r-annotationdbi: new package (#5408)

* r-annotationdbi: Create New Package.

* r-iranges: Create new package.

* r-s4vectors: Create new package.

* r-annotationdbi: Create new package.

* r-s4vectors: Delete file.

* r-annotationdbi: Correct format.

* r-iranges: Correct format.

2 files changed, 89 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
new file mode 100644
index 0000000000..aaac979029
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 RAnnotationdbi(RPackage):
+    """Provides user interface and database connection code for
+    annotation data packages using SQLite data storage."""
+
+    homepage = "https://www.bioconductor.org/packages/AnnotationDbi/"
+    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.38.2.tar.gz"
+    list_url = homepage
+    version('1.38.2', 'aea4a5cd1f752b59cb9f4a8dcca05734')
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-rsqlite', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
new file mode 100644
index 0000000000..1669c05bfe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-iranges/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# 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 RIranges(RPackage):
+    """Provides efficient low-level and highly
+    reusable S4 classes for storing,
+    manipulating and aggregating over annotated ranges of
+    integers. Implements an
+    algebra of range operations, including efficient
+    algorithms for finding overlaps
+    and nearest neighbors. Defines efficient list-like
+    classes for storing, transforming
+    and aggregating large grouped data,
+    i.e., collections of atomic vectors and DataFrames."""
+
+    homepage = "https://www.bioconductor.org/packages/IRanges/"
+    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.10.3.tar.gz"
+    list_url = homepage
+    version('2.10.3', '8fd2a39934de72affef35df8bdf53636')
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))