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Taking in all the great suggestions I tried this:

I hardcoded paths in Makefile

INSTALL_TOP= /home/qsys/lib/lua-5.1.4
INSTALL_BIN= /home/qsys/lib/lua-5.1.4/bin
INSTALL_INC= /home/qsys/lib/lua-5.1.4/include
INSTALL_LIB= /home/qsys/lib/lua-5.1.4/lib
INSTALL_MAN= /home/qsys/lib/lua-5.1.4/man/man1

and I executed

set LUA-PATH=/home/qsys/lib/lua-5.1.4
export LUA_PATH
set LUA_CPATH=/home/qsys/lib/lua-5.1.4
export LUA_CPATH
cd /home/qsys/lib/lua-5.1.4
make clean
make generic
make install

and it seems to work. Is there some test that I can use to verify if it worked?