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Cannot import h5py on macos 10.12

See original GitHub issue

Issue found on macos10.12 with h5py wheel v3.0rc1 (tested with python3.7 and 3.8):

>>> import h5py
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "py37env/lib/python3.7/site-packages/h5py/__init__.py", line 25, in <module>
    from . import _errors
ImportError: dlopen(py37env/lib/python3.7/site-packages/h5py/_errors.cpython-37m-darwin.so, 2): Symbol not found: ____chkstk_darwin
  Referenced from: py37env/lib/python3.7/site-packages/h5py/.dylibs/libsz.2.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 in py37env/lib/python3.7/site-packages/h5py/.dylibs/libsz.2.dylib

It is fine with h5py 2.10.0.

It sounds wheels were built without setting MACOSX_DEPLOYMENT_TARGET environment variable set to enable backward compatibility.

Issue Analytics

State:
Created 3 years ago
Comments:6 (6 by maintainers)

Top GitHub Comments

1reaction

t20100commented, Oct 13, 2020

The missing symbol actually comes from libhdf5 (and libsz) which comes from homebrew. I’m looking into it.

0reactions

takluyvercommented, Oct 13, 2020

It depends how far you want to be backward compatible.

I don’t have a good feel for how quickly old Mac OS versions can be dropped. But if setting an environment variable and building HDF5 from source can easily extend support to older versions, I’m happy for it to support as far back as you want.

For building HDF5, you mean the ci/travis/get_hdf5_if_needed.sh script?

Yup! Thanks 🙂

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