The general problem is that the checkout/update of files does not always match dependency order. This, the makefiles think they need to re-run some commands, but it doesn't work, because you don't have the right versions. So try this: % rm configure.in configure % cvs update configure.in Warning: Remote host denied X11 forwarding. cvs update: warning: configure.in was lost U configure.in % cvs update configure Warning: Remote host denied X11 forwarding. cvs update: warning: configure was lost U configure It is a requirement that the update commands be run seperately, otherwise, you're just going to screw up the dependency order. Then after you do that, re-run configure, run make, and it all should be good.