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Cython compile error when installing with pip #354

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ZuzannaSadowska opened this issue Feb 21, 2024 · 0 comments
Open

Cython compile error when installing with pip #354

ZuzannaSadowska opened this issue Feb 21, 2024 · 0 comments

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@ZuzannaSadowska
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Thank you for your bug report!

Please fill out the following template.

PLATFORM (Mac, PC, Linux, other):

Mac and Linux

OPERATING SYSTEM (eg OSX 10.7, Windows 8.1):

MacOS 12.5.1 (21G83)
Linux a986d33834a9 5.15.49-linuxkit #1 SMP PREEMPT Tue Sep 13 07:51:32 UTC 2022 aarch64 aarch64 aarch64 GNU/Linux

SEVERITY (Critical? Major? Minor? Enhancement?):

DESCRIPTION:

  • What were you trying to do?
    Tried to install cytoflow using pip install cytoflow

  • What happened?

~ pip install cytoflow

Collecting cytoflow
  Downloading cytoflow-1.2.tar.gz (14.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.7/14.7 MB 6.7 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Collecting numpy==1.21.2
  Downloading numpy-1.21.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (13.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.1/13.1 MB 3.9 MB/s eta 0:00:00
Collecting pandas==1.3.5
  Downloading pandas-1.3.5-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (10.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.9/10.9 MB 43.7 MB/s eta 0:00:00
Collecting matplotlib==3.5.0
  Downloading matplotlib-3.5.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 6.9 MB/s eta 0:00:00
Collecting bottleneck==1.3.2
  Downloading Bottleneck-1.3.2.tar.gz (88 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.2/88.2 kB 257.6 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numexpr==2.8.1
  Downloading numexpr-2.8.1.tar.gz (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.8/94.8 kB 330.6 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting scipy==1.7.3
  Downloading scipy-1.7.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (36.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 36.6/36.6 MB 38.6 MB/s eta 0:00:00
Collecting scikit-learn==1.0.1
  Downloading scikit_learn-1.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (26.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 26.4/26.4 MB 7.2 MB/s eta 0:00:00
Collecting seaborn==0.11.2
  Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 292.8/292.8 kB 75.1 MB/s eta 0:00:00
Collecting statsmodels==0.13.0
  Downloading statsmodels-0.13.0.tar.gz (17.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.8/17.8 MB 9.7 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [141 lines of output]
      <string>:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
      <string>:53: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
      <string>:56: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
      <string>:53: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          # smooth
          for i in range(n):
              prev = (n+i-1) % n

              # s[t-m] = xhat[prev, 2+m-1]
              yhat[i] = (xhat[prev, 0] * xhat[prev, 1]**phi) + xhat[prev, 2+m-1]
                                                             ^
      ------------------------------------------------------------

      statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx:156:55: Cannot assign type 'npy_float64 complex' to 'float64_t'

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

              # s[t-m] = xhat[prev, 2+m-1]
              yhat[i] = (xhat[prev, 0] * xhat[prev, 1]**phi) + xhat[prev, 2+m-1]
              # l_t = a * (y_t - s_t-m) + (1-a) * (l_t-1 * b_t-1**phi)
              xhat[i, 0] = (alpha * (y[i] - xhat[prev, 2+m-1])
                            + (1 - alpha) * (xhat[prev, 0] * xhat[prev, 1]**phi))
                            ^
      ------------------------------------------------------------

      statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx:159:22: Cannot assign type 'npy_float64 complex' to 'float64_t'

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              # l_t = a * (y_t - s_t-m) + (1-a) * (l_t-1 * b_t-1**phi)
              xhat[i, 0] = (alpha * (y[i] - xhat[prev, 2+m-1])
                            + (1 - alpha) * (xhat[prev, 0] * xhat[prev, 1]**phi))
              # b_t = (b*) * (l_t / l_t-1) + (1 - (b*)) * b_t-1**phi
              xhat[i, 1] = (beta_star * (xhat[i, 0] / xhat[prev, 0])
                            + (1 - beta_star) * xhat[prev, 1]**phi)
                            ^
      ------------------------------------------------------------

      statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx:162:22: Cannot assign type 'npy_float64 complex' to 'float64_t'

