Unable to install v4.2.1

SCT
21

Ok! Had to do it from another computer, but looks like it worked! Thank a lot!



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



Checking OS type and version...

Linux alicudi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...


SCT version ......... 4.2.1
Installation type ... package
Operating system .... linux (unknown)
Shell config ........ /homes/2/vb922/.cshrc

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: [/homes/2/vb922/sct_4.2.1]

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

Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0): 
/autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1

WARNING: Directory already exists. Files will be overwritten.


Skipping copy of source files (source and destination folders are the same)


Removing sct and isct softlink from /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/bin


Installing conda...


rm -rf /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python


mkdir -p /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python


wget -O /tmp/tmp.x56bCfQH1L/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-01-23 17:12:28--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c94f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.201.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 71785000 (68M) [application/x-sh]
Saving to: ‘/tmp/tmp.x56bCfQH1L/miniconda.sh’

100%[=========================================================================================================>] 71,785,000  60.7MB/s   in 1.1s   

2020-01-23 17:12:29 (60.7 MB/s) - ‘/tmp/tmp.x56bCfQH1L/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.x56bCfQH1L/miniconda.sh -p /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python -b -f

PREFIX=/autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                                                                          
Solving environment: done

## Package Plan ##

  environment location: /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.2.0=py37_0
    - ca-certificates==2019.10.16=0
    - certifi==2019.9.11=py37_0
    - cffi==1.13.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.7.12=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.1=he6710b0_1
    - openssl==1.1.1d=h7b6447c_3
    - pip==19.3.1=py37_0
    - pycosat==0.6.3=py37h14c3975_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.0.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.4=h265db76_1
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_0
    - ruamel_yaml==0.15.46=py37h14c3975_0
    - setuptools==41.4.0=py37_0
    - six==1.12.0=py37_0
    - sqlite==3.30.0=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.36.1=py_0
    - urllib3==1.24.2=py37_0
    - wheel==0.33.6=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cffi               pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.7.12-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  six                pkgs/main/linux-64::six-1.12.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_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: 4.7.12
  latest version: 4.8.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2019.11.27 |                0         124 KB
    certifi-2019.11.28         |           py36_0         153 KB
    ld_impl_linux-64-2.33.1    |       h53a641e_7         568 KB
    openssl-1.1.1d             |       h7b6447c_3         2.5 MB
    pip-19.3.1                 |           py36_0         1.7 MB
    python-3.6.10              |       h0371630_0        29.7 MB
    setuptools-44.0.0          |           py36_0         510 KB
    sqlite-3.30.1              |       h7b6447c_0         1.1 MB
    wheel-0.33.6               |           py36_0          42 KB
    ------------------------------------------------------------
                                           Total:        36.3 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.11.27-0
  certifi            pkgs/main/linux-64::certifi-2019.11.28-py36_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py36_0
  python             pkgs/main/linux-64::python-3.6.10-h0371630_0
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-44.0.0-py36_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.1-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py36_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Proceed ([y]/n)? 

Downloading and Extracting Packages
sqlite-3.30.1        | 1.1 MB    | ######################################################################################################## | 100% 
python-3.6.10        | 29.7 MB   | ######################################################################################################## | 100% 
wheel-0.33.6         | 42 KB     | ######################################################################################################## | 100% 
openssl-1.1.1d       | 2.5 MB    | ######################################################################################################## | 100% 
ld_impl_linux-64-2.3 | 568 KB    | ######################################################################################################## | 100% 
ca-certificates-2019 | 124 KB    | ######################################################################################################## | 100% 
pip-19.3.1           | 1.7 MB    | ######################################################################################################## | 100% 
setuptools-44.0.0    | 510 KB    | ######################################################################################################## | 100% 
certifi-2019.11.28   | 153 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...

