pygraphviz, ImportError: undefined symbol: Agundirected

Question

import pygraphviz

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/pygraphviz/__init__.py", line 58, in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
File "/usr/local/lib/python2.7/dist-packages/pygraphviz/agraph.py", line 26, in <module>
    from . import graphviz as gv
File "/usr/local/lib/python2.7/dist-packages/pygraphviz/graphviz.py", line 28, in <module>
    _graphviz = swig_import_helper()
File "/usr/local/lib/python2.7/dist-packages/pygraphviz/graphviz.py", line 24, in swig_import_helper
    _mod = imp.load_module('_graphviz', fp, pathname, description)
ImportError: /usr/local/lib/python2.7/dist-packages/pygraphviz/_graphviz.so: undefined symbol: Agundirected

I have already tried

pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/"

I have also tried this answer but still not working

Python does not see pygraphviz

Camillacamille

The error is caused by the graphviz library failing to load a dynamic library - check if the library actually exists, and be sure to run ldconfig to update paths to dynamic libraries if the graphviz directory isn't there. – Krypton

can you pls help me to check whether actually the library exists?also how to run idconfig – Camillacamille

@midhunj Use sudo ldconfig. It still doesn't work for me. – Dahna

I have tried ldconfig.Still it is not working. – Camillacamille

When iam trying to import graphviz, its working fine.Then can any one explain why pygraphviz is not getting imported? – Camillacamille

Answer 1

First of all, uninstall your current module:

 pip uninstall pygraphviz

then check your paths with:

 pkg-config --libs-only-L libcgraph
 pkg-config --cflags-only-I libcgraph

That commands should tell the path to the library, for example:

-I/usr/include/graphviz  

Then, using the path from the above output, run [within your virtualenv] the command:

pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/"

Source: https://github.com/pygraphviz/pygraphviz/issues/71

Fanfaron

install-option twice? Why's that? – Froemming

Never mind the output from pkg-config --libs-only-L libcgraph. In my case (Ubuntu 16.04) that command returns an emtpy line, and that is exactly the reason why pip doesn't detect the correct path for the graphviz library. In my case I just installed using: pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/" and then it worked. – Danais

Answer 2

On Ubuntu 14.04 @Martin0x777's answer did not work for me. So I installed pygraphviz from github instructions and the error is gone:

git clone https://github.com/pygraphviz/pygraphviz.git
cd pygraphviz
python setup.py install

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