Unable to install v4.2.1

vb922 · January 16, 2020, 7:44pm

Hello!
I am trying to install the new version of SCT but I’m getting this error:

sct_download_data -d PAM50

./install_sct: line 83: sct_download_data: command not found

ERROR: Command failed.

Installation failed

Can you help me please?
Thanks,
Valeria

jcohenadad · January 16, 2020, 8:02pm

Hi Valeria,
could you please copy/paste the entire Terminal output?
Thanks!

vb922 · January 17, 2020, 4:22pm

vulcano:/autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1 $ ./install_sct


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



Checking OS type and version...

Linux vulcano.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/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1

WARNING: Directory already exists. Files will be overwritten.

./install_sct: line 479: setenv: command not found

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


Installing conda...


rm -rf /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1/python


mkdir -p /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1/python


wget -O /tmp/tmp.ioCzGRa8MN/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-01-16 13:48:25--  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:c84f, ...
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.ioCzGRa8MN/miniconda.sh’

100%[===================================================================================================>] 71,785,000  64.6MB/s   in 1.1s   

2020-01-16 13:48:26 (64.6 MB/s) - ‘/tmp/tmp.ioCzGRa8MN/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.ioCzGRa8MN/miniconda.sh -p /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1/python -b -f

PREFIX=/autofs/cluster/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/cluster/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/cluster/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
python-3.6.10        | 29.7 MB   | ################################################################################################## | 100% 
pip-19.3.1           | 1.7 MB    | ################################################################################################## | 100% 
setuptools-44.0.0    | 510 KB    | ################################################################################################## | 100% 
ld_impl_linux-64-2.3 | 568 KB    | ################################################################################################## | 100% 
openssl-1.1.1d       | 2.5 MB    | ################################################################################################## | 100% 
ca-certificates-2019 | 124 KB    | ################################################################################################## | 100% 
wheel-0.33.6         | 42 KB     | ################################################################################################## | 100% 
sqlite-3.30.1        | 1.1 MB    | ################################################################################################## | 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
  Downloading https://files.pythonhosted.org/packages/62/20/4d43e141b5bc426ba38274933ef8e76e85c7adea2c321ecf9ebf7421cedf/numpy-1.18.1-cp36-cp36m-manylinux1_x86_64.whl (20.1MB)
     |████████████████████████████████| 20.2MB 18.7MB/s 
Installing collected packages: numpy
Successfully installed numpy-1.18.1

Using requirements-freeze.txt (release installation)

