This should make mypackage have all the functions that mynewpackage has, at least this is what I would try.

Are you sure? According to its manual page, base sets up an ISA relationship. Which means that mypackage inherits the methods from mynewpackage. Which is fine if the subs are called as methods, but the OP has to deal with myPackage::foo() calls. He needs mypackage to import from mynewpackage instead.