r-cner: new package (#7228)

2 files changed, 59 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py
new file mode 100644
index 0000000000..8b920b11e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cner/package.py
@@ -0,0 +1,56 @@
+##############################################################################
+# 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 RCner(RPackage):
+    """"Large-scale identification and advanced visualization of sets of
+        conserved noncoding elements."""
+
+    homepage = "http://www.example.co://bioconductor.org/packages/CNEr/"
+    url      = "https://git.bioconductor.org/packages/CNEr"
+
+    version('1.14.0', git='https://git.bioconductor.org/packages/CNEr', commit='b8634d65c51728c815127e22b45eba7c9b9db897')
+
+    depends_on('r-biostrings@2.33.4:', type=('build', 'run'))
+    depends_on('r-dbi@0.7:', type=('build', 'run'))
+    depends_on('r-rsqlite@0.11.4:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.25.5:', type=('build', 'run'))
+    depends_on('r-xvector@0.5.4:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.1.9:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
+    depends_on('r-iranges@2.5.27:', type=('build', 'run'))
+    depends_on('r-readr@0.2.2:', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-reshape2@1.4.1:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.1.0:', type=('build', 'run'))
+    depends_on('r-powerlaw@0.60.3:', type=('build', 'run'))
+    depends_on('r-annotate@1.50.0:', type=('build', 'run'))
+    depends_on('r-go-db@3.3.0:', type=('build', 'run'))
+    depends_on('r-keggrest@1.14.0:', type=('build', 'run'))
+    depends_on('r-utils@2.3.0:', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.14.0')
diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py
index b9a6e6a291..80e7b99024 100644
--- a/var/spack/repos/builtin/packages/r-keggrest/package.py
+++ b/var/spack/repos/builtin/packages/r-keggrest/package.py
@@ -37,8 +37,11 @@ class RKeggrest(RPackage):
     url      = "https://git.bioconductor.org/packages/KEGGREST"
     list_url = homepage
 
+    version('1.18.1', git='https://git.bioconductor.org/packages/KEGGREST', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4')
     version('1.2.0', git='https://git.bioconductor.org/packages/KEGGREST', commit='ed48de0def57a909894e237fa4731c4a052d8849')
 
     depends_on('r-httr', type=('build', 'run'))
     depends_on('r-png', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.2.0')
+    depends_on('r@3.4.3:3.4.9', when='@1.18.1')