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



Checking OS type and version...

Linux ANW-72 4.18.0-240.1.1.el8_3.x86_64 #1 SMP Thu Nov 19 17:20:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...


OK!


SCT version ......... 5.7
Installation type ... package
Operating system .... linux (unknown)
Shell config ........ /home2/yvdwerf/.bashrc

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: 
--> Crash reports will be sent to the SCT development team. Thank you!


SCT will be installed here: [/home2/yvdwerf/sct_5.7]



Do you agree? [y]es/[n]o: 
Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0): 

Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: 
Copying source files from /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/spinalcordtoolbox-5.7 to /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7

..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
rm -rf /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python


mkdir -p /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python


Downloading Miniconda...


wget -nv -O /tmp/tmp.nonmSl8nLx/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

2022-09-28 08:36:48 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [76607678/76607678] -> "/tmp/tmp.nonmSl8nLx/miniconda.sh" [1]

Installing Miniconda...


bash /tmp/tmp.nonmSl8nLx/miniconda.sh -p /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python -b -f

PREFIX=/mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python
Unpacking payload ...

  0%|          | 0/40 [00:00<?, ?it/s]
Extracting : cffi-1.15.0-py39hd667e15_1.conda:   0%|          | 0/40 [00:04<?, ?it/s]
Extracting : cffi-1.15.0-py39hd667e15_1.conda:   2%|▎         | 1/40 [00:04<02:45,  4.24s/it]
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda:   2%|▎         | 1/40 [00:04<02:45,  4.24s/it]
Extracting : python-3.9.12-h12debd9_0.conda:   5%|▌         | 2/40 [02:01<02:41,  4.24s/it]     
Extracting : python-3.9.12-h12debd9_0.conda:   8%|▊         | 3/40 [02:01<27:26, 44.49s/it]
Extracting : xz-5.2.5-h7b6447c_0.conda:   8%|▊         | 3/40 [02:01<27:26, 44.49s/it]     
Extracting : libffi-3.3-he6710b0_2.conda:  10%|█         | 4/40 [02:01<26:41, 44.49s/it]
Extracting : sqlite-3.38.2-hc218d9a_0.conda:  12%|█▎        | 5/40 [02:01<25:57, 44.49s/it]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda:  15%|█▌        | 6/40 [02:01<25:12, 44.49s/it]
Extracting : six-1.16.0-pyhd3eb1b0_1.conda:  18%|█▊        | 7/40 [02:01<24:28, 44.49s/it]    
Extracting : ca-certificates-2022.3.29-h06a4308_1.conda:  20%|██        | 8/40 [02:01<23:43, 44.49s/it]
Extracting : pysocks-1.7.1-py39h06a4308_0.conda:  22%|██▎       | 9/40 [02:01<22:59, 44.49s/it]        
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda:  25%|██▌       | 10/40 [02:01<22:14, 44.49s/it]  
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda:  28%|██▊       | 11/40 [02:01<21:30, 44.49s/it]
Extracting : conda-package-handling-1.8.1-py39h7f8727e_0.conda:  30%|███       | 12/40 [02:01<20:45, 44.49s/it]
Extracting : setuptools-61.2.0-py39h06a4308_0.conda:  32%|███▎      | 13/40 [02:01<20:01, 44.49s/it]           
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda:  35%|███▌      | 14/40 [02:01<19:16, 44.49s/it]
Extracting : openssl-1.1.1n-h7f8727e_0.conda:  38%|███▊      | 15/40 [02:01<18:32, 44.49s/it]             
Extracting : tzdata-2022a-hda174b7_0.conda:  40%|████      | 16/40 [02:01<17:47, 44.49s/it]  
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda:  42%|████▎     | 17/40 [02:01<17:03, 44.49s/it]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  45%|████▌     | 18/40 [02:01<16:18, 44.49s/it]
Extracting : certifi-2021.10.8-py39h06a4308_2.conda:  48%|████▊     | 19/40 [02:01<15:34, 44.49s/it]     
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda:  50%|█████     | 20/40 [02:01<14:49, 44.49s/it]    
Extracting : ncurses-6.3-h7f8727e_2.conda:  52%|█████▎    | 21/40 [02:16<14:05, 44.49s/it]      
Extracting : ncurses-6.3-h7f8727e_2.conda:  55%|█████▌    | 22/40 [02:16<01:25,  4.73s/it]
Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda:  55%|█████▌    | 22/40 [02:16<01:25,  4.73s/it]
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda:  57%|█████▊    | 23/40 [02:16<01:20,  4.73s/it]       
Extracting : readline-8.1.2-h7f8727e_1.conda:  60%|██████    | 24/40 [02:16<01:15,  4.73s/it]  
Extracting : zlib-1.2.12-h7f8727e_1.conda:  62%|██████▎   | 25/40 [02:16<01:10,  4.73s/it]   
Extracting : yaml-0.2.5-h7b6447c_0.conda:  65%|██████▌   | 26/40 [02:16<01:06,  4.73s/it] 
Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda:  68%|██████▊   | 27/40 [02:16<01:01,  4.73s/it]
Extracting : idna-3.3-pyhd3eb1b0_0.conda:  70%|███████   | 28/40 [02:16<00:56,  4.73s/it]         
Extracting : _libgcc_mutex-0.1-main.conda:  72%|███████▎  | 29/40 [02:16<00:52,  4.73s/it]
Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda:  75%|███████▌  | 30/40 [02:16<00:47,  4.73s/it]
Extracting : pycosat-0.6.3-py39h27cfd23_0.conda:  78%|███████▊  | 31/40 [02:16<00:42,  4.73s/it]
Extracting : conda-4.12.0-py39h06a4308_0.conda:  80%|████████  | 32/40 [02:28<00:37,  4.73s/it] 
Extracting : conda-4.12.0-py39h06a4308_0.conda:  82%|████████▎ | 33/40 [02:28<00:22,  3.17s/it]
Extracting : cryptography-36.0.0-py39h9ce1e76_0.conda:  82%|████████▎ | 33/40 [02:28<00:22,  3.17s/it]
Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda:  85%|████████▌ | 34/40 [02:28<00:18,  3.17s/it]  
Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda:  88%|████████▊ | 35/40 [02:28<00:15,  3.17s/it]
Extracting : pip-21.2.4-py39h06a4308_0.conda:  90%|█████████ | 36/40 [02:28<00:12,  3.17s/it]          
Extracting : libgomp-9.3.0-h5101ec6_17.conda:  92%|█████████▎| 37/40 [02:28<00:09,  3.17s/it]
Extracting : tk-8.6.11-h1ccaba5_0.conda:  95%|█████████▌| 38/40 [02:28<00:06,  3.17s/it]     
Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2:  98%|█████████▊| 39/40 [02:28<00:03,  3.17s/it]
                                                                                             
