The whole historic is too long to paste–seems like everything was fine before this.
All requirements installed!
Installing data...
rm -rf /Users/akb46/sct_5.0.0/data
mkdir -p /Users/akb46/sct_5.0.0/data
sct_download_data -d PAM50 -o /Users/akb46/sct_5.0.0/data/PAM50
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Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/PAM50”
Trying URL: https://github.com/sct-data/PAM50/releases/download/r20201104/PAM50-r20201104.zip
Downloading: PAM50-r20201104.zip
Status: 100%|██████████████████████████████| 70.9M/70.9M [00:02<00:00, 28.3MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094748.963278-5o8uird_)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094748.963278-5o8uird_
Removing temporary folders...
Done!
sct_download_data -d gm_model -o /Users/akb46/sct_5.0.0/data/gm_model
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Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/gm_model”
Trying URL: https://osf.io/ugscu/?action=download
Downloading: 20160922_gm_model.zip
Status: 100%|██████████████████████████████| 10.3M/10.3M [00:00<00:00, 17.9MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094752.914972-6y_1adcj)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094752.914972-6y_1adcj
Removing temporary folders...
Done!
sct_download_data -d optic_models -o /Users/akb46/sct_5.0.0/data/optic_models
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Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/optic_models”
Trying URL: https://github.com/sct-data/optic_models/releases/download/r20170413/20170413_optic_models.zip
Downloading: 20170413_optic_models.zip
Status: 100%|██████████████████████████████| 17.7k/17.7k [00:00<00:00, 46.4MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094753.701350-m3hav8q9)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094753.701350-m3hav8q9
Removing temporary folders...
Done!
sct_download_data -d pmj_models -o /Users/akb46/sct_5.0.0/data/pmj_models
--
Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/pmj_models”
Trying URL: https://github.com/sct-data/pmj_models/releases/download/r20170922/20170922_pmj_models.zip
Downloading: 20170922_pmj_models.zip
Status: 100%|██████████████████████████████| 8.87k/8.87k [00:00<00:00, 31.8MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094754.472992-t709hnpv)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094754.472992-t709hnpv
Removing temporary folders...
Done!
sct_download_data -d deepseg_sc_models -o /Users/akb46/sct_5.0.0/data/deepseg_sc_models
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Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/deepseg_sc_models”
Trying URL: https://github.com/sct-data/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip
Downloading: 20180610_deepseg_sc_models.zip
Status: 100%|██████████████████████████████| 58.7M/58.7M [00:02<00:00, 27.8MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094757.314871-5u14n246)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094757.314871-5u14n246
Removing temporary folders...
Done!
sct_download_data -d deepseg_gm_models -o /Users/akb46/sct_5.0.0/data/deepseg_gm_models
--
Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/deepseg_gm_models”
Trying URL: https://github.com/sct-data/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip
Downloading: 20180205_deepseg_gm_models.zip
Status: 100%|██████████████████████████████| 2.28M/2.28M [00:00<00:00, 13.2MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094758.621805-5laql2r4)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094758.621805-5laql2r4
Removing temporary folders...
Done!
sct_download_data -d deepseg_lesion_models -o /Users/akb46/sct_5.0.0/data/deepseg_lesion_models
--
Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/deepseg_lesion_models”
Trying URL: https://github.com/sct-data/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip
Downloading: 20180613_deepseg_lesion_models.zip
Status: 100%|██████████████████████████████| 16.0M/16.0M [00:00<00:00, 25.0MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094800.060726-39l_4l62)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094800.060726-39l_4l62
Removing temporary folders...
Done!
sct_download_data -d c2c3_disc_models -o /Users/akb46/sct_5.0.0/data/c2c3_disc_models
--
Spinal Cord Toolbox (5.0.0)
Removing existing destination folder “/Users/akb46/sct_5.0.0/data/c2c3_disc_models”
Trying URL: https://github.com/sct-data/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip
Downloading: 20190117_c2c3_disc_models.zip
Status: 100%|██████████████████████████████| 8.94k/8.94k [00:00<00:00, 34.4MB/s]
Creating temporary folder (/var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094800.895744-vw05jkh5)
Unzip data to: /var/folders/3x/mvq93r7x7vzcz6929pjtskfmgplfx4/T/sct-20201111094800.895744-vw05jkh5
Removing temporary folders...
