The error “ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject” occurs when there is a binary incompatibility between the installed NumPy package and an extension module that relies on it. This is usually caused by a mismatch in the NumPy versions used during the compilation of the extension module and at runtime.
To resolve this issue, follow these steps:
- Update your packages: First, ensure that both NumPy and the related extension module (e.g., SciPy, scikit-learn, etc.) are up-to-date. You can update your packages using
pip install --upgrade numpy pip install --upgradeIf you are using a different package manager like conda, use the corresponding commands to update your packages.
- Check for version compatibility: Make sure that the NumPy version you have installed is compatible with the extension module. Check the module’s documentation or requirements for any specific NumPy version requirements. If a specific version is required, you can install it using
pip install numpy==
- Reinstall the extension module: Uninstall the extension module and reinstall it to ensure that it is compiled with the correct NumPy version. Use
pipto uninstall and reinstall the package:
- Create a virtual environment: If the issue persists, consider creating a virtual environment to isolate your project’s dependencies. This can help avoid conflicts with other packages or system-wide installations. You can create a virtual environment using
python -m venv myenv source myenv/bin/activate # On Windows, use `myenv\Scripts\activate` pip install numpy
- Seek help from the community: If the issue still occurs after trying the above steps, consider reaching out to the development community or the package maintainers for guidance. They might have encountered similar issues and can provide valuable insights or solutions.
By following these steps, you should be able to resolve the “numpy.ndarray size changed” error and ensure binary compatibility between NumPy and the related extension module.