Collecting absl-py==0.9.0
  Downloading https://files.pythonhosted.org/packages/1a/53/9243c600e047bd4c3df9e69cfabc1e8004a82cac2e0c484580a78a94ba2a/absl-py-0.9.0.tar.gz (104kB)
     |████████████████████████████████| 112kB 2.2MB/s 
Collecting astor==0.8.1
  Downloading https://files.pythonhosted.org/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl
Collecting attrs==19.3.0
  Downloading https://files.pythonhosted.org/packages/a2/db/4313ab3be961f7a763066401fb77f7748373b6094076ae2bda2806988af6/attrs-19.3.0-py2.py3-none-any.whl
Collecting cachetools==4.0.0
  Downloading 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
  Downloading https://files.pythonhosted.org/packages/49/72/0d42f94fe94afa8030350c26e9d787219f3f008ec9bf6b86c66532b29236/cffi-1.13.2-cp36-cp36m-manylinux1_x86_64.whl (397kB)
     |████████████████████████████████| 399kB 8.7MB/s 
Collecting chardet==3.0.4
  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
     |████████████████████████████████| 143kB 43.8MB/s 
Collecting coverage==5.0
  Downloading https://files.pythonhosted.org/packages/fd/83/1f99e79d9b809eaf2a1dfc8a52a197a921501e4d7c592b1902bae0da0897/coverage-5.0-cp36-cp36m-manylinux1_x86_64.whl (226kB)
     |████████████████████████████████| 235kB 43.3MB/s 
Collecting cryptography==2.8
  Downloading https://files.pythonhosted.org/packages/ca/9a/7cece52c46546e214e10811b36b2da52ce1ea7fa203203a629b8dfadad53/cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl (2.3MB)
     |████████████████████████████████| 2.3MB 43.5MB/s 
Collecting cycler==0.10.0
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting decorator==4.4.1
  Downloading https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
Collecting dipy==1.0.0
  Downloading https://files.pythonhosted.org/packages/5c/c1/fbb9b631cb2de6ff21967069144c00f7d06f522a7098f48a04d7f3b46198/dipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl (8.1MB)
     |████████████████████████████████| 8.1MB 45.6MB/s 
Collecting futures==3.1.1
  Downloading https://files.pythonhosted.org/packages/05/80/f41cca0ea1ff69bce7e7a7d76182b47bb4e1a494380a532af3e8ee70b9ec/futures-3.1.1-py3-none-any.whl
Collecting gast==0.2.2
  Downloading https://files.pythonhosted.org/packages/4e/35/11749bf99b2d4e3cceb4d55ca22590b0d7c2c62b9de38ac4a4a7f4687421/gast-0.2.2.tar.gz
Collecting google-auth==1.10.0
  Downloading https://files.pythonhosted.org/packages/36/f8/84b5771faec3eba9fe0c91c8c5896364a8ba08852c0dea5ad2025026dd95/google_auth-1.10.0-py2.py3-none-any.whl (76kB)
     |████████████████████████████████| 81kB 5.4MB/s 
Collecting google-auth-oauthlib==0.4.1
  Downloading 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
  Downloading https://files.pythonhosted.org/packages/c3/fd/1e86bc4837cc9a3a5faf3db9b1854aa04ad35b5f381f9648fbe81a6f94e4/google_pasta-0.1.8-py3-none-any.whl (57kB)
     |████████████████████████████████| 61kB 5.3MB/s 
Collecting grpcio==1.26.0
  Downloading https://files.pythonhosted.org/packages/17/8f/f79c5c174bebece41f824dd7b1ba98da45dc2d4c373b38ac6a7f6a5acb5e/grpcio-1.26.0-cp36-cp36m-manylinux2010_x86_64.whl (2.4MB)
     |████████████████████████████████| 2.4MB 41.8MB/s 
Collecting h5py==2.10.0
  Downloading https://files.pythonhosted.org/packages/60/06/cafdd44889200e5438b897388f3075b52a8ef01f28a17366d91de0fa2d05/h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9MB)
     |████████████████████████████████| 2.9MB 43.1MB/s 
Collecting idna==2.8
  Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB)
     |████████████████████████████████| 61kB 5.3MB/s 
Collecting imageio==2.6.1
  Downloading https://files.pythonhosted.org/packages/1a/de/f7f985018f462ceeffada7f6e609919fbcc934acd9301929cba14bc2c24a/imageio-2.6.1-py3-none-any.whl (3.3MB)
     |████████████████████████████████| 3.3MB 43.2MB/s 
Collecting importlib-metadata==1.3.0
  Downloading https://files.pythonhosted.org/packages/e9/71/1a1e0ed0981bb6a67bce55a210f168126b7ebd2065958673797ea66489ca/importlib_metadata-1.3.0-py2.py3-none-any.whl
Collecting joblib==0.14.1
  Downloading https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl (294kB)
     |████████████████████████████████| 296kB 43.6MB/s 
Collecting Keras==2.3.1
  Downloading https://files.pythonhosted.org/packages/ad/fd/6bfe87920d7f4fd475acd28500a42482b6b84479832bdc0fe9e589a60ceb/Keras-2.3.1-py2.py3-none-any.whl (377kB)
     |████████████████████████████████| 378kB 39.4MB/s 
Collecting Keras-Applications==1.0.8
  Downloading https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl (50kB)
     |████████████████████████████████| 51kB 4.7MB/s 
Collecting Keras-Preprocessing==1.1.0
  Downloading https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl (41kB)
     |████████████████████████████████| 51kB 5.2MB/s 
Collecting kiwisolver==1.1.0
  Downloading https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB)
     |████████████████████████████████| 92kB 7.6MB/s 
Collecting Markdown==3.1.1
  Downloading https://files.pythonhosted.org/packages/c0/4e/fd492e91abdc2d2fcb70ef453064d980688762079397f779758e055f6575/Markdown-3.1.1-py2.py3-none-any.whl (87kB)
     |████████████████████████████████| 92kB 7.2MB/s 
Collecting matplotlib==3.1.2
  Downloading https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1MB)
     |████████████████████████████████| 13.1MB 43.4MB/s 
Collecting more-itertools==8.0.2
  Downloading https://files.pythonhosted.org/packages/68/03/0604cec1ea13c9f063dd50f900d1a36160334dd3cfb01fd0e638f61b46ba/more_itertools-8.0.2-py3-none-any.whl (40kB)
     |████████████████████████████████| 40kB 3.2MB/s 
Collecting networkx==2.4
  Downloading https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl (1.6MB)
     |████████████████████████████████| 1.6MB 43.4MB/s 
Collecting nibabel==3.0.0
  Downloading https://files.pythonhosted.org/packages/0d/fc/2efb2a7c5d117c761b72f6bc00bf057294e9ccdf0a737957c65fa89ecc6f/nibabel-3.0.0-py3-none-any.whl (3.3MB)
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Collecting numpy==1.17.4
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Collecting oauthlib==3.1.0
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Collecting opt-einsum==3.1.0
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Collecting packaging==19.2
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Collecting Pillow==6.2.1
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Collecting pluggy==0.13.1
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Collecting psutil==5.6.7
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Collecting py==1.8.0
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Collecting pyasn1==0.4.8
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Collecting pyasn1-modules==0.2.7
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Collecting pycparser==2.19
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Collecting pytest==5.3.2
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Collecting pytest-cov==2.8.1
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Collecting pytz==2019.3
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Collecting PyWavelets==1.1.1
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Collecting PyYAML==5.2
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Collecting raven==6.10.0
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Collecting requests==2.22.0
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Collecting requests-oauthlib==1.3.0
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Collecting rsa==4.0
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Collecting scikit-image==0.16.2
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Collecting scikit-learn==0.22
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Collecting scipy==1.4.0
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Collecting six==1.13.0
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Collecting tensorboard==2.0.2
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Collecting tensorflow==2.0.0
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Collecting tensorflow-estimator==2.0.1
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Collecting termcolor==1.1.0

