The software underlying Reproducible Research with R and RStudio is constantly changing. This page contains a list of major software updates. I am continually working on an updated version of the Book that will include these updates.
If you have any suggestions for software updates to include on this page please suggest them on the Book's development page.
Note that the book was written with the current development version of RStudio (version 0.98). It has not been officially released yet, but it can be freely downloaded for a variety of operating systems here. I've been using it for months now and it is generally very stable for all of the functions covered in the Book.
Update to Chapter 8 (08-2013): From at least version 1.4.1 the R knitr package is now capable of highlighting syntax from a variety of non-R languages. To make this work properly you will need to install Andre Simon's highlight utility. See his website for download and installation instructions.
Update to Chapter 10 (08-2013):Current versions of knitr allow you to use the fig.align code chunk option with R Markdown documents to align an output figure in a document.
In Chapter 6, the URL has changed for the example downloading the compressed Unified Democracy Scores data set. It was http://www.unified-democracy-scores.org/files/uds_summary.csv.gz but is now http://www.unified-democracy-scores.org/files/20140312/z/uds_summary.csv.gz. The updated bit.ly link is http://bit.ly/1jXJgDh.