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allenai / scispacy

A full spaCy pipeline and models for scientific/biomedical documents.
https://allenai.github.io/scispacy/
Apache License 2.0
1.68k stars 225 forks source link

Error installing scispacy for M1 Mac #442

Closed pika97 closed 2 years ago

pika97 commented 2 years ago

Hi,

I'm trying to install Scispacy on mac m1, python version 3.8.13, pip version 22.1.2, conda 4.11.0.

Error log: (base) ➜ ~ conda activate bio (bio) ➜ ~ pip install scispacy Collecting scispacy Using cached scispacy-0.5.0-py3-none-any.whl (44 kB) Requirement already satisfied: requests<3.0.0,>=2.0.0 in /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib/python3.8/site-packages (from scispacy) (2.28.1) Requirement already satisfied: spacy<3.3.0,>=3.2.0 in /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib/python3.8/site-packages (from scispacy) (3.2.4) Collecting pysbd Using cached pysbd-0.3.4-py3-none-any.whl (71 kB) Requirement already satisfied: numpy in /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib/python3.8/site-packages (from scispacy) (1.23.1) Requirement already satisfied: nmslib>=1.7.3.6 in /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib/python3.8/site-packages (from scispacy) (2.1.1) Collecting conllu Using cached conllu-4.5.1-py2.py3-none-any.whl (16 kB) Collecting scikit-learn>=0.20.3 Using cached scikit-learn-1.1.1.tar.gz (6.8 MB) Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [11073 lines of output] Collecting setuptools<60.0 Using cached setuptools-59.8.0-py3-none-any.whl (952 kB) Collecting wheel Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting Cython>=0.28.5 Using cached Cython-0.29.30-py2.py3-none-any.whl (985 kB) Collecting oldest-supported-numpy Using cached oldest_supported_numpy-2022.5.28-py3-none-any.whl (3.9 kB) Collecting scipy>=1.3.2 Using cached scipy-1.8.1.tar.gz (38.2 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 metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting numpy==1.21.0 Using cached numpy-1.21.0-cp38-cp38-macosx_11_0_arm64.whl (12.1 MB) Building wheels for collected packages: scipy Building wheel for scipy (pyproject.toml): started Building wheel for scipy (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error

    × Building wheel for scipy (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [11041 lines of output]
        scipy/linalg/_generate_pyx.py: all files up-to-date
        scipy/special/_generate_pyx.py: all files up-to-date
        Running scipy/linalg/_generate_pyx.py
        Running scipy/special/_generate_pyx.py
        Running scipy/stats/_generate_pyx.py
        scipy/cluster/_vq.pyx has not changed
        scipy/linalg/_solve_toeplitz.pyx has not changed
        scipy/linalg/cython_blas.pyx has not changed
        scipy/linalg/_decomp_update.pyx.in has not changed
        scipy/optimize/_group_columns.pyx has not changed
        scipy/optimize/_bglu_dense.pyx has not changed
        scipy/optimize/_trlib/_trlib.pyx has not changed
        scipy/optimize/_highs/cython/src/_highs_constants.pyx has not changed
        scipy/optimize/_highs/cython/src/_highs_wrapper.pyx has not changed
        scipy/optimize/_lsq/givens_elimination.pyx has not changed
        scipy/optimize/cython_optimize/_zeros.pyx.in has not changed
        scipy/ndimage/src/_ni_label.pyx has not changed
        scipy/io/matlab/_streams.pyx has not changed
        scipy/io/matlab/_mio_utils.pyx has not changed
        scipy/linalg/cython_lapack.pyx has not changed
        scipy/linalg/_matfuncs_sqrtm_triu.pyx has not changed
        Cythonizing sources
        lapack_opt_info:
        lapack_mkl_info:
        customize UnixCCompiler
          libraries mkl_rt not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        openblas_lapack_info:
          libraries openblas not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        openblas_clapack_info:
          libraries openblas,lapack not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        flame_info:
          libraries flame not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_3_10_threads_info:
        Setting PTATLAS=ATLAS
          libraries lapack_atlas not found in /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib
          libraries tatlas,tatlas not found in /opt/homebrew/Caskroom/miniforge/base/envs/bio/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 /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib
          libraries satlas,satlas not found in /opt/homebrew/Caskroom/miniforge/base/envs/bio/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 /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib
          libraries ptf77blas,ptcblas,atlas not found in /opt/homebrew/Caskroom/miniforge/base/envs/bio/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 /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib
          libraries f77blas,cblas,atlas not found in /opt/homebrew/Caskroom/miniforge/base/envs/bio/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