Done!
Status: 100%|██████████████████████████████| 18.0M/18.0M [00:00<00:00, 25.9MB/s]
In case an old version SCT is already installed (4.0.0-beta.1 or before), remove 'sct_env' declaration in RC file
sed: /Users/akb46/.bashrc: No such file or directory
Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y
Validate installation...
--
Spinal Cord Toolbox (5.0.0)
SCT info:
- version: 5.0.0
- path: /Users/akb46/sct_5.0.0
OS: osx (Darwin-19.6.0-x86_64-i386-64bit)
CPU cores: Available: 12, Used by ITK functions: 12
RAM: Total: 16384MB, Used: 8376MB, Available: 7770MB
Check Python executable.............................[OK]
Using bundled python 3.6.12 |Anaconda, Inc.| (default, Sep 8 2020, 17:50:39)
[GCC Clang 10.0.0 ] at /Users/akb46/sct_5.0.0/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if colored is installed.......................[OK] (1.4.2)
Check if dipy is installed..........................[OK] (1.3.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if ivadomed (2.4.0) is installed..............Generating new fontManager, this may take some time...
Failed to extract font properties from /System/Library/Fonts/Apple Color Emoji.ttc: In FT2Font: Could not set the fontsize (error code 0x17)
Failed to extract font properties from /System/Library/Fonts/Supplemental/NISC18030.ttf: In FT2Font: Could not set the fontsize (error code 0x17)
Failed to extract font properties from /System/Library/Fonts/LastResort.otf: tuple indices must be integers or slices, not str
/Users/akb46/sct_5.0.0/python/envs/venv_sct/lib/python3.6/site-packages/onnxruntime/capi/_pybind_state.py:14: UserWarning: Cannot load onnxruntime.capi. Error: 'dlopen(/Users/akb46/sct_5.0.0/python/envs/venv_sct/lib/python3.6/site-packages/onnxruntime/capi/onnxruntime_pybind11_state.so, 2): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
Referenced from: /Users/akb46/sct_5.0.0/python/envs/venv_sct/lib/python3.6/site-packages/onnxruntime/capi/onnxruntime_pybind11_state.so
Reason: image not found'.
warnings.warn("Cannot load onnxruntime.capi. Error: '{0}'.".format(str(e)))
[FAIL]
cannot import name 'get_all_providers'
Check if Keras (2.1.5) is installed.................[OK] (2.1.5)
Check if matplotlib is installed....................[OK] (3.3.2)
Check if nibabel is installed.......................[OK] (3.2.0)
Check if numpy is installed.........................[OK] (1.19.4)
Check if pandas is installed........................[OK] (1.1.4)
Check if psutil is installed........................[OK] (5.7.3)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (6.1.2)
Check if pytest-cov is installed....................[OK] (__version__ = '2.10.1')
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.24.0)
Check if requirements-parser is installed...........[OK] (0.2.0)
Check if scipy is installed.........................[OK] (1.5.4)
Check if scikit-image is installed..................[OK] (0.17.2)
Check if scikit-learn is installed..................[OK] (0.23.2)
Check if tensorflow (1.5.0) is installed............[OK] (1.5.0)
Check if torch (1.5.0) is installed.................[OK] (1.5.0)
Check if torchvision (0.6.0) is installed...........[OK] (0.6.0)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.51.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.25.11)
Check if pytest_console_scripts is installed........[OK]
Check if pytest-xdist is installed..................[OK] (2.1.0)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if DISPLAY variable is set....................[OK]
Check if figure can be opened with PyQt.............[OK]
Installation validation Failed!
Installation failed!
Please copy the historic of this Terminal (starting with the command install_sct) and paste it in a new created topic on SCT's forum:
