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Daily build tests failing on macOS #971

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rly opened this issue Feb 22, 2025 · 0 comments · Fixed by #972
Closed

Daily build tests failing on macOS #971

rly opened this issue Feb 22, 2025 · 0 comments · Fixed by #972
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rly commented Feb 22, 2025

Describe the issue

https://github.com/NeurodataWithoutBorders/nwb-guide/actions/runs/13414372005 and also
https://github.com/NeurodataWithoutBorders/nwb-guide/actions/runs/13463910009/job/37634708312?pr=970

Started on February 19.

Error:

Error:   File "PyInstaller/loader/pyimod02_importers.py", line 419, in exec_module
  File "manageNeuroconv/__init__.py", line 2, in <module>
  File "PyInstaller/loader/pyimod02_importers.py", line 419, in exec_module
  File "manageNeuroconv/manage_neuroconv.py", line 17, in <module>
  File "PyInstaller/loader/pyimod02_importers.py", line 419, in exec_module
  File "pynwb/__init__.py", line 10, in <module>
  File "PyInstaller/loader/pyimod02_importers.py", line 419, in exec_module
  File "h5py/__init__.py", line 25, in <module>
ImportError: dlopen(/Users/runner/work/nwb-guide/nwb-guide/build/flask/nwb-guide/_internal/h5py/_errors.cpython-39-darwin.so, 0x0002): Symbol not found: _H5T_IEEE_F[16](https://github.com/NeurodataWithoutBorders/nwb-guide/actions/runs/13458366543/job/37607424448#step:15:17)BE_g
  Referenced from: <E63CF6C4-706B-3E0B-953D-CC7FF32770E8> /Users/runner/work/nwb-guide/nwb-guide/build/flask/nwb-guide/_internal/h5py/.dylibs/libhdf5_hl.310.dylib
  Expected in:     <263AC110-613B-362E-8F5B-587BB3E43B61> /Users/runner/work/nwb-guide/nwb-guide/build/flask/nwb-guide/_internal/tables/.dylibs/libhdf5.310.dylib
[1[19](https://github.com/NeurodataWithoutBorders/nwb-guide/actions/runs/13458366543/job/37607424448#step:15:20)26] Failed to execute script 'app' due to unhandled exception!

On February 18, h5py==3.13.0 was released which updates the prebuilt HDF5 library to 1.14.6. I suspect that there is an HDF5 conflict between h5py and tables (pytables). It is also strange that despite python being pinned to 3.9, the 3.10 hdf5 libraries are referenced in the error.

Steps to Reproduce

Run Mac OS (x64) build CI

Operating System

Mac OS x64

GUIDE Version

main

Code of Conduct

Yes

Did you confirm this issue was not already reported?

Yes

@rly rly self-assigned this Feb 22, 2025
@rly rly added the bug Something isn't working label Feb 22, 2025
@rly rly closed this as completed in #972 Feb 24, 2025
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