        lapack_info:
          FOUND:
            libraries = ['lapack', 'lapack']
            library_dirs = ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib']
            language = f77

        blas_opt_info:
        blas_mkl_info:
          libraries mkl_rt not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        blis_info:
          libraries blis not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        openblas_info:
          libraries openblas not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_3_10_blas_threads_info:
        Setting PTATLAS=ATLAS
          libraries tatlas not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_3_10_blas_info:
          libraries satlas not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_blas_threads_info:
        Setting PTATLAS=ATLAS
          libraries ptf77blas,ptcblas,atlas not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_blas_info:
          libraries f77blas,cblas,atlas not found in ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

        blas_info:
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/var
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/var/folders
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/var/folders/y8
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1
        compile options: '-I/opt/homebrew/Caskroom/miniforge/base/envs/bio/include -c'
        clang: /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/source.c
        /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi66amka1/source.c:1:10: fatal error: 'cblas.h' file not found
        #include <cblas.h>
                 ^~~~~~~~~
        1 error generated.
          FOUND:
            libraries = ['blas', 'blas']
            library_dirs = ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib']
            include_dirs = ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/include']

          FOUND:
            define_macros = [('NO_ATLAS_INFO', 1)]
            libraries = ['blas', 'blas']
            library_dirs = ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib']
            include_dirs = ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/include']

          FOUND:
            libraries = ['lapack', 'lapack', 'blas', 'blas']
            library_dirs = ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/lib']
            language = f77
            define_macros = [('NO_ATLAS_INFO', 1)]
            include_dirs = ['/opt/homebrew/Caskroom/miniforge/base/envs/bio/include']

