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jiavila opened this issue Mar 23, 2021 · 4 comments
Open

nipy fails to install using poetry add with mac os #482

jiavila opened this issue Mar 23, 2021 · 4 comments

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@jiavila
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jiavila commented Mar 23, 2021 •
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Hi!

I tried using poetry add nipy on my mac but it fails to install. I keep getting the error below. I've already tried setting up environment variables with export POETRY_<var_name>="" but still fails.

 Traceback (most recent call last):
        File "<string>", line 1, in <module>
        File "/private/var/folders/ly/_t1hns4s3jsd7hdr23nqg2dr0000gn/T/pip-install-zkc70p4q/nipy_bf136dc3170f4bb7af75d1f96dcd18e2/setup.py", line 149, in <module>
          main(**extra_setuptools_args)
        File "/private/var/folders/ly/_t1hns4s3jsd7hdr23nqg2dr0000gn/T/pip-install-zkc70p4q/nipy_bf136dc3170f4bb7af75d1f96dcd18e2/setup.py", line 128, in main
          setup(name=INFO_VARS['NAME'],
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/core.py", line 135, in setup
          config = configuration()
        File "/private/var/folders/ly/_t1hns4s3jsd7hdr23nqg2dr0000gn/T/pip-install-zkc70p4q/nipy_bf136dc3170f4bb7af75d1f96dcd18e2/setup.py", line 40, in configuration
          config.add_subpackage('nipy', 'nipy')
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/misc_util.py", line 1019, in add_subpackage
          config_list = self.get_subpackage(subpackage_name, subpackage_path,
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/misc_util.py", line 985, in get_subpackage
          config = self._get_configuration_from_setup_py(
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/misc_util.py", line 927, in _get_configuration_from_setup_py
          config = setup_module.configuration(*args)
        File "nipy/setup.py", line 64, in configuration
          config.add_subpackage('labs')
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/misc_util.py", line 1019, in add_subpackage
          config_list = self.get_subpackage(subpackage_name, subpackage_path,
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/misc_util.py", line 985, in get_subpackage
          config = self._get_configuration_from_setup_py(
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/misc_util.py", line 927, in _get_configuration_from_setup_py
          config = setup_module.configuration(*args)
        File "nipy/labs/setup.py", line 76, in configuration
          lapack_info = get_info('lapack_opt', 0)
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 584, in get_info
          return cl().get_info(notfound_action)
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 844, in get_info
          self.calc_info()
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 1859, in calc_info
          if self._calc_info(lapack):
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 1849, in _calc_info
          return getattr(self, '_calc_info_{}'.format(name))()
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 1770, in _calc_info_openblas
          info = get_info('openblas_clapack')
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 584, in get_info
          return cl().get_info(notfound_action)
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 844, in get_info
          self.calc_info()
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 2195, in calc_info
          info = self._calc_info()
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 2162, in _calc_info
          info = self.check_libs(lib_dirs, openblas_libs, [])
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 986, in check_libs
          info = self._check_libs(lib_dirs, libs, opt_libs, [ext])
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 1057, in _check_libs
          found_dirs, found_libs = self._find_libs(lib_dirs, libs, exts)
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 1041, in _find_libs
          found_lib = self._find_lib(lib_dir, lib, exts)
        File "/Users/jesusavila/Library/Caches/pypoetry/virtualenvs/nifti2png-activation-map-qZwwQBbT-py3.8/lib/python3.8/site-packages/numpy/distutils/system_info.py", line 1022, in _find_lib
          raise RuntimeError(_accel_msg.format(filename=p[0]))
      RuntimeError: Found /usr/lib/liblapack.dylib, but that file is a symbolic link to the MacOS Accelerate framework, which is not supported by NumPy. You must configure the build to use a different optimized library, or disable the use of optimized BLAS and LAPACK by setting the environment variables NPY_BLAS_ORDER="" and NPY_LAPACK_ORDER="" before building NumPy.
      ----------------------------------------
  WARNING: Discarding https://files.pythonhosted.org/packages/b4/ba/43176080eac00bdd33b11bccf082133f7b212533babd5d9b8090324a4a87/nipy-0.4.2.tar.gz#sha256=d30bed60e1662f0b79ef665396e98b1b2e57b1734d3d11510a3d7fa66d18c7de (from https://pypi.org/simple/nipy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Could not find a version that satisfies the requirement nipy==0.4.2
  ERROR: No matching distribution found for nipy==0.4.2
@matthew-brett
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I don't know poetry I'm afraid - but

  • What architecture is your Mac running on? Intel or M1?
  • Can you install Numpy in a previous step?

@jiavila
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jiavila commented Mar 24, 2021 •
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2.6 GHz 6-Core Intel Core i7

Yes, numpy can be installed separately but, regardless, nipy always tries to build numpy when trying to install with poetry, so nipy cannot be installed successfully with poetry

@matthew-brett
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Yes, I've seen a problem like this now. For the continuous integration, I worked round it thus:

https://github.com/MacPython/nipy-wheels/blob/master/config.sh#L4

In summary, I install OpenBLAS with homebrew, and then configure Numpy to use it instead of Accelerate. I don't know how else to fix this, I'm afraid.

@effigies
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@jiavila Is this resolved in the latest release?

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@matthew-brett @effigies @jiavila