Collecting numpy
  Using cached https://files.pythonhosted.org/packages/62/20/4d43e141b5bc426ba38274933ef8e76e85c7adea2c321ecf9ebf7421cedf/numpy-1.18.1-cp36-cp36m-manylinux1_x86_64.whl
Installing collected packages: numpy
Successfully installed numpy-1.18.1

Using requirements-freeze.txt (release installation)

Processing /homes/2/vb922/.cache/pip/wheels/8e/28/49/fad4e7f0b9a1227708cbbee4487ac8558a7334849cb81c813d/absl_py-0.9.0-cp36-none-any.whl
Collecting astor==0.8.1
  Using cached https://files.pythonhosted.org/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl
Collecting attrs==19.3.0
  Using cached https://files.pythonhosted.org/packages/a2/db/4313ab3be961f7a763066401fb77f7748373b6094076ae2bda2806988af6/attrs-19.3.0-py2.py3-none-any.whl
Collecting cachetools==4.0.0
  Using cached https://files.pythonhosted.org/packages/08/6a/abf83cb951617793fd49c98cb9456860f5df66ff89883c8660aa0672d425/cachetools-4.0.0-py3-none-any.whl
Requirement already satisfied: certifi==2019.11.28 in ./python/envs/venv_sct/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 5)) (2019.11.28)
Collecting cffi==1.13.2
  Using cached https://files.pythonhosted.org/packages/49/72/0d42f94fe94afa8030350c26e9d787219f3f008ec9bf6b86c66532b29236/cffi-1.13.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting chardet==3.0.4
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting coverage==5.0
  Using cached https://files.pythonhosted.org/packages/fd/83/1f99e79d9b809eaf2a1dfc8a52a197a921501e4d7c592b1902bae0da0897/coverage-5.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting cryptography==2.8
  Using cached https://files.pythonhosted.org/packages/ca/9a/7cece52c46546e214e10811b36b2da52ce1ea7fa203203a629b8dfadad53/cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl
Collecting cycler==0.10.0
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting decorator==4.4.1
  Using cached https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
Collecting dipy==1.0.0
  Using cached https://files.pythonhosted.org/packages/5c/c1/fbb9b631cb2de6ff21967069144c00f7d06f522a7098f48a04d7f3b46198/dipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting futures==3.1.1
  Using cached https://files.pythonhosted.org/packages/05/80/f41cca0ea1ff69bce7e7a7d76182b47bb4e1a494380a532af3e8ee70b9ec/futures-3.1.1-py3-none-any.whl
Processing /homes/2/vb922/.cache/pip/wheels/5c/2e/7e/a1d4d4fcebe6c381f378ce7743a3ced3699feb89bcfbdadadd/gast-0.2.2-cp36-none-any.whl
Collecting google-auth==1.10.0
  Using cached https://files.pythonhosted.org/packages/36/f8/84b5771faec3eba9fe0c91c8c5896364a8ba08852c0dea5ad2025026dd95/google_auth-1.10.0-py2.py3-none-any.whl
Collecting google-auth-oauthlib==0.4.1
  Using cached https://files.pythonhosted.org/packages/7b/b8/88def36e74bee9fce511c9519571f4e485e890093ab7442284f4ffaef60b/google_auth_oauthlib-0.4.1-py2.py3-none-any.whl
Collecting google-pasta==0.1.8
  Using cached https://files.pythonhosted.org/packages/c3/fd/1e86bc4837cc9a3a5faf3db9b1854aa04ad35b5f381f9648fbe81a6f94e4/google_pasta-0.1.8-py3-none-any.whl
Collecting grpcio==1.26.0
  Using cached https://files.pythonhosted.org/packages/17/8f/f79c5c174bebece41f824dd7b1ba98da45dc2d4c373b38ac6a7f6a5acb5e/grpcio-1.26.0-cp36-cp36m-manylinux2010_x86_64.whl
Collecting h5py==2.10.0
  Using cached https://files.pythonhosted.org/packages/60/06/cafdd44889200e5438b897388f3075b52a8ef01f28a17366d91de0fa2d05/h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting idna==2.8
  Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting imageio==2.6.1
  Using cached https://files.pythonhosted.org/packages/1a/de/f7f985018f462ceeffada7f6e609919fbcc934acd9301929cba14bc2c24a/imageio-2.6.1-py3-none-any.whl
Collecting importlib-metadata==1.3.0
