problems installing numpy with homebrew python on macOS BigSur

Question

I have macOS BigSur -> installed CommandLineTools 12.3 beta -> installed homebrew -> installed python 3.8 with brew install python@3.8 . Python works well and comes up when I use the python3 command. However when I try to install NumPy with pip3 install numpy i get the following error below. I would really appreciate your help

Collecting numpy
  Using cached numpy-1.19.4.zip (7.3 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/local/opt/python@3.8/bin/python3.8 /usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/tmp7cqupall
         cwd: /private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-install-0ccafnfa/numpy
    Complete output (227 lines):
    Processing numpy/random/_bounded_integers.pxd.in
    Processing numpy/random/_philox.pyx
    Processing numpy/random/_bounded_integers.pyx.in
    Processing numpy/random/_sfc64.pyx
    Processing numpy/random/_mt19937.pyx
    Processing numpy/random/bit_generator.pyx
    Processing numpy/random/mtrand.pyx
    Processing numpy/random/_generator.pyx
    Processing numpy/random/_pcg64.pyx
    Processing numpy/random/_common.pyx
    Cythonizing sources
    blas_opt_info:
    blas_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    blis_info:
      libraries blis not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    openblas_info:
      libraries openblas not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    atlas_3_10_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries tatlas not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    atlas_3_10_blas_info:
      libraries satlas not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    atlas_blas_info:
      libraries f77blas,cblas,atlas not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    accelerate_info:
      libraries accelerate not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
    Library accelerate was not found. Ignoring
      libraries veclib not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
    Library veclib was not found. Ignoring
      FOUND:
        extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
        extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
        define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
    
      FOUND:
        extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
        extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
        define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
    
    non-existing path in 'numpy/distutils': 'site.cfg'
    lapack_opt_info:
    lapack_mkl_info:
      libraries mkl_rt not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    openblas_lapack_info:
      libraries openblas not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    openblas_clapack_info:
      libraries openblas,lapack not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    flame_info:
      libraries flame not found in ['/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE
    
    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
      libraries lapack_atlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries tatlas,tatlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries lapack_atlas not found in /usr/local/lib
      libraries tatlas,tatlas not found in /usr/local/lib
      libraries lapack_atlas not found in /usr/lib
      libraries tatlas,tatlas not found in /usr/lib
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE
    
    atlas_3_10_info:
      libraries lapack_atlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries satlas,satlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries lapack_atlas not found in /usr/local/lib
      libraries satlas,satlas not found in /usr/local/lib
      libraries lapack_atlas not found in /usr/lib
      libraries satlas,satlas not found in /usr/lib
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE
    
    atlas_threads_info:
    Setting PTATLAS=ATLAS
      libraries lapack_atlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries lapack_atlas not found in /usr/local/lib
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
      libraries lapack_atlas not found in /usr/lib
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE
    
    atlas_info:
      libraries lapack_atlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries f77blas,cblas,atlas not found in /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib
      libraries lapack_atlas not found in /usr/local/lib
      libraries f77blas,cblas,atlas not found in /usr/local/lib
      libraries lapack_atlas not found in /usr/lib
      libraries f77blas,cblas,atlas not found in /usr/lib
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE
    
      FOUND:
        extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
        extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
        define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
    
