There's a conflict between Sweave and pdfpages. Try this.
Note this is a .Rnw file (Sweave file) which is being processed into tex via a call like this from R: Sweave("foo.Rnw"). So, it's a specific Sweave issue. Anyhow, change your \usepackage call for Sweave in your .Rnw file to the following. Note the addition of [nogin]
%%%%%%%%%%%% foo.Rnw
\documentclass{article}
\usepackage[nogin]{Sweave}
\usepackage{pdfpages}
\begin{document}
\newpage
\includepdf[fitpaper=true, pages=-]{test.pdf}
\end{document}
What's going on.. So By default, Sweave.sty sets the width of all included graphics to:
\setkeys{Gin}{width=0.8\textwidth}, and it is treating the inserted pdf pages as graphics and setting the size according to the above. You need to override this. If you do this in the \usepackage call, you do this for all graphics. If you don't want that, then you can use this (or something similar)
\setkeys{Gin}{width=8.5in} #um not positive on that syntax
\includepdf[fitpaper=true, pages=-]{test.pdf}
\setkeys{Gin}{width=0.8\textwidth}
noscalingoption AFAIK, try thenoautoscaleoption instead. – Martin Scharrer May 29 '11 at 18:50geometry). – Alan Munn May 29 '11 at 18:51pdfpagesuses thegraphicxpackage, so this order is anyway set. This leavessweave. Please consider adding a minimal working example (MWE) that causes this problem so that other people can have a look on it. – Martin Scharrer May 31 '11 at 12:03