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Here is a minimal working example:

\documentclass{article}
\usepackage{subfig}
\begin{document}
<<echo=FALSE,out.width="0.49\\linewidth",fig.show="hold",fig.align="center",fig.cap="Some figures",fig.subcap=c("first","second","third","fourth")>>=
plot(1:10)
plot(2:12)
plot(3:13)
plot(4:14)
@
\end{document}

The figures go off the page to the right, but if I remove the fig.subcap option they are nicely aligned. Is there a way to add subcaptions to 3 or more plots without ruining the alignment?

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