Failed building wheel of h5py

Autonomous Machines Jetson & Embedded Systems Jetson Nano
1

Hello, I have fresh install of latest image from official nvidia pages. I am trying to make keras or tensorflow or whatever ML platform work, but i get stuck at building wheel of h5py package. I was using official tutorial getting started, didn’t work so I tried solution from youtube from 2020 didn’t work either so then I flashed again and was trying this tutorialhttps://forums.developer.nvidia.com/t/official-tensorflow-for-jetson-nano/71770
, but I always get same error and just don’t know what else to do. Could you help please with this issue? I have been stuck for 3 days on this:

error_log.txt (34.8 KB)

3

Hi,

Thanks for reporting this.
We will give it a try and share more info with you later.

Thanks.

5

Hi,

We have confirmed that the following steps can work.
Please give it a try:

$ sudo apt-get update
$ sudo apt-get install libhdf5-serial-dev hdf5-tools libhdf5-dev zlib1g-dev zip libjpeg8-dev liblapack-dev libblas-dev gfortran
$ sudo apt-get install python3-pip
$ sudo pip3 install -U pip testresources setuptools
$ sudo ln -s /usr/include/locale.h /usr/include/xlocale.h
$ pip3 install Cython==0.29.36
$ pip3 install pkgconfig
$ git clone https://github.com/h5py/h5py.git
$ git checkout 3.1.0
$ git cherry-pick 3bf862daa4ebeb2eeaf3a0491e05f5415c1818e4
$ H5PY_SETUP_REQUIRES=0 pip3 install . --no-deps --no-build-isolation
$ sudo pip3 install -U numpy==1.19.4 future mock keras_preprocessing keras_applications gast==0.2.1 protobuf pybind11 packaging
$ sudo pip3 install --extra-index-url https://developer.download.nvidia.com/compute/redist/jp/v461 tensorflow

Thanks.

5 Likes
6

I have the same problem, I tried to install from the repository but since git checkout 3.1.0 it gives me a git checkout 3.1.0 failure

8

Yes, the same happened to me.

9

@barton @gustavoflor3s I was just able to do git checkout 3.1.0 on h5py, maybe try again now? However, I did not need to manually clone/patch h5py anymore when doing a TensorFlow install in a fresh environment (in nvcr.io/nvidia/l4t-base:r32.7.1 container) :

apt-get update
apt-get install -y python3-pip pkg-config
apt-get install -y libhdf5-serial-dev hdf5-tools libhdf5-dev zlib1g-dev zip libjpeg8-dev liblapack-dev libblas-dev gfortran
ln -s /usr/include/locale.h /usr/include/xlocale.h
pip3 install --verbose 'protobuf<4' 'Cython<3'
wget --no-check-certificate https://developer.download.nvidia.com/compute/redist/jp/v461/tensorflow/tensorflow-2.7.0+nv22.1-cp36-cp36m-linux_aarch64.whl
pip3 install --verbose tensorflow-2.7.0+nv22.1-cp36-cp36m-linux_aarch64.whl

The recent issues seem related to new major releases of protobuf and Cython packages.

1 Like
10

Thank you very much, you are right if it works, I am new to several things, my mistake was silly because it was not inside the h5py folder, that is why it did not pull anymore, this alternative solution also worked for me, thank you very much, I do not understand why the installation of tensorflow did not updated from the main topic. Thank you very much for the help

11

@gustavoflor3s glad it worked for you - new versions of the pip dependencies can be released at any time (in this case - cython, protobuf, h5py) which can cause issues to pop up downstream (this seems to be more a Python thing than anything specific to Jetson). In any case, we’re going to update the documentation, thanks for pointing that out.

12

I didn’t try your solution but if that worked for @gustavoflor3s I would say you can ping this as solution. I eventually used PyTorch and converted pretrained models for it, then ran benchmark all succesfully. I didn’t realize i don’t need to train models on Jetson Nano. Thank you for your time guys.

13

error_log.txt (6.3 KB)
I have tried the above and many other ways. But I still can’t install h5py in any version 2.10.0 or 3.1.0. General error is given:
ERROR: Command errored out with exit status -4:
command: /usr/bin/python3 /usr/local/lib/python3.6/dist-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmph41gi7j9
cwd: /tmp/pip-install-5yql8zku/h5py_cda4d33a7ee44867ab58df7037847fa8
…
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects

Ubuntu 18.04.6 LTS (GNU/Linux 4.9.253-tegra aarch64)
python 3.6.9
jetpack 461
wheel 0.37.1
pip 21.3.1
numpy 1.19.5

15

@minhphuc your log doesn’t contain the actual error - try running “pip3 install” with --verbose so that it gives you more information about the error that occurred.

16

erro_log (28.9 KB)
I try cmd:
sudo pip3 install --verbose h5py

17

Sorry, it is still not capturing the error, did you look for it? Maybe error is printed to stderr instead of stdout, and should be captured like this:

pip3 install --verbose h5py 2>&1 | tee log.txt

Regardless, it is difficult to debug these errors remotely depending on your individual environment and configuration - if you continue having issues, I would try running this in container like l4t-base to start fresh. Or just use l4t-tensorflow container which already has TF and h5py installed in it.

18

pip3 install --verbose h5py 2>&1 | tee log.txt

After running the command I got this log file.

I spent a week trying to fix this. Tried all the methods posted before. .But the result still returns error install h5py.

Vào Th 2, 28 thg 8, 2023 vào lúc 20:03 dusty_nv via NVIDIA Developer Forums <notifications@nvidia.discoursemail.com> đã viết:

log.txt (13.9 KB)

19

@minhphuc have you tried doing it in a container yet to use a fresh environment, or just using l4t-tensorflow? There is still no error, but I found this in your log:

Collecting Cython>=0.29
    Using cached Cython-3.0.2-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (3.3 MB)

It is installing Cython 3, whereas the instruction above is to force Cython<3. Try pip3 install 'Cython<3' as above and make sure it doesn’t upgrade to Cython 3.

20

Thanks, for your suggestion about container . It worked with me. However there is still something stuck, when working with jetpack 461 and installing h5py. Thank you very much

Vào Th 3, 29 thg 8, 2023 vào lúc 00:28 dusty_nv via NVIDIA Developer Forums <notifications@nvidia.discoursemail.com> đã viết:

21

I am having the same issue but with jetson agx xavier using jetpack 5.1 can you give me some guidance in regards to my build?

s
udo pip3 install --verbose --extra-index-url Index of /compute/redist/jp/v51 tensorflow==1.15.5+nv23.01

Using pip 23.2.1 from /usr/local/lib/python3.8/dist-packages/pip (python 3.8)
Looking in indexes: https://pypi.org/simple, https://developer.download.nvidia.com/compute/redist/jp/v51
Collecting tensorflow==1.15.5+nv23.01
  Using cached https://developer.download.nvidia.com/compute/redist/jp/v51/tensorflow/tensorflow-1.15.5%2Bnv23.01-cp38-cp38-linux_aarch64.whl (359.4 MB)
Collecting absl-py>=0.9.0 (from tensorflow==1.15.5+nv23.01)
  Using cached absl_py-1.4.0-py3-none-any.whl (126 kB)
Collecting astunparse==1.6.3 (from tensorflow==1.15.5+nv23.01)
  Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting astor==0.8.1 (from tensorflow==1.15.5+nv23.01)
  Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting gast==0.3.3 (from tensorflow==1.15.5+nv23.01)
  Using cached gast-0.3.3-py2.py3-none-any.whl (9.7 kB)
Collecting google-pasta>=0.1.6 (from tensorflow==1.15.5+nv23.01)
  Using cached google_pasta-0.2.0-py3-none-any.whl (57 kB)
Requirement already satisfied: keras-applications>=1.0.8 in /usr/local/lib/python3.8/dist-packages (from tensorflow==1.15.5+nv23.01) (1.0.8)
Requirement already satisfied: keras-preprocessing>=1.0.5 in /usr/local/lib/python3.8/dist-packages (from tensorflow==1.15.5+nv23.01) (1.1.2)
Collecting opt-einsum>=2.3.2 (from tensorflow==1.15.5+nv23.01)
  Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)
Requirement already satisfied: six>=1.10.0 in /usr/lib/python3/dist-packages (from tensorflow==1.15.5+nv23.01) (1.14.0)
Collecting protobuf<4.0.0,>=3.6.1 (from tensorflow==1.15.5+nv23.01)
  Using cached protobuf-3.20.3-cp38-cp38-manylinux2014_aarch64.whl (918 kB)
Collecting tensorboard<1.16.0,>=1.15.0 (from tensorflow==1.15.5+nv23.01)
  Using cached tensorboard-1.15.0-py3-none-any.whl (3.8 MB)
Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15.5+nv23.01)
  Using cached tensorflow_estimator-1.15.1-py2.py3-none-any.whl (503 kB)
Collecting termcolor>=1.1.0 (from tensorflow==1.15.5+nv23.01)
  Using cached termcolor-2.3.0-py3-none-any.whl (6.9 kB)
Collecting wrapt>=1.11.1 (from tensorflow==1.15.5+nv23.01)
  Using cached wrapt-1.15.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (81 kB)
Collecting h5py==2.10.0 (from tensorflow==1.15.5+nv23.01)
  Using cached h5py-2.10.0.tar.gz (301 kB)
  Running command python setup.py egg_info
  running egg_info
  creating /tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info
  writing /tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info/PKG-INFO
  writing dependency_links to /tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info/dependency_links.txt
  writing requirements to /tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info/requires.txt
  writing top-level names to /tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info/top_level.txt
  writing manifest file '/tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info/SOURCES.txt'
  reading manifest file '/tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  no previously-included directories found matching 'docs/_build'
  no previously-included directories found matching 'docs_api/_build'
  warning: no previously-included files found matching 'h5py/config.pxi'
  warning: no previously-included files found matching 'h5py/defs.pxd'
  warning: no previously-included files found matching 'h5py/defs.pyx'
  warning: no previously-included files matching '.DS_Store' found under directory '*'
  warning: no previously-included files found matching 'ci'
  warning: no previously-included files found matching 'other'
  warning: no previously-included files found matching '.github'
  warning: no previously-included files matching '*' found under directory 'ci'
  warning: no previously-included files matching '*' found under directory 'other'
  warning: no previously-included files matching '*' found under directory '.github'
  warning: no previously-included files found matching 'pavement.py'
  warning: no previously-included files found matching '*.yml'
  warning: no previously-included files found matching '*.yaml'
  warning: no previously-included files matching '__pycache__' found under directory '*'
  warning: no previously-included files matching '*.py[co]' found under directory '*'
  warning: no previously-included files found matching '.coveragerc'
  warning: no previously-included files found matching '.mailmap'
  warning: no previously-included files found matching 'rever.xsh'
  no previously-included directories found matching 'news'
  adding license file 'LICENSE'
  adding license file 'AUTHORS'
  writing manifest file '/tmp/pip-pip-egg-info-xhsz_oki/h5py.egg-info/SOURCES.txt'
  Preparing metadata (setup.py) ... done
Collecting grpcio>=1.8.6 (from tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for grpcio>=1.8.6 from https://files.pythonhosted.org/packages/20/ae/627b64425ce31355824a3f38416ab36e0476895317b1cfe056f9d46c4972/grpcio-1.57.0-cp38-cp38-manylinux_2_17_aarch64.whl.metadata
  Using cached grpcio-1.57.0-cp38-cp38-manylinux_2_17_aarch64.whl.metadata (4.0 kB)
Requirement already satisfied: wheel>=0.26 in /usr/lib/python3/dist-packages (from tensorflow==1.15.5+nv23.01) (0.34.2)
Requirement already satisfied: numpy>=1.20.0 in /usr/local/lib/python3.8/dist-packages (from tensorflow==1.15.5+nv23.01) (1.22.0)
Collecting markdown>=2.6.8 (from tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for markdown>=2.6.8 from https://files.pythonhosted.org/packages/1a/b5/228c1cdcfe138f1a8e01ab1b54284c8b83735476cb22b6ba251656ed13ad/Markdown-3.4.4-py3-none-any.whl.metadata
  Using cached Markdown-3.4.4-py3-none-any.whl.metadata (6.9 kB)
Requirement already satisfied: setuptools>=41.0.0 in /usr/local/lib/python3.8/dist-packages (from tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01) (65.5.0)
Collecting werkzeug>=0.11.15 (from tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for werkzeug>=0.11.15 from https://files.pythonhosted.org/packages/9b/59/a7c32e3d8d0e546a206e0552a2c04444544f15c1da4a01df8938d20c6ffc/werkzeug-2.3.7-py3-none-any.whl.metadata
  Using cached werkzeug-2.3.7-py3-none-any.whl.metadata (4.1 kB)
Collecting importlib-metadata>=4.4 (from markdown>=2.6.8->tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for importlib-metadata>=4.4 from https://files.pythonhosted.org/packages/cc/37/db7ba97e676af155f5fcb1a35466f446eadc9104e25b83366e8088c9c926/importlib_metadata-6.8.0-py3-none-any.whl.metadata
  Using cached importlib_metadata-6.8.0-py3-none-any.whl.metadata (5.1 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=0.11.15->tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for MarkupSafe>=2.1.1 from https://files.pythonhosted.org/packages/8d/66/4a46c7f1402e0377a8b220fd4b53cc4f1b2337ab0d97f06e23acd1f579d1/MarkupSafe-2.1.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata
  Using cached MarkupSafe-2.1.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (3.0 kB)
Collecting zipp>=0.5 (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for zipp>=0.5 from https://files.pythonhosted.org/packages/8c/08/d3006317aefe25ea79d3b76c9650afabaf6d63d1c8443b236e7405447503/zipp-3.16.2-py3-none-any.whl.metadata
  Using cached zipp-3.16.2-py3-none-any.whl.metadata (3.7 kB)
Using cached grpcio-1.57.0-cp38-cp38-manylinux_2_17_aarch64.whl (4.8 MB)
Using cached Markdown-3.4.4-py3-none-any.whl (94 kB)
Using cached werkzeug-2.3.7-py3-none-any.whl (242 kB)
Using cached importlib_metadata-6.8.0-py3-none-any.whl (22 kB)
Using cached MarkupSafe-2.1.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (26 kB)
Using cached zipp-3.16.2-py3-none-any.whl (7.2 kB)
Building wheels for collected packages: h5py
  Running command python setup.py bdist_wheel
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-aarch64-cpython-38
  creating build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/version.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/ipy_completer.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/highlevel.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py
  creating build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/compat.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/dataset.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/base.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/vds.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/datatype.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/attrs.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/selections.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/group.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/dims.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/files.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/filters.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/selections2.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  creating build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_deprecation.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_file.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dimension_scales.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_filters.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/common.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5pl.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_group.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_datatype.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_file2.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_base.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dtype.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_objects.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dataset.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_attrs_data.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_selections.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_threads.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5p.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_file_image.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_attribute_create.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_completions.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5t.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_slicing.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_attrs.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5f.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  creating build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  running build_ext
  Loading library to get version: /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so
  Autodetected HDF5 1.10.4
  ********************************************************************************
                         Summary of the h5py configuration

      Path to HDF5: None
      HDF5 Version: '1.10.4'
       MPI Enabled: False
  Rebuild Required: True

  ********************************************************************************
  Executing api_gen rebuild of defs
  Executing cythonize()
  [ 1/23] Cythonizing /tmp/pip-install-g16hq_w6/h5py_0a8692ab49b44833b48657c74c70266c/h5py/_conv.pyx
  warning: h5py/config.pxi:3:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:4:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:5:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:6:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:7:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:8:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:57:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:59:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:61:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:63:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:65:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:67:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:92:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:94:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:96:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:97:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:99:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:100:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:102:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:168:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:204:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:232:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:234:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:236:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:238:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:240:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:242:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:248:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:250:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:252:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:254:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:256:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:258:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:290:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:292:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:294:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:296:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:298:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:300:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:302:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:304:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:306:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:340:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:342:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:3:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:4:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:5:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:6:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:7:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:8:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_hdf5.pxd:55:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_hdf5.pxd:128:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_hdf5.pxd:197:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  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/config.pxi:3:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:4:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:5:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:6:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:7:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:8:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_ext.pxd:14:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_ext.pxd:35:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_ext.pxd:71:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  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:
  ------------------------------------------------------------
  ...
  # License:  Standard 3-clause BSD; see "license.txt" for full license terms
  #           and contributor agreement.

  from defs cimport *

  from _objects cimport class ObjectID
                        ^
  ------------------------------------------------------------

  h5py/h5t.pxd:12:22: Expected an identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/H5PY_OBJ.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/typewrap.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/py_create.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/TypeID.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
  cdef struct vlen_t:
      size_t len
      void* ptr

  cdef int conv_vlen2ndarray(void* ipt, void* opt, np.dtype elem_dtype,
          TypeID intype, TypeID outtype) except -1:
          ^
  ------------------------------------------------------------

  h5py/_conv.pyx:680:8: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
  cdef struct vlen_t:
      size_t len
      void* ptr

  cdef int conv_vlen2ndarray(void* ipt, void* opt, np.dtype elem_dtype,
          TypeID intype, TypeID outtype) except -1:
                         ^
  ------------------------------------------------------------

  h5py/_conv.pyx:680:23: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...

      return 0


  cdef int conv_ndarray2vlen(void* ipt, void* opt,
          TypeID intype, TypeID outtype) except -1:
          ^
  ------------------------------------------------------------

  h5py/_conv.pyx:788:8: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...

      return 0


  cdef int conv_ndarray2vlen(void* ipt, void* opt,
          TypeID intype, TypeID outtype) except -1:
                         ^
  ------------------------------------------------------------

  h5py/_conv.pyx:788:23: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:620:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
      cdef TypeID outtype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:621:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:718:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
      cdef TypeID outtype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:719:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
          pass

      elif command == H5T_CONV_CONV:

          # need to pass element dtype to converter
          supertype = typewrap(H5Tget_super(src_id))
                      ^
  ------------------------------------------------------------

  h5py/_conv.pyx:640:20: 'typewrap' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      elif command == H5T_CONV_CONV:

          # need to pass element dtype to converter
          supertype = typewrap(H5Tget_super(src_id))
          dt = supertype.dtype
          outtype = py_create(dt)
                    ^
  ------------------------------------------------------------

  h5py/_conv.pyx:642:18: 'py_create' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      cdef char* buf = <char*>buf_i

      if command == H5T_CONV_INIT:

          cdata[0].need_bkg = H5T_BKG_NO
          if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
                                  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:730:32: 'H5PY_OBJ' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      if command == H5T_CONV_INIT:

          cdata[0].need_bkg = H5T_BKG_NO
          if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
              return -2
          supertype = typewrap(H5Tget_super(dst_id))
                      ^
  ------------------------------------------------------------

  h5py/_conv.pyx:732:20: 'typewrap' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
          if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
              return -2
          supertype = typewrap(H5Tget_super(dst_id))
          for i from 0 <= i < nl:
              memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem))
              if supertype != py_create((<np.ndarray> pdata_elem).dtype, 1):
                              ^
  ------------------------------------------------------------

  h5py/_conv.pyx:735:28: 'py_create' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
          if nl == 0:
              return 0

          # need to pass element dtype to converter
          memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
          supertype = py_create((<np.ndarray> pdata_elem).dtype)
                      ^
  ------------------------------------------------------------

  h5py/_conv.pyx:753:20: 'py_create' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
              return 0

          # need to pass element dtype to converter
          memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
          supertype = py_create((<np.ndarray> pdata_elem).dtype)
          outtype = typewrap(H5Tget_super(dst_id))
                    ^
  ------------------------------------------------------------

  h5py/_conv.pyx:754:18: 'typewrap' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...

      enum = H5Tenum_create(H5T_STD_I32LE)

      vlentype = H5Tvlen_create(H5T_STD_I32LE)

      pyobj = H5PY_OBJ
              ^
  ------------------------------------------------------------

  h5py/_conv.pyx:860:12: 'H5PY_OBJ' is not a constant, variable or function identifier
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/tmp/pip-install-g16hq_w6/h5py_0a8692ab49b44833b48657c74c70266c/setup.py", line 140, in <module>
      setup(
    File "/usr/local/lib/python3.8/dist-packages/setuptools/__init__.py", line 87, in setup
      return distutils.core.setup(**attrs)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 968, in run_commands
      self.run_command(cmd)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
      cmd_obj.run()
    File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 223, in run
      self.run_command('build')
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/cmd.py", line 319, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/command/build.py", line 132, in run
      self.run_command(cmd_name)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/cmd.py", line 319, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-g16hq_w6/h5py_0a8692ab49b44833b48657c74c70266c/setup_build.py", line 207, in run
      self.extensions = cythonize(self._make_extensions(config),
    File "/usr/local/lib/python3.8/dist-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
      cythonize_one(*args)
    File "/usr/local/lib/python3.8/dist-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
      raise CompileError(None, pyx_file)
  Cython.Compiler.Errors.CompileError: /tmp/pip-install-g16hq_w6/h5py_0a8692ab49b44833b48657c74c70266c/h5py/_conv.pyx
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /usr/bin/python3 -u -c '
  exec(compile('"'"''"'"''"'"'
  # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
  #
  # - It imports setuptools before invoking setup.py, to enable projects that directly
  #   import from `distutils.core` to work with newer packaging standards.
  # - It provides a clear error message when setuptools is not installed.
  # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
  #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
  #     manifest_maker: standard file '"'"'-c'"'"' not found".
  # - It generates a shim setup.py, for handling setup.cfg-only projects.
  import os, sys, tokenize
  
  try:
      import setuptools
  except ImportError as error:
      print(
          "ERROR: Can not execute `setup.py` since setuptools is not available in "
          "the build environment.",
          file=sys.stderr,
      )
      sys.exit(1)
  
  __file__ = %r
  sys.argv[0] = __file__
  
  if os.path.exists(__file__):
      filename = __file__
      with tokenize.open(__file__) as f:
          setup_py_code = f.read()
  else:
      filename = "<auto-generated setuptools caller>"
      setup_py_code = "from setuptools import setup; setup()"
  
  exec(compile(setup_py_code, filename, "exec"))
  '"'"''"'"''"'"' % ('"'"'/tmp/pip-install-g16hq_w6/h5py_0a8692ab49b44833b48657c74c70266c/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-otppdim9
  cwd: /tmp/pip-install-g16hq_w6/h5py_0a8692ab49b44833b48657c74c70266c/
  Building wheel for h5py (setup.py) ... error
  ERROR: Failed building wheel for h5py
  Running setup.py clean for h5py
  Running command python setup.py clean
  running clean
  removing 'build/lib.linux-aarch64-cpython-38' (and everything under it)
  'build/bdist.linux-aarch64' does not exist -- can't clean it
  'build/scripts-3.8' does not exist -- can't clean it
  removing 'build'
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects

thank you

22

Hi @lucky789, can you try downgrading cython with pip3 install 'Cython<3' ? What does pip3 show Cython show for you?

23

Hi Dusty,

Thank you for the recommendation, I was able to install Cython 0.29.36 and show it, so I tried to reinstall tensorflow but I am getting similar errors not exactly the same ones but very similar output.

$ pip3 install 'Cython<3'

Defaulting to user installation because normal site-packages is not writeable
Collecting Cython<3
  Obtaining dependency information for Cython<3 from https://files.pythonhosted.org/packages/8a/03/16c1f7f497d8d437a115faece43aac2eb269094d255657ac59f4ec00c061/Cython-0.29.36-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl.metadata
  Downloading Cython-0.29.36-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl.metadata (3.1 kB)
Downloading Cython-0.29.36-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl (1.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 8.6 MB/s eta 0:00:00
DEPRECATION: distro-info 0.23ubuntu1 has a non-standard version number. pip 23.3 will enforce this behaviour change. A possible replacement is to upgrade to a newer version of distro-info or contact the author to suggest that they release a version with a conforming version number. Discussion can be found at https://github.com/pypa/pip/issues/12063
DEPRECATION: python-debian 0.1.36ubuntu1 has a non-standard version number. pip 23.3 will enforce this behaviour change. A possible replacement is to upgrade to a newer version of python-debian or contact the author to suggest that they release a version with a conforming version number. Discussion can be found at https://github.com/pypa/pip/issues/12063
Installing collected packages: Cython
  WARNING: The scripts cygdb, cython and cythonize are installed in '/home/nvidia/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed Cython-0.29.36

$ pip3 show Cython

Name: Cython
Version: 0.29.36
Summary: The Cython compiler for writing C extensions for the Python language.
Home-page: http://cython.org/
Author: Robert Bradshaw, Stefan Behnel, Dag Seljebotn, Greg Ewing, et al.
Author-email: cython-devel@python.org
License: Apache
Location: /home/nvidia/.local/lib/python3.8/site-packages
Requires: 
Required-by: 

$ sudo pip3 install --verbose --extra-index-url https://developer.download.nvidia.com/compute/redist/jp/v51 tensorflow==1.15.5+nv23.01

[sudo] password for : 
Using pip 23.2.1 from /usr/local/lib/python3.8/dist-packages/pip (python 3.8)
Looking in indexes: https://pypi.org/simple, https://developer.download.nvidia.com/compute/redist/jp/v51
Collecting tensorflow==1.15.5+nv23.01
  Using cached https://developer.download.nvidia.com/compute/redist/jp/v51/tensorflow/tensorflow-1.15.5%2Bnv23.01-cp38-cp38-linux_aarch64.whl (359.4 MB)
Collecting absl-py>=0.9.0 (from tensorflow==1.15.5+nv23.01)
  Using cached absl_py-1.4.0-py3-none-any.whl (126 kB)
Collecting astunparse==1.6.3 (from tensorflow==1.15.5+nv23.01)
  Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting astor==0.8.1 (from tensorflow==1.15.5+nv23.01)
  Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting gast==0.3.3 (from tensorflow==1.15.5+nv23.01)
  Using cached gast-0.3.3-py2.py3-none-any.whl (9.7 kB)
Collecting google-pasta>=0.1.6 (from tensorflow==1.15.5+nv23.01)
  Using cached google_pasta-0.2.0-py3-none-any.whl (57 kB)
Requirement already satisfied: keras-applications>=1.0.8 in /usr/local/lib/python3.8/dist-packages (from tensorflow==1.15.5+nv23.01) (1.0.8)
Requirement already satisfied: keras-preprocessing>=1.0.5 in /usr/local/lib/python3.8/dist-packages (from tensorflow==1.15.5+nv23.01) (1.1.2)
Collecting opt-einsum>=2.3.2 (from tensorflow==1.15.5+nv23.01)
  Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)
Requirement already satisfied: six>=1.10.0 in /usr/lib/python3/dist-packages (from tensorflow==1.15.5+nv23.01) (1.14.0)
Collecting protobuf<4.0.0,>=3.6.1 (from tensorflow==1.15.5+nv23.01)
  Using cached protobuf-3.20.3-cp38-cp38-manylinux2014_aarch64.whl (918 kB)
Collecting tensorboard<1.16.0,>=1.15.0 (from tensorflow==1.15.5+nv23.01)
  Using cached tensorboard-1.15.0-py3-none-any.whl (3.8 MB)
Collecting tensorflow-estimator==1.15.1 (from tensorflow==1.15.5+nv23.01)
  Using cached tensorflow_estimator-1.15.1-py2.py3-none-any.whl (503 kB)
Collecting termcolor>=1.1.0 (from tensorflow==1.15.5+nv23.01)
  Using cached termcolor-2.3.0-py3-none-any.whl (6.9 kB)
Collecting wrapt>=1.11.1 (from tensorflow==1.15.5+nv23.01)
  Using cached wrapt-1.15.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (81 kB)
Collecting h5py==2.10.0 (from tensorflow==1.15.5+nv23.01)
  Using cached h5py-2.10.0.tar.gz (301 kB)
  Running command python setup.py egg_info
  running egg_info
  creating /tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info
  writing /tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info/PKG-INFO
  writing dependency_links to /tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info/dependency_links.txt
  writing requirements to /tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info/requires.txt
  writing top-level names to /tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info/top_level.txt
  writing manifest file '/tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info/SOURCES.txt'
  reading manifest file '/tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  no previously-included directories found matching 'docs/_build'
  no previously-included directories found matching 'docs_api/_build'
  warning: no previously-included files found matching 'h5py/config.pxi'
  warning: no previously-included files found matching 'h5py/defs.pxd'
  warning: no previously-included files found matching 'h5py/defs.pyx'
  warning: no previously-included files matching '.DS_Store' found under directory '*'
  warning: no previously-included files found matching 'ci'
  warning: no previously-included files found matching 'other'
  warning: no previously-included files found matching '.github'
  warning: no previously-included files matching '*' found under directory 'ci'
  warning: no previously-included files matching '*' found under directory 'other'
  warning: no previously-included files matching '*' found under directory '.github'
  warning: no previously-included files found matching 'pavement.py'
  warning: no previously-included files found matching '*.yml'
  warning: no previously-included files found matching '*.yaml'
  warning: no previously-included files matching '__pycache__' found under directory '*'
  warning: no previously-included files matching '*.py[co]' found under directory '*'
  warning: no previously-included files found matching '.coveragerc'
  warning: no previously-included files found matching '.mailmap'
  warning: no previously-included files found matching 'rever.xsh'
  no previously-included directories found matching 'news'
  adding license file 'LICENSE'
  adding license file 'AUTHORS'
  writing manifest file '/tmp/pip-pip-egg-info-10tcegrw/h5py.egg-info/SOURCES.txt'
  Preparing metadata (setup.py) ... done
Collecting grpcio>=1.8.6 (from tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for grpcio>=1.8.6 from https://files.pythonhosted.org/packages/20/ae/627b64425ce31355824a3f38416ab36e0476895317b1cfe056f9d46c4972/grpcio-1.57.0-cp38-cp38-manylinux_2_17_aarch64.whl.metadata
  Using cached grpcio-1.57.0-cp38-cp38-manylinux_2_17_aarch64.whl.metadata (4.0 kB)
Requirement already satisfied: wheel>=0.26 in /usr/lib/python3/dist-packages (from tensorflow==1.15.5+nv23.01) (0.34.2)
Requirement already satisfied: numpy>=1.20.0 in /usr/local/lib/python3.8/dist-packages (from tensorflow==1.15.5+nv23.01) (1.22.0)
Collecting markdown>=2.6.8 (from tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for markdown>=2.6.8 from https://files.pythonhosted.org/packages/1a/b5/228c1cdcfe138f1a8e01ab1b54284c8b83735476cb22b6ba251656ed13ad/Markdown-3.4.4-py3-none-any.whl.metadata
  Using cached Markdown-3.4.4-py3-none-any.whl.metadata (6.9 kB)
Requirement already satisfied: setuptools>=41.0.0 in /usr/local/lib/python3.8/dist-packages (from tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01) (65.5.0)
Collecting werkzeug>=0.11.15 (from tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for werkzeug>=0.11.15 from https://files.pythonhosted.org/packages/9b/59/a7c32e3d8d0e546a206e0552a2c04444544f15c1da4a01df8938d20c6ffc/werkzeug-2.3.7-py3-none-any.whl.metadata
  Using cached werkzeug-2.3.7-py3-none-any.whl.metadata (4.1 kB)
Collecting importlib-metadata>=4.4 (from markdown>=2.6.8->tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for importlib-metadata>=4.4 from https://files.pythonhosted.org/packages/cc/37/db7ba97e676af155f5fcb1a35466f446eadc9104e25b83366e8088c9c926/importlib_metadata-6.8.0-py3-none-any.whl.metadata
  Using cached importlib_metadata-6.8.0-py3-none-any.whl.metadata (5.1 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=0.11.15->tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for MarkupSafe>=2.1.1 from https://files.pythonhosted.org/packages/8d/66/4a46c7f1402e0377a8b220fd4b53cc4f1b2337ab0d97f06e23acd1f579d1/MarkupSafe-2.1.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata
  Using cached MarkupSafe-2.1.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (3.0 kB)
Collecting zipp>=0.5 (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard<1.16.0,>=1.15.0->tensorflow==1.15.5+nv23.01)
  Obtaining dependency information for zipp>=0.5 from https://files.pythonhosted.org/packages/8c/08/d3006317aefe25ea79d3b76c9650afabaf6d63d1c8443b236e7405447503/zipp-3.16.2-py3-none-any.whl.metadata
  Using cached zipp-3.16.2-py3-none-any.whl.metadata (3.7 kB)
Using cached grpcio-1.57.0-cp38-cp38-manylinux_2_17_aarch64.whl (4.8 MB)
Using cached Markdown-3.4.4-py3-none-any.whl (94 kB)
Using cached werkzeug-2.3.7-py3-none-any.whl (242 kB)
Using cached importlib_metadata-6.8.0-py3-none-any.whl (22 kB)
Using cached MarkupSafe-2.1.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (26 kB)
Using cached zipp-3.16.2-py3-none-any.whl (7.2 kB)
Building wheels for collected packages: h5py
  Running command python setup.py bdist_wheel
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-aarch64-cpython-38
  creating build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/version.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/ipy_completer.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/highlevel.py -> build/lib.linux-aarch64-cpython-38/h5py
  copying h5py/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py
  creating build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/compat.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/dataset.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/base.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/vds.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/datatype.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/attrs.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/selections.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/group.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/dims.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/files.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/filters.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  copying h5py/_hl/selections2.py -> build/lib.linux-aarch64-cpython-38/h5py/_hl
  creating build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_deprecation.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_file.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dimension_scales.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_filters.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/common.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5pl.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_group.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_datatype.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_file2.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_base.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dtype.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_objects.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dataset.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_attrs_data.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_selections.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_threads.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5p.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_file_image.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_attribute_create.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_completions.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5t.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_slicing.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_attrs.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  copying h5py/tests/test_h5f.py -> build/lib.linux-aarch64-cpython-38/h5py/tests
  creating build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  copying h5py/tests/test_vds/__init__.py -> build/lib.linux-aarch64-cpython-38/h5py/tests/test_vds
  running build_ext
  Loading library to get version: /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so
  Autodetected HDF5 1.10.4
  ********************************************************************************
                         Summary of the h5py configuration

      Path to HDF5: None
      HDF5 Version: '1.10.4'
       MPI Enabled: False
  Rebuild Required: True

  ********************************************************************************
  Executing api_gen rebuild of defs
  Executing cythonize()
  [ 1/23] Cythonizing /tmp/pip-install-pom1dbtr/h5py_1410f956ca70420b9396e490fc767c99/h5py/_conv.pyx
  warning: h5py/config.pxi:3:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:4:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:5:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:6:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:7:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:8:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:57:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:59:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:61:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:63:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:65:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:67:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:92:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:94:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:96:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:97:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:99:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:100:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:102:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:168:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:204:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:232:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:234:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:236:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:238:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:240:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:242:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:248:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:250:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:252:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:254:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:256:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:258:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:290:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:292:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:294:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:296:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:298:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:300:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:302:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:304:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:306:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:340:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/defs.pxd:342:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:3:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:4:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:5:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:6:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:7:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:8:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_hdf5.pxd:55:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_hdf5.pxd:128:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_hdf5.pxd:197:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  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/config.pxi:3:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:4:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:5:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:6:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:7:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/config.pxi:8:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_ext.pxd:14:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_ext.pxd:35:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  warning: h5py/api_types_ext.pxd:71:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
  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:
  ------------------------------------------------------------
  ...
  # License:  Standard 3-clause BSD; see "license.txt" for full license terms
  #           and contributor agreement.

  from defs cimport *

  from _objects cimport class ObjectID
                        ^
  ------------------------------------------------------------

  h5py/h5t.pxd:12:22: Expected an identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/H5PY_OBJ.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/typewrap.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/py_create.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      Low-level type-conversion routines.
  """

  from h5 import get_config
  from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
  from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:18:0: 'h5py/h5t/TypeID.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
  cdef struct vlen_t:
      size_t len
      void* ptr

  cdef int conv_vlen2ndarray(void* ipt, void* opt, np.dtype elem_dtype,
          TypeID intype, TypeID outtype) except -1:
          ^
  ------------------------------------------------------------

  h5py/_conv.pyx:680:8: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
  cdef struct vlen_t:
      size_t len
      void* ptr

  cdef int conv_vlen2ndarray(void* ipt, void* opt, np.dtype elem_dtype,
          TypeID intype, TypeID outtype) except -1:
                         ^
  ------------------------------------------------------------

  h5py/_conv.pyx:680:23: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...

      return 0


  cdef int conv_ndarray2vlen(void* ipt, void* opt,
          TypeID intype, TypeID outtype) except -1:
          ^
  ------------------------------------------------------------

  h5py/_conv.pyx:788:8: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...

      return 0


  cdef int conv_ndarray2vlen(void* ipt, void* opt,
          TypeID intype, TypeID outtype) except -1:
                         ^
  ------------------------------------------------------------

  h5py/_conv.pyx:788:23: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:620:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
      cdef TypeID outtype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:621:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      size_t nl, size_t buf_stride, size_t bkg_stride, void *buf_i,
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:718:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
                      void *bkg_i, hid_t dxpl) except -1:

      cdef int command = cdata[0].command
      cdef size_t src_size, dst_size
      cdef TypeID supertype
      cdef TypeID outtype
           ^
  ------------------------------------------------------------

  h5py/_conv.pyx:719:9: 'TypeID' is not a type identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
          pass

      elif command == H5T_CONV_CONV:

          # need to pass element dtype to converter
          supertype = typewrap(H5Tget_super(src_id))
                      ^
  ------------------------------------------------------------

  h5py/_conv.pyx:640:20: 'typewrap' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      elif command == H5T_CONV_CONV:

          # need to pass element dtype to converter
          supertype = typewrap(H5Tget_super(src_id))
          dt = supertype.dtype
          outtype = py_create(dt)
                    ^
  ------------------------------------------------------------

  h5py/_conv.pyx:642:18: 'py_create' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      cdef char* buf = <char*>buf_i

      if command == H5T_CONV_INIT:

          cdata[0].need_bkg = H5T_BKG_NO
          if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
                                  ^
  ------------------------------------------------------------

  h5py/_conv.pyx:730:32: 'H5PY_OBJ' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      if command == H5T_CONV_INIT:

          cdata[0].need_bkg = H5T_BKG_NO
          if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
              return -2
          supertype = typewrap(H5Tget_super(dst_id))
                      ^
  ------------------------------------------------------------

  h5py/_conv.pyx:732:20: 'typewrap' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
          if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
              return -2
          supertype = typewrap(H5Tget_super(dst_id))
          for i from 0 <= i < nl:
              memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem))
              if supertype != py_create((<np.ndarray> pdata_elem).dtype, 1):
                              ^
  ------------------------------------------------------------

  h5py/_conv.pyx:735:28: 'py_create' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
          if nl == 0:
              return 0

          # need to pass element dtype to converter
          memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
          supertype = py_create((<np.ndarray> pdata_elem).dtype)
                      ^
  ------------------------------------------------------------

  h5py/_conv.pyx:753:20: 'py_create' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
              return 0

          # need to pass element dtype to converter
          memcpy(&pdata_elem, pdata, sizeof(pdata_elem))
          supertype = py_create((<np.ndarray> pdata_elem).dtype)
          outtype = typewrap(H5Tget_super(dst_id))
                    ^
  ------------------------------------------------------------

  h5py/_conv.pyx:754:18: 'typewrap' is not a constant, variable or function identifier

  Error compiling Cython file:
  ------------------------------------------------------------
  ...

      enum = H5Tenum_create(H5T_STD_I32LE)

      vlentype = H5Tvlen_create(H5T_STD_I32LE)

      pyobj = H5PY_OBJ
              ^
  ------------------------------------------------------------

  h5py/_conv.pyx:860:12: 'H5PY_OBJ' is not a constant, variable or function identifier
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/tmp/pip-install-pom1dbtr/h5py_1410f956ca70420b9396e490fc767c99/setup.py", line 140, in <module>
      setup(
    File "/usr/local/lib/python3.8/dist-packages/setuptools/__init__.py", line 87, in setup
      return distutils.core.setup(**attrs)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 968, in run_commands
      self.run_command(cmd)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
      cmd_obj.run()
    File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 223, in run
      self.run_command('build')
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/cmd.py", line 319, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/command/build.py", line 132, in run
      self.run_command(cmd_name)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/cmd.py", line 319, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.8/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-pom1dbtr/h5py_1410f956ca70420b9396e490fc767c99/setup_build.py", line 207, in run
      self.extensions = cythonize(self._make_extensions(config),
    File "/usr/local/lib/python3.8/dist-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
      cythonize_one(*args)
    File "/usr/local/lib/python3.8/dist-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
      raise CompileError(None, pyx_file)
  Cython.Compiler.Errors.CompileError: /tmp/pip-install-pom1dbtr/h5py_1410f956ca70420b9396e490fc767c99/h5py/_conv.pyx
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /usr/bin/python3 -u -c '
  exec(compile('"'"''"'"''"'"'
  # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
  #
  # - It imports setuptools before invoking setup.py, to enable projects that directly
  #   import from `distutils.core` to work with newer packaging standards.
  # - It provides a clear error message when setuptools is not installed.
  # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
  #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
  #     manifest_maker: standard file '"'"'-c'"'"' not found".
  # - It generates a shim setup.py, for handling setup.cfg-only projects.
  import os, sys, tokenize
  
  try:
      import setuptools
  except ImportError as error:
      print(
          "ERROR: Can not execute `setup.py` since setuptools is not available in "
          "the build environment.",
          file=sys.stderr,
      )
      sys.exit(1)
  
  __file__ = %r
  sys.argv[0] = __file__
  
  if os.path.exists(__file__):
      filename = __file__
      with tokenize.open(__file__) as f:
          setup_py_code = f.read()
  else:
      filename = "<auto-generated setuptools caller>"
      setup_py_code = "from setuptools import setup; setup()"
  
  exec(compile(setup_py_code, filename, "exec"))
  '"'"''"'"''"'"' % ('"'"'/tmp/pip-install-pom1dbtr/h5py_1410f956ca70420b9396e490fc767c99/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-yg66vsxj
  cwd: /tmp/pip-install-pom1dbtr/h5py_1410f956ca70420b9396e490fc767c99/
  Building wheel for h5py (setup.py) ... error
  ERROR: Failed building wheel for h5py
  Running setup.py clean for h5py
  Running command python setup.py clean
  running clean
  removing 'build/lib.linux-aarch64-cpython-38' (and everything under it)
  'build/bdist.linux-aarch64' does not exist -- can't clean it
  'build/scripts-3.8' does not exist -- can't clean it
  removing 'build'
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects

Thank you for the prompt response!

24

I am having a similar issue for a week now… Very frustrating… I have basic question. What should I set the image to when building using the help here? I have tried both of these:

export JETBOT_BASE_IMAGE=nvcr.io/nvidia/l4t-pytorch:r32.7.1-pth1.10-py3
export JETBOT_BASE_IMAGE=nvcr.io/nvidia/l4t-pytorch:r32.7.4-pth1.6-py3

Seems that this will not work for Python V3.10 or V3.11? Python 3.11 is much faster compiling and running so not sure why we are stuck here on Python 3.8, 3.6.9 and 3.6.15 except for the wish to make it work. I saw that someone on another post got this to work on Python 3.7.7.

In any case I would like to get it to build, so what are the versions of the packages that I should use (for each I would say would be helpful) and how to setup the build correctly?

My stack trace seems similar to lucky789 above, but I am using python 3.6.15… and they are using Python 3.8

I think it would help if someone could give the package versions that work with the Dockerfile that is in the latest jetbot at Master i.e. jetbot Version 0.4.3? The version numbers probably should be fixed in there so that when somoene updates a version of the pypy wheels or other repos outside software, that those of us actually building wont get failures…? Just my 2 cents… Please someone list the packages that worked… We know that Cython<3 works and the latest is 0.29.35 so picking that directly should work. We also already know numpy 1.19.4 is working? or do we? We also saw that in this post protobuf<4 worked before but it may have changed since that as I am using protobuf-3.19.6-py2.py3-none-any.whl (162 kB) So, knowing all of the versions exactly that work for the following would help:

python
tensorflow
h5py
numpy
Cython
gast
opencv
gstreamer
jupyter
jupyter lab
pyzmq
torch2trt

etc.
(others at latest)

Currently I am using
Python 3.6
ARG TENSORFLOW_WHL=tensorflow-1.15.2+nv-cp36-cp36m-linux_aarch64.whl
h5py 3.1.0 with the cherry pick in above post by aastalll
numpy 1.19.4
gast 0.2.1
(others at latest)

Here is my error log:

Step 24/51 : RUN pip3 install -U numpy==1.19.4 future mock keras_preprocessing keras_applications gast==0.2.1 protobuf pybind11 packaging
—> Running in b9f9f541625b
Collecting numpy==1.19.4
Downloading numpy-1.19.4-cp36-cp36m-manylinux2014_aarch64.whl (12.2 MB)
Collecting future
Downloading future-0.18.3.tar.gz (840 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status ‘done’
Collecting mock
Downloading mock-5.1.0-py3-none-any.whl (30 kB)
Collecting keras_preprocessing
Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
Collecting keras_applications
Downloading Keras_Applications-1.0.8-py3-none-any.whl (50 kB)
Collecting gast==0.2.1
Downloading gast-0.2.1.tar.gz (10 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status ‘done’
Collecting protobuf
Downloading protobuf-3.19.6-py2.py3-none-any.whl (162 kB)
Collecting pybind11
Downloading pybind11-2.11.1-py3-none-any.whl (227 kB)
Collecting packaging
Downloading packaging-21.3-py3-none-any.whl (40 kB)
Collecting six>=1.9.0
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting h5py
Downloading h5py-3.1.0.tar.gz (371 kB)
Installing build dependencies: started
Installing build dependencies: finished with status ‘done’
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status ‘done’
Installing backend dependencies: started
Installing backend dependencies: still running…
Installing backend dependencies: still running…
Installing backend dependencies: still running…
Installing backend dependencies: still running…
Installing backend dependencies: finished with status ‘done’
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status ‘done’
Collecting pyparsing!=3.0.5,>=2.0.2
Downloading pyparsing-3.1.1-py3-none-any.whl (103 kB)
Collecting cached-property
Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB)
Building wheels for collected packages: gast, future, h5py
Building wheel for gast (setup.py): started
Building wheel for gast (setup.py): finished with status ‘done’
Created wheel for gast: filename=gast-0.2.1-py3-none-any.whl size=7457 sha256=49305cdafff217d422665d6d3fb317af76d5e556125cc84ce0c29891f5344cb0
Stored in directory: /root/.cache/pip/wheels/5a/de/13/ce88a752efbdba27fa15e3047f3445128e76d6c1a1197a9d5c
Building wheel for future (setup.py): started
Building wheel for future (setup.py): finished with status ‘done’
Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492025 sha256=5a9ceb8275b7bb2d3ca1d327349da3eb877978dd2a552cd33b74591374f3f47e
Stored in directory: /root/.cache/pip/wheels/63/f1/0c/e56d12b3804345ce5ba34279cbfe583ecafdd1401551457330
Building wheel for h5py (pyproject.toml): started
Building wheel for h5py (pyproject.toml): finished with status ‘error’
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/python3.6 /usr/local/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpu5pgouwk
cwd: /tmp/pip-install-ts963com/h5py_0b6290ac88c44264bd92718320fe7eb2
Complete output (478 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/ipy_completer.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/version.py → build/lib.linux-aarch64-3.6/h5py
copying h5py/h5py_warnings.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/base.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/dataset.py → build/lib.linux-aarch64-3.6/h5py/_hl
copying h5py/_hl/attrs.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/filters.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/init.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/files.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/dims.py → build/lib.linux-aarch64-3.6/h5py/_hl
creating build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_errors.py → 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_objects.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_attribute_create.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_dataset_getitem.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/conftest.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_h5f.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_completions.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_file_image.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/common.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/test_filters.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_dimension_scales.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_h5t.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_attrs_data.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/test_h5p.py → build/lib.linux-aarch64-3.6/h5py/tests
copying h5py/tests/test_big_endian_file.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_selections.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_h5pl.py → build/lib.linux-aarch64-3.6/h5py/tests
creating build/lib.linux-aarch64-3.6/h5py/tests/data_files
copying h5py/tests/data_files/init.py → build/lib.linux-aarch64-3.6/h5py/tests/data_files
creating 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_virtual_source.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
copying h5py/tests/data_files/vlen_string_dset.h5 → build/lib.linux-aarch64-3.6/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_dset_utc.h5 → build/lib.linux-aarch64-3.6/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_s390x.h5 → build/lib.linux-aarch64-3.6/h5py/tests/data_files
running build_ext
warning: h5py/config.pxi:3:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:4:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:5:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:6:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:7:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:8:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:9:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:10:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:15:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:62:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:64:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:66:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:68:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:70:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:72:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:74:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:76:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:78:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:102:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:104:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:106:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:107:4: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:109:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:110:4: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:112:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:176:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:193:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:195:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:217:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:245:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:247:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:249:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:251:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:253:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:255:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:261:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:263:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:265:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:267:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:269:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:271:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:273:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:275:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:309:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:311:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:313:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:315:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:317:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:319:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:321:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:323:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:325:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:359:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/defs.pxd:361:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:3:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:4:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:5:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:6:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:7:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:8:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:9:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:10:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_hdf5.pxd:48:2: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_hdf5.pxd:64:2: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_hdf5.pxd:143:2: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_hdf5.pxd:148:2: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_hdf5.pxd:156:2: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_hdf5.pxd:188:2: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_hdf5.pxd:315:2: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:3:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:4:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:5:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:6:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:7:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:8:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:9:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:10:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_ext.pxd:14:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_ext.pxd:25:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/api_types_ext.pxd:52:4: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:3:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:4:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:5:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:6:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:7:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:8:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:9:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:10:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/_conv.pyx:160:8: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/_conv.pyx:421:8: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:3:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:4:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:5:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:6:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:7:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:8:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:9:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/config.pxi:10:0: The ‘DEF’ statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub
warning: h5py/h5r.pxd:17:0: The ‘IF’ statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See Deprecate conditional compilation · Issue #4310 · cython/cython · GitHub

Error compiling Cython file:

…

License: Standard 3-clause BSD; see “license.txt” for full license terms

and contributor agreement.

