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Failed building wheel for pycortex ERROR Windows 10 #475
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Same issue as #248. The error is written at the end of the error message: That being said, we do not support Windows, so even if you fix this issue, the install might break for other reasons.
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@nothingyz, if you need pycortex only for the headcase pipeline, I would strongly recommend using the provided dockerfile to generate a docker container. It will have all the required dependencies, and it should work on windows too. |
Hi, I keep running into an error using
pip install -U pycortex
on my desktop and also a fresh conda environment I created. The error message is:ERROR: Failed building wheel for pycortex
Failed to build pycortex
ERROR: Could not build wheels for pycortex, which is required to install pyproject.toml-based projects
I installed all requirements and followed the documentation available here. I am trying to use this with the headcase pipeline here, and it seems pycortex is the only package that is having issues installing.
I realize this is similar to issue #435 but I am not Ubuntu and the other person on Mac OS was able to install in the end.
Here is the full error message
Collecting pycortex
Using cached pycortex-1.2.5.tar.gz (37.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting wget
Using cached wget-3.2-py3-none-any.whl
Collecting scipy
Using cached scipy-1.10.0-cp38-cp38-win_amd64.whl (42.2 MB)
Collecting future
Using cached future-0.18.2-py3-none-any.whl
Collecting numexpr
Using cached numexpr-2.8.4-cp38-cp38-win_amd64.whl (92 kB)
Collecting h5py
Using cached h5py-3.7.0-cp38-cp38-win_amd64.whl (2.6 MB)
Collecting nibabel
Using cached nibabel-4.0.2-py3-none-any.whl (3.3 MB)
Collecting imageio
Using cached imageio-2.23.0-py3-none-any.whl (3.4 MB)
Collecting pillow
Using cached Pillow-9.4.0-cp38-cp38-win_amd64.whl (2.5 MB)
Collecting tornado>=4.3
Using cached tornado-6.2-cp37-abi3-win_amd64.whl (425 kB)
Collecting matplotlib
Using cached matplotlib-3.6.2-cp38-cp38-win_amd64.whl (7.2 MB)
Collecting lxml
Using cached lxml-4.9.2-cp38-cp38-win_amd64.whl (3.9 MB)
Collecting six
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting shapely
Using cached shapely-2.0.0-cp38-cp38-win_amd64.whl (1.4 MB)
Collecting cython
Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB)
Requirement already satisfied: numpy in c:\users\yao\appdata\local\programs\python\python38\lib\site-packages (from pycortex) (1.24.1)
Collecting networkx>=2.1
Using cached networkx-2.8.8-py3-none-any.whl (2.0 MB)
Collecting html5lib
Using cached html5lib-1.1-py2.py3-none-any.whl (112 kB)
Collecting webencodings
Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting contourpy>=1.0.1
Using cached contourpy-1.0.6-cp38-cp38-win_amd64.whl (163 kB)
Collecting packaging>=20.0
Using cached packaging-22.0-py3-none-any.whl (42 kB)
Collecting cycler>=0.10
Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting pyparsing>=2.2.1
Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB)
Collecting python-dateutil>=2.7
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting fonttools>=4.22.0
Using cached fonttools-4.38.0-py3-none-any.whl (965 kB)
Collecting kiwisolver>=1.0.1
Using cached kiwisolver-1.4.4-cp38-cp38-win_amd64.whl (55 kB)
Requirement already satisfied: setuptools in c:\users\yao\appdata\local\programs\python\python38\lib\site-packages (from nibabel->pycortex) (65.6.3)
Building wheels for collected packages: pycortex
Building wheel for pycortex (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for pycortex (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [423 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-38
creating build\lib.win-amd64-cpython-38\cortex
copying cortex\align.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\anat.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\appdirs.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\brainctm.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\database.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\fmriprep.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\formats_old.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\freesurfer.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\mayavi_aligner.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\mni.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\mp.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\options.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\rois.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\segment.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\surfinfo.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\svgoverlay.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\testing_utils.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\utils.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\version.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\volume.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex\xfm.py -> build\lib.win-amd64-cpython-38\cortex
