New package r-phangorn and its dependencies (#7034)

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

@@ -46,6 +46,10 @@ class RApe(RPackage):
     url      = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
 
+    version('5.0', '82fd2786a502f070ca020797f7b19fa4')
     version('4.1', 'a9ed416d6d172d4b9682556cf692d7c2')
 
     depends_on('r@3.2:')
+    depends_on('r-nlme', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))

var/spack/repos/builtin/packages/r-fastmatch/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/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 RFastmatch(RPackage):
+    """Package providing a fast match() replacement for cases that require
+       repeated look-ups. It is slightly faster that R's built-in match()
+       function on first match against a table, but extremely fast on any
+       subsequent lookup as it keeps the hash table in memory."""
+
+    homepage = "http://www.rforge.net/fastmatch"
+    url      = "https://cran.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fastmatch"
+
+    version('1.1-0', '900c2363c15059ac9d63c4c71ea2d6b2')

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

@@ -34,11 +34,12 @@ class RIgraph(RPackage):
     url      = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/igraph"
 
+    version('1.1.2', 'ca1617aea272852d2856c4661ad1c7d8')
     version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065')
 
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
-    depends_on('r-nmf', type=('build', 'run'))
+    depends_on('r-pkgconfig', type=('build', 'run'))
     depends_on('r-irlba', type=('build', 'run'))
     depends_on('gmp')
     depends_on('libxml2')

var/spack/repos/builtin/packages/r-phangorn/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/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 RPhangorn(RPackage):
+    """Package contains methods for estimation of phylogenetic trees and
+       networks using Maximum Likelihood, Maximum Parsimony, distance methods
+       and Hadamard conjugation. Allows to compare trees, models selection and
+       offers visualizations for trees and split networks."""
+
+    homepage = "http://www.example.co://github.com/KlausVigo/phangorn"
+    url      = "https://cran.r-project.org/src/contrib/phangorn_2.3.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/phangorn"
+
+    version('2.3.1', '85e7309900d061432508ab6f7e3e627e')
+
+    depends_on('r-ape@5.0:', type=('build', 'run'))
+    depends_on('r-quadprog', type=('build', 'run'))
+    depends_on('r-igraph@1.0:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-fastmatch', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.0:', type=('build', 'run'))