How do I avoid this error trying to connect arduino to pc with linux fedora 20
The warning, as I'm sure you can tell, is about a mismatch in version of RXTX arduino is expecting, and what is installed on your system. If everything is functioning, I would not worry about it at all. The versions seem to only be slightly different, maybe just a few bug fixes are missing from the older one. 

RXTX is a library for java to communicate with serial devices, but it is not under development anymore and only available from mirrors, not the original developer site. Arduino has moved on to a library called jSSC, which is currently being maintained, and a much better library IMHO. The change to jSSC is still only in the arduino beta version, 1.5.6r2 at time of writing, but it works very well. Anyway, if RXTX ever actually gives you trouble, you can download the beta version of arduino and not have to deal with it.