Standardize package names: lower-case, not Mixed_CASE (#2475)

* Rename packages

* Upcasing depends_on() in packages.

* Downcased extends('r')

* Fixed erroneously changed URL that had slipped through.

* Fixed typo

* Fixed link from documentation into package source code.

* Fixed another doc problem.

* Changed underscores to dashes in package names.

* Added test to enforce lowercase, no-underscore naming convention.

* Fix r-xgboost

* Downcase more instances of 'R' in package auto-creation.

* Fix test.

* Converted unit test packages to use dashes not underscores

* Downcase `r` in the docs.

* Update module_file_support.rst

Fix r->R for class R.

var/spack/repos/builtin/packages/samrai/no-tool-build.patch

@@ -0,0 +1,20 @@
+--- SAMRAI/Makefile.in	2013-05-31 11:04:32.000000000 -0700
++++ SAMRAI/Makefile.in.notools	2014-05-30 10:31:15.135979900 -0700
+@@ -8,7 +8,7 @@
+ ##
+ #########################################################################
+ 
+-default: library tools
++default: library
+ 
+ SAMRAI  = @top_srcdir@
+ SUBDIR  = .
+@@ -135,7 +135,7 @@
+ 	done
+ 	$(MAKE) archive_remove_obj_names
+ 
+-install: library tools
++install: library
+ 	$(INSTALL) -d -m 755 $(INSTDIR)/config
+ 	$(INSTALL) -d -m 755 $(INSTDIR)/lib
+ 	$(INSTALL) -d -m 755 $(INSTDIR)/bin

var/spack/repos/builtin/packages/samrai/package.py

@@ -0,0 +1,77 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 Samrai(Package):
+    """SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure)
+       is an object-oriented C++ software library enables exploration of
+       numerical, algorithmic, parallel computing, and software issues
+       associated with applying structured adaptive mesh refinement
+       (SAMR) technology in large-scale parallel application development.
+
+    """
+    homepage = "https://computation.llnl.gov/project/SAMRAI/"
+    url      = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz"
+    list_url = homepage
+
+    version('3.9.1',      '232d04d0c995f5abf20d94350befd0b2')
+    version('3.8.0',      'c18fcffa706346bfa5828b36787ce5fe')
+    version('3.7.3',      '12d574eacadf8c9a70f1bb4cd1a69df6')
+    version('3.7.2',      'f6a716f171c9fdbf3cb12f71fa6e2737')
+    version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce')
+    version('3.5.2-beta', 'd072d9d681eeb9ada15ce91bea784274')
+    version('3.5.0-beta', '1ad18a319fc573e12e2b1fbb6f6b0a19')
+    version('3.4.1-beta', '00814cbee2cb76bf8302aff56bbb385b')
+    version('3.3.3-beta', '1db3241d3e1cab913dc310d736c34388')
+    version('3.3.2-beta', 'e598a085dab979498fcb6c110c4dd26c')
+    version('2.4.4',      '04fb048ed0efe7c531ac10c81cc5f6ac')
+
+    depends_on("mpi")
+    depends_on("zlib")
+    depends_on("hdf5+mpi")
+    depends_on("boost")
+
+    # don't build tools with gcc
+    patch('no-tool-build.patch', when='%gcc')
+
+    # TODO: currently hard-coded to use openmpi - be careful!
+    def install(self, spec, prefix):
+        configure(
+            "--prefix=%s" % prefix,
+            "--with-CXX=%s" % spec['mpi'].prefix.bin + "/mpic++",
+            "--with-CC=%s" % spec['mpi'].prefix.bin + "/mpicc",
+            "--with-hdf5=%s" % spec['hdf5'].prefix,
+            "--with-boost=%s" % spec['boost'].prefix,
+            "--with-zlib=%s" % spec['zlib'].prefix,
+            "--without-blas",
+            "--without-lapack",
+            "--with-hypre=no",
+            "--with-petsc=no",
+            "--enable-opt",
+            "--disable-debug")
+
+        make()
+        make("install")