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



Checking OS type and version...

Darwin MACpros-Mac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64 x86_64
ProductVersion:	10.15.6

Checking requirements...


OK!


SCT version ......... 5.0.0
Installation type ... package
Operating system .... osx (15)
Shell config ........ /Users/macpronirims/.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: y

--> Crash reports will be sent to the SCT development team. Thank you!


SCT will be installed here: [/Users/macpronirims/sct_5.0.0]

Do you agree? [y]es/[n]o: y

Copying source files from /Users/macpronirims/Downloads/spinalcordtoolbox-5.0.0 to /Users/macpronirims/sct_5.0.0

................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Installing conda...


rm -rf /Users/macpronirims/sct_5.0.0/python


mkdir -p /Users/macpronirims/sct_5.0.0/python


curl -o /var/folders/sl/lvz0f1gn2v9cfsph2d6p_5b00000gn/T/tmp.2y57wwp3/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 53.2M  100 53.2M    0     0  7512k      0  0:00:07  0:00:07 --:--:-- 5807k
exit status is 0

bash /var/folders/sl/lvz0f1gn2v9cfsph2d6p_5b00000gn/T/tmp.2y57wwp3/miniconda.sh -p /Users/macpronirims/sct_5.0.0/python -b -f

PREFIX=/Users/macpronirims/sct_5.0.0/python
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                                 
Solving environment: done

## Package Plan ##

  environment location: /Users/macpronirims/sct_5.0.0/python

  added / updated specs:
    - ca-certificates==2020.1.1=0
    - certifi==2020.4.5.1=py38_0
    - cffi==1.14.0=py38hc512035_1
    - chardet==3.0.4=py38_1003
    - conda-package-handling==1.6.1=py38h1de35cc_0
    - conda==4.8.3=py38_0
    - cryptography==2.9.2=py38ha12b0ac_0
    - idna==2.9=py_1
    - libcxx==10.0.0=1
    - libedit==3.1.20181209=hb402a30_0
    - libffi==3.3=h0a44026_1
    - ncurses==6.2=h0a44026_1
    - openssl==1.1.1g=h1de35cc_0
    - pip==20.0.2=py38_3
    - pycosat==0.6.3=py38h1de35cc_1
    - pycparser==2.20=py_0
    - pyopenssl==19.1.0=py38_0
    - pysocks==1.7.1=py38_0
    - python.app==2=py38_10
    - python==3.8.3=h26836e1_1
    - readline==8.0=h1de35cc_0
    - requests==2.23.0=py38_0
    - ruamel_yaml==0.15.87=py38h1de35cc_0
    - setuptools==46.4.0=py38_0
    - six==1.14.0=py38_0
    - sqlite==3.31.1=h5c1f38d_1
    - tk==8.6.8=ha441bb4_0
    - tqdm==4.46.0=py_0
    - urllib3==1.25.8=py38_0
    - wheel==0.34.2=py38_0
    - xz==5.2.5=h1de35cc_0
    - yaml==0.1.7=hc338f04_2
    - zlib==1.2.11=h1de35cc_3


