Installation error

[tedeschisunlab]

Hi,
We installed Python 3.10 and Miniconda3 as instructed. We used the following code:
conda env create -f conda_env_python_3_10.yml
conda activate venv_python_3_10

Then we tried to run
pip install -r requirements.txt

We got the following error message:

Using cached numpy-1.19.0.zip (7.3 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
╰─> [88 lines of output]
Running from numpy source directory.
:460: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py:73: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
required_version = LooseVersion('0.29.14')
/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(cython_version) < required_version:
performance hint: _common.pyx:275:19: Exception check after calling 'random_func' will always require the GIL to be acquired. Declare 'random_func' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:299:19: Exception check after calling 'random_func' will always require the GIL to be acquired. Declare 'random_func' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:322:50: Exception check after calling 'random_func' will always require the GIL to be acquired. Declare 'random_func' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:426:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:465:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:509:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:592:36: Exception check after calling 'f0' will always require the GIL to be acquired. Declare 'f0' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:596:36: Exception check after calling 'f1' will always require the GIL to be acquired. Declare 'f1' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:600:36: Exception check after calling 'f2' will always require the GIL to be acquired. Declare 'f2' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:604:36: Exception check after calling 'f3' will always require the GIL to be acquired. Declare 'f3' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:638:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:675:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:712:63: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:754:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:785:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:903:40: Exception check after calling 'f0' will always require the GIL to be acquired. Declare 'f0' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:907:40: Exception check after calling 'fd' will always require the GIL to be acquired. Declare 'fd' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:911:41: Exception check after calling 'fdd' will always require the GIL to be acquired. Declare 'fdd' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:916:40: Exception check after calling 'fi' will always require the GIL to be acquired. Declare 'fi' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:920:41: Exception check after calling 'fdi' will always require the GIL to be acquired. Declare 'fdi' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:924:38: Exception check after calling 'fiii' will always require the GIL to be acquired. Declare 'fiii' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:960:31: Exception check after calling 'f' will always require the GIL to be acquired. Declare 'f' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _common.pyx:1002:32: Exception check after calling 'f1' will always require the GIL to be acquired. Declare 'f1' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: _generator.pyx:706:41: 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:735:45: 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:
  ------------------------------------------------------------
  ...
          for i in range(1, RK_STATE_LEN):
              self.rng_state.key[i] = val[i]
          self.rng_state.pos = i
  
          self._bitgen.state = &self.rng_state
          self._bitgen.next_uint64 = &mt19937_uint64
                                     ^
  ------------------------------------------------------------
  
  _mt19937.pyx:138:35: Cannot assign type 'uint64_t (*)(void *) except? -1 nogil' to 'uint64_t (*)(void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to the type of the value being assigned.
  Processing numpy/random/_bounded_integers.pxd.in
  Processing numpy/random/_bounded_integers.pyx.in
  Processing numpy/random/_common.pyx
  Processing numpy/random/_generator.pyx
  Processing numpy/random/_mt19937.pyx
  Traceback (most recent call last):
    File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 235, in <module>
      main()
    File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 231, in main
      find_process_files(root_dir)
    File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 222, in find_process_files
      process(root_dir, fromfile, tofile, function, hash_db)
    File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 188, in process
      processor_function(fromfile, tofile)
    File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-install-g0bcd_j9/numpy_582a062346a547efa0d6a2ad7910bb71/tools/cythonize.py", line 77, in process_pyx
      subprocess.check_call(
    File "/Users/tedeschia/miniconda3/envs/venv_python_3_10/lib/python3.10/subprocess.py", line 369, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['/Users/tedeschia/miniconda3/envs/venv_python_3_10/bin/python3.10', '-m', 'cython', '-3', '--fast-fail', '-o', '_mt19937.c', '_mt19937.pyx']' returned non-zero exit status 1.
  Cythonizing sources
  Traceback (most recent call last):
    File "/Users/tedeschia/miniconda3/envs/venv_python_3_10/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/Users/tedeschia/miniconda3/envs/venv_python_3_10/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 "/Users/tedeschia/miniconda3/envs/venv_python_3_10/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 "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-build-env-914leq5a/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel
      self.run_setup()
    File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-build-env-914leq5a/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 487, in run_setup
      super().run_setup(setup_script=setup_script)
    File "/private/var/folders/rs/6dqrcxv12lx9_jvf1gv1djw00000gn/T/pip-build-env-914leq5a/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 311, in run_setup
      exec(code, locals())
    File "<string>", line 489, in <module>
    File "<string>", line 469, in setup_package
    File "<string>", line 274, 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.

Our mac operating system is macOS Sierra version 10.12.6 with 16 GB memory.

Any help will be greatly appreciated.

Thanks,

[josh-oloro]

Hi, I got the same error. Was this ever solved?

[sollan]

Hi, if you've installed the libraries with Conda, there should be no need to run pip install.

You could simply run

conda env create -f conda_env_python_3_10.yml
conda activate venv_python_3_10
pythonw ./alma.py

And the program should start.

Can you let me know if that works?

Best,
Annette