Pip install pandas results in error (Python3.8, Pycharm, Apple Silicon)

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Installing pandas via pip install pandas results in the following error. I'm really clueless what to do or how to fix it. I hope I gave enough informations for you. I would appreciate your help a lot!

Setup:

  • macOS BigSur 11.1
  • Apple Silicon, MacBook Pro (13", M1, 2020)
  • PyCharm CE for Apple Silicon 2020.3.2. managed via JetBrains Toolbox
  • Using Python 3.9 (was trying it with python 3.8, too but resulted the same error)

Installed packages:

  • pip 20.3.3
  • setuptools 51.3.3

Error message: Collecting pandas Using cached pandas-1.2.1.tar.gz (5.5 MB) Installing build dependencies: started Installing build dependencies: finished with status 'error'

  ERROR: Command errored out with exit status 1:
   command: /Users/user/PycharmProjects/test1/venv/bin/python /Users/user/PycharmProjects/test1/venv/lib/python3.9/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/vc/_39tpjws3jbb_wprblz865200000gn/T/pip-build-env-pdrftgon/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.29.21,<3' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy; python_version>='"'"'3.9'"'"''
       cwd: None
  Complete output (1081 lines):
  Ignoring numpy: markers 'python_version == "3.7" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.8" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.7" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.8" and platform_system == "AIX"' don't match your environment
  Collecting Cython<3,>=0.29.21
    Using cached Cython-0.29.21-py2.py3-none-any.whl (974 kB)
  Collecting numpy
    Using cached numpy-1.19.5.zip (7.3 MB)
    Installing build dependencies: started
    Installing build dependencies: finished with status 'done'
    Getting requirements to build wheel: started
    Getting requirements to build wheel: finished with status 'done'
      Preparing wheel metadata: started
      Preparing wheel metadata: finished with status 'done'
  Collecting wheel
    Using cached wheel-0.36.2-py2.py3-none-any.whl (35 kB)
  Collecting setuptools
    Using cached setuptools-51.3.3-py3-none-any.whl (786 kB)
  Building wheels for collected packages: numpy
    Building wheel for numpy (PEP 517): started
    Building wheel for numpy (PEP 517): finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /Users/user/PycharmProjects/test1/venv/bin/python /Users/user/PycharmProjects/test1/venv/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/vc/_39tpjws3jbb_wprblz865200000gn/T/tmpt7i8fum9
         cwd: /private/var/folders/vc/_39tpjws3jbb_wprblz865200000gn/T/pip-install-10nrvsom/numpy_27b9d8e3033f43b4964c635b439e0373
    Complete output (1052 lines):
    Running from numpy source directory.
    Cythonizing sources
    numpy/random/_bounded_integers.pxd.in has not changed
    numpy/random/_philox.pyx has not changed
    numpy/random/_bounded_integers.pyx.in has not changed
    numpy/random/_sfc64.pyx has not changed
    numpy/random/_mt19937.pyx has not changed
    numpy/random/bit_generator.pyx has not changed
    Processing numpy/random/_bounded_integers.pyx
    numpy/random/mtrand.pyx has not changed
    numpy/random/_generator.pyx has not changed
    numpy/random/_pcg64.pyx has not changed
    numpy/random/_common.pyx has not changed
    blas_opt_info:
    blas_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/Users/user/PycharmProjects/test1/venv/lib', '/usr/lib']
      NOT AVAILABLE
  
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: clang: errorerror: : the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitlythe clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
  
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
    error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.9-universal2-3.9/numpy/core/src/umath -Ibuild/src.macosx-10.9-universal2-3.9/numpy/core/src/npymath -Ibuild/src.macosx-10.9-universal2-3.9/numpy/core/src/common -Inumpy/core/include -Ibuild/src.macosx-10.9-universal2-3.9/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/user/PycharmProjects/test1/venv/include -I/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9 -Ibuild/src.macosx-10.9-universal2-3.9/numpy/core/src/common -Ibuild/src.macosx-10.9-universal2-3.9/numpy/core/src/npymath -c numpy/core/src/multiarray/buffer.c -o build/temp.macosx-10.9-universal2-3.9/numpy/core/src/multiarray/buffer.o -MMD -MF build/temp.macosx-10.9-universal2-3.9/numpy/core/src/multiarray/buffer.o.d -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers -std=c99" failed with exit status 1
    ----------------------------------------
    ERROR: Failed building wheel for numpy
  Failed to build numpy
  ERROR: Could not build wheels for numpy which use PEP 517 and cannot be installed directly
  ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/user/PycharmProjects/test1/venv/bin/python /Users/user/PycharmProjects/test1/venv/lib/python3.9/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/vc/_39tpjws3jbb_wprblz865200000gn/T/pip-build-env-pdrftgon/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.29.21,<3' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy; python_version>='"'"'3.9'"'"'' Check the logs for full command output.

Hint: I had to cut the error message because it was 90.000 characters long (StackOverflow only accepts 30.000 characters)

apple-silicon pandas pycharm python
3 Answers

Found a similar thread on GitHub related to this issue. The solution is as follows

$ brew install python@3.9
$ brew install openblas
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install cython --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install numpy --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install pandas --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install pybind11 --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install scipy --no-use-pep517
$ brew install libjpeg zlib
$ python3 -m pip install pillow
$ python3 -m pip install matplotlib

Attaching the thread from GitHub for further reference

user_46018540
user_19838540

I had errors for script. Solution by Adithya Kamath almost worked for me. But I still had some error. I checked the root of the problem and found that module 'pythran' is missing.

pip3 install pythran

and then

OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install scipy --no-use-pep517

It works then.

user_172024050
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