The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2020.4.5.1-py38_0
  cffi               pkgs/main/osx-64::cffi-1.14.0-py38hc512035_1
  chardet            pkgs/main/osx-64::chardet-3.0.4-py38_1003
  conda              pkgs/main/osx-64::conda-4.8.3-py38_0
  conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.6.1-py38h1de35cc_0
  cryptography       pkgs/main/osx-64::cryptography-2.9.2-py38ha12b0ac_0
  idna               pkgs/main/noarch::idna-2.9-py_1
  libcxx             pkgs/main/osx-64::libcxx-10.0.0-1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.3-h0a44026_1
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
  pip                pkgs/main/osx-64::pip-20.0.2-py38_3
  pycosat            pkgs/main/osx-64::pycosat-0.6.3-py38h1de35cc_1
  pycparser          pkgs/main/noarch::pycparser-2.20-py_0
  pyopenssl          pkgs/main/osx-64::pyopenssl-19.1.0-py38_0
  pysocks            pkgs/main/osx-64::pysocks-1.7.1-py38_0
  python             pkgs/main/osx-64::python-3.8.3-h26836e1_1
  python.app         pkgs/main/osx-64::python.app-2-py38_10
  readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
  requests           pkgs/main/osx-64::requests-2.23.0-py38_0
  ruamel_yaml        pkgs/main/osx-64::ruamel_yaml-0.15.87-py38h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-46.4.0-py38_0
  six                pkgs/main/osx-64::six-1.14.0-py38_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  tqdm               pkgs/main/noarch::tqdm-4.46.0-py_0
  urllib3            pkgs/main/osx-64::urllib3-1.25.8-py38_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py38_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  yaml               pkgs/main/osx-64::yaml-0.1.7-hc338f04_2
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Preparing transaction: done
Executing transaction: done
installation finished.
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.9.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/macpronirims/sct_5.0.0/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.10.14 |                0         121 KB
    certifi-2020.6.20          |     pyhd3eb1b0_3         155 KB
    libedit-3.1.20191231       |       h1de35cc_1          96 KB
    libffi-3.3                 |       hb1e8313_2          44 KB
    openssl-1.1.1h             |       haf1e3a3_0         2.2 MB
    pip-20.2.4                 |   py36hecd8cb5_0         1.8 MB
    python-3.6.12              |       h26836e1_2        16.9 MB
    setuptools-50.3.1          |   py36hecd8cb5_1         713 KB
    sqlite-3.33.0              |       hffcf06c_0         1.3 MB
    tk-8.6.10                  |       hb0a8c7a_0         3.0 MB
    wheel-0.35.1               |             py_0          37 KB
    ------------------------------------------------------------
                                           Total:        26.2 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.10.14-0
  certifi            pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
  libcxx             pkgs/main/osx-64::libcxx-10.0.0-1
  libedit            pkgs/main/osx-64::libedit-3.1.20191231-h1de35cc_1
  libffi             pkgs/main/osx-64::libffi-3.3-hb1e8313_2
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1h-haf1e3a3_0
  pip                pkgs/main/osx-64::pip-20.2.4-py36hecd8cb5_0
  python             pkgs/main/osx-64::python-3.6.12-h26836e1_2
  readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-50.3.1-py36hecd8cb5_1
  sqlite             pkgs/main/osx-64::sqlite-3.33.0-hffcf06c_0
  tk                 pkgs/main/osx-64::tk-8.6.10-hb0a8c7a_0
  wheel              pkgs/main/noarch::wheel-0.35.1-py_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Proceed ([y]/n)? 

Downloading and Extracting Packages
sqlite-3.33.0        | 1.3 MB    | ############################################################### | 100% 
setuptools-50.3.1    | 713 KB    | ############################################################### | 100% 
certifi-2020.6.20    | 155 KB    | ############################################################### | 100% 
wheel-0.35.1         | 37 KB     | ############################################################### | 100% 
tk-8.6.10            | 3.0 MB    | ############################################################### | 100% 
pip-20.2.4           | 1.8 MB    | ############################################################### | 100% 
ca-certificates-2020 | 121 KB    | ############################################################### | 100% 
openssl-1.1.1h       | 2.2 MB    | ############################################################### | 100% 
libffi-3.3           | 44 KB     | ############################################################### | 100% 
python-3.6.12        | 16.9 MB   | ############################################################### | 100% 
libedit-3.1.20191231 | 96 KB     | ############################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate


Installing Python dependencies...


