Cython errors when compiling h5py with pip
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Jason Greenlaw - NOAA Affiliate
Apr 29, 2020, 10:22:53 PM4/29/20
to h5py
Hello all,
I'm running into some odd Cython errors when attempting to compile h5py from scratch with pip, e.g.:
Error compiling Cython file:------------------------------------------------------------...
# --- open, open_by_name, open_by_idx ---
@with_phildef open(ObjectID loc not None, char* name=NULL, int index=-1, *,
^
------------------------------------------------------------
h5py/h5a.pyx:54:32: Cannot convert 'void *' to Python objectMy environment is h5py v2.10.0 on Amazon Linux (version 2018.03), using a Python 3.7.6 environment installed via pyenv. This is being done in a Docker container.
I'm using HDF5 v1.10.6 libraries, which I also compiled from scratch with the following configuration:
./configure \
--prefix=${INSTALL_PREFIX} \
--with-zlib=/usr/include,/lib64 \
--enable-threadsafe \
# --enable-unsupported required when building high-level libs with thread safety config
--enable-unsupported \
--with-pthread=/usr/include,/lib64I was able to compile h5py v2.10.0 (same version) successfully using the same approach as recently as 2 weeks ago with no issues, but it appears something has changed and I'm unsure what. I have not intentionally changed any library versions since the last successful build, but something must have changed.
So far I'm stumped. If anyone has info that could point me towards the culprit, it would be much appreciated!
Full build output below.
# pip install --no-binary=h5py h5py;Collecting h5py Downloading h5py-2.10.0.tar.gz (301 kB) |████████████████████████████████| 301 kB 2.6 MB/s Collecting numpy>=1.7 Downloading numpy-1.18.3-cp37-cp37m-manylinux1_x86_64.whl (20.2 MB) |████████████████████████████████| 20.2 MB 11.9 MB/s Collecting six Downloading six-1.14.0-py2.py3-none-any.whl (10 kB)Installing collected packages: numpy, six, h5py Running setup.py install for h5py ... error ERROR: Command errored out with exit status 1: command: /opt/.pyenv/versions/3.7.6/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qgbhsiyy/h5py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qgbhsiyy/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 /tmp/pip-record-5n20p1b0/install-record.txt --single-version-externally-managed --compile --install-headers /opt/.pyenv/versions/3.7.6/include/python3.7m/h5py cwd: /tmp/pip-install-qgbhsiyy/h5py/ Complete output (512 lines): running install running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/h5py copying h5py/ipy_completer.py -> build/lib.linux-x86_64-3.7/h5py copying h5py/highlevel.py -> build/lib.linux-x86_64-3.7/h5py copying h5py/h5py_warnings.py -> build/lib.linux-x86_64-3.7/h5py copying h5py/version.py -> build/lib.linux-x86_64-3.7/h5py copying h5py/__init__.py -> build/lib.linux-x86_64-3.7/h5py creating build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/dims.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/files.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/base.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/vds.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/selections.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/filters.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/compat.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/group.py -> build/lib.linux-x86_64-3.7/h5py/_hl copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-3.7/h5py/_hl creating build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_h5t.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_attrs_data.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_h5pl.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_dtype.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_datatype.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_h5.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_h5f.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_objects.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_h5p.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_group.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_dimension_scales.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_file_image.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_selections.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_base.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_completions.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_attribute_create.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_deprecation.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_file.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_slicing.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_threads.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/common.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/__init__.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_dataset.