Fix alpha case of dependencies.

A while ago I was asked to convert packages to all lowercase. That was
done but some dependencies did not get converted in the specification.
This commit fixes that as well as a couple of urls that need to be made
explicit and a missing dependency on jdk.

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

@@ -37,6 +37,8 @@ class RRjava(Package):
 
     extends('R')
 
+    depends_on('jdk')
+
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
           self.stage.source_path)