Using requirements-freeze.txt (release installation)

Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html
Ignoring torch: markers 'sys_platform != "darwin"' don't match your environment
Ignoring torchvision: markers 'sys_platform != "darwin"' don't match your environment
Collecting absl-py==0.11.0
  Using cached absl_py-0.11.0-py3-none-any.whl (127 kB)
Requirement already satisfied: apipkg==1.5 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 2)) (1.5)
Requirement already satisfied: astor==0.8.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 3)) (0.8.1)
Collecting attrs==20.3.0
  Downloading attrs-20.3.0-py2.py3-none-any.whl (49 kB)
     |????????????????????????????????| 49 kB 2.9 MB/s 
Requirement already satisfied: bids-neuropoly==0.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 5)) (0.2)
Requirement already satisfied: bids-validator==1.5.7 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 6)) (1.5.7)
Collecting bleach==1.5.0
  Using cached bleach-1.5.0-py2.py3-none-any.whl (17 kB)
Collecting cachetools==4.1.1
  Using cached cachetools-4.1.1-py3-none-any.whl (10 kB)
Collecting certifi==2020.6.20
  Using cached certifi-2020.6.20-py2.py3-none-any.whl (156 kB)
Collecting cffi==1.14.3
  Using cached cffi-1.14.3-2-cp36-cp36m-macosx_10_9_x86_64.whl (176 kB)
Requirement already satisfied: chardet==3.0.4 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 11)) (3.0.4)
Requirement already satisfied: click==7.1.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 12)) (7.1.2)
Requirement already satisfied: colored==1.4.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 13)) (1.4.2)
Collecting coverage==5.3
  Using cached coverage-5.3-cp36-cp36m-macosx_10_13_x86_64.whl (205 kB)
Collecting cryptography==3.2.1
  Using cached cryptography-3.2.1-cp35-abi3-macosx_10_10_x86_64.whl (1.8 MB)
Requirement already satisfied: cycler==0.10.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 16)) (0.10.0)
Collecting decorator==4.4.2
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting dipy==1.3.0
  Downloading dipy-1.3.0-cp36-cp36m-macosx_10_9_x86_64.whl (7.6 MB)
     |????????????????????????????????| 7.6 MB 3.9 MB/s 
Requirement already satisfied: docopt==0.6.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 19)) (0.6.2)
Requirement already satisfied: execnet==1.7.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 20)) (1.7.1)
Requirement already satisfied: future==0.18.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 21)) (0.18.2)
Requirement already satisfied: futures==3.1.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 22)) (3.1.1)
Requirement already satisfied: gast==0.2.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 23)) (0.2.2)
Collecting google-auth==1.23.0
  Using cached google_auth-1.23.0-py2.py3-none-any.whl (114 kB)
Collecting google-auth-oauthlib==0.4.2
  Using cached google_auth_oauthlib-0.4.2-py2.py3-none-any.whl (18 kB)
Collecting google-pasta==0.2.0
  Using cached google_pasta-0.2.0-py3-none-any.whl (57 kB)
Collecting grpcio==1.33.2
  Using cached grpcio-1.33.2-cp36-cp36m-macosx_10_9_x86_64.whl (3.4 MB)
Requirement already satisfied: h5py==2.10.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 28)) (2.10.0)
Collecting html5lib==0.9999999
  Using cached html5lib-0.9999999.tar.gz (889 kB)
Collecting idna==2.10
  Using cached idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting imageio==2.9.0
  Using cached imageio-2.9.0-py3-none-any.whl (3.3 MB)
Collecting importlib-metadata==2.0.0
  Using cached importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB)
Requirement already satisfied: iniconfig==1.1.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 33)) (1.1.1)
Collecting ivadomed==2.4.0
  Downloading ivadomed-2.4.0-py3-none-any.whl (132 kB)
     |????????????????????????????????| 132 kB 5.7 MB/s 
Collecting joblib==0.17.0