vb922 · January 17, 2020, 4:23pm

 Downloading https://files.pythonhosted.org/packages/8a/48/a76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981/termcolor-1.1.0.tar.gz
Collecting tqdm==4.40.2
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Collecting transforms3d==0.3.1
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Collecting urllib3==1.25.7
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Collecting wcwidth==0.1.7
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Collecting Werkzeug==0.16.0
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Collecting wrapt==1.11.2
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Collecting xlutils==2.0.0
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Collecting xlwt==1.3.0
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Collecting zipp==0.6.0
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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)
Building wheels for collected packages: absl-py, gast, opt-einsum, psutil, pycparser, PyYAML, termcolor, transforms3d, wrapt
  Building wheel for absl-py (setup.py) ... done
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Successfully built absl-py gast opt-einsum psutil pycparser PyYAML termcolor transforms3d wrapt
Installing collected packages: six, absl-py, astor, attrs, cachetools, pycparser, cffi, chardet, coverage, cryptography, cycler, decorator, numpy, scipy, nibabel, h5py, dipy, futures, gast, pyasn1, pyasn1-modules, rsa, google-auth, urllib3, idna, requests, oauthlib, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, PyYAML, Keras-Applications, Keras-Preprocessing, Keras, kiwisolver, Markdown, pyparsing, python-dateutil, 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/cluster/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...

./install_sct: line 595: setenv: command not found

Installing binaries...


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


--
Spinal Cord Toolbox (4.2.1)

Folder /autofs/cluster/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 [00:14<00:00, 5.70MB/s]

Create temporary folder (/tmp/sct-20200116135723.241423-mv9l7z9j)...

Unzip data to: /tmp/sct-20200116135723.241423-mv9l7z9j

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

Remove temporary folders...
Done!


All requirements installed!


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


Installing data...


rm -rf /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1/data


mkdir -p /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1/data


cd /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1/data


sct_download_data -d PAM50

./install_sct: line 83: sct_download_data: command not found

ERROR: Command failed.


Installation failed

vb922 · January 17, 2020, 4:24pm

I had to paste it in two different messages because I was exceeding the allowed character number.
Thank you!

jcohenadad · January 17, 2020, 5:12pm

Thank you. In the future, you can use ~~~ to format Terminal output.

So, the problem is related to the environment. Based on your default .cshrc file, it seems like you are running csh/tcsh shell. However, the command setenv is not recognized (this is an error message that appeared during the installation). So, could you please try to run the following commands and let me know the output:

echo $SHELL
echo $0
echo $HOME
echo ~
ls -la ~/.*rc
ls -la $HOME/.*rc

Lastly: do you happen to know what shell config file you are using? (and where it is located)?

vb922 · January 17, 2020, 7:00pm

Thanks for your reply!
The shell config file .cshrc is located in the path /homes/2/vb922
Do you need me to provide the code?

