*******************************
* Welcome to SCT installation *
*******************************



Checking OS type and version...

Linux 6b7e4ff9b457 6.1.58+ #1 SMP PREEMPT_DYNAMIC Sat Nov 18 15:31:17 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...


OK!


SCT version ......... 6.3.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /root/.bashrc

SCT will be installed here: [/content/spinalcordtoolbox]



Do you agree? [y]es/[n]o: 
Skipping copy of source files (source and destination folders are the same)


Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: 
Downloading Miniconda...


wget -nv -O /tmp/tmp.bCg9nzzsLA/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

2024-03-12 04:04:53 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [144041912/144041912] -> "/tmp/tmp.bCg9nzzsLA/miniconda.sh" [1]

Installing Miniconda...


bash /tmp/tmp.bCg9nzzsLA/miniconda.sh -p /content/spinalcordtoolbox/python -b -f

PREFIX=/content/spinalcordtoolbox/python
Unpacking payload ...

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Extracting : pybind11-abi-4-hd3eb1b0_1.conda:   1%|▏         | 1/73 [00:00<00:14,  5.05it/s]
Extracting : brotli-python-1.0.9-py312h6a678d5_7.conda:   3%|▎         | 2/73 [00:00<00:14,  5.05it/s]
Extracting : conda-libmamba-solver-23.12.0-pyhd3eb1b0_1.conda:   4%|▍         | 3/73 [00:00<00:13,  5.05it/s]
Extracting : idna-3.4-py312h06a4308_0.conda:   5%|▌         | 4/73 [00:00<00:13,  5.05it/s]                  
Extracting : pycosat-0.6.6-py312h5eee18b_0.conda:   7%|▋         | 5/73 [00:00<00:13,  5.05it/s]
Extracting : _libgcc_mutex-0.1-main.conda:   8%|▊         | 6/73 [00:00<00:13,  5.05it/s]       
Extracting : libxml2-2.10.4-hf1b16e4_1.conda:  10%|▉         | 7/73 [00:00<00:13,  5.05it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  11%|█         | 8/73 [00:00<00:12,  5.05it/s]
Extracting : readline-8.2-h5eee18b_0.conda:  12%|█▏        | 9/73 [00:00<00:12,  5.05it/s]              
Extracting : packaging-23.1-py312h06a4308_0.conda:  14%|█▎        | 10/73 [00:00<00:12,  5.05it/s]
Extracting : krb5-1.20.1-h143b758_1.conda:  15%|█▌        | 11/73 [00:00<00:12,  5.05it/s]        
Extracting : krb5-1.20.1-h143b758_1.conda:  16%|█▋        | 12/73 [00:00<00:01, 36.76it/s]
Extracting : jsonpatch-1.32-pyhd3eb1b0_0.conda:  16%|█▋        | 12/73 [00:00<00:01, 36.76it/s]
Extracting : zstandard-0.19.0-py312h5eee18b_0.conda:  18%|█▊        | 13/73 [00:00<00:01, 36.76it/s]
Extracting : conda-24.1.2-py312h06a4308_0.conda:  19%|█▉        | 14/73 [00:00<00:01, 36.76it/s]    
Extracting : ld_impl_linux-64-2.38-h1181459_1.conda:  21%|██        | 15/73 [00:00<00:01, 36.76it/s]
Extracting : ld_impl_linux-64-2.38-h1181459_1.conda:  22%|██▏       | 16/73 [00:00<00:02, 24.05it/s]
Extracting : fmt-9.1.0-hdb19cb5_0.conda:  22%|██▏       | 16/73 [00:00<00:02, 24.05it/s]            
Extracting : pip-23.3.1-py312h06a4308_0.conda:  23%|██▎       | 17/73 [00:01<00:02, 24.05it/s]
Extracting : cryptography-41.0.7-py312hdda0065_0.conda:  25%|██▍       | 18/73 [00:01<00:02, 24.05it/s]
