Opened 11 days ago
Closed 6 days ago
#69938 closed defect (fixed)
py312-h5py @3.11.0: ValueError: Not a datatype (not a datatype)
Reported by: | Michael-P-Allen (Mike Allen) | Owned by: | eborisch (Eric A. Borisch) |
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Priority: | Normal | Milestone: | |
Component: | ports | Version: | |
Keywords: | haspatch | Cc: | Dave-Allured (Dave Allured) |
Port: | py-h5py hdf5 |
Description
Following the upgrade to hdf5 @1.14.4.2_1+cxx+fortran+gfortran+hl I get an error message in Python when I load h5py. I took care to uninstall and reinstall the py-h5py and py312-h5py ports, so now I have:
$ port installed | grep hdf hdf5 @1.14.3_4+cxx+fortran+gfortran+hl hdf5 @1.14.4.2_0+cxx+fortran+gfortran+hl hdf5 @1.14.4.2_1+cxx+fortran+gfortran+hl (active) $ port installed | grep h5 py-h5py @3.11.0_1 (active) py312-h5py @3.11.0_1 (active)
The error I get is:
$ python Python 3.12.3 (main, Apr 12 2024, 20:23:48) [Clang 15.0.0 (clang-1500.1.0.2.5)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import h5py Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/opt/local/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/h5py/__init__.py", line 45, in <module> from ._conv import register_converters as _register_converters, \ File "h5py/_conv.pyx", line 1, in init h5py._conv File "h5py/h5r.pyx", line 1, in init h5py.h5r File "h5py/h5p.pyx", line 1, in init h5py.h5p File "h5py/h5t.pyx", line 235, in init h5py.h5t File "h5py/h5t.pyx", line 80, in h5py.h5t.lockid File "h5py/h5t.pyx", line 49, in h5py.h5t.typewrap ValueError: Not a datatype (not a datatype)
The error message goes away if I do sudo port activate hdf5 @1.14.4.2_0+cxx+fortran+gfortran+hl
and then run python, so it must be associated with the patch introduced in hdf5 in #69861. (Also h5py worked fine with the previous version hdf5 @1.14.3_4+cxx+fortran+gfortran+hl). However, it seemed best to open a new ticket. I am running with Xcode v15.3, Sonoma 14.4.1 on an Intel-based Mac mini.
Change History (6)
comment:1 Changed 11 days ago by jmroot (Joshua Root)
Owner: | set to eborisch |
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Port: | hdf5 added |
Status: | new → assigned |
comment:2 Changed 11 days ago by Michael-P-Allen (Mike Allen)
comment:3 Changed 11 days ago by ryandesign (Ryan Carsten Schmidt)
Keywords: | haspatch added |
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Summary: | Error on loading h5py → py312-h5py @3.11.0: ValueError: Not a datatype (not a datatype) |
Thanks for the pointer to that issue where it looks like two different problems are discussed and for which I've submitted two PR:
- a segfault after running the h5py test suite: https://github.com/macports/macports-ports/pull/23871
ValueError: Not a datatype (not a datatype)
when trying to use h5py at all if hdf5 was built with--disable-nonstandard-feature-float16
(which MacPorts hdf5 now is—that was the fix for #69861): https://github.com/macports/macports-ports/pull/23870
comment:4 Changed 10 days ago by Dave-Allured (Dave Allured)
Cc: | Dave-Allured added |
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comment:5 Changed 6 days ago by ryandesign (Ryan Carsten Schmidt)
comment:6 Changed 6 days ago by ryandesign (Ryan Carsten Schmidt)
Resolution: | → fixed |
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Status: | assigned → closed |
In case it helps, I see (what looks like) the same issue arising in https://github.com/h5py/h5py/issues/2419 . I'm absolutely not competent to follow it up or suggest a fix, though.