after upgrading to the latest kernel (Ubuntu 12.04 126.96.36.199), suddenly Compiz effects werent working.
had to install Nvidia drivers again this time from terminal in recovery mode. After that both Compiz effects worked and fceux compiled normally
strange because in the previous kernel while there were Compiz effects and Opengl worked, fceux wouldnt compile due to libgl.so
now problem has been fixed, mainly due to the new kernel. in the previous kernel even if I reinstalled Nvidia drivers, libgl.so would appear.
2.2.1 released with some bug fixes and new features: https://sourceforge.net/projects/fceultra/files/
I'm not sure why I can't edit the OP anymore, but the new svn repo URL is:
svn checkout http://svn.code.sf.net/p/fceultra/code/fceu/trunk fceultra
I had to
and then everything worked out. Thanks for these instructions because the 1 provided in the repo's for 12.04 would seg fault after only 15 seconds and I found it because I run the Nvidia binary driver for my 8400 GSCode:sudo aptitude install liblua5.1-0-dev