When I run a very simple code with pydot
import pydot graph = pydot.Dot(graph_type=\'graph\') for i in range(3): edge = pydot.Edge(\"king\", \"lord%d\" %
I had the problem again and my above solution did not work. If that is true for you and you are also using Anaconda on a Mac with El Capitan, try this:
conda install --channel https://conda.anaconda.org/RMG graphviz` conda install --channel https://conda.anaconda.org/RMG pydot