Well, I receive this message too and posted this bug long time ago on this forum, but nobody reacted. Anyway, everything is works even with this, I didn't see any problem in work because of this.
It's not an error - just a warning. Most PHP installations have these turned off. For some reason yours isn't. You can repress the warning by putting an @ symbol before the function call.
So $res = chmod($final_fqfn, 0755); becomes $res = @chmod($final_fqfn, 0755); and the "error" should go away.