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Unable to pip install v2.10.0 on macOS

See original GitHub issue
  • macOS 10.14.6
  • Python 3.7.3 from Homebrew
  • h5py version 2.10.0
  • HDF5 version unknown

Traceback during installation:

$ pip install h5py==2.10.0
Collecting h5py==2.10.0
  Using cached https://files.pythonhosted.org/packages/5f/97/a58afbcf40e8abecededd9512978b4e4915374e5b80049af082f49cebe9a/h5py-2.10.0.tar.gz
Requirement already satisfied: numpy>=1.7 in ./venv/lib/python3.7/site-packages (from h5py==2.10.0) (1.17.1)
Requirement already satisfied: six in ./venv/lib/python3.7/site-packages (from h5py==2.10.0) (1.12.0)
Building wheels for collected packages: h5py
  Building wheel for h5py (setup.py) ... error
  Complete output from command /Users/miliu/venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/private/var/folders/_b/kwcscwf12kl4213t2kwdctq00000gn/T/pip-install-svbm5jpc/h5py/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/_b/kwcscwf12kl4213t2kwdctq00000gn/T/pip-wheel-y6az_9nl --python-tag cp37:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.14-x86_64-3.7
  creating build/lib.macosx-10.14-x86_64-3.7/h5py
  copying h5py/h5py_warnings.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
  copying h5py/version.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
  copying h5py/highlevel.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
  copying h5py/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
  copying h5py/ipy_completer.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
  creating build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/files.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/compat.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/selections.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/dataset.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/vds.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/selections2.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/group.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/datatype.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/attrs.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/dims.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/base.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  copying h5py/_hl/filters.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
  creating build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_deprecation.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_attribute_create.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_file_image.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_h5f.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_group.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_slicing.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_h5pl.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_attrs.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_attrs_data.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_h5t.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_h5p.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_datatype.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/common.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_dataset.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_file.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_selections.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_threads.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_dtype.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_h5.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_file2.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_completions.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_filters.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_base.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  copying h5py/tests/test_objects.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
  creating build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
  copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
  running build_ext
  Loading library to get version: libhdf5.dylib
  error: dlopen(libhdf5.dylib, 6): image not found
  
  ----------------------------------------
  Failed building wheel for h5py
  Running setup.py clean for h5py
Failed to build h5py
Installing collected packages: h5py
  Running setup.py install for h5py ... error
    Complete output from command /Users/miliu/venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/private/var/folders/_b/kwcscwf12kl4213t2kwdctq00000gn/T/pip-install-svbm5jpc/h5py/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/_b/kwcscwf12kl4213t2kwdctq00000gn/T/pip-record-73u77dtq/install-record.txt --single-version-externally-managed --compile --install-headers /Users/miliu/venv/include/site/python3.7/h5py:
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.14-x86_64-3.7
    creating build/lib.macosx-10.14-x86_64-3.7/h5py
    copying h5py/h5py_warnings.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
    copying h5py/version.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
    copying h5py/highlevel.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
    copying h5py/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
    copying h5py/ipy_completer.py -> build/lib.macosx-10.14-x86_64-3.7/h5py
    creating build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/files.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/compat.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/selections.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/dataset.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/vds.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/selections2.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/group.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/datatype.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/attrs.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/dims.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/base.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    copying h5py/_hl/filters.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/_hl
    creating build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_deprecation.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_attribute_create.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_file_image.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_h5f.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_group.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_slicing.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_h5pl.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_attrs.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_attrs_data.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_h5t.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_h5p.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_datatype.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/common.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_dataset.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_file.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_selections.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_threads.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_dtype.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_h5.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_file2.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_completions.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_filters.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_base.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    copying h5py/tests/test_objects.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests
    creating build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
    copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
    copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
    copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
    copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-10.14-x86_64-3.7/h5py/tests/test_vds
    running build_ext
    Loading library to get version: libhdf5.dylib
    error: dlopen(libhdf5.dylib, 6): image not found
    
    ----------------------------------------
Command "/Users/miliu/venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/private/var/folders/_b/kwcscwf12kl4213t2kwdctq00000gn/T/pip-install-svbm5jpc/h5py/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/_b/kwcscwf12kl4213t2kwdctq00000gn/T/pip-record-73u77dtq/install-record.txt --single-version-externally-managed --compile --install-headers /Users/miliu/venv/include/site/python3.7/h5py" failed with error code 1 in /private/var/folders/_b/kwcscwf12kl4213t2kwdctq00000gn/T/pip-install-svbm5jpc/h5py/

Issue Analytics

  • State:closed
  • Created 4 years ago
  • Reactions:3
  • Comments:11 (7 by maintainers)

github_iconTop GitHub Comments

1reaction
convoliutioncommented, Sep 9, 2019

Thanks, @tacaswell and @matthew-brett!

I can confirm I’m able to pip install h5py==2.10.0 from wheels on both macOS and Debian. I’ll go ahead and close this issue, as it’s been resolved as far as I’m concerned.

1reaction
tacaswellcommented, Sep 7, 2019

Thanks to @matthew-brett the mac wheel builds have been fixed and are pushed up!

Read more comments on GitHub >

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