r-geomorph and other r fixes (#5961)

var/spack/repos/builtin/packages/r-geomorph/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 RGeomorph(RPackage):
+    """Read, manipulate, and digitize landmark data, generate shape variables
+       via Procrustes analysis for points, curves and surfaces, perform shape
+       analyses, and provide graphical depictions of shapes and patterns of
+       shape variation."""
+
+    homepage = "https://cran.r-project.org/package=geomorph"
+    url      = "https://cran.r-project.org/src/contrib/geomorph_3.0.5.tar.gz"
+
+    version('3.0.5', '240e69fe260ca3ef4d84b4281d61396c')
+
+    depends_on('r-rgl', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-jpeg', type=('build', 'run'))
+    depends_on('r-geiger', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))

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

@@ -41,6 +41,7 @@ class RRgl(RPackage):
     depends_on('r@3.2:3.9')
     depends_on('zlib', type=('link'))
     depends_on('libpng', type=('link'))
+    depends_on('libx11')
     depends_on('freetype', type=('link'))
     depends_on('mesa', type=('link'))
     depends_on('mesa-glu', type=('link'))
@@ -50,3 +51,11 @@ class RRgl(RPackage):
     depends_on('r-jsonlite', type=('build', 'run'))
     depends_on('r-shiny', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
+
+    def configure_args(self):
+        args = ['--x-includes=%s' % self.spec['libx11'].prefix.include,
+                '--x-libraries=%s' % self.spec['libx11'].prefix.lib,
+                '--with-gl-includes=%s' % self.spec['mesa'].prefix.include,
+                '--with-gl-libraries=%s' % self.spec['mesa'].prefix.lib,
+                '--with-gl-prefix=%s' % self.spec['mesa'].prefix]
+        return args

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

@@ -45,3 +45,4 @@ class RShiny(RPackage):
     depends_on('r-digest', type=('build', 'run'))
     depends_on('r-htmltools', type=('build', 'run'))
     depends_on('r-r6', type=('build', 'run'))
+    depends_on('r-sourcetools', type=('build', 'run'))