Make sure the following environment variables are set, and gcc/g++ are the 4.9.1 versions (not sure this is very important in practice):
/media/BBB/lib is the path where the SDL libraries have been installed. And then, just compile, in the classical Linux way:
CC = gcc CXX = g++ AS = as CFLAGS += -O3 -march=armv7-a -mtune=cortex-a8 -mfloat-abi=hard -mfpu=vfpv3-d16 LD_LIBRARY_PATH=/media/BBB/lib
./configure --prefix=/media/BBB/ --program-suffix=-0.7 --disable-gui make make install
The only quirk with this library is that it sometimes fails at loading roms, as the romset names may not match what you have. I have edited my romset definitions to match those of the games I have. I made it public on my github repository, in case this can help: https://github.com/alban-rochel/pixbox-gngeo-romset-definitions Not all games are covered, but this may help you discover Metal Slug, which is the essential part of any emulation system!
To start the emulator, here is the command line I use, which allows me to set the path to the roms, the path to my romset definitions, the scaling (3x, full height on a 720p display), and the key mapping:
gngeo-0.7 --p1key=97,115,100,113,49,53,273,274,276,275 --p2key=102,103,104,98,50,116,105,107,106,108 --scale=3 --romrcdir=/media/BBB/sources/gngeo-0.7/romrc.d/ --rompath=/media/BBB/roms/neogeo/