I had the same problem as Paul details here:

http://mail-index.netbsd.org/port-cobalt/2001/08/14/0000.html

> When I perform a make or make install on any of the pkgsrc packages I
> get the following errors
>
> cannot open vers.c: no such file
> cat: version: No such file or directory
> cannot open vers.c: no such file
> cat: version: No such file or directory
> cannot open vers.c: no such file
> cat: version: No such file or directory
> cannot open vers.c: no such file
> cat: version: No such file or directory
>
> This repeats many times.. But the package eventually installs itself
> anyway.
>
> The only thing I have done to date on the default install is stick
> automake, autoconf and perl5.6.1 on the Qube2.  Could this have broken
> something?

Turns out that Paul had (probably) also done the mod to mk.conf suggested to
build kernels with 'interesting' names that's suggested in the FAQ here:
http://www.netbsd.org/Ports/cobalt/faq.html#install-kernel

since it's in mk.conf, it always gets pulled in, and the vers.c and version
files aren't present anywhere but in the kernel build directory.

Robert