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-rmysql/package.py

@@ -36,7 +36,7 @@ class RRmysql(Package):
 
     extends('R')
 
-    depends_on('r-DBI')
+    depends_on('r-dbi')
     depends_on('mariadb')
 
     def install(self, spec, prefix):