RuntimeError: Running cythonize failed!

[mm3509]

I am interested in vocal cloning from van der Oord et al and found this repo. I try to install on a Google Colab and get:

!pip install -r ZeroSpeech/requirements.txt

Collecting numpy==1.18.2 (from -r ZeroSpeech/requirements.txt (line 1))
  Using cached numpy-1.18.2.zip (5.4 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) 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.
  Preparing metadata (pyproject.toml) ... error
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

I also start a virtual machine on the cloud, clone the repo, try to install, and get a similar error:

$ pip install -r requirements.txt 
Collecting numpy==1.18.2 (from -r requirements.txt (line 1))
  Using cached numpy-1.18.2.zip (5.4 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [63 lines of output]
      Running from numpy source directory.
      <string>:461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
      /tmp/pip-install-d1oosqgf/numpy_df17a3083fa845ed943b7f14bde0105d/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
        required_version = LooseVersion('0.29.14')
      /tmp/pip-install-d1oosqgf/numpy_df17a3083fa845ed943b7f14bde0105d/tools/cythonize.py:77: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
        if LooseVersion(cython_version) < required_version:
      performance hint: _generator.pyx:811:41: Exception check after calling '_shuffle_int' will always require the GIL to be acquired.
      Possible solutions:
          1. Declare '_shuffle_int' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
          2. Use an 'int' return type on '_shuffle_int' to allow an error code to be returned.
      performance hint: _generator.pyx:840:45: Exception check after calling '_shuffle_int' will always require the GIL to be acquired.
      Possible solutions:
          1. Declare '_shuffle_int' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
          2. Use an 'int' return type on '_shuffle_int' to allow an error code to be returned.
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          cdef sfc64_state rng_state
      
          def __init__(self, seed=None):
              BitGenerator.__init__(self, seed)
              self._bitgen.state = <void *>&self.rng_state
              self._bitgen.next_uint64 = &sfc64_uint64
                                         ^
      ------------------------------------------------------------
      
      _sfc64.pyx:90:35: Cannot assign type 'uint64_t (*)(void *) except? -1 nogil' to 'uint64_t (*)(void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to type 'uint64_t (void *) except? -1 nogil'.
      Processing numpy/random/_bounded_integers.pxd.in
      Processing numpy/random/_generator.pyx
      Processing numpy/random/_sfc64.pyx
      Traceback (most recent call last):
        File "/tmp/pip-install-d1oosqgf/numpy_df17a3083fa845ed943b7f14bde0105d/tools/cythonize.py", line 238, in <module>
          main()
        File "/tmp/pip-install-d1oosqgf/numpy_df17a3083fa845ed943b7f14bde0105d/tools/cythonize.py", line 234, in main
          find_process_files(root_dir)
        File "/tmp/pip-install-d1oosqgf/numpy_df17a3083fa845ed943b7f14bde0105d/tools/cythonize.py", line 225, in find_process_files
          process(root_dir, fromfile, tofile, function, hash_db)
        File "/tmp/pip-install-d1oosqgf/numpy_df17a3083fa845ed943b7f14bde0105d/tools/cythonize.py", line 191, in process
          processor_function(fromfile, tofile)
        File "/tmp/pip-install-d1oosqgf/numpy_df17a3083fa845ed943b7f14bde0105d/tools/cythonize.py", line 80, in process_pyx
          subprocess.check_call(
        File "/opt/conda/envs/bshall/lib/python3.10/subprocess.py", line 369, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['/opt/conda/envs/bshall/bin/python3.10', '-m', 'cython', '-3', '--fast-fail', '-o', '_sfc64.c', '_sfc64.pyx']' returned non-zero exit status 1.
      Cythonizing sources
      Traceback (most recent call last):
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/tmp/pip-build-env-ux6kv4on/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/tmp/pip-build-env-ux6kv4on/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 480, in run_setup
          super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-ux6kv4on/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 488, in <module>
        File "<string>", line 469, in setup_package
        File "<string>", line 275, in generate_cython
      RuntimeError: Running cythonize failed!
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

I found this issue with a similar issue on numpy 1.18.5, and they suggest --no-build-isolation, but I still get the error:

$ python -m pip install numpy==1.18.2 --no-build-isolation
Collecting numpy==1.18.2
  Using cached numpy-1.18.2.zip (5.4 MB)
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [63 lines of output]
      Running from numpy source directory.
      <string>:461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
      /tmp/pip-install-bhazifhj/numpy_638e295665ae4b3e88c648f1b94929e4/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
        required_version = LooseVersion('0.29.14')
      /tmp/pip-install-bhazifhj/numpy_638e295665ae4b3e88c648f1b94929e4/tools/cythonize.py:77: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
        if LooseVersion(cython_version) < required_version:
      performance hint: _generator.pyx:811:41: Exception check after calling '_shuffle_int' will always require the GIL to be acquired.
      Possible solutions:
          1. Declare '_shuffle_int' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
          2. Use an 'int' return type on '_shuffle_int' to allow an error code to be returned.
      performance hint: _generator.pyx:840:45: Exception check after calling '_shuffle_int' will always require the GIL to be acquired.
      Possible solutions:
          1. Declare '_shuffle_int' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
          2. Use an 'int' return type on '_shuffle_int' to allow an error code to be returned.
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          cdef sfc64_state rng_state
      
          def __init__(self, seed=None):
              BitGenerator.__init__(self, seed)
              self._bitgen.state = <void *>&self.rng_state
              self._bitgen.next_uint64 = &sfc64_uint64
                                         ^
      ------------------------------------------------------------
      