        [makenpz] scipy/special/tests/data/boost.npz not rebuilt
        [makenpz] scipy/special/tests/data/gsl.npz not rebuilt
        [makenpz] scipy/special/tests/data/local.npz not rebuilt
        non-existing path in 'scipy/signal/windows': 'tests'
        running bdist_wheel
        running build
        running config_cc
        unifing config_cc, config, build_clib, build_ext, build commands --compiler options
        running config_fc
        unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
        running build_src
        build_src
        building py_modules sources
        building library "mach" sources
        building library "quadpack" sources
        building library "lsoda" sources
        building library "vode" sources
        building library "dop" sources
        building library "fitpack" sources
        building library "fwrappers" sources
        building library "odrpack" sources
        building library "minpack" sources
        building library "rectangular_lsap" sources
        building library "rootfind" sources
        building library "basiclu" sources
        building library "superlu_src" sources
        building library "arpack_scipy" sources
        building library "_spropack" sources
        building library "_dpropack" sources
        building library "_cpropack" sources
        building library "_zpropack" sources
        building library "sc_cephes" sources
        building library "sc_mach" sources
        building library "sc_amos" sources
        building library "sc_cdf" sources
        building library "sc_specfun" sources
        building library "statlib" sources
        building library "test_boost_build" sources
        building extension "scipy.cluster._vq" sources
        building extension "scipy.cluster._hierarchy" sources
        building extension "scipy.cluster._optimal_leaf_ordering" sources
        building extension "scipy.fft._pocketfft.pypocketfft" sources
        building extension "scipy.fftpack.convolve" sources
        building extension "scipy.integrate._quadpack" sources
        building extension "scipy.integrate._odepack" sources
        building extension "scipy.integrate._vode" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/integrate/_vode-f2pywrappers.f' to sources.
        building extension "scipy.integrate._lsoda" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/integrate/_lsoda-f2pywrappers.f' to sources.
        building extension "scipy.integrate._dop" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/integrate/_dop-f2pywrappers.f' to sources.
        building extension "scipy.integrate._test_multivariate" sources
        building extension "scipy.integrate._test_odeint_banded" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/integrate' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/integrate/_test_odeint_banded-f2pywrappers.f' to sources.
        building extension "scipy.interpolate.interpnd" sources
        building extension "scipy.interpolate._ppoly" sources
        building extension "scipy.interpolate._bspl" sources
        building extension "scipy.interpolate._fitpack" sources
        building extension "scipy.interpolate.dfitpack" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/interpolate/src/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/interpolate/src' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/interpolate/src/dfitpack-f2pywrappers.f' to sources.
        building extension "scipy.interpolate._rbfinterp_pythran" sources
        building extension "scipy.io._test_fortran" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/io/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/io' to include_dirs.
        building extension "scipy.io.matlab._streams" sources
        building extension "scipy.io.matlab._mio_utils" sources
        building extension "scipy.io.matlab._mio5_utils" sources
        building extension "scipy.linalg._fblas" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg/_fblas-f2pywrappers.f' to sources.
        building extension "scipy.linalg._flapack" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg/_flapack-f2pywrappers.f' to sources.
        building extension "scipy.linalg._flinalg" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg' to include_dirs.
        building extension "scipy.linalg._interpolative" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/linalg' to include_dirs.
        building extension "scipy.linalg._solve_toeplitz" sources
        building extension "scipy.linalg._matfuncs_sqrtm_triu" sources
        building extension "scipy.linalg.cython_blas" sources
        building extension "scipy.linalg.cython_lapack" sources
        building extension "scipy.linalg._decomp_update" sources
        building extension "scipy.linalg._cythonized_array_utils" sources
        building extension "scipy.odr.__odrpack" sources
        building extension "scipy.optimize._minpack" sources
        building extension "scipy.optimize._lsap_module" sources
        building extension "scipy.optimize._zeros" sources
        building extension "scipy.optimize._lbfgsb" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/lbfgsb_src/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/lbfgsb_src' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/optimize/lbfgsb_src/_lbfgsb-f2pywrappers.f' to sources.
        building extension "scipy.optimize._moduleTNC" sources
        building extension "scipy.optimize._cobyla" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/cobyla/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/cobyla' to include_dirs.
        building extension "scipy.optimize._minpack2" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/minpack2/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/minpack2' to include_dirs.
        building extension "scipy.optimize._slsqp" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/slsqp/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/slsqp' to include_dirs.
        building extension "scipy.optimize.__nnls" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/__nnls/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/optimize/__nnls' to include_dirs.
        building extension "scipy.optimize._group_columns" sources
        building extension "scipy.signal._sigtools" sources
        building extension "scipy.signal._max_len_seq_inner" sources
        building extension "scipy.signal._spectral" sources
        building extension "scipy.signal._peak_finding_utils" sources
        building extension "scipy.signal._sosfilt" sources
        building extension "scipy.signal._upfirdn_apply" sources
        building extension "scipy.signal._spline" sources