  Using cached https://files.pythonhosted.org/packages/e9/71/1a1e0ed0981bb6a67bce55a210f168126b7ebd2065958673797ea66489ca/importlib_metadata-1.3.0-py2.py3-none-any.whl
Collecting joblib==0.14.1
  Using cached https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl
Collecting Keras==2.3.1
  Using cached https://files.pythonhosted.org/packages/ad/fd/6bfe87920d7f4fd475acd28500a42482b6b84479832bdc0fe9e589a60ceb/Keras-2.3.1-py2.py3-none-any.whl
Collecting Keras-Applications==1.0.8
  Using cached https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl
Collecting Keras-Preprocessing==1.1.0
  Using cached https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl
Collecting kiwisolver==1.1.0
  Using cached https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting Markdown==3.1.1
  Using cached https://files.pythonhosted.org/packages/c0/4e/fd492e91abdc2d2fcb70ef453064d980688762079397f779758e055f6575/Markdown-3.1.1-py2.py3-none-any.whl
Collecting matplotlib==3.1.2
  Using cached https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting more-itertools==8.0.2
  Using cached https://files.pythonhosted.org/packages/68/03/0604cec1ea13c9f063dd50f900d1a36160334dd3cfb01fd0e638f61b46ba/more_itertools-8.0.2-py3-none-any.whl
Collecting networkx==2.4
  Using cached https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl
Collecting nibabel==3.0.0
  Using cached https://files.pythonhosted.org/packages/0d/fc/2efb2a7c5d117c761b72f6bc00bf057294e9ccdf0a737957c65fa89ecc6f/nibabel-3.0.0-py3-none-any.whl
Collecting numpy==1.17.4
  Using cached https://files.pythonhosted.org/packages/d2/ab/43e678759326f728de861edbef34b8e2ad1b1490505f20e0d1f0716c3bf4/numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl
Collecting oauthlib==3.1.0
  Using cached https://files.pythonhosted.org/packages/05/57/ce2e7a8fa7c0afb54a0581b14a65b56e62b5759dbc98e80627142b8a3704/oauthlib-3.1.0-py2.py3-none-any.whl
Processing /homes/2/vb922/.cache/pip/wheels/2c/b1/94/43d03e130b929aae7ba3f8d15cbd7bc0d1cb5bb38a5c721833/opt_einsum-3.1.0-cp36-none-any.whl
Collecting packaging==19.2
  Using cached https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl
Collecting pandas==0.25.3
  Using cached https://files.pythonhosted.org/packages/52/3f/f6a428599e0d4497e1595030965b5ba455fd8ade6e977e3c819973c4b41d/pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl
Collecting Pillow==6.2.1
  Using cached https://files.pythonhosted.org/packages/10/5c/0e94e689de2476c4c5e644a3bd223a1c1b9e2bdb7c510191750be74fa786/Pillow-6.2.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting pluggy==0.13.1
  Using cached https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl
Collecting protobuf==3.11.1
  Using cached https://files.pythonhosted.org/packages/b8/be/438a8b90701aacfd7d741541571a236edbcf46f772caa25fcb27c4937e9e/protobuf-3.11.1-cp36-cp36m-manylinux1_x86_64.whl
Processing /homes/2/vb922/.cache/pip/wheels/52/41/b0/bf50409fe2b1d3b79afa3eed71b54b3e30fe5b695db2c7ba2e/psutil-5.6.7-cp36-cp36m-linux_x86_64.whl
Collecting py==1.8.0
  Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl
Collecting pyasn1==0.4.8
  Using cached https://files.pythonhosted.org/packages/62/1e/a94a8d635fa3ce4cfc7f506003548d0a2447ae76fd5ca53932970fe3053f/pyasn1-0.4.8-py2.py3-none-any.whl
Collecting pyasn1-modules==0.2.7
  Using cached https://files.pythonhosted.org/packages/52/50/bb4cefca37da63a0c52218ba2cb1b1c36110d84dcbae8aa48cd67c5e95c2/pyasn1_modules-0.2.7-py2.py3-none-any.whl
Processing /homes/2/vb922/.cache/pip/wheels/f2/9a/90/de94f8556265ddc9d9c8b271b0f63e57b26fb1d67a45564511/pycparser-2.19-py2.py3-none-any.whl
Collecting pyOpenSSL==19.1.0
  Using cached https://files.pythonhosted.org/packages/9e/de/f8342b68fa9e981d348039954657bdf681b2ab93de27443be51865ffa310/pyOpenSSL-19.1.0-py2.py3-none-any.whl
