RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

Question

According to MAINT: silence Cython warnings about changes dtype/ufunc size. - numpy/numpy:

These warnings are visible whenever you import scipy (or another package) that was compiled against an older numpy than is installed.

and the checks are inserted by Cython (hence are present in any module compiled with it).

Long story short, these warnings should be benign in the particular case of numpy, and these messages are filtered out since numpy 1.8 (the branch this commit went onto). While scikit-learn 0.18.1 is compiled against numpy 1.6.1.

To filter these warnings yourself, you can do the same as the patch does:

import warnings
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
warnings.filterwarnings("ignore", message="numpy.ufunc size changed")

Of course, you can just recompile all affected modules from source against your local numpy with pip install --no-binary :all:¹ instead if you have the balls tools for that.

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Longer story: the patch's proponent claims there should be no risk specifically with numpy, and 3rd-party packages are intentionally built against older versions:

[Rebuilding everything against current numpy is] not a feasible solution, and certainly shouldn't be necessary. Scipy (as many other packages) is compatible with a number of versions of numpy. So when we distribute scipy binaries, we build them against the lowest supported numpy version (1.5.1 as of now) and they work with 1.6.x, 1.7.x and numpy master as well.

The real correct would be for Cython only to issue warnings when the size of dtypes/ufuncs has changes in a way that breaks the ABI, and be silent otherwise.

As a result, Cython's devs agreed to trust the numpy team with maintaining binary compatibility by hand, so we can probably expect that using versions with breaking ABI changes would yield a specially-crafted exception or some other explicit show-stopper.

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¹_{The previously available --no-use-wheel option has been removed since pip 10.0.0.}

It's the issue of new numpy version (1.15.0)

You can downgrade numpy and this problem will be fixed:

sudo pip uninstall numpy
sudo pip install numpy==1.14.5

Finally numpy 1.15.1 version is released so the warning issues are fixed.

sudo pip install numpy==1.15.1

This is working..

I've tried the above-mentioned ways, but nothing worked. But the issue was gone after I installed the libraries through apt install,

For Python3,

pip3 uninstall -y numpy scipy pandas scikit-learn
sudo apt update
sudo apt install python3-numpy python3-scipy python3-pandas python3-sklearn 

For Python2,

pip uninstall -y numpy scipy pandas scikit-learn
sudo apt update
sudo apt install python-numpy python-scipy python-pandas python-sklearn 

Hope that helps.

Just upgrade your numpy module, right now it is 1.15.4. For windows

pip install numpy --upgrade

if you are in an anaconda environment simply use:

conda update --all

or:

conda update numpy

This error occurs because the installed packages were build agains different version of numpy.
We need to rebuild scipy and scikit-learn against the local numpy.

For new pip (in my case pip 18.0) this worked:

pip uninstall -y scipy scikit-learn
pip install --no-binary scipy,scikit-learn -I scipy scikit-learn

--no-binary takes a list of names of packages that you want to ignore binaries for. In this case we passed --no-binary scipy,scikit-learn which will ignore binaries for packages scipy,scikit-learn. Didn't help me