Poetry fails to install numpy on big sur

[nacaclanga]

Bug report

Please note we will close your issue without comment if you delete, do not read or do not fill out the issue checklist below and provide ALL the requested information. If you repeatedly fail to use the issue template, we will block you from ever submitting issues to Homebrew again.

• ran brew update and can still reproduce the problem?
• ran brew doctor, fixed all issues and can still reproduce the problem?
• ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
• if brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?

What you were trying to do (and why)

Using poetry to manage dependencies and install plattform dependend packages like numpy.

What happened (include command output)

Command output

%poetry add numpy
  Using version ^1.19.4 for numpy
Updating dependencies

Resolving dependencies... (0.9s)
Writing lock file
Package operations: 9 installs, 0 updates, 0 removals
• Installing pyparsing (2.4.7)

• Installing attrs (20.3.0)

• Installing more-itertools (8.6.0)

• Installing packaging (20.7)

• Installing pluggy (0.13.1)

• Installing py (1.9.0)

• Installing wcwidth (0.2.5)

• Installing numpy (1.19.4): Failed
EnvCommandError
Command ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/bin/pip', 'install', '--no-deps', 'file:///Users/sannaj/Library/Caches/pypoetry/artifacts/73/82/44/220b707252fd91e000dd4b03beaa62dad1e7ef8d32db919dd96ad6f104/numpy-1.19.4.zip'] errored with the following return code 1, and output:

Processing /Users/sannaj/Library/Caches/pypoetry/artifacts/73/82/44/220b707252fd91e000dd4b03beaa62dad1e7ef8d32db919dd96ad6f104/numpy-1.19.4.zip

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 'error'

ERROR: Command errored out with exit status 1:

command: /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/bin/python /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/tmpdya657f2

cwd: /private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam

Complete output (209 lines):

Running from numpy source directory.

setup.py:480: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates

run_build = parse_setuppy_commands()

Processing numpy/random/_bounded_integers.pxd.in

Processing numpy/random/_philox.pyx

Processing numpy/random/_bounded_integers.pyx.in

Processing numpy/random/_sfc64.pyx

Processing numpy/random/_mt19937.pyx

Processing numpy/random/bit_generator.pyx

Processing numpy/random/mtrand.pyx

Processing numpy/random/_generator.pyx

Processing numpy/random/_pcg64.pyx

Processing numpy/random/_common.pyx

Cythonizing sources

blas_opt_info:

blas_mkl_info:

customize UnixCCompiler

libraries mkl_rt not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']

NOT AVAILABLE
  blis_info:
    libraries blis not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  openblas_info:
    libraries openblas not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  atlas_3_10_blas_threads_info:
  Setting PTATLAS=ATLAS
    libraries tatlas not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  atlas_3_10_blas_info:
    libraries satlas not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  atlas_blas_threads_info:
  Setting PTATLAS=ATLAS
    libraries ptf77blas,ptcblas,atlas not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  atlas_blas_info:
    libraries f77blas,cblas,atlas not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  accelerate_info:
    libraries accelerate not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
  Library accelerate was not found. Ignoring
    libraries veclib not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
  Library veclib was not found. Ignoring
    FOUND:
      extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
      extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
      define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
  
    FOUND:
      extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
      extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
      define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
  
  non-existing path in 'numpy/distutils': 'site.cfg'
  lapack_opt_info:
  lapack_mkl_info:
    libraries mkl_rt not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  openblas_lapack_info:
    libraries openblas not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  openblas_clapack_info:
    libraries openblas,lapack not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  flame_info:
    libraries flame not found in ['/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib', '/usr/local/lib', '/usr/lib']
    NOT AVAILABLE
  
  atlas_3_10_threads_info:
  Setting PTATLAS=ATLAS
    libraries lapack_atlas not found in /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib
    libraries tatlas,tatlas not found in /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/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 /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib
    libraries satlas,satlas not found in /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/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 /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib
    libraries ptf77blas,ptcblas,atlas not found in /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/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 /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib
    libraries f77blas,cblas,atlas not found in /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib
    libraries lapack_atlas not found in /usr/local/lib
    libraries f77blas,cblas,atlas not found in /usr/local/lib
    libraries lapack_atlas not found in /usr/lib
    libraries f77blas,cblas,atlas not found in /usr/lib
  <class 'numpy.distutils.system_info.atlas_info'>
    NOT AVAILABLE
  
    FOUND:
      extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
      extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
      define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
  
