A .rnw-file like this (call it "test.rnw") :
\documentclass{article}
\begin{document}
<<foo, cache = FALSE>>=
library(knitr)
x <- FALSE
@
<<bar, eval = x>>=
1+1
@
\end{document}
is fine for knitr::knit("test.rnw"). (In the "foo"-chunk a variable x is defined to determine wether the "bar"-chunk should be evaluated.) However, checkpoint::checkpoint("test.rnw") fails since it is unable to parse this file - which I assume is due to utils::Stangle("test.rnw") also failing.
Would it be perhaps be possible to get the option to use knitr::purl for parsing the .rnw files instead? knitr::purl("test.rnw") does produce an output.