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          # smooth
          for i in range(n):
              prev = (n+i-1) % n

              # s[t-m] = xhat[prev, 2+m-1]
              yhat[i] = (xhat[prev, 0] * xhat[prev, 1]**phi) * xhat[prev, 2+m-1]
                                                             ^
      ------------------------------------------------------------

      statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx:191:55: Cannot assign type 'npy_float64 complex' to 'float64_t'

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

              # s[t-m] = xhat[prev, 2+m-1]
              yhat[i] = (xhat[prev, 0] * xhat[prev, 1]**phi) * xhat[prev, 2+m-1]
              # l_t = a * (y_t / s_t-m) + (1-a) * (l_t-1 * b_t-1**phi)
              xhat[i, 0] = (alpha * (y[i] / xhat[prev, 2+m-1])
                            + (1 - alpha) * (xhat[prev, 0] * xhat[prev, 1]**phi))
                            ^
      ------------------------------------------------------------

      statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx:194:22: Cannot assign type 'npy_float64 complex' to 'float64_t'

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              # l_t = a * (y_t / s_t-m) + (1-a) * (l_t-1 * b_t-1**phi)
              xhat[i, 0] = (alpha * (y[i] / xhat[prev, 2+m-1])
                            + (1 - alpha) * (xhat[prev, 0] * xhat[prev, 1]**phi))
              # b_t = (b*) * (l_t / l_t-1) + (1 - (b*)) * b_t-1**phi
              xhat[i, 1] = (beta_star * (xhat[i, 0] / xhat[prev, 0])
                            + (1 - beta_star) * xhat[prev, 1]**phi)
                            ^
      ------------------------------------------------------------

      statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx:197:22: Cannot assign type 'npy_float64 complex' to 'float64_t'
      Compiling statsmodels/tsa/_stl.pyx because it changed.
      Compiling statsmodels/tsa/holtwinters/_exponential_smoothers.pyx because it changed.
      Compiling statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx because it changed.
      Compiling statsmodels/tsa/_innovations.pyx because it changed.
      Compiling statsmodels/tsa/regime_switching/_hamilton_filter.pyx because it changed.
      Compiling statsmodels/tsa/regime_switching/_kim_smoother.pyx because it changed.
      Compiling statsmodels/tsa/innovations/_arma_innovations.pyx because it changed.
      Compiling statsmodels/nonparametric/linbin.pyx because it changed.
      Compiling statsmodels/robust/_qn.pyx because it changed.
      Compiling statsmodels/nonparametric/_smoothers_lowess.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_initialization.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_representation.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_kalman_filter.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_filters/_conventional.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_filters/_inversions.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_filters/_univariate.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_filters/_univariate_diffuse.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_kalman_smoother.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_smoothers/_alternative.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_smoothers/_classical.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_smoothers/_conventional.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_smoothers/_univariate.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_smoothers/_univariate_diffuse.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_simulation_smoother.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_cfa_simulation_smoother.pyx because it changed.
      Compiling statsmodels/tsa/statespace/_tools.pyx because it changed.
      [ 1/26] Cythonizing statsmodels/nonparametric/_smoothers_lowess.pyx
      [ 2/26] Cythonizing statsmodels/nonparametric/linbin.pyx
      [ 3/26] Cythonizing statsmodels/robust/_qn.pyx
      [ 4/26] Cythonizing statsmodels/tsa/_innovations.pyx
      [ 5/26] Cythonizing statsmodels/tsa/_stl.pyx
      [ 6/26] Cythonizing statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx
      Traceback (most recent call last):
        File "/opt/conda/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/opt/conda/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/opt/conda/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-vmg419vk/overlay/lib/python3.9/site-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-vmg419vk/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-vmg419vk/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 480, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-vmg419vk/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 304, in <module>
        File "/tmp/pip-build-env-vmg419vk/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
          cythonize_one(*args)
        File "/tmp/pip-build-env-vmg419vk/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: statsmodels/tsa/exponential_smoothing/_ets_smooth.pyx
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
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.
  • What did you expect to happen?
    Expected the install to work

Don't forget to attach the log file to this bug report!

If you are having trouble with a particular FCS file, please attach that file too.
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@ZuzannaSadowska