  Using cached joblib-0.17.0-py3-none-any.whl (301 kB)
Collecting Keras==2.1.5
  Using cached Keras-2.1.5-py2.py3-none-any.whl (334 kB)
Requirement already satisfied: Keras-Applications==1.0.8 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 37)) (1.0.8)
Collecting Keras-Preprocessing==1.1.2
  Using cached Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
Collecting kiwisolver==1.3.1
  Using cached kiwisolver-1.3.1-cp36-cp36m-macosx_10_9_x86_64.whl (61 kB)
Collecting Markdown==3.3.3
  Using cached Markdown-3.3.3-py3-none-any.whl (96 kB)
Collecting matplotlib==3.3.2
  Using cached matplotlib-3.3.2-cp36-cp36m-macosx_10_9_x86_64.whl (8.5 MB)
Requirement already satisfied: mock==4.0.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 42)) (4.0.2)
Collecting networkx==2.5
  Using cached networkx-2.5-py3-none-any.whl (1.6 MB)
Collecting nibabel==3.2.0
  Using cached nibabel-3.2.0-py3-none-any.whl (3.3 MB)
Requirement already satisfied: num2words==0.5.10 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 45)) (0.5.10)
Collecting numpy==1.19.4
  Downloading numpy-1.19.4-cp36-cp36m-macosx_10_9_x86_64.whl (15.3 MB)
     |????????????????????????????????| 15.3 MB 11.4 MB/s 
Requirement already satisfied: oauthlib==3.1.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 47)) (3.1.0)
Requirement already satisfied: onnxruntime==1.5.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 48)) (1.5.2)
Collecting opt-einsum==3.2.1
  Downloading opt_einsum-3.2.1-py3-none-any.whl (63 kB)
     |????????????????????????????????| 63 kB 4.5 MB/s 
Collecting packaging==20.4
  Using cached packaging-20.4-py2.py3-none-any.whl (37 kB)
Collecting pandas==1.1.4
  Using cached pandas-1.1.4-cp36-cp36m-macosx_10_9_x86_64.whl (10.2 MB)
Requirement already satisfied: patsy==0.5.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 52)) (0.5.1)
Collecting Pillow==8.0.1
  Using cached Pillow-8.0.1-cp36-cp36m-macosx_10_10_x86_64.whl (2.2 MB)
Requirement already satisfied: pluggy==0.13.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 54)) (0.13.1)
Collecting protobuf==3.13.0
  Using cached protobuf-3.13.0-cp36-cp36m-macosx_10_9_x86_64.whl (1.3 MB)
Collecting psutil==5.7.3
  Using cached psutil-5.7.3.tar.gz (465 kB)
Collecting py==1.9.0
  Using cached py-1.9.0-py2.py3-none-any.whl (99 kB)
Requirement already satisfied: pyasn1==0.4.8 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 58)) (0.4.8)
Collecting pyasn1-modules==0.2.8
  Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
Requirement already satisfied: pybids==0.12.3 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 60)) (0.12.3)
Collecting pycparser==2.20
  Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB)
Requirement already satisfied: pyOpenSSL==19.1.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 62)) (19.1.0)
Collecting pyparsing==2.4.7
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Requirement already satisfied: PyQt5==5.11.3 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 64)) (5.11.3)
Requirement already satisfied: PyQt5-sip==4.19.19 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 65)) (4.19.19)
Collecting pytest==6.1.2
  Using cached pytest-6.1.2-py3-none-any.whl (272 kB)
Requirement already satisfied: pytest-console-scripts==1.0.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 67)) (1.0.0)
Collecting pytest-cov==2.10.1
  Using cached pytest_cov-2.10.1-py2.py3-none-any.whl (19 kB)
Requirement already satisfied: pytest-forked==1.3.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 69)) (1.3.0)
Requirement already satisfied: pytest-xdist==2.1.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 70)) (2.1.0)
Requirement already satisfied: python-dateutil==2.8.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 71)) (2.8.1)
Collecting pytz==2020.4
  Using cached pytz-2020.4-py2.py3-none-any.whl (509 kB)
