Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[BUG] pypi version mismatch #828

Open
jxchen01 opened this issue May 22, 2023 · 2 comments
Open

[BUG] pypi version mismatch #828

jxchen01 opened this issue May 22, 2023 · 2 comments
Labels
bug

Comments

@jxchen01
Copy link

Describe the bug
when installing the package via pypi, there is a meta data mismatch:

Requested pyradiomics from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz has inconsistent version: expected '3.1.0', but metadata has '3.0.1a1'

PyRadiomics configuration

N/A

To Reproduce

pip install pyradiomics with Python=3.9

Version (please complete the following information):

  • OS: MacOS 13.3.1
  • Python version: 3.9
  • PyRadiomics version: 3.1.0
@jxchen01 jxchen01 added the bug label May 22, 2023
@jxchen01
Copy link
Author

further error message:

 Using cached pyradiomics-3.0.1.tar.gz (34.5 MB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy>=1.9.2 in ./opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages (from pyradiomics) (1.24.3)
Collecting SimpleITK>=0.9.1
  Downloading SimpleITK-2.2.1-cp38-cp38-macosx_10_9_x86_64.whl (45.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.5/45.5 MB 9.1 MB/s eta 0:00:00
Collecting PyWavelets>=0.4.0
  Using cached PyWavelets-1.4.1-cp38-cp38-macosx_10_13_x86_64.whl (4.3 MB)
Collecting pykwalify>=1.6.0
  Using cached pykwalify-1.8.0-py2.py3-none-any.whl (24 kB)
Collecting six>=1.10.0
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting ruamel.yaml>=0.16.0
  Using cached ruamel.yaml-0.17.26-py3-none-any.whl (109 kB)
Collecting docopt>=0.6.2
  Using cached docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py) ... done
Collecting python-dateutil>=2.8.0
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting ruamel.yaml.clib>=0.2.7
  Downloading ruamel.yaml.clib-0.2.7-cp38-cp38-macosx_10_9_x86_64.whl (143 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.4/143.4 kB 4.9 MB/s eta 0:00:00
Building wheels for collected packages: pyradiomics, docopt
  Building wheel for pyradiomics (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [41 lines of output]
      /Users/jianxuchen/opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages/setuptools/dist.py:770: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
        warnings.warn(
      /Users/jianxuchen/opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages/setuptools/dist.py:529: UserWarning: Normalizing 'v3.0.1' to '3.0.1'
        warnings.warn(tmpl.format(**locals()))
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-10.9-x86_64-cpython-38
      creating build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/featureextractor.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/glcm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/shape2D.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/_version.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/gldm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/firstorder.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/ngtdm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/glrlm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/glszm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/imageoperations.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/shape.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/generalinfo.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/base.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      creating build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      copying radiomics/scripts/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      copying radiomics/scripts/voxel.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      copying radiomics/scripts/segment.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      creating build/lib.macosx-10.9-x86_64-cpython-38/radiomics/schemas
      copying radiomics/schemas/paramSchema.yaml -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/schemas
      copying radiomics/schemas/schemaFuncs.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/schemas
      UPDATING build/lib.macosx-10.9-x86_64-cpython-38/radiomics/_version.py
      set build/lib.macosx-10.9-x86_64-cpython-38/radiomics/_version.py to 'v3.0.1'
      running build_ext
      building 'radiomics._cmatrices' extension
      creating build/temp.macosx-10.9-x86_64-cpython-38
      creating build/temp.macosx-10.9-x86_64-cpython-38/radiomics
      creating build/temp.macosx-10.9-x86_64-cpython-38/radiomics/src
      gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include -arch x86_64 -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include -arch x86_64 -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include/python3.8 -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages/numpy/core/include -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include/python3.8 -c radiomics/src/_cmatrices.c -o build/temp.macosx-10.9-x86_64-cpython-38/radiomics/src/_cmatrices.o
      xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pyradiomics
  Running setup.py clean for pyradiomics
  Building wheel for docopt (setup.py) ... done
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=dcdd99741564d8ed51da9385f913854283e5b4b9dc3c0bc9e7ec07a87a72f36e
  Stored in directory: /Users/jianxuchen/Library/Caches/pip/wheels/56/ea/58/ead137b087d9e326852a851351d1debf4ada529b6ac0ec4e8c
Successfully built docopt
Failed to build pyradiomics
Installing collected packages: SimpleITK, docopt, six, ruamel.yaml.clib, PyWavelets, ruamel.yaml, python-dateutil, pykwalify, pyradiomics
  Running setup.py install for pyradiomics ... error
  error: subprocess-exited-with-error

  × Running setup.py install for pyradiomics did not run successfully.
  │ exit code: 1
  ╰─> [43 lines of output]
      /Users/jianxuchen/opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages/setuptools/dist.py:770: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
        warnings.warn(
      /Users/jianxuchen/opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages/setuptools/dist.py:529: UserWarning: Normalizing 'v3.0.1' to '3.0.1'
        warnings.warn(tmpl.format(**locals()))
      running install
      /Users/jianxuchen/opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      running build_py
      creating build
      creating build/lib.macosx-10.9-x86_64-cpython-38
      creating build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/featureextractor.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/glcm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/shape2D.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/_version.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/gldm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/firstorder.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/ngtdm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/glrlm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/glszm.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/imageoperations.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/shape.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/generalinfo.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      copying radiomics/base.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics
      creating build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      copying radiomics/scripts/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      copying radiomics/scripts/voxel.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      copying radiomics/scripts/segment.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/scripts
      creating build/lib.macosx-10.9-x86_64-cpython-38/radiomics/schemas
      copying radiomics/schemas/paramSchema.yaml -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/schemas
      copying radiomics/schemas/schemaFuncs.py -> build/lib.macosx-10.9-x86_64-cpython-38/radiomics/schemas
      UPDATING build/lib.macosx-10.9-x86_64-cpython-38/radiomics/_version.py
      set build/lib.macosx-10.9-x86_64-cpython-38/radiomics/_version.py to 'v3.0.1'
      running build_ext
      building 'radiomics._cmatrices' extension
      creating build/temp.macosx-10.9-x86_64-cpython-38
      creating build/temp.macosx-10.9-x86_64-cpython-38/radiomics
      creating build/temp.macosx-10.9-x86_64-cpython-38/radiomics/src
      gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include -arch x86_64 -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include -arch x86_64 -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include/python3.8 -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/lib/python3.8/site-packages/numpy/core/include -I/Users/jianxuchen/opt/anaconda3/envs/validomics_dev/include/python3.8 -c radiomics/src/_cmatrices.c -o build/temp.macosx-10.9-x86_64-cpython-38/radiomics/src/_cmatrices.o
      xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pyradiomics

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

@lyhyl lyhyl mentioned this issue Jun 5, 2023
Open
@Solene81
Copy link

Hi yes we have the same issue, is there any workaround ?

@sjswerdloff sjswerdloff mentioned this issue Aug 14, 2023
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@jxchen01 @Solene81