unable to run autoconf in peardoc folder

I checked out peardoc from CVS and tried to run autoconf, in Cygwin, and 
instead got this error:

' is already registered with AC_CONFIG_FILES.
/usr/src/autoconf/26/autoconf2.5-2.61-1/src/autoconf-2.61/lib/autoconf/status.m4
:300: AC_CONFIG_FILES is expanded from...
configure.in:504: the top level
autom4te-2.61: /usr/bin/m4 failed with exit status: 1

I tried to run make partial INCLUDE="packages package.database" and got 
htis back:
make: *** No rule to make target 'partial'.  Stop.

Does the configure file need to exist before I can run make, be it for a 
partial build or not?