I also get that error on Ubuntu 16.04 x64. The issue is described here:
https://github.com/libretro/parallel-n64/issues/441
After installing libclang-dev and adding /usr/lib/llvm-3.8/include to the include path I had this error:
In file included from /usr/lib/llvm-3.8/include/clang/Basic/DiagnosticOptions.h:13:0,
from mupen64plus-rsp-paraLLEl/jit.cpp:3:
/usr/lib/llvm-3.8/include/clang/Basic/LLVM.h:22:34: fatal error: llvm/Support/Casting.h: No such file or directory
So I installed llvm-dev and then I could compile fine.
Any chance to get this incorporated into RetroPie?