        building extension "scipy.sparse.linalg._isolve._iterative" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve/iterative/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve/iterative' to include_dirs.
        building extension "scipy.sparse.linalg._dsolve._superlu" sources
        building extension "scipy.sparse.linalg._eigen.arpack._arpack" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/arpack/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/arpack' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/arpack/_arpack-f2pywrappers.f' to sources.
        building extension "scipy.sparse.linalg._propack._spropack" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/_spropack-f2pywrappers.f' to sources.
        building extension "scipy.sparse.linalg._propack._dpropack" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/_dpropack-f2pywrappers.f' to sources.
        building extension "scipy.sparse.linalg._propack._cpropack" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/_cpropack-f2pywrappers.f' to sources.
        building extension "scipy.sparse.linalg._propack._zpropack" sources
        f2py options: []
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/fortranobject.c' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_propack/_zpropack-f2pywrappers.f' to sources.
        building extension "scipy.sparse.csgraph._shortest_path" sources
        building extension "scipy.sparse.csgraph._traversal" sources
        building extension "scipy.sparse.csgraph._min_spanning_tree" sources
        building extension "scipy.sparse.csgraph._matching" sources
        building extension "scipy.sparse.csgraph._flow" sources
        building extension "scipy.sparse.csgraph._reordering" sources
        building extension "scipy.sparse.csgraph._tools" sources
        building extension "scipy.sparse._csparsetools" sources
        building extension "scipy.sparse._sparsetools" sources
        [generate_sparsetools] 'scipy/sparse/sparsetools/bsr_impl.h' already up-to-date
        [generate_sparsetools] 'scipy/sparse/sparsetools/csr_impl.h' already up-to-date
        [generate_sparsetools] 'scipy/sparse/sparsetools/csc_impl.h' already up-to-date
        [generate_sparsetools] 'scipy/sparse/sparsetools/other_impl.h' already up-to-date
        [generate_sparsetools] 'scipy/sparse/sparsetools/sparsetools_impl.h' already up-to-date
        building extension "scipy.spatial.transform._rotation" sources
        building extension "scipy.spatial._qhull" sources
        building extension "scipy.spatial._ckdtree" sources
        building extension "scipy.spatial._distance_wrap" sources
        building extension "scipy.spatial._distance_pybind" sources
        building extension "scipy.spatial._voronoi" sources
        copying scipy/sparse/_dia.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/_lil.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/_matrix_io.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/csr.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/construct.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/_csc.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/extract.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/base.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/_construct.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/data.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/_arrays.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/_extract.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        copying scipy/sparse/_dok.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse
        creating build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/isolve.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/_interface.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/matfuncs.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/interface.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/_expm_multiply.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/_matfuncs.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/_svdp.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/_norm.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/dsolve.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/_onenormest.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        copying scipy/sparse/linalg/eigen.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg
        creating build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/lsqr.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/tfqmr.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/iterative.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/utils.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/_gcrotmk.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/minres.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/lsmr.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        copying scipy/sparse/linalg/_isolve/lgmres.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_isolve
        creating build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_dsolve
        copying scipy/sparse/linalg/_dsolve/_add_newdocs.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_dsolve
        copying scipy/sparse/linalg/_dsolve/linsolve.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_dsolve
        copying scipy/sparse/linalg/_dsolve/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_dsolve
        copying scipy/sparse/linalg/_dsolve/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_dsolve
        creating build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen
        copying scipy/sparse/linalg/_eigen/_svds.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen
        copying scipy/sparse/linalg/_eigen/_svds_doc.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen
        copying scipy/sparse/linalg/_eigen/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen
        copying scipy/sparse/linalg/_eigen/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen
        creating build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/arpack
        copying scipy/sparse/linalg/_eigen/arpack/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/arpack
        copying scipy/sparse/linalg/_eigen/arpack/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/arpack
        copying scipy/sparse/linalg/_eigen/arpack/arpack.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/arpack
        creating build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/lobpcg
        copying scipy/sparse/linalg/_eigen/lobpcg/lobpcg.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/lobpcg