      _sfc64.pyx:90:35: Cannot assign type 'uint64_t (*)(void *) except? -1 nogil' to 'uint64_t (*)(void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to type 'uint64_t (void *) except? -1 nogil'.
      Processing numpy/random/_bounded_integers.pxd.in
      Processing numpy/random/_generator.pyx
      Processing numpy/random/_sfc64.pyx
      Traceback (most recent call last):
        File "/tmp/pip-install-bhazifhj/numpy_638e295665ae4b3e88c648f1b94929e4/tools/cythonize.py", line 238, in <module>
          main()
        File "/tmp/pip-install-bhazifhj/numpy_638e295665ae4b3e88c648f1b94929e4/tools/cythonize.py", line 234, in main
          find_process_files(root_dir)
        File "/tmp/pip-install-bhazifhj/numpy_638e295665ae4b3e88c648f1b94929e4/tools/cythonize.py", line 225, in find_process_files
          process(root_dir, fromfile, tofile, function, hash_db)
        File "/tmp/pip-install-bhazifhj/numpy_638e295665ae4b3e88c648f1b94929e4/tools/cythonize.py", line 191, in process
          processor_function(fromfile, tofile)
        File "/tmp/pip-install-bhazifhj/numpy_638e295665ae4b3e88c648f1b94929e4/tools/cythonize.py", line 80, in process_pyx
          subprocess.check_call(
        File "/opt/conda/envs/bshall/lib/python3.10/subprocess.py", line 369, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['/opt/conda/envs/bshall/bin/python', '-m', 'cython', '-3', '--fast-fail', '-o', '_sfc64.c', '_sfc64.pyx']' returned non-zero exit status 1.
      Cythonizing sources
      Traceback (most recent call last):
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/setuptools/build_meta.py", line 480, in run_setup
          super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
        File "/opt/conda/envs/bshall/lib/python3.10/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 488, in <module>
        File "<string>", line 469, in setup_package
        File "<string>", line 275, in generate_cython
      RuntimeError: Running cythonize failed!
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.

One possible problem is that I'm not sure that Nvidia/Apex is installed. So I follow this thread to install it on Colab. I get this error:

DEPRECATION: --build-option and --global-option are deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use --config-settings. Discussion can be found at https://github.com/pypa/pip/issues/11859
WARNING: Implying --no-binary=:all: due to the presence of --build-option / --global-option. 
Processing /content/gdrive/MyDrive/apex
  Running command pip subprocess to install build dependencies
  Using pip 23.1.2 from /usr/local/lib/python3.10/dist-packages/pip (python 3.10)
  Collecting setuptools
    Using cached setuptools-69.0.3-py3-none-any.whl
  Collecting wheel
    Using cached wheel-0.42.0-py3-none-any.whl
  Installing collected packages: wheel, setuptools
    Creating /tmp/pip-build-env-f0jjytpy/overlay/local/bin
    changing mode of /tmp/pip-build-env-f0jjytpy/overlay/local/bin/wheel to 755
  ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
  ipython 7.34.0 requires jedi>=0.16, which is not installed.
  lida 0.0.10 requires fastapi, which is not installed.
  lida 0.0.10 requires kaleido, which is not installed.
  lida 0.0.10 requires python-multipart, which is not installed.
  lida 0.0.10 requires uvicorn, which is not installed.
  Successfully installed setuptools-69.0.3 wheel-0.42.0
  Installing build dependencies ... done
  Running command Getting requirements to build wheel
  Traceback (most recent call last):
    File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-f0jjytpy/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
      return self._get_build_requires(config_settings, requirements=['wheel'])
    File "/tmp/pip-build-env-f0jjytpy/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 295, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-f0jjytpy/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 311, in run_setup
      exec(code, locals())
    File "<string>", line 5, in <module>
  ModuleNotFoundError: No module named 'packaging'
  error: subprocess-exited-with-error
  
  × Getting requirements to build 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 /usr/local/lib/python3.10/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py get_requires_for_build_wheel /tmp/tmpp0zh_uyr
  cwd: /content/gdrive/MyDrive/apex
  Getting requirements to build wheel ... error
error: subprocess-exited-with-error

× Getting requirements to build 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.

I install packaging with !pip install packaging but I get the same error.

How can I install the numpy requirements for running this project?

[yanshui177]

Same error