SylarSong
Reputation: 43
How do I install pygraphviz with pip
this is brew list and pip list
(lebienv) ➜ lebi git:(master) ✗ brew list
graphviz libpng libxml2 mysql openssl
(lebienv) ➜ lebi git:(master) ✗ pip list
Flask (0.10.1)
itsdangerous (0.24)
Jinja2 (2.8)
MarkupSafe (0.23)
pip (8.0.3)
setuptools (20.1.1)
Werkzeug (0.11.4)
wheel (0.29.0)
(lebienv) ➜ lebi git:(master) ✗
and excute pip install pygraphviz
(lebienv) ➜ lebi git:(master) ✗ 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 ... error
Complete output from command /Users/zyl/song/lebi/lebienv/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/5t/965cgdc56ks37w8pmlmw4vx40000gn/T/pip-build-x2Vstw/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /var/folders/5t/965cgdc56ks37w8pmlmw4vx40000gn/T/tmp7z72M3pip-wheel- --python-tag cp27:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.11-intel-2.7
creating build/lib.macosx-10.11-intel-2.7/pygraphviz
copying pygraphviz/__init__.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz
copying pygraphviz/agraph.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz
copying pygraphviz/release.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz
copying pygraphviz/version.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz
creating build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_attributes.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-10.11-intel-2.7/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-10.11-intel-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-10.11-intel-2.7/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-10.11-intel-2.7/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.macosx-10.11-intel-2.7
creating build/temp.macosx-10.11-intel-2.7/pygraphviz
cc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.11-intel-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.
pygraphviz/graphviz_wrap.c:3295:15: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
len = strlen(val);
~ ^~~~~~~~~~~
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:3313:15: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
len = strlen(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 ;
^
11 warnings generated.
cc -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -Wl,-F. build/temp.macosx-10.11-intel-2.7/pygraphviz/graphviz_wrap.o -lcgraph -lcdt -o build/lib.macosx-10.11-intel-2.7/pygraphviz/_graphviz.so
ld: warning: ignoring file /usr/local/lib/libcdt.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libcdt.dylib
ld: warning: ignoring file /usr/local/lib/libcgraph.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libcgraph.dylib
installing to build/bdist.macosx-10.11-intel/wheel
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 (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.
----------------------------------------
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 /Users/zyl/song/lebi/lebienv/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/5t/965cgdc56ks37w8pmlmw4vx40000gn/T/pip-build-x2Vstw/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/5t/965cgdc56ks37w8pmlmw4vx40000gn/T/pip-1imEXi-record/install-record.txt --single-version-externally-managed --compile --install-headers /Users/zyl/song/lebi/lebienv/include/site/python2.7/pygraphviz:
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 (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.
----------------------------------------
Command "/Users/zyl/song/lebi/lebienv/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/5t/965cgdc56ks37w8pmlmw4vx40000gn/T/pip-build-x2Vstw/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/5t/965cgdc56ks37w8pmlmw4vx40000gn/T/pip-1imEXi-record/install-record.txt --single-version-externally-managed --compile --install-headers /Users/zyl/song/lebi/lebienv/include/site/python2.7/pygraphviz" failed with error code 1 in /private/var/folders/5t/965cgdc56ks37w8pmlmw4vx40000gn/T/pip-build-x2Vstw/pygraphviz
System :Mac OS X Version:10.11.1
how to fix the problem.
Upvotes: 4
Views: 11727
Answers (5)
Yuri Santos
Reputation: 67
The @jamjar and @Faccion answers did not work properly for me. So, I looked at the documentation and found a path config that worked for me. (Remember to install grapgviz first)
pip install --config-settings="--global-option=build_ext"
--config-settings="--global-option=-IC:\Program Files\Graphviz\include"
--config-settings="--global-option=-LC:\Program Files\Graphviz\lib"
pygraphviz
documentation: https://pygraphviz.github.io/documentation/stable/install.html#manual-download
Upvotes: 0
Sameer Mahajan
Reputation: 598
latest pip versions (e.g. 24.2 and later) have deprecated the --build-option and --global-option for newer --config-settings as can be seen here
DEPRECATION: --build-option and --global-option are deprecated. pip 24.2 will enforce this behaviour change. A possible replacement is to use --config-settings. Discussion can be found at https://github.com/pypa/pip/issues/11859
Now you need something like
pip install --config-settings="--build-option=build_ext" --config-settings="--build-option=--library-dirs=$GRAPHVIZ_DIR/lib" --config-settings="--build-option=--include-dirs=$GRAPHVIZ_DIR/include" pygraphviz
where $GRAPHVIZ_DIR is the directory where you have installed graphviz
Upvotes: 0
Rob
Reputation: 1909
It is not helpful to randomly attempt to paste in people's paths for the install location.
If you installed it successfully with brew, you can get your own path and use it to install pygraphviz:
brew install graphviz
brew info graphviz
# This will print out the install location
# Look for this line:
# **/usr/local/Cellar/graphviz/3.0.0** (292 files, 6.8MB) *
# Path is part I've bolded above
export GRAPHVIZ_DIR="[path from above command]"
# Ensure you are in the virtual environment
pip install pygraphviz --global-option=build_ext --global-option="-I$GRAPHVIZ_DIR/include" --global-option="-L$GRAPHVIZ_DIR/lib"
Upvotes: 2
jamjar
Reputation: 635
Setting library_dirs and include_dirs as suggested in the error message worked for me. This article shows how to set them. However, first make sure pygraphviz is actually installed.
pip install --install-option="--include-path=/usr/local/include/graphviz/" --install-option="--library-path=/usr/local/lib/graphviz" pygraphviz
Upvotes: 3
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