8000 Installation fails on MacOS 10.11 El Capitan with Python 3.10 · Issue #24113 · scikit-learn/scikit-learn · GitHub
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OBgoneSouth opened this issue Aug 4, 2022 · 1 comment · Fixed by #23833
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Installation fails on MacOS 10.11 El Capitan with Python 3.10 #24113

OBgoneSouth opened this issue Aug 4, 2022 · 1 comment · Fixed by #23833
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Bug Needs Triage Issue requires triage

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@OBgoneSouth
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Describe the bug

There is a scikit_learn-1.1.1-cp310-cp310-macosx_10_13_x86_64.whl Wheel available on PyPi, but nothing compatible with earlier versions of MacOS running Python 3.10

As a result, pip attempts to compile from source. This fails as below.

Numpy and SciPy are already installed.

python3 -m pip show numpy
Name: numpy
Version: 1.21.3
Summary: NumPy is the fundamental package for array computing with Python.
Home-page: https://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email: 
License: BSD
Location: /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages
Requires: 
Required-by: matplotlib, pandas, pytorch-lightning, scipy, tensorboard, torchmetrics, transformers

Steps/Code to Reproduce

python3 -m pip install scikit-learn

Expected Results

Something like

Downloading scikit_learn-1.1.1-cp310-cp310-macosx_10_9_x86_64.whl

Actual Results

Collecting scikit-learn
  Downloading scikit-learn-1.1.1.tar.gz (6.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.8/6.8 MB 3.5 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [139 lines of output]
      Partial import of sklearn during the build process.
      C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
      
      compile options: '-c'
      clang: test_program.c
      In file included from test_program.c:1:
      In file included from /usr/include/stdio.h:64:
      /usr/include/sys/cdefs.h:707:2: error: Unsupported architecture
      #error Unsupported architecture
       ^
      In file included from test_program.c:1:
      In file included from /usr/include/stdio.h:67:
      In file included from /usr/include/_types.h:27:
      In file included from /usr/include/sys/_types.h:33:
      /usr/include/machine/_types.h:34:2: error: architecture not supported
      #error architecture not supported
       ^
      In file included from test_program.c:1:
      In file included from /usr/include/stdio.h:67:
      In file included from /usr/include/_types.h:27:
      /usr/include/sys/_types.h:55:9: error: unknown type name '__int64_t'; did you mean '__int128_t'?
      typedef __int64_t       __darwin_blkcnt_t;      /* total blocks */
              ^
      note: '__int128_t' declared here
      /usr/include/sys/_types.h:56:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
      typedef __int32_t       __darwin_blksize_t;     /* preferred block size */
              ^
      note: '__int128_t' declared here
      /usr/include/sys/_types.h:57:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
      typedef __int32_t       __darwin_dev_t;         /* dev_t */
              ^
      note: '__int128_t' declared here
      /usr/include/sys/_types.h:60:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
      typedef __uint32_t      __darwin_gid_t;         /* [???] process and group IDs */
              ^
      note: '__uint128_t' declared here
      /usr/include/sys/_types.h:61:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
      typedef __uint32_t      __darwin_id_t;          /* [XSI] pid_t, uid_t, or gid_t*/
              ^
      note: '__uint128_t' declared here
      /usr/include/sys/_types.h:62:9: error: unknown type name '__uint64_t'; did you mean '__uint128_t'?
      typedef __uint64_t      __darwin_ino64_t;       /* [???] Used for 64 bit inodes */
              ^
      note: '__uint128_t' declared here
      /usr/include/sys/_types.h:68:9: error: unknown type name '__darwin_natural_t'
      typedef __darwin_natural_t __darwin_mach_port_name_t; /* Used by mach */
              ^
      /usr/include/sys/_types.h:70:9: error: unknown type name '__uint16_t'; did you mean '__uint128_t'?
      typedef __uint16_t      __darwin_mode_t;        /* [???] Some file attributes */
              ^
      note: '__uint128_t' declared here
      /usr/include/sys/_types.h:71:9: error: unknown type name '__int64_t'; did you mean '__int128_t'?
      typedef __int64_t       __darwin_off_t;         /* [???] Used for file sizes */
              ^
      note: '__int128_t' declared here
      /usr/include/sys/_types.h:72:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
      typedef __int32_t       __darwin_pid_t;         /* [???] process and group IDs */
              ^
      note: '__int128_t' declared here
      /usr/include/sys/_types.h:73:9: error: unknown 
8000
type name '__uint32_t'; did you mean '__uint128_t'?
      typedef __uint32_t      __darwin_sigset_t;      /* [???] signal set */
              ^
      note: '__uint128_t' declared here
      /usr/include/sys/_types.h:74:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
      typedef __int32_t       __darwin_suseconds_t;   /* [???] microseconds */
              ^
      note: '__int128_t' declared here
      /usr/include/sys/_types.h:75:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
      typedef __uint32_t      __darwin_uid_t;         /* [???] user IDs */
              ^
      note: '__uint128_t' declared here
      /usr/include/sys/_types.h:76:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
      typedef __uint32_t      __darwin_useconds_t;    /* [???] microseconds */
              ^
      note: '__uint128_t' declared here
      In file included from test_program.c:1:
      In file included from /usr/include/stdio.h:67:
      /usr/include/_types.h:42:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
      typedef __uint32_t      __darwin_wctype_t;
              ^
      note: '__uint128_t' declared here
      In file included from test_program.c:1:
      In file included from /usr/include/stdio.h:71:
      /usr/include/sys/_types/_va_list.h:31:9: error: unknown type name '__darwin_va_list'
      typedef __darwin_va_list va_list;
              ^
      In file included from test_program.c:1:
      In file included from /usr/include/stdio.h:72:
      /usr/include/sys/_types/_size_t.h:30:9: error: unknown type name '__darwin_size_t'
      typedef __darwin_size_t        size_t;
              ^
      fatal error: too many errors emitted, stopping now [-ferror-limit=]
      20 errors generated.
      Traceback (most recent call last):
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 164, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 267, in run_setup
          super(_BuildMetaLegacyBackend,
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 158, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 328, in <module>
          setup_package()
        File "setup.py", line 324, in setup_package
          setup(**metadata)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/core.py", line 135, in setup
          config = configuration()
        File "setup.py", line 187, in configuration
          config.add_subpackage("sklearn")
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/misc_util.py", line 1014, in add_subpackage
          config_list = self.get_subpackage(subpackage_name, subpackage_path,
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/misc_util.py", line 980, in get_subpackage
          config = self._get_configuration_from_setup_py(
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/misc_util.py", line 922, in _get_configuration_from_setup_py
          config = setup_module.configuration(*args)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-install-nsycs__4/scikit-learn_cf1850107767490faaca5f091aa388b9/sklearn/setup.py", line 85, in configuration
          cythonize_extensions(top_path, config)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-install-nsycs__4/scikit-learn_cf1850107767490faaca5f091aa388b9/sklearn/_build_utils/__init__.py", line 47, in cythonize_extensions
          basic_check_build()
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-install-nsycs__4/scikit-learn_cf1850107767490faaca5f091aa388b9/sklearn/_build_utils/pre_build_helpers.py", line 119, in basic_check_build
          compile_test_program(code)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-install-nsycs__4/scikit-learn_cf1850107767490faaca5f091aa388b9/sklearn/_build_utils/pre_build_helpers.py", line 75, in compile_test_program
          ccompiler.compile(
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/ccompiler.py", line 89, in <lambda>
          m = lambda self, *args, **kw: func(self, *args, **kw)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/ccompiler.py", line 366, in CCompiler_compile
          single_compile(o)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/ccompiler.py", line 326, in single_compile
          self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/ccompiler.py", line 89, in <lambda>
          m = lambda self, *args, **kw: func(self, *args, **kw)
        File "/private/var/folders/9j/28vfzp751lbf5yhsr208gkp00000gn/T/pip-build-env-i5bosgpj/overlay/lib/python3.10/site-packages/numpy/distutils/unixccompiler.py", line 57, in UnixCCompiler__compile
          raise CompileError(msg) from None
      distutils.errors.CompileError: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -c test_program.c -o objects/test_program.o" failed with exit status 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Versions

