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Error installing PyGraphviz (Mac OS X, Anaconda)

I'm having trouble installing PyGraphviz. I am using Anaconda on Mac OS X.

Error messages indicate some causes, but I have already verified that it is installed in the anaconda directory.

Sundongui-MacBook-Pro:site-packages sundong$ pwd /Users/sundong/anaconda/lib/python2.7/site-packages Sundongui-MacBook-Pro:site-packages sundong$ pip install graphviz --upgrade Requirement already up-to-date: graphviz in /Users/sundong/anaconda/lib/python2.7/site-packages

According to the error messages, how to change the include_dirs and library_dirs variables in setup.py ??

Here is the error message that I meet

 Sundongui-MacBook-Pro:anaconda sundong$ pip install pygraphviz Collecting pygraphviz Using cached pygraphviz-1.3.1.tar.gz Building wheels for collected packages: pygraphviz Running setup.py bdist_wheel for pygraphviz Complete output from command /Users/sundong/anaconda/bin/python -c "import setuptools;__file__='/private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/tmpwR_08Dpip-wheel-: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.5-x86_64-2.7 creating build/lib.macosx-10.5-x86_64-2.7/pygraphviz copying pygraphviz/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz copying pygraphviz/agraph.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz copying pygraphviz/graphviz.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz copying pygraphviz/release.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz copying pygraphviz/version.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz creating build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_attributes.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_clear.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_graph.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_html.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_layout.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_string.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests running egg_info writing pygraphviz.egg-info/PKG-INFO writing top-level names to pygraphviz.egg-info/top_level.txt writing dependency_links to pygraphviz.egg-info/dependency_links.txt warning: manifest_maker: standard file '-c' not found reading manifest file 'pygraphviz.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '.svn' found anywhere in distribution no previously-included directories found matching 'doc/build' writing manifest file 'pygraphviz.egg-info/SOURCES.txt' copying pygraphviz/graphviz.i -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz running build_ext building 'pygraphviz._graphviz' extension creating build/temp.macosx-10.5-x86_64-2.7 creating build/temp.macosx-10.5-x86_64-2.7/pygraphviz gcc -fno-strict-aliasing -I/Users/sundong/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sundong/anaconda/include/python2.7 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.5-x86_64-2.7/pygraphviz/graphviz_wrap.o pygraphviz/graphviz_wrap.c:2954:10: fatal error: 'graphviz/cgraph.h' file not found #include "graphviz/cgraph.h" ^ 1 error generated. error: command 'gcc' failed with exit status 1 ---------------------------------------- Failed building wheel for pygraphviz Failed to build pygraphviz Installing collected packages: pygraphviz Running setup.py install for pygraphviz Complete output from command /Users/sundong/anaconda/bin/python -c "import setuptools, tokenize;__file__='/private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-qgosXm-record/install-record.txt --single-version-externally-managed --compile: running install Trying pkg-config Failed to find pkg-config Trying dotneato-config Failed to find dotneato-config Failed to find dotneato-config Your Graphviz installation could not be found. 1) You don't have Graphviz installed: Install Graphviz (http://graphviz.org) 2) Your Graphviz package might incomplete. Install the binary development subpackage (eg libgraphviz-dev or similar.) 3) You are using Windows There are no PyGraphviz binary packages for Windows but you might be able to build it from this source. See http://networkx.lanl.gov/pygraphviz/reference/faq.html If you think your installation is correct you will need to manually change the include_dirs and library_dirs variables in setup.py to point to the correct locations of your graphviz installation. The current setting of library_dirs and include_dirs is: library_dirs=None include_dirs=None error: Error locating graphviz. ---------------------------------------- Command "/Users/sundong/anaconda/bin/python -c "import setuptools, tokenize;__file__='/private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-qgosXm-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz
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python install macos pygraphviz
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3 answers

try the following (make sure the anaconda client is installed and updated):

 conda install --channel https://conda.anaconda.org/garylschultz pygraphviz
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Graphviz can be installed using homebrew: brew install graphviz .

Then do:

 cd /usr/local/Cellar/graphviz/VERSION/include/graphviz mkdir graphviz cp cgraph.h graphviz/

And finally:

 pip install graphviz

Tested on Sierra and good.

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Assuming you have already installed Graphviz software:

As described in this blog post , use the following options when trying to run pip install pygraphviz

 --install-option="--include-path=/usr/local/include/graphviz/" \ --install-option="--library-path=/usr/local/lib/graphviz"

So, the last command will look like pip install pygraphviz --install-option="--include-path=/usr/local/include/graphviz/" --install-option="--library-path=/usr/local/lib/graphviz" .

What this does is explicitly indicated where the source program libraries (graphviz) for the python extension exist. Unfortunately, this does not seem to be automatically recognized.

Worked on MacOS Sierra with Python 3.6

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