Extracting : cryptography-41.0.7-py312hdda0065_0.conda:  26%|██▌       | 19/73 [00:01<00:04, 10.81it/s]
Extracting : bzip2-1.0.8-h7b6447c_0.conda:  26%|██▌       | 19/73 [00:01<00:04, 10.81it/s]             
Extracting : requests-2.31.0-py312h06a4308_1.conda:  27%|██▋       | 20/73 [00:01<00:04, 10.81it/s]
Extracting : distro-1.8.0-py312h06a4308_0.conda:  29%|██▉       | 21/73 [00:01<00:04, 10.81it/s]   
Extracting : truststore-0.8.0-py312h06a4308_0.conda:  30%|███       | 22/73 [00:01<00:04, 10.81it/s]
Extracting : menuinst-2.0.2-py312h06a4308_0.conda:  32%|███▏      | 23/73 [00:01<00:04, 10.81it/s]  
Extracting : archspec-0.2.1-pyhd3eb1b0_0.conda:  33%|███▎      | 24/73 [00:01<00:04, 10.81it/s]   
Extracting : cffi-1.16.0-py312h5eee18b_0.conda:  34%|███▍      | 25/73 [00:01<00:04, 10.81it/s]
Extracting : jsonpointer-2.1-pyhd3eb1b0_0.conda:  36%|███▌      | 26/73 [00:01<00:04, 10.81it/s]
Extracting : wheel-0.41.2-py312h06a4308_0.conda:  37%|███▋      | 27/73 [00:01<00:04, 10.81it/s]
Extracting : lz4-c-1.9.4-h6a678d5_0.conda:  38%|███▊      | 28/73 [00:01<00:04, 10.81it/s]      
Extracting : xz-5.4.5-h5eee18b_0.conda:  40%|███▉      | 29/73 [00:01<00:04, 10.81it/s]   
Extracting : xz-5.4.5-h5eee18b_0.conda:  41%|████      | 30/73 [00:01<00:02, 19.66it/s]
Extracting : libmambapy-1.5.3-py312h2dafd23_0.conda:  41%|████      | 30/73 [00:01<00:02, 19.66it/s]
Extracting : python-3.12.1-h996f2a0_0.conda:  42%|████▏     | 31/73 [00:03<00:02, 19.66it/s]        
Extracting : tk-8.6.12-h1ccaba5_0.conda:  44%|████▍     | 32/73 [00:03<00:02, 19.66it/s]    
Extracting : tk-8.6.12-h1ccaba5_0.conda:  45%|████▌     | 33/73 [00:03<00:06,  5.92it/s]
Extracting : sqlite-3.41.2-h5eee18b_0.conda:  45%|████▌     | 33/73 [00:03<00:06,  5.92it/s]
Extracting : libcurl-8.5.0-h251f7ec_0.conda:  47%|████▋     | 34/73 [00:03<00:06,  5.92it/s]
Extracting : openssl-3.0.13-h7f8727e_0.conda:  48%|████▊     | 35/73 [00:03<00:06,  5.92it/s]
Extracting : reproc-14.2.4-h295c915_1.conda:  49%|████▉     | 36/73 [00:03<00:06,  5.92it/s] 
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda:  51%|█████     | 37/73 [00:03<00:06,  5.92it/s]
Extracting : certifi-2024.2.2-py312h06a4308_0.conda:  52%|█████▏    | 38/73 [00:03<00:05,  5.92it/s]
Extracting : boltons-23.0.0-py312h06a4308_0.conda:  53%|█████▎    | 39/73 [00:03<00:05,  5.92it/s]  
Extracting : setuptools-68.2.2-py312h06a4308_0.conda:  55%|█████▍    | 40/73 [00:03<00:05,  5.92it/s]
Extracting : libev-4.33-h7f8727e_1.conda:  56%|█████▌    | 41/73 [00:03<00:05,  5.92it/s]            
Extracting : conda-content-trust-0.2.0-py312h06a4308_0.conda:  58%|█████▊    | 42/73 [00:03<00:05,  5.92it/s]
Extracting : libffi-3.4.4-h6a678d5_0.conda:  59%|█████▉    | 43/73 [00:03<00:05,  5.92it/s]                  
Extracting : libnghttp2-1.57.0-h2d74bed_0.conda:  60%|██████    | 44/73 [00:03<00:04,  5.92it/s]
Extracting : c-ares-1.19.1-h5eee18b_0.conda:  62%|██████▏   | 45/73 [00:03<00:04,  5.92it/s]    
Extracting : libarchive-3.6.2-h6ac8c49_2.conda:  63%|██████▎   | 46/73 [00:03<00:04,  5.92it/s]
