+    depends_on('r-bit', type=('build', 'run'))