        copying scipy/sparse/linalg/_eigen/lobpcg/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/lobpcg
        copying scipy/sparse/linalg/_eigen/lobpcg/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/linalg/_eigen/lobpcg
        creating build/lib.macosx-11.0-arm64-3.8/scipy/sparse/csgraph
        copying scipy/sparse/csgraph/_laplacian.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/csgraph
        copying scipy/sparse/csgraph/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/csgraph
        copying scipy/sparse/csgraph/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/csgraph
        copying scipy/sparse/csgraph/_validation.py -> build/lib.macosx-11.0-arm64-3.8/scipy/sparse/csgraph
        creating build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/_spherical_voronoi.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/_procrustes.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/_kdtree.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/distance.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/kdtree.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/_geometric_slerp.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/_plotutils.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/ckdtree.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        copying scipy/spatial/qhull.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial
        creating build/lib.macosx-11.0-arm64-3.8/scipy/spatial/transform
        copying scipy/spatial/transform/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial/transform
        copying scipy/spatial/transform/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial/transform
        copying scipy/spatial/transform/_rotation_spline.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial/transform
        copying scipy/spatial/transform/rotation.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial/transform
        copying scipy/spatial/transform/_rotation_groups.py -> build/lib.macosx-11.0-arm64-3.8/scipy/spatial/transform
        creating build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_spfun_stats.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_sf_error.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/spfun_stats.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_testutils.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_add_newdocs.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/sf_error.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/add_newdocs.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_spherical_bessel.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_mptestutils.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_ellip_harm.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_generate_pyx.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_lambertw.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/basic.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_orthogonal.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/orthogonal.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/specfun.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_basic.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        copying scipy/special/_logsumexp.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special
        creating build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/wright_bessel_data.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/expn_asy.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/zetac.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/struve_convergence.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/loggamma.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/wright_bessel.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/gammainc_asy.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/wrightomega.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/gammainc_data.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/utils.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/cosine_cdf.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/lambertw.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        copying scipy/special/_precompute/hyp2f1_data.py -> build/lib.macosx-11.0-arm64-3.8/scipy/special/_precompute
        creating build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_multivariate.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_constants.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_result_classes.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_binned_statistic.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_distr_params.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_stats_py.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_tukeylambda_stats.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_rvs_sampling.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_relative_risk.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_stats_mstats_common.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_binomtest.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/mvn.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_bootstrap.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_hypotests_pythran.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stats
        copying scipy/stats/_ksstats.py -> build/lib.macosx-11.0-arm64-3.8/scipy/stat
        copying scipy/_lib/_testutils.py -> build/lib.macosx-11.0-arm64-3.8/scipy/_lib
        copying scipy/_lib/_pep440.py -> build/lib.macosx-11.0-arm64-3.8/scipy/_lib
        copying scipy/_lib/doccer.py -> build/lib.macosx-11.0-arm64-3.8/scipy/_lib
        creating build/lib.macosx-11.0-arm64-3.8/scipy/_lib/_uarray
        copying scipy/_lib/_uarray/_backend.py -> build/lib.macosx-11.0-arm64-3.8/scipy/_lib/_uarray
        copying scipy/_lib/_uarray/__init__.py -> build/lib.macosx-11.0-arm64-3.8/scipy/_lib/_uarray
        copying scipy/_lib/_uarray/setup.py -> build/lib.macosx-11.0-arm64-3.8/scipy/_lib/_uarray
        running build_clib
        customize UnixCCompiler
        #### ['clang', '-Wno-unused-result', '-Wsign-compare', '-Wunreachable-code', '-DNDEBUG', '-fwrapv', '-O2', '-Wall', '-fPIC', '-O2', '-isystem', '/opt/homebrew/Caskroom/miniforge/base/envs/bio/include', '-arch', 'arm64', '-fPIC', '-O2', '-isystem', '/opt/homebrew/Caskroom/miniforge/base/envs/bio/include', '-arch', 'arm64'] #######
        customize UnixCCompiler using build_clib
        CCompilerOpt.cc_test_flags[999] : testing flags (-march=native)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn
        creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay
        creating

