I had the same issue. What I did was I unzipped my rom and placed it in the mupen64plus folder, I also overclocked my pi to the pi2 1000 mhz overclocking, then I changed the video plugin from mupen64gles2 to mupen64rice in the mupen64plus.cfg file. Once I opened up the game again in the emulator it fixed it, then I exited back out and changed the screen update setting from 6 to 4
Even Floob replied :). Your error looks familiar to me, I think I had the same, and that it was fixed by adding the ‘sudo’ in front of the command line for the N64 and if I’m not mistaken, it was in the retroarch.cfg. but I could be wrong, I need to check on that at home.