I've been worn down by my quest for a comparable product to SQLite written in pure Java and have come to the conclusion that it doesn't exit. I've looked at Derby, QED, Axion, blah blah and I'm not too impressed by any of them. None of them are as good as SQLite and they all use multiple files for their storage.
Sqlite is portable to pretty much anything more advanced than an abacus, so I don't see your problem. If there were gcc for abacus it would work on that too :-).