RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb

Question

I'm trying to learn Machine Learning, but I cannot resolve below error.

[My environment]

• Mac High Sierra 10.13.2
• Python3.4.5
• Numpy1.13.3

[Command]

$ python3 -c "import jupyter, matplotlib, numpy, pandas, scipy, sklearn"

[Error]

RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb
Traceback (most recent call last):
  File "/Users/uekyo/ml/env/lib/python3.4/site-packages/pandas/__init__.py", line 26, in <module>
    from pandas._libs import (hashtable as _hashtable,
  File "/Users/uekyo/ml/env/lib/python3.4/site-packages/pandas/_libs/__init__.py", line 4, in <module>
    from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
  File "pandas/_libs/tslib.pyx", line 1, in init pandas._libs.tslib
ImportError: numpy.core.multiarray failed to import

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/uekyo/ml/env/lib/python3.4/site-packages/pandas/__init__.py", line 35, in <module>
    "the C extensions first.".format(module))
ImportError: C extension: numpy.core.multiarray failed to import not built. If you want to import pandas from the source directory, you may need to run 'python setup.py build_ext --inplace --force' to build the C extensions first.

[Things I tried]

I understood numpy is wrong. So I tried below things, but the error still appears.

~1~

sudo mv /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy_old

~2~

pip3 uninstall numpy
pip3 install numpy  -I

Thanks.

Answer 1

Seems like this is due to pandas version higher than 0.21.0 and numpy version 1.13.3 that is pulled by TensorFlow not playing well together.

Here is how I fixed it in my end:

# ipython
Python 2.7.6 (default, Nov 23 2017, 15:49:48)
Type "copyright", "credits" or "license" for more information.

IPython 4.2.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import tensorflow as tf
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb
    
In [2]: !pip install pandas==0.21.0
Collecting pandas==0.21.0
/usr/local/lib/python2.7/dist-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPS request
has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server
to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve
 this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#snimissingwarning.
  SNIMissingWarning
/usr/local/lib/python2.7/dist-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLC
ontext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to f
ail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest
/security.html#insecureplatformwarning.
  InsecurePlatformWarning
  Downloading pandas-0.21.0-cp27-cp27mu-manylinux1_x86_64.whl (24.3MB)
    100% |################################| 24.3MB 52kB/s
Requirement already satisfied: pytz>=2011k in /usr/local/lib/python2.7/dist-packages (from pandas==0.21.0)
Requirement already satisfied: numpy>=1.9.0 in /usr/local/lib/python2.7/dist-packages (from pandas==0.21.0)
Requirement already satisfied: python-dateutil in /usr/local/lib/python2.7/dist-packages (from pandas==0.21.0)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python2.7/dist-packages (from python-dateutil->pandas==0.21.0)
Installing collected packages: pandas
  Found existing installation: pandas 0.21.1
    Uninstalling pandas-0.21.1:
      Successfully uninstalled pandas-0.21.1
Successfully installed pandas-0.21.0

In [3]: del tf

In [4]: import tensorflow as tf

Answer 2

Most likely due to version of numpy too low; this one solved my problem:

pip3 install "numpy == 1.15.0" --user 

conda install can't solve because currently it only have numpy version 1.13.1, but is may due to my mirror site choosen is not the latest