Make R extensable and add a couple of packages for verification.

Added R as a build system so that the create template will have the
correct configure line.
Added a regex for version parsing as the R URLs are a little odd.

3 files changed, 84 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 2471dff09b..3a76416f27 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -1,4 +1,14 @@
+import functools
+import glob
+import inspect
+import os
+import re
+from contextlib import closing
+
+import spack
+from llnl.util.lang import match_predicate
 from spack import *
+from spack.util.environment import *
 
 
 class R(Package):
@@ -9,6 +19,8 @@ class R(Package):
     """
     homepage = "https://www.r-project.org"
     url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
+    
+    extendable = True
 
     version('3.2.3', '1ba3dac113efab69e706902810cc2970')
     version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
@@ -47,3 +59,45 @@ class R(Package):
         configure(*options)
         make()
         make('install')
+
+    # ========================================================================
+    # Set up environment to make install easy for R extensions.
+    # ========================================================================
+
+    @property
+    def r_lib_dir(self):
+        return os.path.join('lib64', 'R', 'library')
+
+    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        # Set R_LIBS to include the library dir for the
+        # extension and any other R extensions it depends on.
+        r_libs_path = []
+        for d in extension_spec.traverse():
+            if d.package.extends(self.spec):
+                r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
+
+        r_libs_path = ':'.join(r_libs_path)
+        spack_env.set('R_LIBS', r_libs_path)
+
+        # For run time environment set only the path for extension_spec and prepend it to R_LIBS
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir))
+
+
+    def setup_dependent_package(self, module, ext_spec):
+        """
+        Called before R modules' install() methods.
+
+        In most cases, extensions will only need to have one line::
+
+	R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+        """
+        # R extension builds can have a global R executable function
+        module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
+
+        # Add variable for library directry
+        module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
+
+        # Make the site packages directory for extensions, if it does not exist already.
+        if ext_spec.package.is_extension:
+            mkdirp(module.r_lib_dir)
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py
new file mode 100644
index 0000000000..54d399c432
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-abind/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class RAbind(Package):
+    """Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays. Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays."""
+
+    homepage = "https://cran.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz"
+
+    version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False)
+
+    extends('R')
+
+    def install(self, spec, prefix):
+
+        R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py
new file mode 100644
index 0000000000..5f25b2a162
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class RMagic(Package):
+    """A collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays."""
+    homepage = "https://cran.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
+
+    version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False)
+
+    extends('R')
+
+    depends_on('r-abind')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)