This is the Terminal output for your commands:

/usr/local/bin/tcsh
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ echo $0
tcsh
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ echo $HOME
/homes/2/vb922
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ echo ~
/homes/2/vb922
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ ls -la ~/.*rc
-rw-r----- 1 vb922 vb922   304 Oct  3  2016 /homes/2/vb922/.bashrc
-rw-rwxr-- 1 vb922 vb922  1742 Oct 29 12:06 /homes/2/vb922/.cshrc
-rw------- 1 vb922 vb922 17390 Oct  3  2016 /homes/2/vb922/.pinerc
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ ls -la $HOME/.*rc
-rw-r----- 1 vb922 vb922   304 Oct  3  2016 /homes/2/vb922/.bashrc
-rw-rwxr-- 1 vb922 vb922  1742 Oct 29 12:06 /homes/2/vb922/.cshrc
-rw------- 1 vb922 vb922 17390 Oct  3  2016 /homes/2/vb922/.pinerc
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $

jcohenadad · January 17, 2020, 7:30pm

Thanks, what are the output of:

setenv 
export

vb922 · January 17, 2020, 8:15pm

OSTYPE=linux
QT_GRAPHICSSYSTEM_CHECKED=1
KDEDIRS=/usr
LANG=en_US.UTF-8
DISPLAY=:0
SHLVL=2
LOGNAME=vb922
VENDOR=unknown
CVS_RSH=ssh
IMSETTINGS_MODULE=none
QTLIB=/usr/lib64/qt-3.3/lib
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
XAUTHORITY=/run/gdm/auth-for-vb922-M3rZXS/database
XDG_VTNR=1
QTDIR=/usr/lib64/qt-3.3
LPDEST=InvalidPrinter
IMSETTINGS_INTEGRATE_DESKTOP=yes
XDG_SESSION_ID=1
PWD=/autofs/cluster/mscat/users/caterina/recons_fsv5.3
DESKTOP_SESSION=0-mate
XDG_SESSION_DESKTOP=0-mate
GDMSESSION=0-mate
USERNAME=vb922
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
WINDOWPATH=1
COLORTERM=truecolor
MATE_DESKTOP_SESSION_ID=this-is-deprecated
HOST=vulcano.nmr.mgh.harvard.edu
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-wtWmVAgS5S,guid=bc8aee3670c6e70d6a9267975e1cdcff
GROUP=vb922
MAIL=/var/spool/mail/vb922
HOSTTYPE=x86_64-linux
XDG_DATA_DIRS=/homes/2/vb922/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/
PRINTER=InvalidPrinter
MODULESHOME=/usr/share/Modules
LESSOPEN=||/usr/bin/lesspipe.sh %s
SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/3397,unix/unix:/tmp/.ICE-unix/3397
PATHSET=1
GDM_LANG=en_US.UTF-8
SHELL=/usr/local/bin/tcsh
XDG_SESSION_TYPE=x11
GTK_OVERLAY_SCROLLING=0
HOSTNAME=vulcano.nmr.mgh.harvard.edu
SSH_AGENT_PID=3366
TERM=xterm-256color
SSH_AUTH_SOCK=/run/user/4016374/keyring/ssh
XDG_CURRENT_DESKTOP=MATE
PATH=/usr/pubsw/packages/python/anaconda/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fsfast/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/tktools:/usr/pubsw/packages/fsl/current/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/bin:/homes/2/vb922/bin:/usr/pubsw/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/pubsw/packages/AFNI/current/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fillLesion/src/:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/
WINDOWID=44205621
COBBLER_SERVER=spacewalk.nmr.mgh.harvard.edu
HOME=/homes/2/vb922
XDG_SEAT=seat0
MACHTYPE=x86_64
XDG_RUNTIME_DIR=/run/user/4016374
QTINC=/usr/lib64/qt-3.3/include
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
USER=vb922
VTE_VERSION=5202
LOADEDMODULES=
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
FREESURFER_HOME=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
SUBJECTS_DIR=/autofs/cluster/mscat/users/caterina/recons_fsv5.3
FUNCTIONALS_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/sessions
OS=Linux
FS_OVERRIDE=0
FSFAST_HOME=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fsfast
MINC_BIN_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/bin
MNI_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni
MINC_LIB_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/lib
MNI_DATAPATH=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/data
FSL_DIR=/usr/pubsw/packages/fsl/current
LOCAL_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/local
FSF_OUTPUT_FORMAT=nii.gz
FMRI_ANALYSIS_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fsfast
MNI_PERL5LIB=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/lib/perl5/5.8.5
PERL5LIB=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/lib/perl5/5.8.5
FSLDIR=/usr/pubsw/packages/fsl/current
FSL_BIN=/usr/pubsw/packages/fsl/current/bin
FSLOUTPUTTYPE=NIFTI_GZ
FSLMULTIFILEQUIT=TRUE
FSLTCLSH=/usr/pubsw/packages/fsl/current/bin/fsltclsh
FSLWISH=/usr/pubsw/packages/fsl/current/bin/fslwish
FSLLOCKDIR=
FSLMACHINELIST=
FSLREMOTECALL=
FSLGECUDAQ=cuda.q
FSLDISPLAY=/usr/bin/display
FSLCONVERT=/usr/bin/convert
FIX_VERTEX_AREA=
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ export
export: Command not found.
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $

vb922 · January 17, 2020, 8:17pm

Sorry I think I copied the wrong thing…

vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ setenv
OSTYPE=linux
QT_GRAPHICSSYSTEM_CHECKED=1
KDEDIRS=/usr
LANG=en_US.UTF-8
DISPLAY=:0
SHLVL=2
LOGNAME=vb922
VENDOR=unknown
CVS_RSH=ssh
IMSETTINGS_MODULE=none
QTLIB=/usr/lib64/qt-3.3/lib
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
XAUTHORITY=/run/gdm/auth-for-vb922-M3rZXS/database
XDG_VTNR=1
QTDIR=/usr/lib64/qt-3.3
LPDEST=InvalidPrinter
IMSETTINGS_INTEGRATE_DESKTOP=yes
XDG_SESSION_ID=1
PWD=/autofs/cluster/mscat/users/caterina/recons_fsv5.3
DESKTOP_SESSION=0-mate
XDG_SESSION_DESKTOP=0-mate
GDMSESSION=0-mate
USERNAME=vb922
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
WINDOWPATH=1
COLORTERM=truecolor
MATE_DESKTOP_SESSION_ID=this-is-deprecated
HOST=vulcano.nmr.mgh.harvard.edu
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-wtWmVAgS5S,guid=bc8aee3670c6e70d6a9267975e1cdcff
GROUP=vb922
MAIL=/var/spool/mail/vb922
HOSTTYPE=x86_64-linux
XDG_DATA_DIRS=/homes/2/vb922/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/
PRINTER=InvalidPrinter
MODULESHOME=/usr/share/Modules
LESSOPEN=||/usr/bin/lesspipe.sh %s
SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/3397,unix/unix:/tmp/.ICE-unix/3397
PATHSET=1
GDM_LANG=en_US.UTF-8
SHELL=/usr/local/bin/tcsh
XDG_SESSION_TYPE=x11
GTK_OVERLAY_SCROLLING=0
HOSTNAME=vulcano.nmr.mgh.harvard.edu
SSH_AGENT_PID=3366
TERM=xterm-256color
SSH_AUTH_SOCK=/run/user/4016374/keyring/ssh
XDG_CURRENT_DESKTOP=MATE
PATH=/usr/pubsw/packages/python/anaconda/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fsfast/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/tktools:/usr/pubsw/packages/fsl/current/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/bin:/homes/2/vb922/bin:/usr/pubsw/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/pubsw/packages/AFNI/current/bin:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fillLesion/src/:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/
WINDOWID=44205621
COBBLER_SERVER=spacewalk.nmr.mgh.harvard.edu
HOME=/homes/2/vb922
XDG_SEAT=seat0
MACHTYPE=x86_64
XDG_RUNTIME_DIR=/run/user/4016374
QTINC=/usr/lib64/qt-3.3/include
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
USER=vb922
VTE_VERSION=5202
LOADEDMODULES=
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
FREESURFER_HOME=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
SUBJECTS_DIR=/autofs/cluster/mscat/users/caterina/recons_fsv5.3
FUNCTIONALS_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/sessions
OS=Linux
FS_OVERRIDE=0
FSFAST_HOME=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fsfast
MINC_BIN_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/bin
MNI_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni
MINC_LIB_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/lib
MNI_DATAPATH=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/data
FSL_DIR=/usr/pubsw/packages/fsl/current
LOCAL_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/local
FSF_OUTPUT_FORMAT=nii.gz
FMRI_ANALYSIS_DIR=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/fsfast
MNI_PERL5LIB=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/lib/perl5/5.8.5
PERL5LIB=/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013/mni/lib/perl5/5.8.5
FSLDIR=/usr/pubsw/packages/fsl/current
FSL_BIN=/usr/pubsw/packages/fsl/current/bin
FSLOUTPUTTYPE=NIFTI_GZ
FSLMULTIFILEQUIT=TRUE
FSLTCLSH=/usr/pubsw/packages/fsl/current/bin/fsltclsh
FSLWISH=/usr/pubsw/packages/fsl/current/bin/fslwish
FSLLOCKDIR=
FSLMACHINELIST=
FSLREMOTECALL=
FSLGECUDAQ=cuda.q
FSLDISPLAY=/usr/bin/display
FSLCONVERT=/usr/bin/convert
FIX_VERTEX_AREA=
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $ export
export: Command not found.
vulcano:/autofs/cluster/mscat/users/caterina/recons_fsv5.3 $

