Python crashes after each start (H5check_version) about qgis-mac-packager HOT 11 CLOSED

found issue, looking how to fix it

0   libsystem_kernel.dylib            0x00007fff7ae512c6 __pthread_kill + 10
1   libsystem_pthread.dylib           0x00007fff7af0cbf1 pthread_kill + 284
2   libsystem_c.dylib                 0x00007fff7adbb6a6 abort + 127
3   libhdf5.103.dylib                 0x0000000114268a1f H5check_version + 587
4   h5f.cpython-37m-darwin.so         0x0000000139a2e161 __pyx_pymod_exec_h5f + 13505
5   org.python.python                 0x00000001279c3b6c PyModule_ExecDef + 115

https://support.hdfgroup.org/HDF5/doc1.6/RM_H5.html#Library-VersCheck

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The cause:

h5py used same library (libhdf5.103.dylib) as qgis binary. However those 2 libraries have different minor version and the abort() check in H5check_version aborted execution when used in pyqgis.

Fix is to install h5py with flag --no-binaries to compile h5py binaries ourselves.
The bug should be fixed in the next build

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@gubuntu can you try with https://qgis.org/downloads/macos/ltr/qgis_ltr_final-3_4_8_20190528_075201.dmg

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fixed, thanks!

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It's doing this again on both the latest builds

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@gubuntu is is on nightly builds or also LTR and PR builds?

the fix is already deployed and I haven't reinstalled the deps recently.. Are you sure it is the same error message?

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LTR and PR builds, I didn't try nightly

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Hi Gavin, how can I reproduce this bug?

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@gubuntu could you start with a new profile?

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@gubuntu is it solved with new profile? If yes, maybe there is some plugin that ships hdf5 (py)library that conflicts with the official one from installation... which plugins do you have installed that uses pyhdf5?

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fixed in qgis-deps-0.5.4 (nightly2 builds)

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