Extracting : _openmp_mutex-5.1-1_gnu.conda:  64%|██████▍   | 47/73 [00:03<00:04,  5.92it/s]    
Extracting : libgomp-11.2.0-h1234567_1.conda:  66%|██████▌   | 48/73 [00:03<00:04,  5.92it/s]
Extracting : tzdata-2023d-h04d1e81_0.conda:  67%|██████▋   | 49/73 [00:03<00:04,  5.92it/s]  
Extracting : libuuid-1.41.5-h5eee18b_0.conda:  68%|██████▊   | 50/73 [00:03<00:03,  5.92it/s]
Extracting : libmamba-1.5.3-haf1ee3a_0.conda:  70%|██████▉   | 51/73 [00:03<00:03,  5.92it/s]
Extracting : libmamba-1.5.3-haf1ee3a_0.conda:  71%|███████   | 52/73 [00:03<00:01, 14.66it/s]
Extracting : libssh2-1.10.0-hdbd6064_2.conda:  71%|███████   | 52/73 [00:03<00:01, 14.66it/s]
Extracting : conda-package-streaming-0.9.0-py312h06a4308_0.conda:  73%|███████▎  | 53/73 [00:03<00:01, 14.66it/s]
Extracting : pysocks-1.7.1-py312h06a4308_0.conda:  74%|███████▍  | 54/73 [00:03<00:01, 14.66it/s]                
Extracting : libgcc-ng-11.2.0-h1234567_1.conda:  75%|███████▌  | 55/73 [00:04<00:01, 14.66it/s]  
Extracting : expat-2.5.0-h6a678d5_0.conda:  77%|███████▋  | 56/73 [00:04<00:01, 14.66it/s]     
Extracting : libstdcxx-ng-11.2.0-h1234567_1.conda:  78%|███████▊  | 57/73 [00:04<00:01, 14.66it/s]
Extracting : libstdcxx-ng-11.2.0-h1234567_1.conda:  79%|███████▉  | 58/73 [00:04<00:00, 15.22it/s]
Extracting : reproc-cpp-14.2.4-h295c915_1.conda:  79%|███████▉  | 58/73 [00:04<00:00, 15.22it/s]  
Extracting : urllib3-2.1.0-py312h06a4308_1.conda:  81%|████████  | 59/73 [00:04<00:00, 15.22it/s]
Extracting : ncurses-6.4-h6a678d5_0.conda:  82%|████████▏ | 60/73 [00:05<00:00, 15.22it/s]       
Extracting : yaml-cpp-0.8.0-h6a678d5_0.conda:  84%|████████▎ | 61/73 [00:05<00:00, 15.22it/s]
Extracting : platformdirs-3.10.0-py312h06a4308_0.conda:  85%|████████▍ | 62/73 [00:05<00:00, 15.22it/s]
Extracting : platformdirs-3.10.0-py312h06a4308_0.conda:  86%|████████▋ | 63/73 [00:05<00:01,  8.88it/s]
Extracting : conda-package-handling-2.2.0-py312h06a4308_0.conda:  86%|████████▋ | 63/73 [00:05<00:01,  8.88it/s]
Extracting : ruamel.yaml-0.17.21-py312h5eee18b_0.conda:  88%|████████▊ | 64/73 [00:05<00:01,  8.88it/s]         
Extracting : libedit-3.1.20230828-h5eee18b_0.conda:  89%|████████▉ | 65/73 [00:05<00:00,  8.88it/s]    
Extracting : zlib-1.2.13-h5eee18b_0.conda:  90%|█████████ | 66/73 [00:05<00:00,  8.88it/s]         
Extracting : tqdm-4.65.0-py312he106c6f_0.conda:  92%|█████████▏| 67/73 [00:05<00:00,  8.88it/s]
Extracting : zstd-1.5.5-hc292b87_0.conda:  93%|█████████▎| 68/73 [00:05<00:00,  8.88it/s]      
Extracting : icu-73.1-h6a678d5_0.conda:  95%|█████████▍| 69/73 [00:05<00:00,  8.88it/s]  
Extracting : libsolv-0.7.24-he621ea3_0.conda:  96%|█████████▌| 70/73 [00:05<00:00,  8.88it/s]
Extracting : pluggy-1.0.0-py312h06a4308_1.conda:  97%|█████████▋| 71/73 [00:05<00:00,  8.88it/s]
Extracting : ca-certificates-2023.12.12-h06a4308_0.conda:  99%|█████████▊| 72/73 [00:05<00:00,  8.88it/s]
                                                                                                         
