phpDocumentor has a few dependencies in order to work correctly on OSX. If you get the following error message when generating documentation in phpdoc:
Unable to find the `dot` command of the GraphViz package
you will need to install the GraphViz package via homebrew.
If you don’t have homebrew installed on OSX, here is a link to it: http://mxcl.github.com/homebrew/
brew install graphviz
This will quickly install GraphViz on OSX. PhpDocumentor will be able to generate the Class Inheritance Diagrams after GraphViz is installed.