Bump
I’m suprised that this issue has not been resolved and there are 3+ posts about it. From what i have read the guy who was forking the build from official repos has depreciated the project so it’s not as confusing.
The build process is the same, but I can’t test it on the RetroPie right now>

To setup, run the following commands:

sudo apt-get install git # to install git if you don’t have it.
git clone http://github.com/ricrpi/mupen64plus # to clone the repository
cd mupen64plus
./build.sh # to build the binaries and shared libraries
sudo ./install.sh # to install mupen64plus into /usr/local/bin

You can also try reading my post on the bottom of this page if it won’t compile. Like I stated I haven’t had a chance to test.