Installing base environment...


Downloading and Extracting Packages: ...working... done

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
WARNING:
    You currently have a PYTHONPATH environment variable set. This may cause
    unexpected behavior when running the Python interpreter in Miniconda3.
    For best results, please verify that your PYTHONPATH only points to
    directories of packages that are compatible with the Python interpreter
    in Miniconda3: /content/spinalcordtoolbox/python

Creating conda environment...

Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /content/spinalcordtoolbox/python/envs/venv_sct

  added / updated specs:
    - python=3.9


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pip-23.3.1                 |   py39h06a4308_0         2.6 MB
    python-3.9.18              |       h955ad1f_0        25.1 MB
    setuptools-68.2.2          |   py39h06a4308_0         948 KB
    tzdata-2024a               |       h04d1e81_0         116 KB
    wheel-0.41.2               |   py39h06a4308_0         108 KB
    xz-5.4.6                   |       h5eee18b_0         651 KB
    ------------------------------------------------------------
                                           Total:        29.4 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main 
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0 
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 
  openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_0 
  pip                pkgs/main/linux-64::pip-23.3.1-py39h06a4308_0 
  python             pkgs/main/linux-64::python-3.9.18-h955ad1f_0 
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 
  setuptools         pkgs/main/linux-64::setuptools-68.2.2-py39h06a4308_0 
  sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0 
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0 
  tzdata             pkgs/main/noarch::tzdata-2024a-h04d1e81_0 
  wheel              pkgs/main/linux-64::wheel-0.41.2-py39h06a4308_0 
  xz                 pkgs/main/linux-64::xz-5.4.6-h5eee18b_0 
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0 



Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate /content/spinalcordtoolbox/python/envs/venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /content/spinalcordtoolbox/python/envs/venv_sct

  added / updated specs:
    - libstdcxx-ng


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
    ca-certificates-2024.2.2   |       hbcca054_0         152 KB  conda-forge
    libgcc-ng-13.2.0           |       h807b86a_5         752 KB  conda-forge
    libgomp-13.2.0             |       h807b86a_5         410 KB  conda-forge
    libstdcxx-ng-13.2.0        |       h7e041cc_5         3.7 MB  conda-forge
    openssl-3.2.1              |       hd590300_0         2.7 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         7.7 MB

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-hbcca054_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 
  openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0 

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu 



Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)
Collecting pip!=21.2.*
  Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Downloading pip-24.0-py3-none-any.whl (2.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 23.0 MB/s eta 0:00:00
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.3.1
    Uninstalling pip-23.3.1:
      Successfully uninstalled pip-23.3.1
Successfully installed pip-24.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

Installing Python dependencies...


Using requirements.txt (git installation)

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7))
  Downloading dipy-1.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.0 kB)
Collecting ivadomed (from -r requirements.txt (line 11))
  Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)
Collecting matplotlib (from -r requirements.txt (line 12))
  Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-5.2.1-py3-none-any.whl.metadata (8.8 kB)
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)
Collecting nnunetv2 (from -r requirements.txt (line 23))
  Downloading nnunetv2-2.3.1.tar.gz (182 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 182.5/182.5 kB 4.2 MB/s eta 0:00:00
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
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  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
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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.

Failed running pip install: 1


Installation failed!

Please find the file "/content/spinalcordtoolbox/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> http://forum.spinalcordmri.org/c/sct