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

Question

I have this error for trying to load a saved SVM model. I have tried uninstalling sklearn, NumPy and SciPy, reinstalling the latest versions all-together again (using pip). I am still getting this error. Why?

In [1]: import sklearn; print sklearn.__version__
0.18.1
In [3]: import numpy; print numpy.__version__
1.11.2
In [5]: import scipy; print scipy.__version__
0.18.1
In [7]: import pandas; print pandas.__version__
0.19.1

In [10]: clf = joblib.load('model/trained_model.pkl')
---------------------------------------------------------------------------
RuntimeWarning                            Traceback (most recent call last)
<ipython-input-10-5e5db1331757> in <module>()
----> 1 clf = joblib.load('sentiment_classification/model/trained_model.pkl')

/usr/local/lib/python2.7/dist-packages/sklearn/externals/joblib/numpy_pickle.pyc in load(filename, mmap_mode)
    573                     return load_compatibility(fobj)
    574
--> 575                 obj = _unpickle(fobj, filename, mmap_mode)
    576
    577     return obj

/usr/local/lib/python2.7/dist-packages/sklearn/externals/joblib/numpy_pickle.pyc in _unpickle(fobj, filename, mmap_mode)
    505     obj = None
    506     try:
--> 507         obj = unpickler.load()
    508         if unpickler.compat_mode:
    509             warnings.warn("The file '%s' has been generated with a "

/usr/lib/python2.7/pickle.pyc in load(self)
    862             while 1:
    863                 key = read(1)
--> 864                 dispatch[key](self)
    865         except _Stop, stopinst:
    866             return stopinst.value

/usr/lib/python2.7/pickle.pyc in load_global(self)
   1094         module = self.readline()[:-1]
   1095         name = self.readline()[:-1]
-> 1096         klass = self.find_class(module, name)
   1097         self.append(klass)
   1098     dispatch[GLOBAL] = load_global

/usr/lib/python2.7/pickle.pyc in find_class(self, module, name)
   1128     def find_class(self, module, name):
   1129         # Subclasses may override this
-> 1130         __import__(module)
   1131         mod = sys.modules[module]
   1132         klass = getattr(mod, name)

/usr/local/lib/python2.7/dist-packages/sklearn/svm/__init__.py in <module>()
     11 # License: BSD 3 clause (C) INRIA 2010
     12
---> 13 from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
     14         LinearSVR
     15 from .bounds import l1_min_c

/usr/local/lib/python2.7/dist-packages/sklearn/svm/classes.py in <module>()
      2 import numpy as np
      3
----> 4 from .base import _fit_liblinear, BaseSVC, BaseLibSVM
      5 from ..base import BaseEstimator, RegressorMixin
      6 from ..linear_model.base import LinearClassifierMixin, SparseCoefMixin, \

/usr/local/lib/python2.7/dist-packages/sklearn/svm/base.py in <module>()
      6 from abc import ABCMeta, abstractmethod
      7
----> 8 from . import libsvm, liblinear
      9 from . import libsvm_sparse
     10 from ..base import BaseEstimator, ClassifierMixin

__init__.pxd in init sklearn.svm.libsvm (sklearn/svm/libsvm.c:10207)()

RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 80

UPDATE: OK, by following here, and

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

The error has now gone, though I still have no idea why it occurred in the first place...

Answer 1

pip install numpy==1.26.4

This worked for me

Answer 2

I had the same issue in my context, someone was installing a certain module:

pip install biopython==1.81

and I saw in the old CI (Docker container build) logs, that this used to implicitly download numpy as transitive dependency:

Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)

since recently, for whatever reason, this now downloads

 Downloading numpy-2.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)

probably the dependency spec in biopython is wrong. In any case, this then breaks at rutime with the OP's error.

Anyways, I solved it by freezing the numpy version to the old one:

pip install biopython==1.81 numpy==1.26.4

and another day where everything breaks all the time and needs to be fixed all the time ends :)

Answer 3

We are getting this error :

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

with the latest release of numpy 2.0 as well.

https://github.com/numpy/numpy/releases

We expect that some modules will need time to support NumPy 2

till then:

pip install numpy==1.26.4

Answer 4

if you are in an anaconda environment simply use:

conda update --all

or:

conda update numpy

Answer 5

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

pip install numpy --upgrade

Answer 6

Note that as of cython 0.29 there is a new check_size option that eliminates the warning at the source, so no work-arounds should be needed once that version percolates to the various packages

Answer 7

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..

Answer 8

Meta-information: The recommended way to install sklearn

If you already have a working installation of numpy and scipy, the easiest way to install scikit-learn is using pip

pip install -U scikit-learn 

or conda:

conda install scikit-learn

[... do not compile from source using pip]

If you don’t already have a python installation with numpy and scipy, we recommend to install either via your package manager or via a python bundle. These come with numpy, scipy, scikit-learn, matplotlib and many other helpful scientific and data processing libraries.

Answer 9

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.

Answer 10

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.

---

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.

---

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

Answer 11

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

Answer 12

My enviroment is Python 2.7.15

I try

pip uninstall
pip install --no-use-wheel

but it does not work. It shows the error:

no such option: --no-use-wheel

Then I try:

pip uninstall
pip install --user --install-option="--prefix=" -U scikit-learn

And it works: the useless warnings do not show.

Answer 13

When import scipy, error info shows: RuntimeWarning: builtin.type size changed, may indicate binary incompatibility. Expected zd, got zd

I solved this problem by updating python version from 2.7.2 to 2.7.13