Can't install numpy on pypy3/Mac OSX

Issue #2949 new
champagne_alexandre created an issue

I've been trying to install numpy on the latest pypy3. I tried both the precompiled binaries on pypy.org and the latest brew version, and both yield the same output. I also tried pypy2, installing xcode command line tools, installing the full xcode - nothing.

The output I get is the following. I can't seem to wrap my head over this one.

Alexandres-MBP ~ pip_pypy3 install numpy
Collecting numpy
  Using cached https://files.pythonhosted.org/packages/2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c/numpy-1.16.1.zip
Installing collected packages: numpy
  Running setup.py install for numpy ... error
    Complete output from command /usr/local/Cellar/pypy3/6.0.0/bin/pypy3 -u -c "import setuptools, tokenize;__file__='/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-record-csvehs47/install-record.txt --single-version-externally-managed --compile:
    Running from numpy source directory.

    Note: if you need reliable uninstall behavior, then install
    with pip instead of using `setup.py install`:

      - `pip install .`       (from a git repo or downloaded source
                               release)
      - `pip install numpy`   (last NumPy release on PyPi)


    blas_opt_info:
    blas_mkl_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpj6ky3mz7/file.c
      libraries mkl_rt not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    blis_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp_qfz2skb/file.c
      libraries blis not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    openblas_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmprx9e1fn5/file.c
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpiv6n26aa/file.c
      libraries openblas not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    atlas_3_10_blas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp13puxf7n/file.c
      libraries tatlas not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    atlas_3_10_blas_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkr81mv8t/file.c
      libraries satlas not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpjyy9xzn_/file.c
      libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    atlas_blas_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpad2wybxr/file.c
      libraries f77blas,cblas,atlas not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    accelerate_info:
      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:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpvivpla8q/file.c
      libraries mkl_rt not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    openblas_lapack_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpukmeglqd/file.c
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpeudl3irx/file.c
      libraries openblas not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

    openblas_clapack_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp7jh7fy0v/file.c
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp83v2a7ej/file.c
      libraries openblas,lapack not found in ['/usr/local/Cellar/pypy3/6.0.0/libexec/lib', '/usr/local/lib', '/usr/lib']
      NOT AVAILABLE

[...]

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpcwipzrv9/file.c
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpg0zj9qr_/file.c
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp16sr7wk2/file.c
      libraries lapack_atlas not found in /usr/local/Cellar/pypy3/6.0.0/libexec/lib
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp3q4ns9eu/file.c
      libraries f77blas,cblas,atlas not found in /usr/local/Cellar/pypy3/6.0.0/libexec/lib
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpmtsagm8c/file.c
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpkw31na5h/file.c
      libraries f77blas,cblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmp4oghquyx/file.c
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/var
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/var/folders
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/var/folders/rn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T
    creating /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l
    compile options: '-MMD -MF /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/file.c.d -c'
    cc: /var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/tmpf3oghm2l/file.c
      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)]

    /usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/dist.py:261: UserWarning: Unknown distribution option: 'define_macros'
      warnings.warn(msg)
    running install
    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
    creating build
    creating build/src.macosx-10.14-x86_64-3.5
    creating build/src.macosx-10.14-x86_64-3.5/numpy
    creating build/src.macosx-10.14-x86_64-3.5/numpy/distutils
    building library "npymath" sources
    get_default_fcompiler: matching types: '['gnu95', 'nag', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']'
    customize Gnu95FCompiler
    Found executable /usr/local/bin/gfortran
    /private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/fcompiler/gnu.py:353: UserWarning: Env. variable MACOSX_DEPLOYMENT_TARGET set to 10.3
      flags = GnuFCompiler.get_flags_linker_so(self)
    customize Gnu95FCompiler
    customize Gnu95FCompiler using config
    C compiler: cc -pthread -arch x86_64 -DNDEBUG -O2 -fPIC

    compile options: '-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/usr/local/Cellar/pypy3/6.0.0/libexec/include -c'
    cc: _configtest.c
    cc -pthread -arch x86_64 _configtest.o -o _configtest
    ld: library not found for -lgcc_s.10.4
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    failure.
    removing: _configtest.c _configtest.o _configtest.o.d
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/setup.py", line 415, in <module>
        setup_package()
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/setup.py", line 407, in setup_package
        setup(**metadata)
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/core.py", line 171, in setup
        return old_setup(**new_attr)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/site-packages/setuptools/__init__.py", line 145, in setup
        return distutils.core.setup(**attrs)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/dist.py", line 955, in run_commands
        self.run_command(cmd)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/command/install.py", line 62, in run
        r = self.setuptools_run()
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/command/install.py", line 36, in setuptools_run
        return distutils_install.run(self)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/command/install.py", line 549, in run
        self.run_command('build')
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/command/build.py", line 47, in run
        old_build.run(self)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/local/Cellar/pypy3/6.0.0/libexec/lib-python/3/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/command/build_src.py", line 148, in run
        self.build_sources()
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/command/build_src.py", line 159, in build_sources
        self.build_library_sources(*libname_info)
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/command/build_src.py", line 292, in build_library_sources
        sources = self.generate_sources(sources, (lib_name, build_info))
      File "/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/numpy/distutils/command/build_src.py", line 375, in generate_sources
        source = func(extension, build_dir)
      File "numpy/core/setup.py", line 667, in get_mathlib_info
        raise RuntimeError("Broken toolchain: cannot link a simple C program")
    RuntimeError: Broken toolchain: cannot link a simple C program

    ----------------------------------------
Command "/usr/local/Cellar/pypy3/6.0.0/bin/pypy3 -u -c "import setuptools, tokenize;__file__='/private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-record-csvehs47/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/rn/d8wvxv0n7kg2jq31bfhfpxw00000gn/T/pip-install-gsqxbr53/numpy/

Comments (7)

  1. Andrew Stepanov

    Try installing with

    $ MACOSX_DEPLOYMENT_TARGET=10.14 pip install numpy
    

    I don't think this is PyPy's fault. You get the exact same error when building from source on CPython.

  2. William Hua

    I'm experiencing the same issue.

    I've tried installing with the above recommendation( MACOSX_DEPLOYMENT_TARGET=10.14 pip install numpy) and it's not working as well.

    I'm trying this with PyPy3.6 v7.0.0 on OSX 10.14 (Mojave).

  3. Julian Berman

    @mattip this I think is a difference with CPython, since on this machine for me, I don't in fact need to set it (even when running pip install --no-binary numpy).

  4. Julian Berman

    I haven’t yet gotten a chance to fully write up and verify I have this fixed – too many other things, but am trying to get to that by EOW --

    For anyone else having this issue, the only other thing I am already aware of that messes things up, is if you have binutils (and therefore a /usr/local/bin/ar) installed via homebrew, uninstall that, since gnu ar appears to not work on macOS, or at least, what it outputs neither clang nor gcc are happy with. I couldn’t even get them to be happy after removing /usr/local/bin from my path, until I fully uninstalled it somehow.

    But yeah hoping to find time to come back to this and write up whatever I’ve figured out – I can say I believe I’ve successfully gotten a numpy installation on pypy3 now, so I just need to fully bisect all the things that I did that were needed to get there.

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