Asghar is evidently a bit shy to post to the group, but he had been having trouble launching Onyx from within R. Here's his note:
I finally managed to resolve the issue.
It turns out that onyxR is not compatible with the latest version of Onyx (onyx-10-1044). I switched to the older version, onyx-1.0-1026, and everything worked perfectly. The diagram was successfully generated without any problems.