Hi Yunyu, This is a common question with Rgraphviz. You might want to search the bioconductor mailing list for answers. "Zhang, Yunyu" <yunyu_zhang@dfci.harvard.edu> writes: > checking for graphviz... checking for dotneato-config... not found > failed > configure: error: please specify a valid path to 'dotneato-config' version >= > 1.12 using --with-graphviz=DIR Rgraphviz depends on the graphviz libraries and header files being installed on the system. Assuming you are on a unix-like syste, you need to install graphviz. dotneato-config is a configuration script that comes with graphviz. After installing graphviz, make sure that this script is in your path as it is used during the build process to find the graphviz library that Rgraphviz needs to link against. Best, + seth