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py39h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py39h06a4308_2
    - cffi==1.15.0=py39hd667e15_1
    - charset-normalizer==2.0.4=pyhd3eb1b0_0
    - colorama==0.4.4=pyhd3eb1b0_0
    - conda-content-trust==0.1.1=pyhd3eb1b0_0
    - conda-package-handling==1.8.1=py39h7f8727e_0
    - conda==4.12.0=py39h06a4308_0
    - cryptography==36.0.0=py39h9ce1e76_0
    - idna==3.3=pyhd3eb1b0_0
    - ld_impl_linux-64==2.35.1=h7274673_9
    - libffi==3.3=he6710b0_2
    - libgcc-ng==9.3.0=h5101ec6_17
    - libgomp==9.3.0=h5101ec6_17
    - libstdcxx-ng==9.3.0=hd4cf53a_17
    - ncurses==6.3=h7f8727e_2
    - openssl==1.1.1n=h7f8727e_0
    - pip==21.2.4=py39h06a4308_0
    - pycosat==0.6.3=py39h27cfd23_0
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py39h06a4308_0
    - python==3.9.12=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py39h27cfd23_0
    - setuptools==61.2.0=py39h06a4308_0
    - six==1.16.0=pyhd3eb1b0_1
    - sqlite==3.38.2=hc218d9a_0
    - tk==8.6.11=h1ccaba5_0
    - tqdm==4.63.0=pyhd3eb1b0_0
    - tzdata==2022a=hda174b7_0
    - urllib3==1.26.8=pyhd3eb1b0_0
    - wheel==0.37.1=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.12=h7f8727e_1


