In this file I get 9 warnings of \"assumed special\". They are
;;;*** Warning in CHECK-ROW: CHECKARRAY assumed special in SETQ ;;;*** Warning in CHECK-ROW: R
The difference is that setq is not, strictly speaking, supposed to be used to define a variable (I am not exactly sure why, since it does define a variable).
Use defvar for globals and the let construct for locals.
defvar
let