Collecting pyparsing==2.4.5
  Using cached https://files.pythonhosted.org/packages/c0/0c/fc2e007d9a992d997f04a80125b0f183da7fb554f1de701bbb70a8e7d479/pyparsing-2.4.5-py2.py3-none-any.whl
Collecting PyQt5==5.11.3
  Using cached https://files.pythonhosted.org/packages/d4/bf/d884da8e2f7096d201c891d515eb6813a8e85df5eb6f5e12e867bf1d831c/PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl
Collecting PyQt5-sip==4.19.19
  Using cached https://files.pythonhosted.org/packages/f2/5e/da07d1977cf54d636e44a50271bc0ad1f7f34b502e484b4cefd6a1a6962a/PyQt5_sip-4.19.19-cp36-cp36m-manylinux1_x86_64.whl
Collecting pytest==5.3.2
  Using cached https://files.pythonhosted.org/packages/19/cf/711f1d887cb92c5155c9a1eb338f1b5d2411b50e4492a3b20e4a188a22b2/pytest-5.3.2-py3-none-any.whl
Collecting pytest-cov==2.8.1
  Using cached https://files.pythonhosted.org/packages/b9/54/3673ee8be482f81527678ac894276223b9814bb7262e4f730469bb7bf70e/pytest_cov-2.8.1-py2.py3-none-any.whl
Collecting python-dateutil==2.8.1
  Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting pytz==2019.3
  Using cached https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl
Collecting PyWavelets==1.1.1
  Using cached https://files.pythonhosted.org/packages/59/bb/d2b85265ec9fa3c1922210c9393d4cdf7075cc87cce6fe671d7455f80fbc/PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl
Processing /homes/2/vb922/.cache/pip/wheels/54/b7/c7/2ada654ee54483c9329871665aaf4a6056c3ce36f29cf66e67/PyYAML-5.2-cp36-cp36m-linux_x86_64.whl
Collecting raven==6.10.0
  Using cached https://files.pythonhosted.org/packages/bd/8e/62e26a88c0a1bbae677200baf0767c1022321a6555634f8129e6d55c5ddc/raven-6.10.0-py2.py3-none-any.whl
Collecting requests==2.22.0
  Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl
Collecting requests-oauthlib==1.3.0
  Using cached https://files.pythonhosted.org/packages/a3/12/b92740d845ab62ea4edf04d2f4164d82532b5a0b03836d4d4e71c6f3d379/requests_oauthlib-1.3.0-py2.py3-none-any.whl
Collecting rsa==4.0
  Using cached https://files.pythonhosted.org/packages/02/e5/38518af393f7c214357079ce67a317307936896e961e35450b70fad2a9cf/rsa-4.0-py2.py3-none-any.whl
Collecting scikit-image==0.16.2
  Using cached https://files.pythonhosted.org/packages/c8/bb/771800366f41d66eef51e4b80515f8ef7edab234a3f244fdce3bafe89b39/scikit_image-0.16.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting scikit-learn==0.22
  Using cached https://files.pythonhosted.org/packages/2e/d0/860c4f6a7027e00acff373d9f5327f4ae3ed5872234b3cbdd7bcb52e5eff/scikit_learn-0.22-cp36-cp36m-manylinux1_x86_64.whl
Collecting scipy==1.4.0
  Using cached https://files.pythonhosted.org/packages/f0/7a/579f4659bb488f19f6b458a003b36b86bacaedcb28530f8d25cb153fc5cd/scipy-1.4.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting six==1.13.0
  Using cached https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
Collecting tensorboard==2.0.2
  Using cached https://files.pythonhosted.org/packages/76/54/99b9d5d52d5cb732f099baaaf7740403e83fe6b0cedde940fabd2b13d75a/tensorboard-2.0.2-py3-none-any.whl
Collecting tensorflow==2.0.0
  Using cached https://files.pythonhosted.org/packages/46/0f/7bd55361168bb32796b360ad15a25de6966c9c1beb58a8e30c01c8279862/tensorflow-2.0.0-cp36-cp36m-manylinux2010_x86_64.whl
Collecting tensorflow-estimator==2.0.1
  Using cached https://files.pythonhosted.org/packages/fc/08/8b927337b7019c374719145d1dceba21a8bb909b93b1ad6f8fb7d22c1ca1/tensorflow_estimator-2.0.1-py2.py3-none-any.whl
Processing /homes/2/vb922/.cache/pip/wheels/7c/06/54/bc84598ba1daf8f970247f550b175aaaee85f68b4b0c5ab2c6/termcolor-1.1.0-cp36-none-any.whl
Collecting tqdm==4.40.2
  Using cached https://files.pythonhosted.org/packages/7f/32/5144caf0478b1f26bd9d97f510a47336cf4ac0f96c6bc3b5af20d4173920/tqdm-4.40.2-py2.py3-none-any.whl
