This is not a question, but an information that may be useful to everybody having problems with Rgraphviz similar to the one described in this post. I succeeded in solving the problem in installing Graphviz in a directory such as its path does not include any blank character. Everything worked well as soon as I installed Graphviz in the following directory "C:\Graphviz2.20" instead of "C:\Program Files\Graphviz2.20", which has a blank character between Program and Files. -- output of sessionInfo(): -- Sent via the guest posting facility at bioconductor.org.