Add package r-reportingtools and update url for its dependencies. (#6071)

* r-reportingtools: Create new package.

* r-go-db: Update url.

* r-gseabase: Update url.

* r-pfam-db: Update url.

var/spack/repos/builtin/packages/r-go-db/package.py

@@ -30,8 +30,7 @@ class RGoDb(RPackage):
     Ontology assembled using data from GO."""
 
     homepage = "https://www.bioconductor.org/packages/GO.db/"
-    url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz"
-    list_url = homepage
+    url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz"
 
     version('3.4.1', 'e16ee8921d8adc1ed3cbac2a3e35e386')
     depends_on('r-annotationdbi', type=('build', 'run'))

var/spack/repos/builtin/packages/r-gseabase/package.py

@@ -30,9 +30,9 @@ class RGseabase(RPackage):
     Set Enrichment Analysis (GSEA)."""
 
     homepage = "https://www.bioconductor.org/packages/GSEABase/"
-    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/GSEABase_1.38.2.tar.gz"
+    url      = "https://git.bioconductor.org/packages/GSEABase"
 
-    version('1.38.2', '027bdf1c9811f4991f3d11075ca40226')
+    version('1.38.2', git='https://git.bioconductor.org/packages/GSEABase', commit='84c9f10c316163118ca990900a7a67555b96e75b')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.2')
     depends_on('r-biocgenerics', type=('build', 'run'))

var/spack/repos/builtin/packages/r-pfam-db/package.py

@@ -30,7 +30,7 @@ class RPfamDb(RPackage):
     public repositories."""
 
     homepage = "https://www.bioconductor.org/packages/PFAM.db/"
-    url      = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz"
+    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz"
 
     version('3.4.1', '65ed35887ecc44f5ac9f9c8563e03f44')
 

var/spack/repos/builtin/packages/r-reportingtools/package.py

@@ -0,0 +1,67 @@
+##############################################################################
+# 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 RReportingtools(RPackage):
+    """The ReportingTools software package enables users to easily
+    display reports of analysis results generated from sources such
+    as microarray and sequencing data. The package allows users to
+    create HTML pages that may be viewed on a web browser such as
+    Safari, or in other formats readable by programs such as Excel.
+    Users can generate tables with sortable and filterable columns,
+    make and display plots, and link table entries to other data
+    sources such as NCBI or larger plots within the HTML page. Using
+    the package, users can also produce a table of contents page to
+    link various reports together for a particular project that can
+    be viewed in a web browser. For more examples, please visit our
+    site: http:// research-pub.gene.com/ReportingTools."""
+
+    homepage = "https://bioconductor.org/packages/ReportingTools/"
+    url      = "https://git.bioconductor.org/packages/ReportingTools"
+
+    version('2.16.0', git='https://git.bioconductor.org/packages/ReportingTools', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.16.0')
+    depends_on('r-knitr', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-hwriter', type=('build', 'run'))
+    depends_on('r-category', type=('build', 'run'))
+    depends_on('r-gostats', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-edger', type=('build', 'run'))
+    depends_on('r-annotate', type=('build', 'run'))
+    depends_on('r-pfam-db', type=('build', 'run'))
+    depends_on('r-gseabase', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
+    depends_on('r-utils', type=('build', 'run'))
+    depends_on('r-deseq2', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-ggbio', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))