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-4.5-1_gnu
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py39hd667e15_1
  charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
  colorama           pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
  conda              pkgs/main/linux-64::conda-4.12.0-py39h06a4308_0
  conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py39h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py39h9ce1e76_0
  idna               pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openssl            pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.4-py39h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0
  pycparser          pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
  pyopenssl          pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.12-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
  requests           pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py39h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  tqdm               pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
  tzdata             pkgs/main/noarch::tzdata-2022a-hda174b7_0
  urllib3            pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1


Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.

Creating conda environment...

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 22.9.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/$CONDA_WORKING_DIR/envs/venv_sct

  added / updated specs:
    - python=3.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |             main           3 KB
    _openmp_mutex-5.1          |            1_gnu          21 KB
    ca-certificates-2022.07.19 |       h06a4308_0         124 KB
    certifi-2022.9.14          |   py37h06a4308_0         155 KB
    ld_impl_linux-64-2.38      |       h1181459_1         654 KB
    libffi-3.3                 |       he6710b0_2          50 KB
    libgcc-ng-11.2.0           |       h1234567_1         5.3 MB
    libgomp-11.2.0             |       h1234567_1         474 KB
    libstdcxx-ng-11.2.0        |       h1234567_1         4.7 MB
    ncurses-6.3                |       h5eee18b_3         781 KB
    openssl-1.1.1q             |       h7f8727e_0         2.5 MB
    pip-22.1.2                 |   py37h06a4308_0         2.4 MB
    python-3.7.13              |       h12debd9_0        46.2 MB
    readline-8.1.2             |       h7f8727e_1         354 KB
    setuptools-63.4.1          |   py37h06a4308_0         1.1 MB
    sqlite-3.39.2              |       h5082296_0         1.1 MB
    tk-8.6.12                  |       h1ccaba5_0         3.0 MB
    wheel-0.37.1               |     pyhd3eb1b0_0          33 KB
    xz-5.2.6                   |       h5eee18b_0         394 KB
    zlib-1.2.12                |       h5eee18b_3         103 KB
    ------------------------------------------------------------
                                           Total:        69.4 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-2022.07.19-h06a4308_0
  certifi            pkgs/main/linux-64::certifi-2022.9.14-py37h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  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-6.3-h5eee18b_3
  openssl            pkgs/main/linux-64::openssl-1.1.1q-h7f8727e_0
  pip                pkgs/main/linux-64::pip-22.1.2-py37h06a4308_0
  python             pkgs/main/linux-64::python-3.7.13-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
  setuptools         pkgs/main/linux-64::setuptools-63.4.1-py37h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.39.2-h5082296_0
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.6-h5eee18b_0
  zlib               pkgs/main/linux-64::zlib-1.2.12-h5eee18b_3



Downloading and Extracting Packages

wheel-0.37.1         | 33 KB     |            |   0% 
wheel-0.37.1         | 33 KB     | ####9      |  49% 
wheel-0.37.1         | 33 KB     | ########## | 100% 
wheel-0.37.1         | 33 KB     | ########## | 100% 

readline-8.1.2       | 354 KB    |            |   0% 
readline-8.1.2       | 354 KB    | ########## | 100% 
readline-8.1.2       | 354 KB    | ########## | 100% 

ncurses-6.3          | 781 KB    |            |   0% 
ncurses-6.3          | 781 KB    | ########## | 100% 
ncurses-6.3          | 781 KB    | ########## | 100% 

