numpy issue on Python 2.7 -- numpy.dtype has the wrong size

Question

Wondering if anyone met with similar issues before and any solutions? Using Python 2.7 on Mac OSX.

import numpy as np
import matplotlib.pyplot as plt
from sklearn import linear_model, datasets

# import some data to play with
iris = datasets.load_iris()
X = iris.data[:, :2]  # we only take the first two features.
Y = iris.target

h = .02  # step size in the mesh

logreg = linear_model.LogisticRegression(C=1e5)

# we create an instance of Neighbours Classifier and fit the data.
logreg.fit(X, Y)

Traceback (most recent call last):
  File "/Users/foo/Downloads/PycharmProjects/testLogisticRegressionSimple.py", line 23, in <module>
    from sklearn import linear_model, datasets
  File "/Library/Python/2.7/site-packages/sklearn/__init__.py", line 57, in <module>
    from .base import clone
  File "/Library/Python/2.7/site-packages/sklearn/base.py", line 11, in <module>
    from .utils.fixes import signature
  File "/Library/Python/2.7/site-packages/sklearn/utils/__init__.py", line 10, in <module>
    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

Edit 1, met with errors when trying to re-install, here are the command and error message,

sudo /usr/local/bin/pip install --upgrade --force-reinstall numpy sklearn
The directory '/Users/foo/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/foo/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting numpy
  Downloading numpy-1.11.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.9MB)
    100% |████████████████████████████████| 3.9MB 296kB/s
Collecting sklearn
Collecting scikit-learn (from sklearn)
  Downloading scikit_learn-0.17.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.9MB)
    100% |████████████████████████████████| 3.9MB 317kB/s
Installing collected packages: numpy, scikit-learn, sklearn
  Found existing installation: numpy 1.8.0rc1
    DEPRECATION: Uninstalling a distutils installed project (numpy) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
    Uninstalling numpy-1.8.0rc1:
Exception:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip-8.1.1-py2.7.egg/pip/basecommand.py", line 209, in main
    status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip-8.1.1-py2.7.egg/pip/commands/install.py", line 317, in run
    prefix=options.prefix_path,
  File "/Library/Python/2.7/site-packages/pip-8.1.1-py2.7.egg/pip/req/req_set.py", line 726, in install
    requirement.uninstall(auto_confirm=True)
  File "/Library/Python/2.7/site-packages/pip-8.1.1-py2.7.egg/pip/req/req_install.py", line 746, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/Library/Python/2.7/site-packages/pip-8.1.1-py2.7.egg/pip/req/req_uninstall.py", line 115, in remove
    renames(path, new_path)
  File "/Library/Python/2.7/site-packages/pip-8.1.1-py2.7.egg/pip/utils/__init__.py", line 267, 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: '/tmp/pip-TDvKH6-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info'
You are using pip version 8.1.1, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Answer 1

Your code works fine for me, which suggests it's an environment error.

Try running sudo pip install --upgrade --force-reinstall numpy sklearn and see if that does the trick.

If you installed via Homebrew: brew install --force numpy (there's no sklearn homebrew package)

If you installed via MacPorts:

port -f uninstall py27-numpy
port install py27-numpy

(But if you installed via either Homebrew or MacPorts, I recommend uninstalling (port -f uninstall py27-numpy || brew uninstall numpy) and installing via pip instead.