/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils creating /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks compile options: '-c' extra options: '-march=native' CCompilerOpt.dist_test[576] : CCompilerOpt._dist_test_spawn[711] : Command (clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -c /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/test_flags.c -o /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/test_flags.o.d -march=native) failed with exit status 1 output -> clang-14: error: the clang compiler does not support '-march=native'

        CCompilerOpt.cc_test_flags[1003] : testing failed
        CCompilerOpt.cc_test_flags[999] : testing flags (-O3)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-O3'
        CCompilerOpt.cc_test_flags[999] : testing flags (-Werror)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-Werror'
        CCompilerOpt.__init__[1674] : check requested baseline
        CCompilerOpt.feature_test[1444] : testing feature 'NEON_FP16' with flags ()
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-Werror'
        CCompilerOpt.feature_test[1444] : testing feature 'NEON' with flags ()
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-Werror'
        CCompilerOpt.feature_test[1444] : testing feature 'NEON_VFPV4' with flags ()
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-Werror'
        CCompilerOpt.feature_test[1444] : testing feature 'ASIMD' with flags ()
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-Werror'
        CCompilerOpt.__init__[1683] : check requested dispatch-able features
        CCompilerOpt.cc_test_flags[999] : testing flags (-march=armv8.2-a+fp16)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-march=armv8.2-a+fp16'
        CCompilerOpt.feature_test[1444] : testing feature 'ASIMDHP' with flags (-march=armv8.2-a+fp16)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-march=armv8.2-a+fp16 -Werror'
        CCompilerOpt.cc_test_flags[999] : testing flags (-march=armv8.2-a+fp16fml)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-march=armv8.2-a+fp16fml'
        CCompilerOpt.feature_test[1444] : testing feature 'ASIMDFHM' with flags (-march=armv8.2-a+fp16+fp16fml)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-march=armv8.2-a+fp16+fp16fml -Werror'
        CCompilerOpt.dist_test[576] : CCompilerOpt._dist_test_spawn[711] : Command (clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -c /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.c -o /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.o -MMD -MF /var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/tmpi02bn307/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.o.d -march=armv8.2-a+fp16+fp16fml -Werror) failed with exit status 1 output ->
        /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.c:13:35: error: implicit declaration of function 'vfmlal_low_u32' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
            int ret  = (int)vget_lane_f32(vfmlal_low_u32(vlf, vlhp, vlhp), 0);
                                          ^
        /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.c:13:35: note: did you mean 'vfmlal_low_f16'?
        /opt/homebrew/Cellar/llvm/14.0.6_1/lib/clang/14.0.6/include/arm_neon.h:43651:18: note: 'vfmlal_low_f16' declared here
        __ai float32x2_t vfmlal_low_f16(float32x2_t __p0, float16x4_t __p1, float16x4_t __p2) {
                         ^
        /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.c:13:21: error: initializing 'float32x2_t' (vector of 2 'float32_t' values) with an expression of incompatible type 'int'
            int ret  = (int)vget_lane_f32(vfmlal_low_u32(vlf, vlhp, vlhp), 0);
                            ^             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        /opt/homebrew/Cellar/llvm/14.0.6_1/lib/clang/14.0.6/include/arm_neon.h:7978:15: note: expanded from macro 'vget_lane_f32'
          float32x2_t __s0 = __p0; \
                      ^      ~~~~
        /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.c:14:36: error: implicit declaration of function 'vfmlslq_high_u32' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
                ret += (int)vgetq_lane_f32(vfmlslq_high_u32(vf, vhp, vhp), 0);
                                           ^
        /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.c:14:36: note: did you mean 'vmlsl_high_u32'?
        /opt/homebrew/Cellar/llvm/14.0.6_1/lib/clang/14.0.6/include/arm_neon.h:69446:17: note: 'vmlsl_high_u32' declared here
        __ai uint64x2_t vmlsl_high_u32(uint64x2_t __p0, uint32x4_t __p1, uint32x4_t __p2) {
                        ^
        /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_asimdfhm.c:14:21: error: initializing 'float32x4_t' (vector of 4 'float32_t' values) with an expression of incompatible type 'int'
                ret += (int)vgetq_lane_f32(vfmlslq_high_u32(vf, vhp, vhp), 0);
                            ^              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        /opt/homebrew/Cellar/llvm/14.0.6_1/lib/clang/14.0.6/include/arm_neon.h:7788:15: note: expanded from macro 'vgetq_lane_f32'
          float32x4_t __s0 = __p0; \
                      ^      ~~~~
        4 errors generated.

