Can't install h5py on Jetpack 4.3

Robotics & Edge Computing Jetson & Embedded Systems Jetson TX2
1

I flashed 4.3 because…4.4 sucks. Now I’m having issues installing tensorflow.

One of the pre-reqs for it is h5py. There is a note about it at the bottom to fix dependency issues, but that didn’t work.

I get a long red text output during install…

Building wheel for h5py (setup.py) … error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’"’/tmp/pip-install-8ef0zuxm/h5py/setup.py’“'”‘; file=’“'”‘/tmp/pip-install-8ef0zuxm/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 /tmp/pip-wheel-x7u2z71a
cwd: /tmp/pip-install-8ef0zuxm/h5py/
Complete output (512 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-aarch64-3.6
creating build/lib.linux-aarch64-3.6/h5py
copying h5py/h5py_warnings.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/highlevel.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/version.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/ipy_completer.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/init.py → build/lib.linux-aarch64-3.6/h5py
creating build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/datatype.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/filters.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/files.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/group.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/vds.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/selections.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/base.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/dims.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/compat.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/init.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/dataset.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/selections2.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/attrs.py → build/lib.linux-aarch64-3.6/h5py/_hl
creating build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_group.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dtype.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_completions.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_objects.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5pl.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_file.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_base.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_attribute_create.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_selections.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_threads.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_deprecation.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_filters.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5t.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dataset.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_file2.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dims_dimensionproxy.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_attrs_data.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_datatype.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_attrs.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/common.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_file_image.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_slicing.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5f.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dataset_getitem.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dimension_scales.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/init.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dataset_swmr.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5d_direct_chunk.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5p.py → build/lib.linux-aarch64-3.6/h5py/tests
creating build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/test_virtual_source.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/test_lowlevel_vds.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/test_highlevel_vds.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/init.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
running build_ext
Loading library to get version: /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so
Autodetected HDF5 1.10.0

                     Summary of the h5py configuration

  Path to HDF5: None
  HDF5 Version: '1.10.0'
   MPI Enabled: False

Rebuild Required: True

Executing api_gen rebuild of defs
Executing cythonize()
[ 1/23] Cythonizing /tmp/pip-install-8ef0zuxm/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-8ef0zuxm/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-8ef0zuxm/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-8ef0zuxm/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-8ef0zuxm/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-8ef0zuxm/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-8ef0zuxm/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 “”, line 1, in
File “/tmp/pip-install-8ef0zuxm/h5py/setup.py”, line 159, in
cmdclass = CMDCLASS,
File “/usr/lib/python3/dist-packages/setuptools/init.py”, line 129, in setup
return distutils.core.setup(**attrs)
File “/usr/lib/python3.6/distutils/core.py”, line 148, in setup
dist.run_commands()
File “/usr/lib/python3.6/distutils/dist.py”, line 955, in run_commands
self.run_command(cmd)
File “/usr/lib/python3.6/distutils/dist.py”, line 974, in run_command
cmd_obj.run()
File “/usr/lib/python3/dist-packages/wheel/bdist_wheel.py”, line 204, in run
self.run_command(‘build’)
File “/usr/lib/python3.6/distutils/cmd.py”, line 313, in run_command
self.distribution.run_command(command)
File “/usr/lib/python3.6/distutils/dist.py”, line 974, in run_command
cmd_obj.run()
File “/usr/lib/python3.6/distutils/command/build.py”, line 135, in run
self.run_command(cmd_name)
File “/usr/lib/python3.6/distutils/cmd.py”, line 313, in run_command
self.distribution.run_command(command)
File “/usr/lib/python3.6/distutils/dist.py”, line 974, in run_command
cmd_obj.run()
File “/tmp/pip-install-8ef0zuxm/h5py/setup_build.py”, line 209, in run
language_level=2)
File “/tmp/pip-install-8ef0zuxm/h5py/.eggs/Cython-3.0a5-py3.6.egg/Cython/Build/Dependencies.py”, line 1105, in cythonize
cythonize_one(*args)
File “/tmp/pip-install-8ef0zuxm/h5py/.eggs/Cython-3.0a5-py3.6.egg/Cython/Build/Dependencies.py”, line 1263, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /tmp/pip-install-8ef0zuxm/h5py/h5py/h5a.pyx

