Error "GraphViz's executables not found" when calling GraphViz layout from NetworkX in iPython notebook
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I received the error "InvocationException: GraphViz's executables not found, error GraphViz's executables not found" when trying to use the method graphviz_layout in my code. The code works fine when graphviz_layout is replaced by spring_layout. From the throwback exception information, it looks like it calls pydot_layout. I have the pydot module installed through Canopy's package manager, but importing it does not help. I have also pip installed graphviz and imported it with no luck.
Here is my code:
import networkx as nx import matplotlib.pyplot as plt keywordTreeFile = open('decode_wordnet/keywordTreeFile.TXT','r') #keyword generation file keywordTreeFileLineData = keywordTreeFile.readlines() G = nx.Graph() pairData =  for i in range(0,len(keywordTreeFileLineData)): pairData = pairData + [keywordTreeFileLineData[i].split('\t')] pairData[i] = pairData[i].rstrip('\n') G.add_edge(pairData[i],pairData[i]) pos = nx.graphviz_layout(G) nx.draw(G, pos=pos, width = 1.0, with_labels = True, font_size = 3, linewidths=.1 ) plt.savefig("graph.pdf")
Here is the throwback exception information:
--------------------------------------------------------------------------- InvocationException Traceback (most recent call last) <ipython-input-1-e85a11cf6191> in <module>() 15 16 #pos = nx.spring_layout(G,k=.15,iterations=50,scale=100) ---> 17 pos = nx.graphviz_layout(G) 18 #labels = nx.draw_networkx_labels(G,pos) 19 nx.draw(G, /Users/scott/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/networkx/drawing/nx_pydot.pyc in graphviz_layout(G, prog, root, **kwds) 245 This is a wrapper for pydot_layout. 246 """ --> 247 return pydot_layout(G=G,prog=prog,root=root,**kwds) 248 249 /Users/scott/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/networkx/drawing/nx_pydot.pyc in pydot_layout(G, prog, root, **kwds) 269 P.set("root",make_str(root)) 270 --> 271 D=P.create_dot(prog=prog) 272 273 if D=="": # no data returned /Users/scott/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/pydot.pyc in <lambda>(f, prog) 1800 self.__setattr__( 1801 'create_'+frmt, -> 1802 lambda f=frmt, prog=self.prog : self.create(format=f, prog=prog)) 1803 f = self.__dict__['create_'+frmt] 1804 f.__doc__ = '''Refer to the docstring accompanying the 'create' method for more information.''' /Users/scott/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/pydot.pyc in create(self, prog, format) 1951 if self.progs is None: 1952 raise InvocationException( -> 1953 'GraphViz\'s executables not found' ) 1954 1955 if not self.progs.has_key(prog): InvocationException: GraphViz's executables not found
System information: I am using the lastest version and modules of Enthought Canopy on a 64-bit Mac with OS X 10.9.5. Also, I am using an iPython notebook.
I solved this by installing GraphViz on my Mac using macports:
sudo port install graphviz
Installing python packages is not enough in this case. Nonetheless, this is a dependency that should have been taken of by Enthought.
Mean Error: Definition, error, mistake, and blunder mean an act or statement that is not right or true or proper. error is used for failure to follow a model correctly. There was an error in the Error, in applied mathematics, the difference between a true value and an estimate, or approximation, of that value. In statistics, a common example is the difference between the mean of an entire population and the mean of a sample drawn from that population.
Often, you should start with a fresh installation of Macports
Remove old Macports
sudo port -f uninstall installed sudo port clean --work --archive all
Import, install and compile recent Macports sources files
cd ~ curl -O https://distfiles.macports.org/MacPorts/MacPorts-2.3.3.tar.bz2 tar xf MacPorts-2.3.3.tar.bz2 cd MacPorts-2.3.3/ ./configure make sudo make install port version
(Optional) update Macports
sudo port selfupdate sudo port upgrade outdated
Install Graphviz using your fresh Macports
sudo port install graphviz sudo pip install --upgrade graphviz
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For ubuntu users:-
sudo apt-get install -y graphviz libgraphviz-dev
This installs the graphviz executables needed by python to display plots
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- I'm getting
Error: Port graphviz not found
- 4 years later, I'd suggest installing anaconda (or at least a conda env). After doing so, it becomes a one liner to install both the Python package and the Mac app:
conda install -c anaconda graphviz python-graphviz