I have added an unserscore to the extention of the vignette file, i.e., it is called ShortRead_and_HilbertCurveDisplay.Rnw_, so that it does not get processed automatically. This is because it takes quite long to get build the vignette and you have to download some example data before building it. If you do want to rebuild the vignette: In the same directory that contains the Rnw file, make two subdirecties, called H3K4me1 and H3K4me3. Go to http://www.ebi.ac.uk/~anders/ShortReadExampleData/, download the content of the two directories H3K4me1 and H3K4me3 there and put these files in the directories just created. Then run Sweave.