I don't know if these errors are specific to cygwin, but when I build I consistently see the message:
Checking if your kit is complete... Looks good 'INSTALLSITESEARCH' is not a known MakeMaker parameter name. 'SITE_PREFIX' is not a known MakeMaker parameter name. Writing Makefile for <packagename> --- Are INSTALLSITESEARCH/SITE_PREFIX supposed to be sent or recognized by makemaker?
