mac OS X10.11.5安装scikit-learn后运行出现ValueError: numpy.dtype has the wrong size的错误

1. 安装机器学习类库
   通过pip命令安装机器学习类库 numpy,scipy,scikit-learn

   sudo pip install numpy scipy scikit-learn 

   但是安装后，运行机器学习算法，报错如下：

   Traceback (most recent call last): File "", line 1, in  File "/Library/Python/2.7/site-packages/sklearn/__init__.py", line 57, in  from .base import clone File "/Library/Python/2.7/site-packages/sklearn/base.py", line 11, in  from .utils.fixes import signature File "/Library/Python/2.7/site-packages/sklearn/utils/__init__.py", line 10, in  from .murmurhash import murmurhash3_32 File "numpy.pxd", line 155, in init sklearn.utils.murmurhash (sklearn/utils/murmurhash.c:5029) ValueError: numpy.dtype has the wrong size, try recompiling 

2. 排查错误原因

   网上给的建议大都是直接卸载再全部重装，将 numpy 、 scipy 和 scikit-learn 全部卸载了，然后在安装，操作如下
   我在操作时候发现，不能通过简单的安装和卸载方式重新安装，因为重新安装可能某些类库仍然是低版本，所以要选择升级，这样能保证版本都是最新的

   sudo pip install -U numpy scipy scikit-learn 

   安装在执行这个命令时候，会报错如下：

   Exception:
   Traceback (most recent call last):
     File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/basecommand.py", line 211, in main
       status = self.run(options, args)
     File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/commands/install.py", line 311, in run
       root=options.root_path,
     File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_set.py", line 640, in install
       requirement.uninstall(auto_confirm=True)
     File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_install.py", line 716, in uninstall
       paths_to_remove.remove(auto_confirm)
     File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_uninstall.py", line 125, in remove
       renames(path, new_path)
     File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/utils/__init__.py", line 315, in renames
       shutil.move(old, new)
     File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 302, in move
       copy2(src, real_dst)
     File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 131, in copy2
       copystat(src, dst)
     File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 103, in copystat
       os.chflags(dst, st.st_flags)
   OSError: [Errno 1] Operation not permitted: 
   

   ---

3. 继续剖析错误原因
   查了资料，找到如下解决方案：
   1、重启电脑，按command+R进入恢复模式，点击菜单【实用工具】，打开【终端】，输入 csrutil disable
   2、重启电脑，正常进入，打开【终端】输入 csrutil status

   这是macosx 10.11 EI Capitan使用了Rootlees，可以理解为一个更高等级的内核保护，系统会默认锁定/system , /sbin , /usr这三个目录，

   通过上面方法可以将这个保护关闭。

   如果没有关闭，安装一些软件时会出现

   Operation not permitted

   重新执行如下命令：

   sudo pip install -U numpy scipy scikit-learn 

   可以正常执行

   但是重新运行机器学习算法，还是报上面的错

   ---

4. 尝试新思路解决问题

   继续查资料时终于发现有用的方法了:

   http://scikit-learn-general.narkive.com/kMA6mRCk/valueerror-numpy-dtype-has-the-wrong-size-try-recompiling

   就是不用使用 pip install scikit-learn 安装，卸载之后直接使用git上 https://github.com/scikit-learn/scikit-learn 的自己安装
   操作流程如下：

   sudo pip uninstall scikit-learn 
   
   git clone https://github.com/scikit-learn/scikit-learn.git
   
   cd scikit-learn
   sudo make
   执行make会报错如下：
   RuntimeError: Running cythonize failed! 
   Error提示,这时候安装一下 cpython 即可
   sudo pip install cython
   
   然后 继续执行make
   最后执行install
   sudo python setup.py install
   
   copying sklearn/datasets/data/digits.csv.gz -> /Library/Python/2.7/site-packages/sklearn/datasets/data/
   copying sklearn/datasets/data/linnerud_physiological.csv -> /Library/Python/2.7/site-packages/sklearn/datasets/data/
   copying sklearn/datasets/data/breast_cancer.csv -> /Library/Python/2.7/site-packages/sklearn/datasets/data/
   copying sklearn/datasets/data/linnerud_exercise.csv -> /Library/Python/2.7/site-packages/sklearn/datasets/data/
   creating /Library/Python/2.7/site-packages/sklearn/datasets/images
   copying sklearn/datasets/images/flower.jpg -> /Library/Python/2.7/site-packages/sklearn/datasets/images/
   copying sklearn/datasets/images/README.txt -> /Library/Python/2.7/site-packages/sklearn/datasets/images/
   copying sklearn/datasets/images/china.jpg -> /Library/Python/2.7/site-packages/sklearn/datasets/images/
   creating /Library/Python/2.7/site-packages/sklearn/datasets/descr
   copying sklearn/datasets/descr/digits.rst -> /Library/Python/2.7/site-packages/sklearn/datasets/descr/
   copying sklearn/datasets/descr/linnerud.rst -> /Library/Python/2.7/site-packages/sklearn/datasets/descr/
   copying sklearn/datasets/descr/breast_cancer.rst -> /Library/Python/2.7/site-packages/sklearn/datasets/descr/
   copying sklearn/datasets/descr/iris.rst -> /Library/Python/2.7/site-packages/sklearn/datasets/descr/
   copying sklearn/datasets/descr/boston_house_prices.rst -> /Library/Python/2.7/site-packages/sklearn/datasets/descr/
   copying sklearn/datasets/descr/diabetes.rst -> /Library/Python/2.7/site-packages/sklearn/datasets/descr/
   running install_egg_info
   Writing /Library/Python/2.7/site-packages/scikit_learn-0.18.dev0-py2.7.egg-info
   running install_clib

   “running install_clib” 表示顺利安装成功

   再次运行机器学习算法，不再报错了

经常在自己mac运行下机器学习算法，记得之前就遇到过这样问题，这次正好又遇到了，就整理下， 希望能对大家有所帮助吧，也不是啥干货，就是简单整理一下。

---

作者:stark_summer
出处:http://blog.csdn.net/stark_summer/article/details/51980888