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I have troubles installing pygraphviz on macOS 10.10.5. I have a fully functional installation of Python 2.7.x, and I'd like to run the test example of queueing-tool, which requires installing pygraphviz using pip.
When executing the command pip install pygraphviz, I get the following lengthy error message:
Collecting pygraphviz
Using cached pygraphviz-1.3.1.zip
Building wheels for collected packages: pygraphviz
Running setup.py bdist_wheel for pygraphviz ... error
Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/tmpcYcoACpip-wheel- --python-tag cp27:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.10-x86_64-2.7
creating build/lib.macosx-10.10-x86_64-2.7/pygraphviz
copying pygraphviz/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz
copying pygraphviz/agraph.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz
copying pygraphviz/release.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz
copying pygraphviz/version.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz
creating build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_attributes.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-10.10-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-10.10-x86_64-2.7/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-10.10-x86_64-2.7/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.macosx-10.10-x86_64-2.7
creating build/temp.macosx-10.10-x86_64-2.7/pygraphviz
clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.10-x86_64-2.7/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:3321:12: warning: incompatible pointer to integer conversion returning 'Agsym_t *' (aka 'struct Agsym_s *') from a function with result type 'int' [-Wint-conversion]
return agattr(g, kind, name, val);
^~~~~~~~~~~~~~~~~~~~~~~~~~
pygraphviz/graphviz_wrap.c:3405:7: warning: unused variable 'fd1' [-Wunused-variable]
int fd1 ;
^
pygraphviz/graphviz_wrap.c:3406:13: warning: unused variable 'mode_obj1' [-Wunused-variable]
PyObject *mode_obj1 ;
^
pygraphviz/graphviz_wrap.c:3407:13: warning: unused variable 'mode_byte_obj1' [-Wunused-variable]
PyObject *mode_byte_obj1 ;
^
pygraphviz/graphviz_wrap.c:3408:9: warning: unused variable 'mode1' [-Wunused-variable]
char *mode1 ;
^
pygraphviz/graphviz_wrap.c:3463:7: warning: unused variable 'fd2' [-Wunused-variable]
int fd2 ;
^
pygraphviz/graphviz_wrap.c:3464:13: warning: unused variable 'mode_obj2' [-Wunused-variable]
PyObject *mode_obj2 ;
^
pygraphviz/graphviz_wrap.c:3465:13: warning: unused variable 'mode_byte_obj2' [-Wunused-variable]
PyObject *mode_byte_obj2 ;
^
pygraphviz/graphviz_wrap.c:3466:9: warning: unused variable 'mode2' [-Wunused-variable]
char *mode2 ;
^
9 warnings generated.
clang -bundle -undefined dynamic_lookup build/temp.macosx-10.10-x86_64-2.7/pygraphviz/graphviz_wrap.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -lcgraph -lcdt -o build/lib.macosx-10.10-x86_64-2.7/pygraphviz/_graphviz.so
installing to build/bdist.macosx-10.10-x86_64/wheel
running install
Trying pkg-config
Package libcgraph was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcgraph.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcgraph' found
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup.py", line 87, in <module>
tests_require=['nose>=0.10.1', 'doctest-ignore-unicode>=0.1.0',],
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/local/lib/python2.7/site-packages/wheel/bdist_wheel.py", line 215, in run
self.run_command('install')
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup_commands.py", line 44, in modified_run
self.include_path, self.library_path = get_graphviz_dirs()
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup_extra.py", line 121, in get_graphviz_dirs
include_dirs, library_dirs = _pkg_config()
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup_extra.py", line 44, in _pkg_config
output = S.check_output(['pkg-config', '--libs-only-L', 'libcgraph'])
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 574, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['pkg-config', '--libs-only-L', 'libcgraph']' returned non-zero exit status 1
----------------------------------------
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
Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-7HXgN6-record/install-record.txt --single-version-externally-managed --compile:
running install
Trying pkg-config
Package libcgraph was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcgraph.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcgraph' found
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup.py", line 87, in <module>
tests_require=['nose>=0.10.1', 'doctest-ignore-unicode>=0.1.0',],
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup_commands.py", line 44, in modified_run
self.include_path, self.library_path = get_graphviz_dirs()
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup_extra.py", line 121, in get_graphviz_dirs
include_dirs, library_dirs = _pkg_config()
File "/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup_extra.py", line 44, in _pkg_config
output = S.check_output(['pkg-config', '--libs-only-L', 'libcgraph'])
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 574, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['pkg-config', '--libs-only-L', 'libcgraph']' returned non-zero exit status 1
----------------------------------------
Command "/usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-7HXgN6-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/x3/nr48r8q10dv1lb9l9t_yx7kh0000gq/T/pip-build-Ljj4Ox/pygraphviz/
I am unsure about how to address the above error. All other Python packages, such as numpy or networkx, were straightforward to install. Any help would be greatly appreciated. Thanks a lot in advance.
601
Try this :
sudo apt-get install python-dev graphviz libgraphviz-dev pkg-config
or the following might be needed if you're using Python 3:
sudo apt-get install python3-dev graphviz libgraphviz-dev pkg-config
then
sudo pip install pygraphviz
Basically you need to download graphviz first using brew:
brew install graphviz
pip install graphviz
pip install pygraphviz
You can also try using pip3 in place of pip just in case there is Python's version issue. Hope it helps.
9
The comment by Andrew brought me on the right path. Thank you for that.
It turns out that a detailed solution for installing pygraphviz on macOS is already available on stackoverflow, see this solution by teut.
5
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