this should produce 2 figures per column:

\documentclass{article}
\begin{document}
<<,fig.show = "hold",out.width = "2cm",fig.ncol=2>>=
plot(1:100); plot(100:1); plot(1:100); plot(100:1); plot(1:100) 
@
\end{document}

it used to work.

now it produces this:

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