Processing /homes/2/vb922/.cache/pip/wheels/3d/3c/84/28d36677f3c760c048bd02b5a547ea0c4027770cc9cdb9af1e/transforms3d-0.3.1-cp36-none-any.whl
Collecting urllib3==1.25.7
  Using cached https://files.pythonhosted.org/packages/b4/40/a9837291310ee1ccc242ceb6ebfd9eb21539649f193a7c8c86ba15b98539/urllib3-1.25.7-py2.py3-none-any.whl
Collecting wcwidth==0.1.7
  Using cached https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Collecting Werkzeug==0.16.0
  Using cached https://files.pythonhosted.org/packages/ce/42/3aeda98f96e85fd26180534d36570e4d18108d62ae36f87694b476b83d6f/Werkzeug-0.16.0-py2.py3-none-any.whl
Processing /homes/2/vb922/.cache/pip/wheels/d7/de/2e/efa132238792efb6459a96e85916ef8597fcb3d2ae51590dfd/wrapt-1.11.2-cp36-cp36m-linux_x86_64.whl
Collecting xlrd==1.2.0
  Using cached https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl
Collecting xlutils==2.0.0
  Using cached https://files.pythonhosted.org/packages/c7/55/e22ac73dbb316cabb5db28bef6c87044a95914f713a6e81b593f8a0d2f79/xlutils-2.0.0-py2.py3-none-any.whl
Collecting xlwt==1.3.0
  Using cached https://files.pythonhosted.org/packages/44/48/def306413b25c3d01753603b1a222a011b8621aed27cd7f89cbc27e6b0f4/xlwt-1.3.0-py2.py3-none-any.whl
Collecting zipp==0.6.0
  Using cached https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools>=40.3.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth==1.10.0->-r requirements-freeze.txt (line 15)) (44.0.0.post20200106)
Requirement already satisfied: wheel>=0.26; python_version >= "3" in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard==2.0.2->-r requirements-freeze.txt (line 64)) (0.33.6)
Installing collected packages: six, absl-py, astor, attrs, cachetools, pycparser, cffi, chardet, coverage, cryptography, cycler, decorator, numpy, h5py, scipy, nibabel, dipy, futures, gast, pyasn1, rsa, pyasn1-modules, google-auth, idna, urllib3, requests, oauthlib, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, Keras-Applications, PyYAML, Keras-Preprocessing, Keras, kiwisolver, Markdown, python-dateutil, pyparsing, matplotlib, networkx, opt-einsum, packaging, pytz, pandas, pluggy, protobuf, psutil, py, pyOpenSSL, PyQt5-sip, PyQt5, wcwidth, pytest, pytest-cov, PyWavelets, raven, scikit-image, scikit-learn, Werkzeug, tensorboard, wrapt, termcolor, tensorflow-estimator, tensorflow, tqdm, transforms3d, xlrd, xlwt, xlutils
  Found existing installation: numpy 1.18.1
    Uninstalling numpy-1.18.1:
      Successfully uninstalled numpy-1.18.1
Successfully installed Keras-2.3.1 Keras-Applications-1.0.8 Keras-Preprocessing-1.1.0 Markdown-3.1.1 Pillow-6.2.1 PyQt5-5.11.3 PyQt5-sip-4.19.19 PyWavelets-1.1.1 PyYAML-5.2 Werkzeug-0.16.0 absl-py-0.9.0 astor-0.8.1 attrs-19.3.0 cachetools-4.0.0 cffi-1.13.2 chardet-3.0.4 coverage-5.0 cryptography-2.8 cycler-0.10.0 decorator-4.4.1 dipy-1.0.0 futures-3.1.1 gast-0.2.2 google-auth-1.10.0 google-auth-oauthlib-0.4.1 google-pasta-0.1.8 grpcio-1.26.0 h5py-2.10.0 idna-2.8 imageio-2.6.1 importlib-metadata-1.3.0 joblib-0.14.1 kiwisolver-1.1.0 matplotlib-3.1.2 more-itertools-8.0.2 networkx-2.4 nibabel-3.0.0 numpy-1.17.4 oauthlib-3.1.0 opt-einsum-3.1.0 packaging-19.2 pandas-0.25.3 pluggy-0.13.1 protobuf-3.11.1 psutil-5.6.7 py-1.8.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.7 pycparser-2.19 pyparsing-2.4.5 pytest-5.3.2 pytest-cov-2.8.1 python-dateutil-2.8.1 pytz-2019.3 raven-6.10.0 requests-2.22.0 requests-oauthlib-1.3.0 rsa-4.0 scikit-image-0.16.2 scikit-learn-0.22 scipy-1.4.0 six-1.13.0 tensorboard-2.0.2 tensorflow-2.0.0 tensorflow-estimator-2.0.1 termcolor-1.1.0 tqdm-4.40.2 transforms3d-0.3.1 urllib3-1.25.7 wcwidth-0.1.7 wrapt-1.11.2 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0 zipp-0.6.0
Obtaining file:///autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox

Creating launchers for Python scripts...


Make shell scripts executable...


Creating symbolic links for Shell scripts...


Installing binaries...


sct_download_data -d binaries_debian -o /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/bin


--
Spinal Cord Toolbox (4.2.1)

Folder /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/bin has been created.

Trying URL: https://osf.io/bt58d/?action=download
Downloading 20190930_sct_binaries_linux.tar.gz...
Status: 100%|#################################################################################################| 81.1M/81.1M [00:06<00:00, 12.7MB/s]

Create temporary folder (/tmp/sct-20200123171344.932626-8ey9hg_p)...

Unzip data to: /tmp/sct-20200123171344.932626-8ey9hg_p

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


All requirements installed!


. /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python/bin/activate /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python


Installing data...


rm -rf /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/data


mkdir -p /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/data


cd /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/data


sct_download_data -d PAM50


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/u79sr/?pid=6zbyf/?action=download
Unexpected: link doesn't provide a filename

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20191029_PAM50.zip
Downloading 20191029_pam50.zip...
Status: 70.8MB [00:13, 5.17MB/s]
22 

Unzip data to: /tmp/sct-20200123171403.287208-us7k1ff3

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d gm_model


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/ugscu/?action=download
Downloading 20160922_gm_model.zip...
Status: 100%|#################################################################################################| 10.3M/10.3M [00:00<00:00, 15.1MB/s]

Create temporary folder (/tmp/sct-20200123171406.537373-xehhp7go)...

Unzip data to: /tmp/sct-20200123171406.537373-xehhp7go

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d optic_models


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/g4fwn/?action=download
Downloading 20170413_optic_models.zip...
Status: 100%|#################################################################################################| 17.7k/17.7k [00:00<00:00, 15.0MB/s]

Create temporary folder (/tmp/sct-20200123171409.392833-wsttbeh3)...

Unzip data to: /tmp/sct-20200123171409.392833-wsttbeh3

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d pmj_models


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/4gufr/?action=download
Downloading 20170922_pmj_models.zip...
Status: 100%|#################################################################################################| 8.87k/8.87k [00:00<00:00, 10.7MB/s]

Create temporary folder (/tmp/sct-20200123171411.386932-uuuqyjkr)...

Unzip data to: /tmp/sct-20200123171411.386932-uuuqyjkr

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_sc_models


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/avf97/?action=download
Downloading 20180610_deepseg_sc_models.zip...
Status: 100%|#################################################################################################| 58.7M/58.7M [00:04<00:00, 14.0MB/s]

Create temporary folder (/tmp/sct-20200123171417.342787-85mfxt0b)...

Unzip data to: /tmp/sct-20200123171417.342787-85mfxt0b

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_gm_models


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/b9y4x/?action=download
Downloading 20180205_deepseg_gm_models.zip...
Status: 100%|#################################################################################################| 2.28M/2.28M [00:00<00:00, 5.47MB/s]

Create temporary folder (/tmp/sct-20200123171421.029635-d7yi41gq)...

Unzip data to: /tmp/sct-20200123171421.029635-d7yi41gq

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_lesion_models


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/eg7v9/?action=download
Downloading 20180613_deepseg_lesion_models.zip...
Status: 100%|#################################################################################################| 16.0M/16.0M [00:01<00:00, 14.5MB/s]

Create temporary folder (/tmp/sct-20200123171424.037988-btb6qe_b)...

