Cannot install pygraphviz on Mac OS 10.11.6

[manthis]

I have installed graphviz on my Mac using:

brew install graphviz

Every time I'm trying to install pygraphviz with:

pip install pygraphviz

I get the following results:

          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 (e.g. 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.

I have tried to specify library_path and include_path with the following command:

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

But it tells me:

error: option --include-path not recognized

I have tried with "include-dirs" and "library_dirs" too but without success.
How can I install it successfully? Should I built it from source?

[jiangpengnju]

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

Both path in bold should NOT contain "graphviz".

[manthis]

@jiangpengnju

Actually paths should include "graphviz". My mistake was that I was trying to install graphviz with pip instead of pygraphviz. Sorry for the inconvenience.

[szeitlin]

fwiw I just had the same problem - was following the dask tutorial and initially tried installing pygraphviz and graphviz inside a conda env. That didn't work - but installing them both globally seems to have solved it. I also added the graphviz path to my .bash_profile, not sure if that was really necessary.

[iamihgam]

Use
conda install pygraphviz.
It solved the problem for me.

[jolespin]

@iamihgam what conda, python, and operating system/version do you have?

I have

(python3_test) jespinozlt-osx:~ jespinoz$ conda install pygraphviz
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - defaults/osx-64::dbus==1.12.2=h5243cc1_1
  - pygraphviz
  - r/osx-64::r-xtable==1.8_2=r342hb9d8108_0
Use "conda info <package>" to see the dependencies for each package.

Here are my versions:

(python3_test) jespinozlt-osx:~ jespinoz$ conda --version
conda 4.4.10
(python3_test) jespinozlt-osx:~ jespinoz$ python --version
Python 3.6.4 :: Anaconda, Inc.
(python3_test) jespinozlt-osx:~ jespinoz$ sw_vers
ProductName:	Mac OS X
ProductVersion:	10.11.6

[iamihgam]

@jolespin
conda version : conda 4.5.0
Python 3.6.4 :: Anaconda custom (x86_64)
Mac version : El capitan version : 10.11.6

[iamihgam]

tryp updating conda

[jolespin]

Just updated my conda :(

(python3_test) jespinozlt-osx:~ jespinoz$ conda --version
conda 4.5.0
(python3_test) jespinozlt-osx:~ jespinoz$ conda install pygraphviz
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - defaults/osx-64::dbus==1.12.2=h5243cc1_1
  - pygraphviz
  - r/osx-64::r-xtable==1.8_2=r342hb9d8108_0
Use "conda info <package>" to see the dependencies for each package.

I think it has to do with my backend?

[abrahamrhoffman]

For me, brew install placed the bin appropriately, but when I attempted to pip3 install pygraphviz in my virtualenv, I got the error: Error locating graphviz. error. The fix was installing with the appropriate --install-options (as mentioned by @jiangpengnju):

pip3 install --install-option="--include-path=/usr/local/include/" --install-option="--library-path=/usr/local/lib/" pygraphviz

Thank you for the help!

[jolespin]

Thanks @abrahamrhoffman I tried my version of this but still got an error:

pip install --install-option="--include-path=~/anaconda/envs/python3_test/include/graphviz/" --install-option="--library-path=~/anaconda/envs/python3_test/lib/graphviz/" pygraphviz

It looks like the original source for this is:
https://pygraphviz.github.io/documentation/development/install.html

Installation error:

(python3_test) jespinozlt-osx:~ jespinoz$ pip install --install-option="--include-path=~/anaconda/envs/python3_test/include/graphviz/" --install-option="--library-path=~/anaconda/envs/python3_test/lib/graphviz/" pygraphviz
/Users/jespinoz/anaconda/envs/python3_test/lib/python3.6/site-packages/pip/commands/install.py:194: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
  cmdoptions.check_install_build_global(options)
Collecting pygraphviz
  Downloading https://files.pythonhosted.org/packages/98/bb/a32e33f7665b921c926209305dde66fe41003a4ad934b10efb7c1211a419/pygraphviz-1.3.1.tar.gz (103kB)
    100% |████████████████████████████████| 112kB 1.4MB/s
Skipping bdist_wheel for pygraphviz, due to binaries being disabled for it.
Installing collected packages: pygraphviz
  Running setup.py install for pygraphviz ... error
    Complete output from command /Users/jespinoz/anaconda/envs/python3_test/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/6z/5vbtz_gmkr76ftgc3149dvtr0003c0/T/pip-build-cb44s6jl/pygraphviz/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/6z/5vbtz_gmkr76ftgc3149dvtr0003c0/T/pip-kyj15wnc-record/install-record.txt --single-version-externally-managed --compile --include-path=~/anaconda/envs/python3_test/include/graphviz/ --library-path=~/anaconda/envs/python3_test/lib/graphviz/:
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.6
    creating build/lib.macosx-10.9-x86_64-3.6/pygraphviz
    copying pygraphviz/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz
    copying pygraphviz/agraph.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz
    copying pygraphviz/graphviz.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz
    copying pygraphviz/release.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz
    copying pygraphviz/version.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz
    creating build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_attributes.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_clear.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_graph.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_html.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_layout.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_string.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz/tests
    running egg_info
    writing pygraphviz.egg-info/PKG-INFO
    writing dependency_links to pygraphviz.egg-info/dependency_links.txt
    writing top-level names to pygraphviz.egg-info/top_level.txt
    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-10.9-x86_64-3.6/pygraphviz
    copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-10.9-x86_64-3.6/pygraphviz
    running build_ext
    building 'pygraphviz._graphviz' extension
    creating build/temp.macosx-10.9-x86_64-3.6
    creating build/temp.macosx-10.9-x86_64-3.6/pygraphviz
    x86_64-apple-darwin13.4.0-clang -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I~/anaconda/envs/python3_test/include/graphviz/ -I/Users/jespinoz/anaconda/envs/python3_test/include/python3.6m -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.9-x86_64-3.6/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 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1

    ----------------------------------------
Command "/Users/jespinoz/anaconda/envs/python3_test/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/6z/5vbtz_gmkr76ftgc3149dvtr0003c0/T/pip-build-cb44s6jl/pygraphviz/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/6z/5vbtz_gmkr76ftgc3149dvtr0003c0/T/pip-kyj15wnc-record/install-record.txt --single-version-externally-managed --compile --include-path=~/anaconda/envs/python3_test/include/graphviz/ --library-path=~/anaconda/envs/python3_test/lib/graphviz/" failed with error code 1 in /private/var/folders/6z/5vbtz_gmkr76ftgc3149dvtr0003c0/T/pip-build-cb44s6jl/pygraphviz/

[abrahamrhoffman]

You're welcome @jolespin : Try removing graphviz and reinstalling it. Might do the trick.

[jolespin]

Finally got it working :) for my conda environment

# PyGraphViz
conda install graphviz --yes
pip download git+git://github.com/pygraphviz/pygraphviz.git#egg=pygraphviz
unzip pygraphviz*.zip
cd pygraphviz
python setup.py install --include-path=$CONDA_PREFIX/include --library-path=$CONDA_PREFIX/lib
pip install pydot

[ddahan]

I have the same problem but I'm using pipenv. How to solve this in that case?