Trying to install the latest version, but same seems to apply to earlier ones.

Release 0.24.0 in December 2020 appears to be the last one with a MacOS 10.9 build, but for Python 3.9

scikit_learn-0.24.0-cp39-cp39-macosx_10_9_x86_64.whl


(Incidentally, the same problem exists with scikit-image after release 0.18.3 in August 2021.)
@OBgoneSouth OBgoneSouth added Bug Needs Triage Issue requires triage labels Aug 4, 2022
@thomasjpfan thomasjpfan mentioned this issue Aug 4, 2022
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@OBgoneSouth
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Thanks so much for doing this: very much appreciated.

Just to expand on why there may be reasonable demand for support of older versions of MacOS if there's no fundamental limitation: it's down to 32-bit support and APFS in a multitude of different scenarios.

Just as an example, it might make sense to upgrade a well-spec'd Late-2012 Mac Mini to 10.14 Mojave, as the last version to still support 32-bit applications.

Normally, why even hesitate?

But APFS doesn't support booting from an AppleRAID volume, so if your higher spec included RAID1 redundancy, you suddenly have a new obstacle. MacOS 10.13 High Sierra may or may not require APFS conversion, depending on whether you've previously upgraded to SSD; but 10.14 Mojave definitely will.

It still makes sense to upgrade, but not so much to 10.13; and it also makes sense to delay further whilst you solve data security (and/or other practical) issues.

@OBgoneSouth OBgoneSouth mentioned this issue Aug 8, 2022
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CI Set MACOSX_DEPLOYMENT_TARGET=10.9 thomasjpfan/scikit-learn
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