I must admit that I have never used that package. And after scouring the github page there doesn't seem to be much of help there, but I did notice that there were comments mentioning the problem you are having with no responses.
What sticks out to me is the trying to install to /root/Retropie instead of /home/pi/Retropie. Did that happen in your 4.3 build?
I don't see what difference it should make but have you tried installing via the command line instead of SSH? Updating via managing experimental packages after installing?