Requirement already satisfied: PyWavelets==1.1.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 73)) (1.1.1)
Collecting PyYAML==5.3.1
  Using cached PyYAML-5.3.1.tar.gz (269 kB)
Requirement already satisfied: raven==6.10.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 75)) (6.10.0)
Collecting requests==2.24.0
  Using cached requests-2.24.0-py2.py3-none-any.whl (61 kB)
Requirement already satisfied: requests-oauthlib==1.3.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 77)) (1.3.0)
Requirement already satisfied: requirements-parser==0.2.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 78)) (0.2.0)
Collecting rsa==4.6
  Using cached rsa-4.6-py3-none-any.whl (47 kB)
Collecting scikit-image==0.17.2
  Using cached scikit_image-0.17.2-cp36-cp36m-macosx_10_13_x86_64.whl (12.1 MB)
Collecting scikit-learn==0.23.2
  Using cached scikit_learn-0.23.2-cp36-cp36m-macosx_10_9_x86_64.whl (7.2 MB)
Collecting scipy==1.5.4
  Downloading scipy-1.5.4-cp36-cp36m-macosx_10_9_x86_64.whl (28.8 MB)
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Requirement already satisfied: seaborn==0.11.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 83)) (0.11.0)
Collecting six==1.15.0
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Requirement already satisfied: SQLAlchemy==1.3.20 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 85)) (1.3.20)
Collecting tensorboard==2.3.0
  Using cached tensorboard-2.3.0-py3-none-any.whl (6.8 MB)
Requirement already satisfied: tensorboard-plugin-wit==1.7.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 87)) (1.7.0)
Collecting tensorflow==1.5.0
  Downloading tensorflow-1.5.0-cp36-cp36m-macosx_10_11_x86_64.whl (42.5 MB)
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Collecting tensorflow-estimator==1.15.1
  Using cached tensorflow_estimator-1.15.1-py2.py3-none-any.whl (503 kB)
Collecting tensorflow-tensorboard==1.5.1
  Using cached tensorflow_tensorboard-1.5.1-py3-none-any.whl (3.0 MB)
Requirement already satisfied: termcolor==1.1.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 91)) (1.1.0)
Requirement already satisfied: threadpoolctl==2.1.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 92)) (2.1.0)
Requirement already satisfied: tifffile==2020.9.3 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 93)) (2020.9.3)
Requirement already satisfied: toml==0.10.2 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 94)) (0.10.2)
Requirement already satisfied: torch==1.5.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 101)) (1.5.0)
Requirement already satisfied: torchvision==0.6.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 103)) (0.6.0)
Collecting tqdm==4.51.0
  Using cached tqdm-4.51.0-py2.py3-none-any.whl (70 kB)
Requirement already satisfied: transforms3d==0.3.1 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 105)) (0.3.1)
Collecting urllib3==1.25.11
  Using cached urllib3-1.25.11-py2.py3-none-any.whl (127 kB)
Collecting Werkzeug==1.0.1
  Using cached Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
Requirement already satisfied: xlwt==1.3.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 108)) (1.3.0)
Collecting zipp==3.4.0
  Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB)
Requirement already satisfied: setuptools>=40.3.0 in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from google-auth==1.23.0->-r requirements-freeze.txt (line 24)) (50.3.2)
Requirement already satisfied: wheel>=0.26; python_version >= "3" in /Users/macpronirims/.pyenv/versions/3.6.9/lib/python3.6/site-packages (from tensorboard==2.3.0->-r requirements-freeze.txt (line 86)) (0.35.1)
Building wheels for collected packages: html5lib, psutil, PyYAML
  Building wheel for html5lib (setup.py) ... done
  Created wheel for html5lib: filename=html5lib-0.9999999-py3-none-any.whl size=107219 sha256=f3262eee35b5ba9fdcc2242086a3e224c0d83071d608bb6b77782651f257e1bd
