Thought I would post this in case anyone else runs into the issue.
I'm building latest AFNI version(AFNI_2008_07_18_1710 ) on recent cygwin installation, and had to do the following debugging to get make to finish.
1. had to install obsolete version 6.x of xorg-x11-devel from cygwin setup, found link to similar problem for reference (http://www.mail-archive.com/xastir@lists.xastir.org/msg00025.html)
2. ccalc.c - change strcasestr to simply strstr. Apparently strcasestr doesn't exist in cygwin
3. Not really sure how this fell through the cracks, but line 1025 of 3dAllineate.c is missing the end parenthesis and semicolon.
things seem to be working fine now. Hope this helps anyone in a similar situation...
Nick