jcohenadad · January 17, 2020, 8:33pm

OK, I think I found what the problem is: the install script is running under bash, but launched tcsh commands such as setenv (which should be run outside of the script).

Could you please copy this script install_sct_test (20.9 KB) under SCT’s folder and run this modified installer:

./install_sct_test

vb922 · January 21, 2020, 4:32pm

This is what I got:



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

Checking OS type and version...

Linux vulcano.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: y

Copying source files from /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1 to /homes/2/vb922/sct_4.2.1

.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5WebEngineCore.so.5’: Disk quota exceeded
...........cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Multimedia.so.5’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5QuickWidgets.so.5’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Location.so.5’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Bluetooth.so.5’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtMultimedia.so’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtPrintSupport.so’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtDesigner.so’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtWebSockets.so’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtNfc.so’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtQuickWidgets.so’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/pyrcc.so’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/_QOpenGLFunctions_2_0.so’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtWidgets.so’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtWebEngineCore.so’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/QtMultimediaWidgets.so’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/PyQt5/sip.so’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/cryptography-2.8.dist-info’: Disk quota exceeded
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cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/site-packages/pytz-2019.3.dist-info’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/keyword.py’: Disk quota exceeded
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.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/ensurepip’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/datetime.py’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/asyncio’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/sysconfig.py’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/dummy_threading.py’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/pkgutil.py’: Disk quota exceeded
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.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/sqlite3’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/bisect.py’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/pathlib.py’: Disk quota exceeded
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.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/python3.6/lib2to3’: Disk quota exceeded
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...cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/liblsan.so.0.0.0’: Disk quota exceeded
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.............cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libpanelw.so.6.1’: Disk quota exceeded
..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libhistory.so.7.0’: Disk quota exceeded
..cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/tdbcpostgres1.0.6’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/tclooConfig.sh’: Disk quota exceeded
..cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/tk8.6’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libpython3.6m.a’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libtk8.6.so’: Disk quota exceeded
...cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libssl.a’: Disk quota exceeded
..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libffi.la’: Disk quota exceeded
..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libpanelw.a’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libz.so.1.2.11’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/tcl8’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libquadmath.so.0.0.0’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libtinfow.a’: Disk quota exceeded
..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libhistory.a’: Disk quota exceeded
..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libformw.so.6.1’: Disk quota exceeded
..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/liblzma.a’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/liblzma.so.5.2.4’: Disk quota exceeded
...cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/tclConfig.sh’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libssl.so.1.1’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libncursesw.so.6.1’: Disk quota exceeded
....cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/tkConfig.sh’: Disk quota exceeded
...cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/pkgconfig’: Disk quota exceeded
...cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libitm.so.1.0.0’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libreadline.so.7.0’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libasan.so.5.0.0’: Disk quota exceeded

vb922 · January 21, 2020, 4:32pm

..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libstdc++.so.6.0.26’: Disk quota exceeded
...cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libtinfow.so.6.1’: Disk quota exceeded
..cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libncursesw.a’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libmenuw.so.6.1’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libedit.a’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libcrypto.so.1.1’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/libsqlite3.a’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/lib/tdbcodbc1.0.6’: Disk quota exceeded
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.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/envs/venv_sct/conda-meta’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/etc’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/python/include’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/requirements-freeze.txt’: Disk quota exceeded
.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/requirements.txt’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/scripts’: Disk quota exceeded
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.cp: failed to close ‘/homes/2/vb922/sct_4.2.1/setup.py’: Disk quota exceeded
.cp: cannot create directory ‘/homes/2/vb922/sct_4.2.1/shell’: Disk quota exceeded
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cp: failed to close ‘/homes/2/vb922/sct_4.2.1/version.txt’: Disk quota exceeded
.
Removing sct and isct softlink from /homes/2/vb922/sct_4.2.1/bin