  Stored in directory: /Users/macpronirims/Library/Caches/pip/wheels/90/1c/cb/a87fd097ff74648ecc468a703001f6c7c86d8a71d459e65c98
  Building wheel for psutil (setup.py) ... done
  Created wheel for psutil: filename=psutil-5.7.3-cp36-cp36m-macosx_10_15_x86_64.whl size=234497 sha256=75cc8385cfca3b8fa6f99e942b53935beacc00a0698baa4fa20b8c37ccd34f09
  Stored in directory: /Users/macpronirims/Library/Caches/pip/wheels/fa/ad/67/90bbaacdcfe970960dd5158397f23a6579b51d853720d7856d
  Building wheel for PyYAML (setup.py) ... done
  Created wheel for PyYAML: filename=PyYAML-5.3.1-cp36-cp36m-macosx_10_15_x86_64.whl size=44626 sha256=cfd682fb0c2fccc3503c9cf9194c29c495b042217642066263675866a1cce968
  Stored in directory: /Users/macpronirims/Library/Caches/pip/wheels/e5/9d/ad/2ee53cf262cba1ffd8afe1487eef788ea3f260b7e6232a80fc
Successfully built html5lib psutil PyYAML
Installing collected packages: six, absl-py, attrs, html5lib, bleach, cachetools, certifi, pycparser, cffi, coverage, cryptography, decorator, numpy, scipy, tqdm, pyparsing, packaging, nibabel, dipy, rsa, pyasn1-modules, google-auth, google-auth-oauthlib, google-pasta, grpcio, idna, Pillow, imageio, zipp, importlib-metadata, pytz, pandas, kiwisolver, matplotlib, joblib, scikit-learn, py, pytest, networkx, scikit-image, urllib3, requests, Werkzeug, Markdown, protobuf, tensorboard, ivadomed, PyYAML, Keras, Keras-Preprocessing, opt-einsum, psutil, pytest-cov, tensorflow-tensorboard, tensorflow, tensorflow-estimator
  Attempting uninstall: six
    Found existing installation: six 1.13.0
    Uninstalling six-1.13.0:
      Successfully uninstalled six-1.13.0
  Attempting uninstall: absl-py
    Found existing installation: absl-py 0.9.0
    Uninstalling absl-py-0.9.0:
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  Attempting uninstall: attrs
    Found existing installation: attrs 19.3.0
    Uninstalling attrs-19.3.0:
      Successfully uninstalled attrs-19.3.0
  Attempting uninstall: cachetools
    Found existing installation: cachetools 4.0.0
    Uninstalling cachetools-4.0.0:
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  Attempting uninstall: certifi
    Found existing installation: certifi 2019.11.28
    Uninstalling certifi-2019.11.28:
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  Attempting uninstall: pycparser
    Found existing installation: pycparser 2.19
    Uninstalling pycparser-2.19:
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  Attempting uninstall: cffi
    Found existing installation: cffi 1.13.2
    Uninstalling cffi-1.13.2:
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  Attempting uninstall: coverage
    Found existing installation: coverage 5.0
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  Attempting uninstall: cryptography
    Found existing installation: cryptography 2.8
    Uninstalling cryptography-2.8:
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  Attempting uninstall: decorator
    Found existing installation: decorator 4.4.1
    Uninstalling decorator-4.4.1:
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  Attempting uninstall: numpy
    Found existing installation: numpy 1.17.4
    Uninstalling numpy-1.17.4:
      Successfully uninstalled numpy-1.17.4
  Attempting uninstall: scipy
    Found existing installation: scipy 1.4.0
    Uninstalling scipy-1.4.0:
      Successfully uninstalled scipy-1.4.0
  Attempting uninstall: tqdm
    Found existing installation: tqdm 4.40.2
    Uninstalling tqdm-4.40.2:
      Successfully uninstalled tqdm-4.40.2
  Attempting uninstall: pyparsing
    Found existing installation: pyparsing 2.4.5
    Uninstalling pyparsing-2.4.5:
      Successfully uninstalled pyparsing-2.4.5
  Attempting uninstall: packaging
    Found existing installation: packaging 19.2
    Uninstalling packaging-19.2:
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  Attempting uninstall: nibabel
    Found existing installation: nibabel 3.0.0
    Uninstalling nibabel-3.0.0:
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  Attempting uninstall: dipy
    Found existing installation: dipy 1.0.0
    Uninstalling dipy-1.0.0:
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  Attempting uninstall: rsa
    Found existing installation: rsa 4.0
    Uninstalling rsa-4.0:
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  Attempting uninstall: pyasn1-modules
    Found existing installation: pyasn1-modules 0.2.7
    Uninstalling pyasn1-modules-0.2.7:
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  Attempting uninstall: google-auth
    Found existing installation: google-auth 1.10.0
    Uninstalling google-auth-1.10.0:
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  Attempting uninstall: google-auth-oauthlib
    Found existing installation: google-auth-oauthlib 0.4.1
    Uninstalling google-auth-oauthlib-0.4.1:
      Successfully uninstalled google-auth-oauthlib-0.4.1
  Attempting uninstall: google-pasta
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  Attempting uninstall: grpcio
    Found existing installation: grpcio 1.26.0
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  Attempting uninstall: idna
    Found existing installation: idna 2.8
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  Attempting uninstall: Pillow
    Found existing installation: Pillow 6.2.1
    Uninstalling Pillow-6.2.1:
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  Attempting uninstall: imageio
    Found existing installation: imageio 2.6.1
    Uninstalling imageio-2.6.1:
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  Attempting uninstall: zipp
    Found existing installation: zipp 0.6.0
    Uninstalling zipp-0.6.0:
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  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 1.3.0
    Uninstalling importlib-metadata-1.3.0:
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  Attempting uninstall: pytz
    Found existing installation: pytz 2019.3
    Uninstalling pytz-2019.3:
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  Attempting uninstall: pandas
    Found existing installation: pandas 0.25.3
    Uninstalling pandas-0.25.3:
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  Attempting uninstall: kiwisolver
    Found existing installation: kiwisolver 1.1.0
    Uninstalling kiwisolver-1.1.0:
      Successfully uninstalled kiwisolver-1.1.0
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.1.2
    Uninstalling matplotlib-3.1.2:
      Successfully uninstalled matplotlib-3.1.2
  Attempting uninstall: joblib
    Found existing installation: joblib 0.14.1
    Uninstalling joblib-0.14.1:
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  Attempting uninstall: scikit-learn
    Found existing installation: scikit-learn 0.22
    Uninstalling scikit-learn-0.22:
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  Attempting uninstall: py
    Found existing installation: py 1.8.0
    Uninstalling py-1.8.0:
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  Attempting uninstall: pytest
    Found existing installation: pytest 5.3.2
    Uninstalling pytest-5.3.2:
      Successfully uninstalled pytest-5.3.2
  Attempting uninstall: networkx
    Found existing installation: networkx 2.4
    Uninstalling networkx-2.4:
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  Attempting uninstall: scikit-image
    Found existing installation: scikit-image 0.16.2
    Uninstalling scikit-image-0.16.2:
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  Attempting uninstall: urllib3
    Found existing installation: urllib3 1.25.7
    Uninstalling urllib3-1.25.7:
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  Attempting uninstall: requests
    Found existing installation: requests 2.22.0
    Uninstalling requests-2.22.0:
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  Attempting uninstall: Werkzeug
    Found existing installation: Werkzeug 0.16.0
    Uninstalling Werkzeug-0.16.0:
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  Attempting uninstall: Markdown
    Found existing installation: Markdown 3.1.1
    Uninstalling Markdown-3.1.1:
      Successfully uninstalled Markdown-3.1.1
  Attempting uninstall: protobuf
    Found existing installation: protobuf 3.11.1
    Uninstalling protobuf-3.11.1:
      Successfully uninstalled protobuf-3.11.1
  Attempting uninstall: tensorboard
    Found existing installation: tensorboard 2.0.2
    Uninstalling tensorboard-2.0.2:
      Successfully uninstalled tensorboard-2.0.2
  Attempting uninstall: ivadomed
    Found existing installation: ivadomed 2.0.2
    Uninstalling ivadomed-2.0.2:
      Successfully uninstalled ivadomed-2.0.2
  Attempting uninstall: PyYAML
    Found existing installation: PyYAML 5.2
    Uninstalling PyYAML-5.2:
      Successfully uninstalled PyYAML-5.2
  Attempting uninstall: Keras
    Found existing installation: Keras 2.3.1
    Uninstalling Keras-2.3.1:
      Successfully uninstalled Keras-2.3.1
  Attempting uninstall: Keras-Preprocessing
    Found existing installation: Keras-Preprocessing 1.1.0
    Uninstalling Keras-Preprocessing-1.1.0:
      Successfully uninstalled Keras-Preprocessing-1.1.0
  Attempting uninstall: opt-einsum
    Found existing installation: opt-einsum 3.1.0
    Uninstalling opt-einsum-3.1.0:
      Successfully uninstalled opt-einsum-3.1.0
  Attempting uninstall: psutil
    Found existing installation: psutil 5.6.7
    Uninstalling psutil-5.6.7:
      Successfully uninstalled psutil-5.6.7
  Attempting uninstall: pytest-cov
    Found existing installation: pytest-cov 2.8.1
    Uninstalling pytest-cov-2.8.1:
      Successfully uninstalled pytest-cov-2.8.1
  Attempting uninstall: tensorflow
    Found existing installation: tensorflow 2.0.1
    Uninstalling tensorflow-2.0.1:
      Successfully uninstalled tensorflow-2.0.1
  Attempting uninstall: tensorflow-estimator
    Found existing installation: tensorflow-estimator 2.0.1
    Uninstalling tensorflow-estimator-2.0.1:
      Successfully uninstalled tensorflow-estimator-2.0.1
Successfully installed Keras-2.1.5 Keras-Preprocessing-1.1.2 Markdown-3.3.3 Pillow-8.0.1 PyYAML-5.3.1 Werkzeug-1.0.1 absl-py-0.11.0 attrs-20.3.0 bleach-1.5.0 cachetools-4.1.1 certifi-2020.6.20 cffi-1.14.3 coverage-5.3 cryptography-3.2.1 decorator-4.4.2 dipy-1.3.0 google-auth-1.23.0 google-auth-oauthlib-0.4.2 google-pasta-0.2.0 grpcio-1.33.2 html5lib-0.9999999 idna-2.10 imageio-2.9.0 importlib-metadata-2.0.0 ivadomed-2.4.0 joblib-0.17.0 kiwisolver-1.3.1 matplotlib-3.3.2 networkx-2.5 nibabel-3.2.0 numpy-1.19.4 opt-einsum-3.2.1 packaging-20.4 pandas-1.1.4 protobuf-3.13.0 psutil-5.7.3 py-1.9.0 pyasn1-modules-0.2.8 pycparser-2.20 pyparsing-2.4.7 pytest-6.1.2 pytest-cov-2.10.1 pytz-2020.4 requests-2.24.0 rsa-4.6 scikit-image-0.17.2 scikit-learn-0.23.2 scipy-1.5.4 six-1.15.0 tensorboard-2.3.0 tensorflow-1.5.0 tensorflow-estimator-1.15.1 tensorflow-tensorboard-1.5.1 tqdm-4.51.0 urllib3-1.25.11 zipp-3.4.0
Obtaining file:///Users/macpronirims/sct_5.0.0
Installing collected packages: spinalcordtoolbox
  Attempting uninstall: spinalcordtoolbox
    Found existing installation: spinalcordtoolbox 4.2.2
    Uninstalling spinalcordtoolbox-4.2.2:
      Successfully uninstalled spinalcordtoolbox-4.2.2
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox

Creating launchers for Python scripts...

cp: /Users/macpronirims/sct_5.0.0/python/envs/venv_sct/bin/*sct*: No such file or directory

Problem creating launchers!


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:

--> http://forum.spinalcordmri.org/c/sct