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_attrs.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_file2.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-x86_64-3.7/h5py/tests copying h5py/tests/test_filters.py -> build/lib.linux-x86_64-3.7/h5py/tests creating build/lib.linux-x86_64-3.7/h5py/tests/test_vds copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-x86_64-3.7/h5py/tests/test_vds copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-x86_64-3.7/h5py/tests/test_vds copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-x86_64-3.7/h5py/tests/test_vds copying h5py/tests/test_vds/__init__.py -> build/lib.linux-x86_64-3.7/h5py/tests/test_vds running build_ext ******************************************************************************** Summary of the h5py configuration Path to HDF5: '/usr/local' HDF5 Version: '1.10.6' MPI Enabled: False Rebuild Required: True ******************************************************************************** Executing api_gen rebuild of defs Executing cythonize() [ 1/23] Cythonizing /tmp/pip-install-qgbhsiyy/h5py/h5py/_conv.pyx warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared [ 2/23] Cythonizing /tmp/pip-install-qgbhsiyy/h5py/h5py/_errors.pyx warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared [ 3/23] Cythonizing /tmp/pip-install-qgbhsiyy/h5py/h5py/_objects.pyx warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared [ 4/23] Cythonizing /tmp/pip-install-qgbhsiyy/h5py/h5py/_proxy.pyx warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared [ 5/23] Cythonizing /tmp/pip-install-qgbhsiyy/h5py/h5py/defs.pyx warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared [ 6/23] Cythonizing /tmp/pip-install-qgbhsiyy/h5py/h5py/h5.pyx warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared [ 7/23] Cythonizing /tmp/pip-install-qgbhsiyy/h5py/h5py/h5a.pyx warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared Error compiling Cython file: ------------------------------------------------------------ ... # --- open, open_by_name, open_by_idx --- @with_phil def open(ObjectID loc not None, char* name=NULL, int index=-1, *, ^ ------------------------------------------------------------ h5py/h5a.pyx:54:32: Cannot convert 'void *' to Python object Error compiling Cython file: ------------------------------------------------------------ ... """ H5Arename_by_name(loc.id, obj_name, name, new_name, pdefault(lapl)) @with_phil def delete(ObjectID loc not None, char* name=NULL, int index=-1, *, ^ ------------------------------------------------------------ h5py/h5a.pyx:122:34: Cannot convert 'void *' to Python object Error compiling Cython file: ------------------------------------------------------------ ... def _hash(self): return hash((self.corder_valid, self.corder, self.cset, self.data_size)) @with_phil def get_info(ObjectID loc not None, char* name=NULL, int index=-1, *, ^ ------------------------------------------------------------ h5py/h5a.pyx:184:36: Cannot convert 'void *' to Python object Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-install-qgbhsiyy/h5py/setup.py", line 159, in <module> cmdclass = CMDCLASS, File "/opt/.pyenv/versions/3.7.6/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup return distutils.core.setup(**attrs) File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/opt/.pyenv/versions/3.7.6/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run return orig.install.run(self) File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/command/install.py", line 545, in run self.run_command('build') File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/opt/.pyenv/versions/3.7.6/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-qgbhsiyy/h5py/setup_build.py", line 209, in run language_level=2) File "/tmp/pip-install-qgbhsiyy/h5py/.eggs/Cython-3.0a3-py3.7-linux-x86_64.egg/Cython/Build/Dependencies.py", line 1105, in cythonize cythonize_one(*args) File "/tmp/pip-install-qgbhsiyy/h5py/.eggs/Cython-3.0a3-py3.7-linux-x86_64.egg/Cython/Build/Dependencies.py", line 1263, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: /tmp/pip-install-qgbhsiyy/h5py/h5py/h5a.pyx ----------------------------------------ERROR: Command errored out with exit status 1: /opt/.pyenv/versions/3.7.6/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qgbhsiyy/h5py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qgbhsiyy/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 /tmp/pip-record-5n20p1b0/install-record.txt --single-version-externally-managed --compile --install-headers /opt/.pyenv/versions/3.7.6/include/python3.7m/h5py Check the logs for full command output.Jason Greenlaw - NOAA Affiliate
Apr 29, 2020, 10:55:45 PM4/29/20
to h5py
And of course 10 minutes after I posted this, I found the GitHub issue about it: https://github.com/h5py/h5py/issues/1533
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