Installing conda...


rm -rf /homes/2/vb922/sct_4.2.1/python


mkdir -p /homes/2/vb922/sct_4.2.1/python


wget -O /tmp/tmp.dWmmNaQwc3/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-01-17 15:59:36--  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:c84f, ...
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.dWmmNaQwc3/miniconda.sh’

100%[===================================================================================================>] 71,785,000  67.3MB/s   in 1.0s   

2020-01-17 15:59:37 (67.3 MB/s) - ‘/tmp/tmp.dWmmNaQwc3/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.dWmmNaQwc3/miniconda.sh -p /homes/2/vb922/sct_4.2.1/python -b -f

PREFIX=/homes/2/vb922/sct_4.2.1/python
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                                                                    
Solving environment: done

## Package Plan ##

  environment location: /homes/2/vb922/sct_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: /homes/2/vb922/sct_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
ca-certificates-2019 | 124 KB    | ################################################################################################## | 100% 
wheel-0.33.6         | 42 KB     | ################################################################################################## | 100% 
python-3.6.10        | 29.7 MB   | ################################################################################################## | 100% 
certifi-2019.11.28   | 153 KB    | ################################################################################################## | 100% 
pip-19.3.1           | 1.7 MB    | ################################################################################################## | 100% 
openssl-1.1.1d       | 2.5 MB    | ################################################################################################## | 100% 
sqlite-3.30.1        | 1.1 MB    | ################################################################################################## | 100% 
ld_impl_linux-64-2.3 | 568 KB    | ################################################################################################## | 100% 
setuptools-44.0.0    | 510 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)

Obtaining file:///homes/2/vb922/sct_4.2.1
ERROR: Files/directories not found in /homes/2/vb922/sct_4.2.1/

Failed to pip install sct.


Installation failed

vulcano:/autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1 $

vb922 · January 23, 2020, 3:05pm

Oops sorry just noticed a huge mistake. Re-launching it now! I will let you know. Thank you!

jcohenadad · January 23, 2020, 8:30pm

Hi,
did the installation work with the modified script?

vb922 · January 23, 2020, 8:58pm

I think it did not…



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



Checking OS type and version...

Linux vulcano.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.


Copying source files from /autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1 to /autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1

.........................................................................................................................................................................................................................................................................................................................
  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
openssl-1.1.1d       | 2.5 MB    | ################################################################################################## | 100% 
pip-19.3.1           | 1.7 MB    | ################################################################################################## | 100% 
sqlite-3.30.1        | 1.1 MB    | ################################################################################################## | 100% 
setuptools-44.0.0    | 510 KB    | ################################################################################################## | 100% 
ca-certificates-2019 | 124 KB    | ################################################################################################## | 100% 
certifi-2019.11.28   | 153 KB    | ################################################################################################## | 100% 
ld_impl_linux-64-2.3 | 568 KB    | ################################################################################################## | 100% 
wheel-0.33.6         | 42 KB     | ################################################################################################## | 100% 
python-3.6.10        | 29.7 MB   | ################################################################################################## | 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, nibabel, scipy, h5py, dipy, futures, gast, pyasn1, pyasn1-modules, rsa, google-auth, oauthlib, urllib3, idna, requests, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, Keras-Applications, Keras-Preprocessing, PyYAML, Keras, kiwisolver, Markdown, pyparsing, python-dateutil, 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, tensorflow-estimator, termcolor, wrapt, 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, 13.4MB/s]

Create temporary folder (/tmp/sct-20200123101802.914909-oudy713n)...

Unzip data to: /tmp/sct-20200123101802.914909-oudy713n

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, 5.20MB/s]                                                                                                             

Create temporary folder (/tmp/sct-20200123101825.279214-_u92w510)...

Unzip data to: /tmp/sct-20200123101825.279214-_u92w510

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 [00:01<00:00, 9.26MB/s]

Create temporary folder (/tmp/sct-20200123101830.000029-gdthalpd)...