        CCompilerOpt.feature_test[1458] : testing failed
        CCompilerOpt.cc_test_flags[999] : testing flags (-march=armv8.2-a+dotprod)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

        compile options: '-c'
        extra options: '-march=armv8.2-a+dotprod'
        CCompilerOpt.feature_test[1444] : testing feature 'ASIMDDP' with flags (-march=armv8.2-a+dotprod)
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64

1 warning and 2 errors generated. Running from SciPy source directory. /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/distutils/system_info.py:1989: UserWarning: Optimized (vendor) Blas libraries are not found. Falls back to netlib Blas library which has worse performance. A better performance should be easily gained by switching Blas library. if self._calc_info(blas):

        ########### EXT COMPILER OPTIMIZATION ###########
        Platform      :
          Architecture: aarch64
          Compiler    : clang

        CPU baseline  :
          Requested   : 'min'
          Enabled     : NEON NEON_FP16 NEON_VFPV4 ASIMD
          Flags       : none
          Extra checks: none

        CPU dispatch  :
          Requested   : 'max -xop -fma4'
          Enabled     : ASIMDHP ASIMDDP
          Generated   : none
        CCompilerOpt._cache_write[796] : write cache to path -> /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-install-uuwdcljm/scipy_1e5a8d6662c746f79ba39bfdd004ca74/build/temp.macosx-11.0-arm64-3.8/ccompiler_opt_cache_ext.py

        ########### CLIB COMPILER OPTIMIZATION ###########
        Platform      :
          Architecture: aarch64
          Compiler    : clang

        CPU baseline  :
          Requested   : 'min'
          Enabled     : NEON NEON_FP16 NEON_VFPV4 ASIMD
          Flags       : none
          Extra checks: none

        CPU dispatch  :
          Requested   : 'max -xop -fma4'
          Enabled     : ASIMDHP ASIMDDP
          Generated   : none
        CCompilerOpt._cache_write[796] : write cache to path -> /private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-install-uuwdcljm/scipy_1e5a8d6662c746f79ba39bfdd004ca74/build/temp.macosx-11.0-arm64-3.8/ccompiler_opt_cache_clib.py
        error: Command "clang++ -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/bio/include -arch arm64 -DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DPYTHRAN_BLAS_NONE -I/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/pythran -I/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/core/include -I/private/var/folders/y8/jrbkx6m56ls9z35szl2w0qmm0000gn/T/pip-build-env-_rz1_rsn/overlay/lib/python3.8/site-packages/numpy/core/include -Ibuild/src.macosx-11.0-arm64-3.8/numpy/distutils/include -I/opt/homebrew/Caskroom/miniforge/base/envs/bio/include/python3.8 -c scipy/interpolate/_rbfinterp_pythran.cpp -o build/temp.macosx-11.0-arm64-3.8/scipy/interpolate/_rbfinterp_pythran.o -MMD -MF build/temp.macosx-11.0-arm64-3.8/scipy/interpolate/_rbfinterp_pythran.o.d -std=c++11 -fno-math-errno -Wno-unused-function" failed with exit status 1
        [end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed building wheel for scipy
  Failed to build scipy
  ERROR: Could not build wheels for scipy, which is required to install pyproject.toml-based projects
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× pip subprocess to install build dependencies 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.

dakinggg commented 2 years ago

The error looks like it is an error installing scipy, not scispacy. Can you confirm this by trying to install scipy separately?

pika97 commented 2 years ago

I already have scipy installed

(bio) ➜ ~ pip install scipy Requirement already satisfied: scipy in /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib/python3.8/site-packages (1.8.1) Requirement already satisfied: numpy<1.25.0,>=1.17.3 in /opt/homebrew/Caskroom/miniforge/base/envs/bio/lib/python3.8/site-packages (from scipy) (1.23.1)

dakinggg commented 2 years ago

I can't reproduce as I don't have an M1 mac unfortunately. Can you make sure you can install spacy and nmslib? If you can install those two libraries, everything else should go smoothly. I'd expect one of those to be the problem. Also, please try in a new, clean environment.

dakinggg commented 2 years ago

Closing due to inactivity