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I'm having trouble installing pygraphviz and I'm using Anaconda on macOS Monterey.
I already had graphviz on Anaconda. I then did
brew install graphviz
and then
pip install pygraphviz
but I keep getting this error:
Collecting pygraphviz
Using cached pygraphviz-1.7.zip (118 kB)
Building wheels for collected packages: pygraphviz
Building wheel for pygraphviz (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/susiekim4/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/setup.py'"'"'; __file__='"'"'/private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-wheel-4fuwg_2b
cwd: /private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/
Complete output (71 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/scraper.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/agraph.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/testing.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
creating build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.macosx-10.9-x86_64-3.8/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 files found matching '*.png' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
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_64-3.8/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/pygraphviz
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/susiekim4/opt/anaconda3/include -arch x86_64 -I/Users/susiekim4/opt/anaconda3/include -arch x86_64 -I/Users/susiekim4/opt/anaconda3/include/python3.8 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.9-x86_64-3.8/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:1756:7: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /* tp_print */
^
/Users/susiekim4/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/susiekim4/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pygraphviz/graphviz_wrap.c:1923:7: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /* tp_print */
^
/Users/susiekim4/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/susiekim4/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pygraphviz/graphviz_wrap.c:2711:10: fatal error: 'graphviz/cgraph.h' file not found
#include "graphviz/cgraph.h"
^~~~~~~~~~~~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for pygraphviz
Running setup.py clean for pygraphviz
Failed to build pygraphviz
Installing collected packages: pygraphviz
Running setup.py install for pygraphviz ... error
ERROR: Command errored out with exit status 1:
command: /Users/susiekim4/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/setup.py'"'"'; __file__='"'"'/private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-record-pnja99aw/install-record.txt --single-version-externally-managed --compile --install-headers /Users/susiekim4/opt/anaconda3/include/python3.8/pygraphviz
cwd: /private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/
Complete output (71 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/scraper.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/agraph.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
copying pygraphviz/testing.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
creating build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.macosx-10.9-x86_64-3.8/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 files found matching '*.png' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
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_64-3.8/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-10.9-x86_64-3.8/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/pygraphviz
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/susiekim4/opt/anaconda3/include -arch x86_64 -I/Users/susiekim4/opt/anaconda3/include -arch x86_64 -I/Users/susiekim4/opt/anaconda3/include/python3.8 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.9-x86_64-3.8/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:1756:7: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /* tp_print */
^
/Users/susiekim4/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/susiekim4/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pygraphviz/graphviz_wrap.c:1923:7: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /* tp_print */
^
/Users/susiekim4/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/susiekim4/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pygraphviz/graphviz_wrap.c:2711:10: fatal error: 'graphviz/cgraph.h' file not found
#include "graphviz/cgraph.h"
^~~~~~~~~~~~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/susiekim4/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/setup.py'"'"'; __file__='"'"'/private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-install-zr2twxnl/pygraphviz_e78bc2c823034812a5ffbd6ef61160d7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/j5/z34rlnbj2l94p1hh0x_hkkjw0000gn/T/pip-record-pnja99aw/install-record.txt --single-version-externally-managed --compile --install-headers /Users/susiekim4/opt/anaconda3/include/python3.8/pygraphviz Check the logs for full command output.
I've tried pip3 install, pip install cgraph, and the other solutions.
What am I missing?
769
asked Sep 05 '25 09:09
On Mac, you must pass the path of the install directory so the wheel compiler can find the graphviz header and library files. Here's how:
Use Homebrew to install graphviz:
brew install graphviz
Get the install directory:
brew --prefix graphviz
Set GRAPHVIZ_DIR to where it was installed:
export GRAPHVIZ_DIR="[INSTALL PATH HERE]"
Install graphviz specifying the path:
If using pip 23.2 or later:
export GRAPHVIZ_DIR="$(brew --prefix graphviz)"
pip install pygraphviz \
--global-option=build_ext \
--global-option="-I$GRAPHVIZ_DIR/include" \
--global-option="-L$GRAPHVIZ_DIR/lib"
If using an earlier version of pip:
export GRAPHVIZ_DIR="$(brew --prefix graphviz)"
pip install pygraphviz \
--config-settings=--global-option=build_ext \
--config-settings=--global-option="-I$GRAPHVIZ_DIR/include" \
--config-settings=--global-option="-L$GRAPHVIZ_DIR/lib"
With these additions, the package should be compiled and installed successfully:
Collecting pygraphviz
Using cached pygraphviz-1.11.zip (120 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: pygraphviz
Building wheel for pygraphviz (pyproject.toml) ... done
Created wheel for pygraphviz: filename=pygraphviz-1.11-cp311-cp311-macosx_13_0_arm64.whl size=100586 sha256=0d6e56168321d335706a6c6789a006b8d2831bbd32b1cd28bd8fb2238122f73b
Stored in directory: .../pip/wheels/c8/03/73/b754941d55845a8b326f6de528bc70e65774838c76effa6d51
Successfully built pygraphviz
Installing collected packages: pygraphviz
Successfully installed pygraphviz-1.11
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