Unzip data to: /tmp/sct-20200123171424.037988-btb6qe_b

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d c2c3_disc_models


--
Spinal Cord Toolbox (4.2.1)


Trying URL: https://osf.io/t97ap/?action=download
Downloading 20190117_c2c3_disc_models.zip...
Status: 100%|#################################################################################################| 8.94k/8.94k [00:00<00:00, 10.9MB/s]

Create temporary folder (/tmp/sct-20200123171426.192905-zw4gp6f6)...

Unzip data to: /tmp/sct-20200123171426.192905-zw4gp6f6

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


In case an old version SCT is already installed (4.0.0-beta.1 or before), remove 'sct_env' declaration in RC file


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


Validate installation...


--
Spinal Cord Toolbox (4.2.1)

SCT info:
- version: 4.2.1
- path: /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1
OS: linux (Linux-3.10.0-1062.4.3.el7.x86_64-x86_64-with-centos-7.7.1908-Core)
CPU cores: Available: 40, Used by SCT: 40
RAM: MemTotal:       65723344 kB
total        used        free      shared  buff/cache   available
Mem:          64182       12749        7825         381       43608       50568
Swap:         40599         819       39780
Check Python executable.............................[OK]
  Using bundled python 3.6.10 |Anaconda, Inc.| (default, Jan  7 2020, 21:14:29) 
[GCC 7.3.0] at /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.17.4)
Check if cryptography is installed..................[OK] (2.8)
Check if dipy is installed..........................[OK] (1.0.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras is installed.........................Could not open font file /usr/share/fonts/google-noto-emoji/NotoColorEmoji.ttf: In FT2Font: Can not load face.  Unknown file format.
generated new fontManager
[OK] (2.3.1)
Check if matplotlib is installed....................[OK] (3.1.2)
Check if nibabel is installed.......................[OK] (3.0.0)
Check if pandas is installed........................[OK] (0.25.3)
Check if psutil is installed........................[OK] (5.6.7)
Check if pyqt5 (5.11.3) is installed................[OK]
Check if pytest is installed........................[OK] (5.3.2)
Check if pytest-cov is installed....................[OK] (2.8.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.4.0)
Check if scikit-image is installed..................[OK] (0.16.2)
Check if scikit-learn is installed..................[OK] (0.22)
Check if tensorflow is installed....................[OK] (2.0.0)
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.40.2)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.7)
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]


Open a new Terminal window to load environment variables, or run:
source /homes/2/vb922/.cshrc


Installation finished successfully!

alicudi:/autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1 $
1 Like
23

Hi Valeria,

I’m following up on the issue you were having here, where you observed an Illegal instruction (core dumped) Error related to the incompatibility with Keras/Tensoflow.

We have solved that issue in a pre-release, and we would like to ask users who have experienced that issue to make sure this solution works in most cases.

Could you please go back to the computer that produced that error, and try the following (copy/paste the Terminal output):

git clone --branch=jca/2562-tensorflow-1.5 --depth=1 https://github.com/neuropoly/spinalcordtoolbox.git sct-tf1.5
cd sct-tf1.5/
yes | ./install_sct

Open a new Terminal and run (send us this terminal output if at least one test fails):

sct_testing

Thanks!
Julien

24

Hello Julien!
Sorry for the late answer, I was abroad the past week.
So shall I copy the entire first command:
git clone --branch=jca/2562-tensorflow-1.5 --depth=1 https://github.com/neuropoly/spinalcordtoolbox.git sct-tf1.5
cd sct-tf1.5/
yes | ./install_sct

Also, shall I enter the folder in which I installed SCT before?

Thanks,
Vale

25

Hi Vale,

In the meantime we had other users testing this branch and confirming it works. So we have now closed that branch (meaning: you cannot do the git clone as instructed here), however you can already try the development version directly from master:

git clone https://github.com/neuropoly/spinalcordtoolbox.git sct-master
cd sct-master/
yes | ./install_sct

Then, open a new Terminal and run (send us this terminal output if at least one test fails):

sct_testing

If everything works, then you can re-do this procedure using the installation folder that you used before (if you want to keep SCT at a specific location).

Cheers,
Julien

26

Everything worked, thank you!
Vale

1 Like