Building wheel for stardist-sparse (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for stardist-sparse (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [152 lines of output]
:4: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2025-Mar-03, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
********************************************************************************
!!
opt = self.warn_dash_deprecation(opt, section)
running bdist_wheel
running build
running build_py
creating build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/version.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/rays3d.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/sample_patches.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/nms.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/__init__.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/matching.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/bioimageio_utils.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/utils.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
copying stardist/big.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist
creating build/lib.macosx-11.1-arm64-cpython-311/stardist/plot
copying stardist/plot/plot.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/plot
copying stardist/plot/render.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/plot
copying stardist/plot/__init__.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/plot
creating build/lib.macosx-11.1-arm64-cpython-311/stardist/models
copying stardist/models/model3d.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/models
copying stardist/models/model2d.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/models
copying stardist/models/__init__.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/models
copying stardist/models/base.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/models
creating build/lib.macosx-11.1-arm64-cpython-311/stardist/scripts
copying stardist/scripts/__init__.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/scripts
copying stardist/scripts/predict2d.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/scripts
copying stardist/scripts/predict3d.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/scripts
creating build/lib.macosx-11.1-arm64-cpython-311/stardist/geometry
copying stardist/geometry/__init__.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/geometry
copying stardist/geometry/geom3d.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/geometry
copying stardist/geometry/geom2d.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/geometry
creating build/lib.macosx-11.1-arm64-cpython-311/stardist/data
copying stardist/data/__init__.py -> build/lib.macosx-11.1-arm64-cpython-311/stardist/data
creating build/lib.macosx-11.1-arm64-cpython-311/stardist/kernels
copying stardist/kernels/stardist2d.cl -> build/lib.macosx-11.1-arm64-cpython-311/stardist/kernels
copying stardist/kernels/stardist3d.cl -> build/lib.macosx-11.1-arm64-cpython-311/stardist/kernels
creating build/lib.macosx-11.1-arm64-cpython-311/stardist/data/images
copying stardist/data/images/mask2d.tif -> build/lib.macosx-11.1-arm64-cpython-311/stardist/data/images
copying stardist/data/images/mask3d.tif -> build/lib.macosx-11.1-arm64-cpython-311/stardist/data/images
copying stardist/data/images/img3d.tif -> build/lib.macosx-11.1-arm64-cpython-311/stardist/data/images
copying stardist/data/images/img2d.tif -> build/lib.macosx-11.1-arm64-cpython-311/stardist/data/images
copying stardist/data/images/histo.jpg -> build/lib.macosx-11.1-arm64-cpython-311/stardist/data/images
running build_ext
building 'stardist.lib.stardist2d' extension
>>> compiling with '-fopenmp' failed
building 'stardist.lib.stardist2d' extension
>>> compiling with '-Xpreprocessor -fopenmp' failed
>>> compiling with OpenMP support failed, re-trying without
building 'stardist.lib.stardist2d' extension
Traceback (most recent call last):
File "/opt/anaconda3/envs/cellsparse-api/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/opt/anaconda3/envs/cellsparse-api/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/cellsparse-api/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 438, in build_wheel
return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 426, in _build
return self._build_with_temp_dir(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
self.run_setup()
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 320, in run_setup
exec(code, locals())
File "<string>", line 80, in <module>
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 117, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 183, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
dist.run_commands()
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
self.run_command(cmd)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 995, in run_command
super().run_command(command)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
cmd_obj.run()
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/command/bdist_wheel.py", line 381, in run
self.run_command("build")
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 995, in run_command
super().run_command(command)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
cmd_obj.run()
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 995, in run_command
super().run_command(command)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
cmd_obj.run()
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 99, in run
_build_ext.run(self)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 476, in build_extensions
self._build_extensions_serial()
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 502, in _build_extensions_serial
self.build_extension(ext)
File "<string>", line 53, in build_extension
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 264, in build_extension
_build_ext.build_extension(self, ext)
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 557, in build_extension
objects = self.compiler.compile(
^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/numpy/distutils/ccompiler.py", line 89, in <lambda>
m = lambda self, *args, **kw: func(self, *args, **kw)
^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/numpy/distutils/ccompiler.py", line 272, in CCompiler_compile
jobs = get_num_build_jobs()
^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/numpy/distutils/misc_util.py", line 91, in get_num_build_jobs
from numpy.distutils.core import get_distribution
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/numpy/distutils/core.py", line 24, in <module>
from numpy.distutils.command import config, config_compiler, \
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/numpy/distutils/command/config.py", line 19, in <module>
from numpy.distutils.mingw32ccompiler import generate_manifest
File "/private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-build-env-xia83o31/overlay/lib/python3.11/site-packages/numpy/distutils/mingw32ccompiler.py", line 28, in <module>
from distutils.msvccompiler import get_build_version as get_build_msvc_version
ModuleNotFoundError: No module named 'distutils.msvccompiler'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for stardist-sparse
Building wheel for cellpose (setup.py) ... done
Created wheel for cellpose: filename=cellpose-0.1.dev621+g5098105-py3-none-any.whl size=170599 sha256=0b99bf4b32336f24a8f2cd3024909dfdadd64a520a651db665f631442d56e0e7
Stored in directory: /private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-ephem-wheel-cache-30twmsan/wheels/31/4b/46/91befb9700a702f1a673e1722ca9db17b37e6a8002bf53353c
Building wheel for elephant (setup.py) ... done
Created wheel for elephant: filename=elephant-0.5.2-py3-none-any.whl size=69492 sha256=a753c8f735ba35a9acc095b4521b6d0abcb9c33842dbe2af6b17efe752f8d636
Stored in directory: /private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-ephem-wheel-cache-30twmsan/wheels/a9/b1/bf/091cb728623cdf01d15767a8c88977adf5ff26dba7255f03b0
Successfully built cellsparse-api cellsparse cellpose elephant
Failed to build stardist-sparse
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (stardist-sparse)
@ksugar I am having issues downloading cellsparse on my Mac M1 using the instructions provided. I get the following error:
Building wheel for stardist-sparse (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for stardist-sparse (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [152 lines of output]
:4: DeprecationWarning:
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for stardist-sparse
Building wheel for cellpose (setup.py) ... done
Created wheel for cellpose: filename=cellpose-0.1.dev621+g5098105-py3-none-any.whl size=170599 sha256=0b99bf4b32336f24a8f2cd3024909dfdadd64a520a651db665f631442d56e0e7
Stored in directory: /private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-ephem-wheel-cache-30twmsan/wheels/31/4b/46/91befb9700a702f1a673e1722ca9db17b37e6a8002bf53353c
Building wheel for elephant (setup.py) ... done
Created wheel for elephant: filename=elephant-0.5.2-py3-none-any.whl size=69492 sha256=a753c8f735ba35a9acc095b4521b6d0abcb9c33842dbe2af6b17efe752f8d636
Stored in directory: /private/var/folders/pv/1b4v_5xx1zdcx6nfk94r99scvc5cld/T/pip-ephem-wheel-cache-30twmsan/wheels/a9/b1/bf/091cb728623cdf01d15767a8c88977adf5ff26dba7255f03b0
Successfully built cellsparse-api cellsparse cellpose elephant
Failed to build stardist-sparse
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (stardist-sparse)