That's just a warning and no problem because autogen.sh calls gnome- autogen.sh which detects GNOME_DOC_INIT in configure.ac and then calls aclocal with appropriate parameters so that GNOME_DOC_INIT is in aclocal.m4 (just grep for it).
-- newly created documentation isn't valid https://launchpad.net/bugs/76562 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs