bug/will not pip install unstructured[pdf] on gitpod

[thams]

Describe the bug
pip install unstructured[pdf] results in ERROR: Could not build wheels for onnx, which is required to install pyproject.toml-based projects

To Reproduce
% pip install unstructured[pdf]

Expected behavior
unstructured[pdf] to be installed without error.

Screenshots
Building wheels for collected packages: onnx
Building wheel for onnx (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for onnx (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [112 lines of output]
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
running bdist_wheel
running build
running build_py
running create_version
running cmake_build
Using cmake args: ['/home/linuxbrew/.linuxbrew/bin/cmake', '-DPYTHON_INCLUDE_DIR=/home/gitpod/.pyenv/versions/3.12.2/include/python3.12', '-DPYTHON_EXECUTABLE=/home/gitpod/.pyenv/versions/3.12.2/bin/python3.12', '-DBUILD_ONNX_PYTHON=ON', '-DCMAKE_EXPORT_COMPILE_COMMANDS=ON', '-DONNX_NAMESPACE=onnx', '-DPY_EXT_SUFFIX=.cpython-312-x86_64-linux-gnu.so', '-DCMAKE_BUILD_TYPE=Release', '-DONNX_ML=1', '/tmp/pip-install-vdhok58s/onnx_5f1b4c51f66549599449a17a03800247']
CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
  
  
  -- The C compiler identification is GNU 11.4.0
  -- The CXX compiler identification is GNU 11.4.0
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working C compiler: /usr/bin/cc - skipped
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  CMake Warning (dev) at CMakeLists.txt:119 (find_package):
    Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
    are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
    the cmake_policy command to set the policy and suppress this warning.
  
  This warning is for project developers.  Use -Wno-dev to suppress it.
  
  -- Found PythonInterp: /home/gitpod/.pyenv/versions/3.12.2/bin/python3.12 (found version "3.12.2")
  CMake Warning (dev) at CMakeLists.txt:121 (find_package):
    Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
    are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
    the cmake_policy command to set the policy and suppress this warning.
  
  This warning is for project developers.  Use -Wno-dev to suppress it.
  
  -- Found PythonLibs: /home/gitpod/.pyenv/versions/3.12.2/lib/libpython3.12.so (found version "3.12.2")
  Generated: /tmp/pip-install-vdhok58s/onnx_5f1b4c51f66549599449a17a03800247/.setuptools-cmake-build/onnx/onnx-ml.proto
  CMake Error at CMakeLists.txt:303 (message):
    Protobuf compiler not found
  Call Stack (most recent call first):
    CMakeLists.txt:334 (relative_protobuf_generate_cpp)
  
  
  -- Configuring incomplete, errors occurred!
  Traceback (most recent call last):
    File "/home/gitpod/.pyenv/versions/3.12.2/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/home/gitpod/.pyenv/versions/3.12.2/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/gitpod/.pyenv/versions/3.12.2/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 410, in build_wheel
      return self._build_with_temp_dir(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 395, in _build_with_temp_dir
      self.run_setup()
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 487, in run_setup
      super().run_setup(setup_script=setup_script)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 311, in run_setup
      exec(code, locals())
    File "<string>", line 342, in <module>
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 104, in setup
      return distutils.core.setup(**attrs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
             ^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 967, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-e_rbr27s/normal/lib/python3.12/site-packages/wheel/bdist_wheel.py", line 368, in run
      self.run_command("build")
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 967, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/command/build.py", line 131, in run
      self.run_command(cmd_name)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 967, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "<string>", line 236, in run
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 967, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-e_rbr27s/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "<string>", line 222, in run
    File "/home/gitpod/.pyenv/versions/3.12.2/lib/python3.12/subprocess.py", line 413, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['/home/linuxbrew/.linuxbrew/bin/cmake', '-DPYTHON_INCLUDE_DIR=/home/gitpod/.pyenv/versions/3.12.2/include/python3.12', '-DPYTHON_EXECUTABLE=/home/gitpod/.pyenv/versions/3.12.2/bin/python3.12', '-DBUILD_ONNX_PYTHON=ON', '-DCMAKE_EXPORT_COMPILE_COMMANDS=ON', '-DONNX_NAMESPACE=onnx', '-DPY_EXT_SUFFIX=.cpython-312-x86_64-linux-gnu.so', '-DCMAKE_BUILD_TYPE=Release', '-DONNX_ML=1', '/tmp/pip-install-vdhok58s/onnx_5f1b4c51f66549599449a17a03800247']' returned non-zero exit status 1.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for onnx
Failed to build onnx
ERROR: Could not build wheels for onnx, which is required to install pyproject.toml-based projects

Environment Info
Please run python scripts/collect_env.py and paste the output here.

No such file or directory
/home/gitpod/.pyenv/versions/3.12.2/bin/python: can't open file '/workspace/template-jupyter-notebook/collect_env.py': [Errno 2] No such file or directory

Additional context
Running on a simple gitpod such as this one: https://github.com/gitpod-samples/template-jupyter-notebook

[vykhovanets]

can be related Unstructured-IO/unstructured-inference#336

[zeionara]

I have the same error, is there any progress in solving the problem?

[scanny]

This is worth trying again with the latest version of unstructured. This problem was addressed in a new release of unstructured-inference and a new release of unstructured that uses that new version of unstructured-inference.

Let us know how you go.

[MthwRobinson]

@thams - Do you know if this is still an issue on the latest version?

[scsudo]

I have exactly the same problem under macOS 15.1 with Python 3.13.0. Can anyone help me?

[jotahcm]

Same as @scsudo for me.