安装 PyGraphviz（Mac OS X、Anaconda）时出错

Posted 2023-03-12

【中文标题】安装 PyGraphviz（Mac OS X、Anaconda）时出错

【英文标题】：Error while installing PyGraphviz (Mac OS X, Anaconda)

【发布时间】：2016-01-01 05:12:36

【问题描述】：

我在安装 PyGraphviz 时遇到问题。 我在 Mac OS X 中使用 Anaconda。

错误消息指出了一些原因，但我已经检查过它安装在 anaconda 目录中。

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

根据错误信息，如何更改 setup.py 中的 include_dirs 和 library_dirs 变量？？

这是我遇到的错误信息

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 (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/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

【参考方案1】：

尝试以下操作（确保安装并更新了 anaconda-client）：

conda install --channel https://conda.anaconda.org/garylschultz pygraphviz

【参考方案2】：

Graphviz 可以通过自制软件安装：brew install graphviz。

然后做：

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

最后：

pip install graphviz

在 Sierra 上测试过，可以正常工作。

【讨论】：

我宁愿建议创建一个符号链接 (ln -s . graphviz) 而不是复制文件，而不是步骤 2 和 3。

【参考方案3】：

假设您已经安装了 graphviz 软件：

如this blog post 中所述，在尝试运行pip install pygraphviz 时使用以下参数

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

所以最终的命令看起来像pip install pygraphviz --install-option="--include-path=/usr/local/include/graphviz/" --install-option="--library-path=/usr/local/lib/graphviz"。

这样做的目的是明确指定原始程序 (graphviz) 的库存在于何处以供 python 扩展使用。不幸的是，这似乎没有被自动识别。

使用 Python 3.6 在 MacOS Sierra 上工作

【讨论】：

对我有用的小变化 MacOS Sierra、Python 2.7+、随 MacPorts 安装的 Graphviz：pip install pygraphviz --install-option="--include-path=/opt/local/include/" --install-option="--library-path=/opt/local/lib/graphviz"

如果我使用 pipenv 会怎样？

【参考方案4】：

brew install graphviz

然后：

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

两个粗体路径都不应包含“graphviz”。

https://github.com/pygraphviz/pygraphviz/issues/100#issuecomment-237560404

在 OSX 10.14.1 上为我工作

【讨论】：

已于 2019 年 6 月 8 日验证可在 OS X 10.14.5 (Mojave) 上运行。谢谢！

在 OSX 10.13.6 和 pygraphviz 1.6 上工作