Install on IpadOS v16.6

[Nicolaeus]

Describe the bug
When I install with pip I have this issue :

Defaulting to user installation because normal site-packages is not writeable
Collecting SimpleITK
Using cached SimpleITK-2.1.1.2.tar.gz (2.0 MB)
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'

error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [55 lines of output]
running dist_info
creating /private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK.egg-info
writing /private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK.egg-info/PKG-INFO
writing dependency_links to /private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK.egg-info/dependency_links.txt
writing top-level names to /private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK.egg-info/top_level.txt
writing manifest file '/private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK.egg-info/SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file '/private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'SimpleITK/.ExternalData'
warning: no previously-included files matching '.git*' found anywhere in distribution
writing manifest file '/private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK.egg-info/SOURCES.txt'
creating '/private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-modern-metadata-55jiw8v6/SimpleITK-2.1.1.2.dist-info'
Traceback (most recent call last):
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in
main()
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/build_meta.py", line 377, in prepare_metadata_for_build_wheel
self.run_setup()
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/build_meta.py", line 335, in run_setup
exec(code, locals())
File "", line 9, in
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/scikit_build-0.11.2.dev202+g9cc7823-py3.11.egg/skbuild/setuptools_wrap.py", line 507, in setup
return setuptools.setup(**kw)
^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/init.py", line 108, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/dist.py", line 1213, in run_command
super().run_command(command)
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/command/dist_info.py", line 101, in run
bdist_wheel = self.get_finalized_command('bdist_wheel')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 305, in get_finalized_command
cmd_obj.ensure_finalized()
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 111, in ensure_finalized
self.finalize_options()
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/scikit_build-0.11.2.dev202+g9cc7823-py3.11.egg/skbuild/command/bdist_wheel.py", line 54, in finalize_options
if sys.platform == 'darwin' and self.plat_name is None and self.distribution.has_ext_modules():
^^^
NameError: name 'sys' is not defined
[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.

To Reproduce
Steps to reproduce the behavior:

1. Operating system, version, and architecture

• OS: [IpadOs v16.6 ]
• Architecture: [Ipad gen6]

2. Programming language, and version [Python 3.11, ].
3. Version of SimpleITK : no version.
4. How was SimpleITK installed?

• binary distribution : pip install SimpleITK in app Carnets

Expected behavior

Fix it ^^

Images
If applicable, include a minimal sized sample input and output image. Or SimpleITK commands to synthetically generate
an input.

Additional context

If you can fix it, it will be cool!
Thank you !!
Nicolaeus

[blowekamp]

The error message comes from scikit-build. And the path includes "scikit_build-0.11.2.dev202+g9cc7823-py3.11.egg" which I will presume is the version of the tool. I suggest update scikit-build to a recent release.

[Nicolaeus]

I test to upgrade but I have this now about scikit-learn :

error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [43 lines of output]
Partial import of sklearn during the build process.
clang: command not found
Traceback (most recent call last):
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/unixccompiler.py", line 186, in _compile
self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs)
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/ccompiler.py", line 1007, in spawn
spawn(cmd, dry_run=self.dry_run, **kwargs)
File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/spawn.py", line 70, in spawn
raise DistutilsExecError(
distutils.errors.DistutilsExecError: command 'clang' failed with exit code 127

  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
      main()
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
      return hook(metadata_directory, config_settings)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/build_meta.py", line 377, in prepare_metadata_for_build_wheel
      self.run_setup()
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/build_meta.py", line 485, in run_setup
      self).run_setup(setup_script=setup_script)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/build_meta.py", line 335, in run_setup
      exec(code, locals())
    File "<string>", line 632, in <module>
    File "<string>", line 626, in setup_package
    File "<string>", line 554, in configure_extension_modules
    File "/private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-install-452fswso/scikit-learn_654e8b0618a14185b79e74b4848aab21/sklearn/_build_utils/__init__.py", line 46, in cythonize_extensions
      basic_check_build()
    File "/private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-install-452fswso/scikit-learn_654e8b0618a14185b79e74b4848aab21/sklearn/_build_utils/pre_build_helpers.py", line 73, in basic_check_build
      compile_test_program(code)
    File "/private/var/mobile/Containers/Data/Application/215DDBCB-76A7-41AB-9C97-9B17FEAAD2F6/tmp/pip-install-452fswso/scikit-learn_654e8b0618a14185b79e74b4848aab21/sklearn/_build_utils/pre_build_helpers.py", line 31, in compile_test_program
      ccompiler.compile(
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/ccompiler.py", line 599, in compile
      self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
    File "/private/var/containers/Bundle/Application/DFC8B3A9-6316-49EC-8A77-53F902881EFC/Carnets-sci.app/Library/lib/python3.11/site-packages/setuptools/_distutils/unixccompiler.py", line 188, in _compile
      raise CompileError(msg)
  distutils.errors.CompileError: command 'clang' failed with exit code 127
  [end of output]

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

[zivy]

Closing due to long time since question was asked. If still relevant please feel free to reopen.