ERROR: Failed building wheel for h5py
Running setup.py clean for h5py
Failed to build h5py
Installing collected packages: h5py, astor, termcolor, protobuf, keras-applications, keras-preprocessing, wrapt, google-pasta
Running setup.py install for h5py … error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’"’/tmp/pip-install-8ef0zuxm/h5py/setup.py’“'”‘; file=’“'”‘/tmp/pip-install-8ef0zuxm/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-l7tms7nl/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6/h5py
cwd: /tmp/pip-install-8ef0zuxm/h5py/
Complete output (201 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-aarch64-3.6
creating build/lib.linux-aarch64-3.6/h5py
copying h5py/h5py_warnings.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/highlevel.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/version.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/ipy_completer.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/init.py → build/lib.linux-aarch64-3.6/h5py
creating build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/datatype.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/filters.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/files.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/group.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/vds.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/selections.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/base.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/dims.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/compat.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/init.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/dataset.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/selections2.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/attrs.py → build/lib.linux-aarch64-3.6/h5py/_hl
creating build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_group.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dtype.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_completions.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_objects.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5pl.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_file.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_base.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_attribute_create.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_selections.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_threads.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_deprecation.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_filters.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5t.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dataset.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_file2.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dims_dimensionproxy.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_attrs_data.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_datatype.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_attrs.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/common.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_file_image.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_slicing.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5f.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dataset_getitem.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dimension_scales.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/init.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_dataset_swmr.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5d_direct_chunk.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_h5p.py → build/lib.linux-aarch64-3.6/h5py/tests
creating build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/test_virtual_source.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/test_lowlevel_vds.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/test_highlevel_vds.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
copying h5py/tests/test_vds/init.py → build/lib.linux-aarch64-3.6/h5py/tests/test_vds
running build_ext
Loading library to get version: /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so
Autodetected HDF5 1.10.0
********************************************************************************
Summary of the h5py configuration

    Path to HDF5: None
    HDF5 Version: '1.10.0'
     MPI Enabled: False
Rebuild Required: True

********************************************************************************
Executing cythonize()
[ 1/23] Cythonizing /tmp/pip-install-8ef0zuxm/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-8ef0zuxm/h5py/setup.py", line 159, in <module>
    cmdclass = CMDCLASS,
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 129, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib/python3.6/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib/python3.6/distutils/dist.py", line 955, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 61, in run
    return orig.install.run(self)
  File "/usr/lib/python3.6/distutils/command/install.py", line 589, in run
    self.run_command('build')
  File "/usr/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/usr/lib/python3.6/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/usr/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.6
2

ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’"’/tmp/pip-install-8ef0zuxm/h5py/setup.py’“'”‘; file=’“'”‘/tmp/pip-install-8ef0zuxm/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-l7tms7nl/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6/h5py Check the logs for full command output.

3

ended up doing sudo apt install python3-h5py

I suggest updating the instructions…

5

Hi,

It’s recommended to install h5py via pip3.
The version from apt-get may be different.

The detail installation steps can be found in our document here:

Please make sure you have all the dependencies installed first.
Thanks.

6

I was following those very instructions. It failed.

8

I had the exact same issue. There’s references to a workaround:

https://github.com/h5py/h5py/issues/1533

9

This was on Jetpack 4.4 but should still apply to anyone who finds themselves here.
h5py version 3 resolves the issue, it was not on pip yet but you can install from the git repo using the following.

git clone https://github.com/h5py/h5py.git
cd h5py/
pip3 install .

You may also be able to

pip3 install git+https://github.com/h5py/h5py.git

1 Like
10

The issue still exists in Jetpack 4.5.

Running

sudo pip3 install -U cython

prior to step 4 under Prerequisites and Dependencies resolved the issue for me.

1 Like