sqlite-3.39.2        | 1.1 MB    |            |   0% 
sqlite-3.39.2        | 1.1 MB    | ########## | 100% 
sqlite-3.39.2        | 1.1 MB    | ########## | 100% 

certifi-2022.9.14    | 155 KB    |            |   0% 
certifi-2022.9.14    | 155 KB    | ########## | 100% 
certifi-2022.9.14    | 155 KB    | ########## | 100% 

tk-8.6.12            | 3.0 MB    |            |   0% 
tk-8.6.12            | 3.0 MB    | ########## | 100% 
tk-8.6.12            | 3.0 MB    | ########## | 100% 

libgcc-ng-11.2.0     | 5.3 MB    |            |   0% 
libgcc-ng-11.2.0     | 5.3 MB    | #######7   |  78% 
libgcc-ng-11.2.0     | 5.3 MB    | ########## | 100% 

python-3.7.13        | 46.2 MB   |            |   0% 
python-3.7.13        | 46.2 MB   | 8          |   9% 
python-3.7.13        | 46.2 MB   | ##7        |  27% 
python-3.7.13        | 46.2 MB   | #####6     |  56% 
python-3.7.13        | 46.2 MB   | #######7   |  77% 
python-3.7.13        | 46.2 MB   | #########7 |  97% 
python-3.7.13        | 46.2 MB   | ########## | 100% 

libffi-3.3           | 50 KB     |            |   0% 
libffi-3.3           | 50 KB     | ########## | 100% 
libffi-3.3           | 50 KB     | ########## | 100% 

pip-22.1.2           | 2.4 MB    |            |   0% 
pip-22.1.2           | 2.4 MB    | ########## | 100% 
pip-22.1.2           | 2.4 MB    | ########## | 100% 

_libgcc_mutex-0.1    | 3 KB      |            |   0% 
_libgcc_mutex-0.1    | 3 KB      | ########## | 100% 
_libgcc_mutex-0.1    | 3 KB      | ########## | 100% 

ca-certificates-2022 | 124 KB    |            |   0% 
ca-certificates-2022 | 124 KB    | ########## | 100% 
ca-certificates-2022 | 124 KB    | ########## | 100% 

zlib-1.2.12          | 103 KB    |            |   0% 
zlib-1.2.12          | 103 KB    | ########## | 100% 
zlib-1.2.12          | 103 KB    | ########## | 100% 

_openmp_mutex-5.1    | 21 KB     |            |   0% 
_openmp_mutex-5.1    | 21 KB     | ########## | 100% 
_openmp_mutex-5.1    | 21 KB     | ########## | 100% 

libgomp-11.2.0       | 474 KB    |            |   0% 
libgomp-11.2.0       | 474 KB    | ########## | 100% 
libgomp-11.2.0       | 474 KB    | ########## | 100% 

ld_impl_linux-64-2.3 | 654 KB    |            |   0% 
ld_impl_linux-64-2.3 | 654 KB    | ########## | 100% 
ld_impl_linux-64-2.3 | 654 KB    | ########## | 100% 

xz-5.2.6             | 394 KB    |            |   0% 
xz-5.2.6             | 394 KB    | ########## | 100% 
xz-5.2.6             | 394 KB    | ########## | 100% 

openssl-1.1.1q       | 2.5 MB    |            |   0% 
openssl-1.1.1q       | 2.5 MB    | ########## | 100% 
openssl-1.1.1q       | 2.5 MB    | ########## | 100% 

setuptools-63.4.1    | 1.1 MB    |            |   0% 
setuptools-63.4.1    | 1.1 MB    | ########## | 100% 
setuptools-63.4.1    | 1.1 MB    | ########## | 100% 

libstdcxx-ng-11.2.0  | 4.7 MB    |            |   0% 
libstdcxx-ng-11.2.0  | 4.7 MB    | #########7 |  98% 
libstdcxx-ng-11.2.0  | 4.7 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

./install_sct: line 605: /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python/envs/venv_sct/pyvenv.cfg: No such file or directory

Installation failed!

Please find the file "/mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/spinalcordtoolbox-5.7/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