  /usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
    warnings.warn(msg)
  running dist_info
  running build_src
  build_src
  building py_modules sources
  creating build
  creating build/src.macosx-11-x86_64-3.9
  creating build/src.macosx-11-x86_64-3.9/numpy
  creating build/src.macosx-11-x86_64-3.9/numpy/distutils
  building library "npymath" sources
  Traceback (most recent call last):
    File "/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 280, in <module>
      main()
    File "/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 263, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 133, in prepare_metadata_for_build_wheel
      return hook(metadata_directory, config_settings)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-build-env-xia9l98z/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 157, in prepare_metadata_for_build_wheel
      self.run_setup()
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-build-env-xia9l98z/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 248, in run_setup
      super(_BuildMetaLegacyBackend,
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-build-env-xia9l98z/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 142, in run_setup
      exec(compile(code, __file__, 'exec'), locals())
    File "setup.py", line 508, in <module>
      setup_package()
    File "setup.py", line 500, in setup_package
      setup(**metadata)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/core.py", line 169, in setup
      return old_setup(**new_attr)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-build-env-xia9l98z/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 165, in setup
      return distutils.core.setup(**attrs)
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-build-env-xia9l98z/overlay/lib/python3.9/site-packages/setuptools/command/dist_info.py", line 31, in run
      egg_info.run()
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/command/egg_info.py", line 24, in run
      self.run_command("build_src")
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/command/build_src.py", line 144, in run
      self.build_sources()
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/command/build_src.py", line 155, in build_sources
      self.build_library_sources(*libname_info)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/command/build_src.py", line 288, in build_library_sources
      sources = self.generate_sources(sources, (lib_name, build_info))
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/command/build_src.py", line 378, in generate_sources
      source = func(extension, build_dir)
    File "numpy/core/setup.py", line 658, in get_mathlib_info
      st = config_cmd.try_link('int main(void) { return 0;}')
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/command/config.py", line 241, in try_link
      self._check_compiler()
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/command/config.py", line 80, in _check_compiler
      self.fcompiler = new_fcompiler(compiler=self.fcompiler,
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/__init__.py", line 880, in new_fcompiler
      compiler = get_default_fcompiler(plat, requiref90=requiref90,
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/__init__.py", line 851, in get_default_fcompiler
      compiler_type =  _find_existing_fcompiler(matching_compiler_types,
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/__init__.py", line 802, in _find_existing_fcompiler
      c.customize(dist)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/__init__.py", line 526, in customize
      linker_so_flags = self.flag_vars.linker_so
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/environment.py", line 37, in __getattr__
      return self._get_var(name, conf_desc)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/environment.py", line 53, in _get_var
      var = self._hook_handler(name, hook)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/__init__.py", line 705, in _environment_hook
      return hook()
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/gnu.py", line 346, in get_flags_linker_so
      flags = GnuFCompiler.get_flags_linker_so(self)
    File "/private/var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/pip-req-build-zkhrmwam/numpy/distutils/fcompiler/gnu.py", line 136, in get_flags_linker_so
      os.environ['MACOSX_DEPLOYMENT_TARGET'] = target
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 684, in __setitem__
      value = self.encodevalue(value)
    File "/usr/local/Cellar/[email protected]/3.9.0_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 756, in encode
      raise TypeError("str expected, not %s" % type(value).__name__)
  TypeError: str expected, not int
  ----------------------------------------

ERROR: Command errored out with exit status 1: /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/bin/python /Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/kf/25msxpx52j98k6qm2pgq11rh0000gn/T/tmpdya657f2 Check the logs for full command output.

WARNING: You are using pip version 20.2.4; however, version 20.3.1 is available.

You should consider upgrading via the '/Users/sannaj/Library/Caches/pypoetry/virtualenvs/bigsurtest-oBpdMjZr-py3.9/bin/python -m pip install --upgrade pip' command.
at /usr/local/Cellar/poetry/1.1.4/libexec/lib/python3.9/site-packages/poetry/utils/env.py:1074 in run

1070│                 output = subprocess.check_output(

1071│                     cmd, stderr=subprocess.STDOUT, **kwargs

1072│                 )

1073│         except CalledProcessError as e:

→ 1074│             raise EnvCommandError(e, input=input)

1075│

1076│         return decode(output)

1077│

1078│     def execute(self, bin, *args, **kwargs):
• Installing pytest (5.4.3)
Failed to add packages, reverting the pyproject.toml file to its original content.
  

What you expected to happen

Successfull installation

Step-by-step reproduction instructions (by running brew install commands)

brew install poetry
poetry new bigsurtest
cd bigsurtest
poetry add numpy

I suspect that this is due to homebrew using an older version of "packaging" for poetry, that fails to use macOS 10.X wheels on Big Sur. See e.g. pypa/pip#9138 pypa/packaging#319. The poetry formula installes pinned versions different from https://github.com/python-poetry/poetry/blob/master/poetry.lock so this likely issue.

[fxcoudert]

This is an issue in numpy: numpy/numpy#17906