How are you trying to install jUnit library? I am no expert but I presume you can just add the jar file to the project library and use it from there.
I had some problem when I was trying to update jMP from nightly. I was using ubuntu. In my case the problem was the jMP executable and the adjacent folders didn’t had the permission to write the updated files in the correct location. I had to update the permission of the jMP files and folders.