> AC_OUTPUT(src/app/Makefile, src/Random/Makefile, Makefile) If you want to pass two or more files to AC_OUTPUT, you must separate them by white spaces, not by commas. Otherwise, only the first one is considered (in this case only `src/app/Makefile'), which is hardly what you want.
That said, it seems you are using Autoconf and Automake macros in ways that have been deprecated for a long time (in particular, AC_OUTPUT should now be used only without arguments). I think you should follow the advices of Jason and William and modernize your setup. By the way, which versions of Automake and Autoconf are you using? Regards, Stefano
