If you use flycheck (#9) then you should disable flymake:
(setq rnc-enable-flymake nil ; now do it with flycheck
However, rnc-configure-flymake doesn't respect this option and is called unconditionally.
Until this is fixed, one can use the following:
(defadvice rnc-configure-flymake (around rnc-enable-flymake activate)
"Don't run rnc-configure-flymake unless rnc-enable-flymake is set.
Else the function produces a distracting error message"
(if rnc-enable-flymake ad-do-it))