from .defs cimport *

from ._objects cimport class ObjectID
^

h5py/h5t.pxd:13:23: Expected an identifier

Error compiling Cython file:

…

from logging import getLogger

from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^

h5py/_conv.pyx:21:0: ‘h5py/h5t/H5PY_OBJ.pxd’ not found

Error compiling Cython file:

…

from logging import getLogger

from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^

h5py/_conv.pyx:21:0: ‘h5py/h5t/typewrap.pxd’ not found

Error compiling Cython file:

…

from logging import getLogger

from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^

h5py/_conv.pyx:21:0: ‘h5py/h5t/py_create.pxd’ not found

Error compiling Cython file:

…

from logging import getLogger

from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^

h5py/_conv.pyx:21:0: ‘h5py/h5t/TypeID.pxd’ not found

Error compiling Cython file:

…

from logging import getLogger

from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^

h5py/_conv.pyx:21:0: ‘h5py/h5t/H5PY_PYTHON_OPAQUE_TAG.pxd’ not found

Error compiling Cython file:

…
void* ptr

cdef int conv_vlen2ndarray(void* ipt,
void* opt,
cnp.dtype elem_dtype,
TypeID intype,
^

h5py/_conv.pyx:686:27: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…

cdef int conv_vlen2ndarray(void* ipt,
void* opt,
cnp.dtype elem_dtype,
TypeID intype,
TypeID outtype) except -1:
^

h5py/_conv.pyx:687:27: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…
return 0

cdef int conv_ndarray2vlen(void* ipt,
void* opt,
TypeID intype,
^

h5py/_conv.pyx:809:27: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…

cdef int conv_ndarray2vlen(void* ipt,
void* opt,
TypeID intype,
TypeID outtype) except -1:
^

h5py/_conv.pyx:810:27: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…
:return: error-code
“”"
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
^

h5py/_conv.pyx:628:8: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…
“”"
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
TypeID outtype
^

h5py/_conv.pyx:629:8: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…
void *bkg_i,
hid_t dxpl) except -1 with gil:
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
^

h5py/_conv.pyx:741:8: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…
hid_t dxpl) except -1 with gil:
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
TypeID outtype
^

h5py/_conv.pyx:742:8: ‘TypeID’ is not a type identifier

Error compiling Cython file:

…
cdef char* ctag = NULL
try:
if H5Tget_class(obj) == H5T_OPAQUE:
ctag = H5Tget_tag(obj)
if ctag != NULL:
if strcmp(ctag, H5PY_PYTHON_OPAQUE_TAG) == 0:
^

h5py/_conv.pyx:156:32: undeclared name not builtin: H5PY_PYTHON_OPAQUE_TAG

Error compiling Cython file:

…
elif command == H5T_CONV_FREE:
pass

  elif command == H5T_CONV_CONV:
      # need to pass element dtype to converter
      supertype = typewrap(H5Tget_super(src_id))
                  ^

h5py/_conv.pyx:644:20: undeclared name not builtin: typewrap

Error compiling Cython file:

…

  elif command == H5T_CONV_CONV:
      # need to pass element dtype to converter
      supertype = typewrap(H5Tget_super(src_id))
      dt = supertype.dtype
      outtype = py_create(dt)
                ^

h5py/_conv.pyx:646:18: undeclared name not builtin: py_create

Error compiling Cython file:

…
PyObject pdata_elem
char buf = <char*>buf_i

  if command == H5T_CONV_INIT:
      cdata[0].need_bkg = H5T_BKG_NO
      if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
                              ^

h5py/_conv.pyx:750:32: undeclared name not builtin: H5PY_OBJ
Loading library to get version: /usr/lib/aarch64-linux-gnu/hdf5/serial/lib/libhdf5.so

                     Summary of the h5py configuration

HDF5 include dirs: [
‘/usr/lib/aarch64-linux-gnu/hdf5/serial/include’
]
HDF5 library dirs: [
‘/usr/lib/aarch64-linux-gnu/hdf5/serial/lib’
]
HDF5 Version: (1, 10, 0)
MPI Enabled: False
Rebuild Required: True

Executing api_gen rebuild of defs
Executing cythonize()
[ 1/24] Cythonizing /tmp/pip-install-ts963com/h5py_0b6290ac88c44264bd92718320fe7eb2/h5py/_conv.pyx
Traceback (most recent call last):
File “/usr/local/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py”, line 363, in
main()
File “/usr/local/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py”, line 345, in main
json_out[‘return_val’] = hook(**hook_input[‘kwargs’])
File “/usr/local/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py”, line 262, in build_wheel
metadata_directory)
File “/tmp/pip-build-env-99_xr_f6/overlay/lib/python3.6/site-packages/setuptools/build_meta.py”, line 231, in build_wheel
wheel_directory, config_settings)
File “/tmp/pip-build-env-99_xr_f6/overlay/lib/python3.6/site-packages/setuptools/build_meta.py”, line 215, in _build_with_temp_dir
self.run_setup()
File “/tmp/pip-build-env-99_xr_f6/overlay/lib/python3.6/site-packages/setuptools/build_meta.py”, line 158, in run_setup
exec(compile(code, file, ‘exec’), locals())
File “setup.py”, line 183, in
cmdclass = CMDCLASS,
File “/tmp/pip-build-env-99_xr_f6/overlay/lib/python3.6/site-packages/setuptools/init.py”, line 153, in setup
return distutils.core.setup(**attrs)
File “/usr/local/lib/python3.6/distutils/core.py”, line 148, in setup
dist.run_commands()
File “/usr/local/lib/python3.6/distutils/dist.py”, line 955, in run_commands
self.run_command(cmd)
File “/usr/local/lib/python3.6/distutils/dist.py”, line 974, in run_command
cmd_obj.run()
File “/tmp/pip-build-env-99_xr_f6/overlay/lib/python3.6/site-packages/wheel/bdist_wheel.py”, line 299, in run
self.run_command(‘build’)
File “/usr/local/lib/python3.6/distutils/cmd.py”, line 313, in run_command
self.distribution.run_command(command)
File “/usr/local/lib/python3.6/distutils/dist.py”, line 974, in run_command
cmd_obj.run()
File “/usr/local/lib/python3.6/distutils/command/build.py”, line 135, in run
self.run_command(cmd_name)
File “/usr/local/lib/python3.6/distutils/cmd.py”, line 313, in run_command
self.distribution.run_command(command)
File “/usr/local/lib/python3.6/distutils/dist.py”, line 974, in run_command
cmd_obj.run()
File “/tmp/pip-install-ts963com/h5py_0b6290ac88c44264bd92718320fe7eb2/setup_build.py”, line 171, in run
language_level=3)
File “/tmp/pip-build-env-99_xr_f6/normal/lib/python3.6/site-packages/Cython/Build/Dependencies.py”, line 1134, in cythonize
cythonize_one(*args)
File “/tmp/pip-build-env-99_xr_f6/normal/lib/python3.6/site-packages/Cython/Build/Dependencies.py”, line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /tmp/pip-install-ts963com/h5py_0b6290ac88c44264bd92718320fe7eb2/h5py/_conv.pyx

ERROR: Failed building wheel for h5py
Successfully built gast future
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects
The command ‘/bin/sh -c pip3 install -U numpy==1.19.4 future mock keras_preprocessing keras_applications gast==0.2.1 protobuf pybind11 packaging’ returned a non-zero code: 1
: