Robert the author of jamvm has been assisting me with this and he has managed find another error message, which does give a good clue as to what the problem is.
I am using RXTXcomm package, which of course on my dev. system works because there are supported libraries, however on the Yun I don't think they're are.
So I will probably need to roll my own native library and JNI package to provide the serial interfacing.
There is no need to build your own RXTX library on the Yun: if you have an usb/serial connector and installed the correct driver (see the opkg packages) you have a /dev/ttyUSB 'file' (mind the quotes). You can open it both for reading (FileInputStream) and writing (FileOutputStream) from Java and voila.
Ty, but this is polling the port instead of interrupt driven, there is a chance the app. could miss data, I'll try it out, could always create a thread just to poll te port I guess.
I've tried opening the device as a stream and I just can't get it to read anything, having spent a while searching, it seems that others use either javax or rxtx.
Since neither are available in jamvm I'm back to writing a native library.
I'm away from home atm, will try it this weekend, when I get home.
JSSC is no different from RXTX in that it relies on a native library to do the actual hardware interfacing, I don't see any native library or support for the Yun.
I started installing the SDK for the Yun in Ubuntu last night, will try to get that complete and working,
SPlatten, if you manage to make it, please share your script as it could be turned into an openwrt Makefile, thus making that package available to everyone