I don't know about RetroPie, but in normal Raspbian you clone the git repository:
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git clone --depth 1 https://github.com/libretro/libretro-fceumm.git
Then you cd into the directory where it has been cloned:
And then you build the core with the Raspberry Pi 1 platform definitions which will activate the right compiler flags:
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make -f Makefile.libretro platform=rpi1 -j8
You can load the core manualy with RetroArch doing:
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retroarch -L libretro-fceumm.so game.nes
What I do personally is put all the cores in a directory, and create a simple script for each system.
For example, the NES script is simply called "nes" and contains:
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./retroarch -L cores/libretro-fceumm.so -c cfg/nes.cfg "$1"
You can give it execution rights with chmod +x
Then you simply do
./nes nintendo/mario.nes
So use Raspbian instead and learn on your way to NES playing. Or use Lakka (
http://www.lakka.tv) instead of RetroPie: it's far better and you can easily chose what core you want to use.
I know how you feel, but be patient. My advice is to use normal Raspbian, disable X server, learn how to disable un-needed services (I can help you if you want), become friends with the text console, and you will soon see you can do ANYTHING you want and your Pi is actually very capable for your retro-gaming projects.
But by using RetroPie you are very restricted I guess...