copying cortex_init_.py -> build\lib.win-amd64-cpython-38\cortex
creating build\lib.win-amd64-cpython-38\cortex\webgl
copying cortex\webgl\data.py -> build\lib.win-amd64-cpython-38\cortex\webgl
copying cortex\webgl\FallbackLoader.py -> build\lib.win-amd64-cpython-38\cortex\webgl
copying cortex\webgl\htmlembed.py -> build\lib.win-amd64-cpython-38\cortex\webgl
copying cortex\webgl\serve.py -> build\lib.win-amd64-cpython-38\cortex\webgl
copying cortex\webgl\view.py -> build\lib.win-amd64-cpython-38\cortex\webgl
copying cortex\webgl_init_.py -> build\lib.win-amd64-cpython-38\cortex\webgl
creating build\lib.win-amd64-cpython-38\cortex\mapper
copying cortex\mapper\line.py -> build\lib.win-amd64-cpython-38\cortex\mapper
copying cortex\mapper\mapper.py -> build\lib.win-amd64-cpython-38\cortex\mapper
copying cortex\mapper\patch.py -> build\lib.win-amd64-cpython-38\cortex\mapper
copying cortex\mapper\point.py -> build\lib.win-amd64-cpython-38\cortex\mapper
copying cortex\mapper\samplers.py -> build\lib.win-amd64-cpython-38\cortex\mapper
copying cortex\mapper\volume.py -> build\lib.win-amd64-cpython-38\cortex\mapper
copying cortex\mapper_init_.py -> build\lib.win-amd64-cpython-38\cortex\mapper
creating build\lib.win-amd64-cpython-38\cortex\dataset
copying cortex\dataset\braindata.py -> build\lib.win-amd64-cpython-38\cortex\dataset
copying cortex\dataset\dataset.py -> build\lib.win-amd64-cpython-38\cortex\dataset
copying cortex\dataset\view2D.py -> build\lib.win-amd64-cpython-38\cortex\dataset
copying cortex\dataset\viewRGB.py -> build\lib.win-amd64-cpython-38\cortex\dataset
copying cortex\dataset\views.py -> build\lib.win-amd64-cpython-38\cortex\dataset
copying cortex\dataset_init_.py -> build\lib.win-amd64-cpython-38\cortex\dataset
creating build\lib.win-amd64-cpython-38\cortex\blender
copying cortex\blender\blendlib.py -> build\lib.win-amd64-cpython-38\cortex\blender
copying cortex\blender_init_.py -> build\lib.win-amd64-cpython-38\cortex\blender
creating build\lib.win-amd64-cpython-38\cortex\tests
copying cortex\tests\test_dataset.py -> build\lib.win-amd64-cpython-38\cortex\tests
copying cortex\tests\test_freesurfer.py -> build\lib.win-amd64-cpython-38\cortex\tests
copying cortex\tests\test_polyutils.py -> build\lib.win-amd64-cpython-38\cortex\tests
copying cortex\tests\test_quickflat.py -> build\lib.win-amd64-cpython-38\cortex\tests
copying cortex\tests\test_utils.py -> build\lib.win-amd64-cpython-38\cortex\tests
copying cortex\tests_init_.py -> build\lib.win-amd64-cpython-38\cortex\tests
creating build\lib.win-amd64-cpython-38\cortex\quickflat
copying cortex\quickflat\composite.py -> build\lib.win-amd64-cpython-38\cortex\quickflat
copying cortex\quickflat\utils.py -> build\lib.win-amd64-cpython-38\cortex\quickflat
copying cortex\quickflat\view.py -> build\lib.win-amd64-cpython-38\cortex\quickflat
copying cortex\quickflat_init_.py -> build\lib.win-amd64-cpython-38\cortex\quickflat
creating build\lib.win-amd64-cpython-38\cortex\polyutils
copying cortex\polyutils\distortion.py -> build\lib.win-amd64-cpython-38\cortex\polyutils
copying cortex\polyutils\exact_geodesic.py -> build\lib.win-amd64-cpython-38\cortex\polyutils
copying cortex\polyutils\misc.py -> build\lib.win-amd64-cpython-38\cortex\polyutils
copying cortex\polyutils\subsurface.py -> build\lib.win-amd64-cpython-38\cortex\polyutils
copying cortex\polyutils\surface.py -> build\lib.win-amd64-cpython-38\cortex\polyutils
copying cortex\polyutils_init_.py -> build\lib.win-amd64-cpython-38\cortex\polyutils
creating build\lib.win-amd64-cpython-38\cortex\export
copying cortex\export\panels.py -> build\lib.win-amd64-cpython-38\cortex\export
copying cortex\export\save_views.py -> build\lib.win-amd64-cpython-38\cortex\export
copying cortex\export_default_params.py -> build\lib.win-amd64-cpython-38\cortex\export
copying cortex\export_init_.py -> build\lib.win-amd64-cpython-38\cortex\export
running egg_info
writing pycortex.egg-info\PKG-INFO
writing dependency_links to pycortex.egg-info\dependency_links.txt
writing requirements to pycortex.egg-info\requires.txt
writing top-level names to pycortex.egg-info\top_level.txt
reading manifest file 'pycortex.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'pycortex.egg-info\SOURCES.txt'
:5: DeprecationWarning:
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pycortex
Failed to build pycortex
ERROR: Could not build wheels for pycortex, which is required to install pyproject.toml-based projects
I am running python 3.8.0 and Windows 10 and would greatly appreciate any suggestions. Thank you in advance!
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