    running dist_info
    running build_src
    build_src
    building py_modules sources
    creating build
    creating build/src.macosx-11.0-x86_64-3.8
    creating build/src.macosx-11.0-x86_64-3.8/numpy
    creating build/src.macosx-11.0-x86_64-3.8/numpy/distutils
    building library "npymath" sources
    Could not locate executable gfortran
    Could not locate executable f95
    Could not locate executable f90
    Could not locate executable f77
    Could not locate executable xlf90
    Could not locate executable xlf
    Could not locate executable ifort
    Could not locate executable ifc
    Could not locate executable g77
    Could not locate executable g95
    Could not locate executable pgfortran
    don't know how to compile Fortran code on platform 'posix'
    creating build/src.macosx-11.0-x86_64-3.8/numpy/core
    creating build/src.macosx-11.0-x86_64-3.8/numpy/core/src
    creating build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npymath
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npymath/npy_math_internal.h
      adding 'build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npymath' to include_dirs.
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npymath/ieee754.c
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npymath/npy_math_complex.c
    None - nothing done with h_files = ['build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npymath/npy_math_internal.h']
    building library "npysort" sources
    creating build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common/npy_sort.h
      adding 'build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common' to include_dirs.
    creating build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort/quicksort.c
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort/mergesort.c
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort/timsort.c
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort/heapsort.c
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort/radixsort.c
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common/npy_partition.h
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort/selection.c
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common/npy_binsearch.h
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/npysort/binsearch.c
    None - nothing done with h_files = ['build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common/npy_sort.h', 'build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common/npy_partition.h', 'build/src.macosx-11.0-x86_64-3.8/numpy/core/src/common/npy_binsearch.h']
    building library "npyrandom" sources
    building extension "numpy.core._multiarray_tests" sources
    creating build/src.macosx-11.0-x86_64-3.8/numpy/core/src/multiarray
    conv_template:> build/src.macosx-11.0-x86_64-3.8/numpy/core/src/multiarray/_multiarray_tests.c
    building extension "numpy.core._multiarray_umath" sources
    Running from numpy source directory.
    setup.py:480: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
      run_build = parse_setuppy_commands()
    /usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib/python3.8/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
      warnings.warn(msg)
    Traceback (most recent call last):
      File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 280, in <module>
        main()
      File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 263, in main
        json_out['return_val'] = hook(**hook_input['kwargs'])
      File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 133, in prepare_metadata_for_build_wheel
        return hook(metadata_directory, config_settings)
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-build-env-e1y5szqo/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 157, in prepare_metadata_for_build_wheel
        self.run_setup()
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-build-env-e1y5szqo/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 248, in run_setup
        super(_BuildMetaLegacyBackend,
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-build-env-e1y5szqo/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 142, in run_setup
        exec(compile(code, __file__, 'exec'), locals())
      File "setup.py", line 508, in <module>
        setup_package()
      File "setup.py", line 500, in setup_package
        setup(**metadata)
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-install-0ccafnfa/numpy/numpy/distutils/core.py", line 169, in setup
        return old_setup(**new_attr)
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-build-env-e1y5szqo/overlay/lib/python3.8/site-packages/setuptools/__init__.py", line 165, in setup
        return distutils.core.setup(**attrs)
      File "/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib/python3.8/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib/python3.8/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-build-env-e1y5szqo/overlay/lib/python3.8/site-packages/setuptools/command/dist_info.py", line 31, in run
        egg_info.run()
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-install-0ccafnfa/numpy/numpy/distutils/command/egg_info.py", line 24, in run
        self.run_command("build_src")
      File "/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib/python3.8/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/local/Cellar/python@3.8/3.8.6_1/Frameworks/Python.framework/Versions/3.8/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-install-0ccafnfa/numpy/numpy/distutils/command/build_src.py", line 144, in run
        self.build_sources()
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-install-0ccafnfa/numpy/numpy/distutils/command/build_src.py", line 161, in build_sources
        self.build_extension_sources(ext)
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-install-0ccafnfa/numpy/numpy/distutils/command/build_src.py", line 318, in build_extension_sources
        sources = self.generate_sources(sources, ext)
      File "/private/var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/pip-install-0ccafnfa/numpy/numpy/distutils/command/build_src.py", line 378, in generate_sources
        source = func(extension, build_dir)
      File "numpy/core/setup.py", line 436, in generate_config_h
        moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
      File "numpy/core/setup.py", line 47, in check_types
        out = check_types(*a, **kw)
      File "numpy/core/setup.py", line 292, in check_types
        raise SystemError(
    SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/opt/python@3.8/bin/python3.8 /usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/pt/_zy2t2xj0mvbh41_pm942s8m0000gn/T/tmp7cqupall Check the logs for full command output.

Answer 1

I was able to solve a similar problem on a brand new Macbook Air (M1 chip) by using the Rosetta compatibility layer:

1. Go to Applications/Utilities and Duplicate then Rename Terminal to Terminal x86
2. Right click Terminal x86 , click Get Info, and check Open using Rosetta

You should now be able to use homebrew/pip/etc without issue

Answer 2

A problem was reported to numpy dev a few days ago, and an issue opened. Maybe you want to subscribe to this thread;

BUG: Error installing NumPy via Pip on macOS Big Sur with python from HomeBrew #17784

It is still a bit of a mess, but a number of good people are working on solutions; It is not ideal, but if you can, maybe you wait for a little while?

Answer 3

Open your terminal using Rosetta and do the installation, None of these issues would occur.

For Iterm, you can search iterm in Finder -> Right click -> Get info -> Choose the option "Open with Rosetta"

For Pycharm terminal, you can open Preferences -> Tools -> Terminal -> Update script path to "env /usr/bin/arch -x86_64 /bin/zsh --login"

If you are using a terminal apart from this, you could just google and figure out the steps to run that terminal using Rosetta.

Answer 4

转到Applications/Utilities复制它，然后将终端重命名为Terminal x86右键单击Terminal x86 ，单击获取信息，然后选中使用 Rosetta 打开