Merge pull request spack#1343 from glennpj/r_unfilter

becker33 · web-flow · commit b892cebe8ae1 · 2016-08-01T13:51:13.000-07:00
R extension dependencies with compiler wrapper
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
@@ -22,10 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
-
 from spack import *
 from spack.util.environment import *
+import shutil
 
 
 class R(Package):
@@ -74,6 +73,10 @@ class R(Package):
     depends_on('pcre')
     depends_on('jdk')
 
+    @property
+    def etcdir(self):
+        return join_path(prefix, 'rlib', 'R', 'etc')
+
     def install(self, spec, prefix):
         rlibdir = join_path(prefix, 'rlib')
         configure_args = ['--prefix=%s' % prefix,
@@ -88,6 +91,12 @@ def install(self, spec, prefix):
         make()
         make('install')
 
+        # Make a copy of Makeconf because it will be needed to properly build R
+        # dependencies in Spack.
+        src_makeconf = join_path(self.etcdir, 'Makeconf')
+        dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
+        shutil.copy(src_makeconf, dst_makeconf)
+
         self.filter_compilers(spec, prefix)
 
     def filter_compilers(self, spec, prefix):
@@ -98,42 +107,46 @@ def filter_compilers(self, spec, prefix):
         cc and c++. We want them to be bound to whatever compiler
         they were built with."""
 
-        etcdir = join_path(prefix, 'rlib', 'R', 'etc')
-
         kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
 
-        filter_file(env['CC'],  self.compiler.cc,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+        filter_file(env['CC'], self.compiler.cc,
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['CXX'], self.compiler.cxx,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['F77'], self.compiler.f77,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['FC'], self.compiler.fc,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
 
     # ========================================================================
     # Set up environment to make install easy for R extensions.
     # ========================================================================
 
     @property
     def r_lib_dir(self):
-        return os.path.join('rlib', 'R', 'library')
+        return join_path('rlib', '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(deptype=nolink, deptype_query='run'):
             if d.package.extends(self.spec):
-                r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
+                r_libs_path.append(join_path(d.prefix, self.r_lib_dir))
 
         r_libs_path = ':'.join(r_libs_path)
         spack_env.set('R_LIBS', r_libs_path)
+        spack_env.set('R_MAKEVARS_SITE',
+                      join_path(self.etcdir, 'Makeconf.spack'))
+
+        # Use the number of make_jobs set in spack. The make program will
+        # determine how many jobs can actually be started.
+        spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
 
         # 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(
+            run_env.prepend_path('R_LIBS', join_path(
                 extension_spec.prefix, self.r_lib_dir))
 
     def setup_environment(self, spack_env, run_env):
@@ -147,13 +160,14 @@ def setup_environment(self, spack_env, run_env):
     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.source_path)"""
+            R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+              self.stage.source_path)"""
+
         # 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)
+        module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir)
 
         # Make the site packages directory for extensions, if it does not exist
         # already.