Unzip data to: /tmp/sct-20200123101830.000029-gdthalpd

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, 4.07MB/s]

Create temporary folder (/tmp/sct-20200123101832.392560-zp80svhp)...

Unzip data to: /tmp/sct-20200123101832.392560-zp80svhp

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, 17.9MB/s]

Create temporary folder (/tmp/sct-20200123101835.564710-a2ohseav)...

Unzip data to: /tmp/sct-20200123101835.564710-a2ohseav

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, 14.4MB/s]

Create temporary folder (/tmp/sct-20200123101841.417436-la6fzcj7)...

Unzip data to: /tmp/sct-20200123101841.417436-la6fzcj7

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, 4.39MB/s]

Create temporary folder (/tmp/sct-20200123101846.255466-_i58chfg)...

Unzip data to: /tmp/sct-20200123101846.255466-_i58chfg

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, 11.9MB/s]

Create temporary folder (/tmp/sct-20200123101851.100398-_xlx5s_e)...

Unzip data to: /tmp/sct-20200123101851.100398-_xlx5s_e

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, 15.6MB/s]

Create temporary folder (/tmp/sct-20200123101854.933524-6_ujko7e)...

Unzip data to: /tmp/sct-20200123101854.933524-6_ujko7e

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: 8, Used by SCT: 8
RAM: MemTotal:       24512016 kB
total        used        free      shared  buff/cache   available
Mem:          23937        2503       13684         344        7749       20728
Swap:         23999           5       23994
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........................../install_sct_test: line 673: 50512 Illegal instruction     (core dumped) sct_check_dependencies

Installation validation Failed!

Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):

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

Installation failed

vulcano:/autofs/cluster/mscat/users/valeria/spinalcordtoolbox-4.2.1 $

jcohenadad · January 23, 2020, 9:16pm

this is another problem now, not related to the shell environment. It looks like your RAM is maxed out:

total        used        free      shared  buff/cache   available
Mem:          23937        2503       13684         344        7749       20728

you need at least 2GB of RAM to run SCT

can you free your RAM and re-run the installation?

vb922 · January 23, 2020, 9:38pm

Done…



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



Checking OS type and version...

Linux vulcano.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.z03g0kxHoW/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-01-23 16:28:41--  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.z03g0kxHoW/miniconda.sh’

100%[====================================================================================================================================================================================================>] 71,785,000  52.9MB/s   in 1.3s   

2020-01-23 16:28:43 (52.9 MB/s) - ‘/tmp/tmp.z03g0kxHoW/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.z03g0kxHoW/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
python-3.6.10        | 29.7 MB   | ################################################################################################################# | 100% 
certifi-2019.11.28   | 153 KB    | ################################################################################################################# | 100% 
ca-certificates-2019 | 124 KB    | ################################################################################################################# | 100% 
setuptools-44.0.0    | 510 KB    | ################################################################################################################# | 100% 
wheel-0.33.6         | 42 KB     | ################################################################################################################################################################################################### | 100% 
pip-19.3.1           | 1.7 MB    | ################################################################################################################################################################################################### | 100% 
ld_impl_linux-64-2.3 | 568 KB    | ################################################################################################################################################################################################### | 100% 
openssl-1.1.1d       | 2.5 MB    | ################################################################################################################################################################################################### | 100% 
sqlite-3.30.1        | 1.1 MB    | ################################################################################################################################################################################################### | 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, scipy, h5py, nibabel, dipy, futures, gast, pyasn1, pyasn1-modules, rsa, google-auth, oauthlib, urllib3, idna, requests, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, PyYAML, Keras-Preprocessing, Keras-Applications, Keras, kiwisolver, Markdown, pyparsing, python-dateutil, 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, termcolor, wrapt, 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 [00:05<00:00, 15.5MB/s]

Create temporary folder (/tmp/sct-20200123163300.573610-gyz9dulz)...

Unzip data to: /tmp/sct-20200123163300.573610-gyz9dulz

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

vb922 · January 23, 2020, 9:38pm



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, 5.19MB/s]                                                                                                                                                                                                              

Create temporary folder (/tmp/sct-20200123163323.261601-j97s45yv)...

Unzip data to: /tmp/sct-20200123163323.261601-j97s45yv

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 [00:01<00:00, 10.2MB/s]

Create temporary folder (/tmp/sct-20200123163329.021173-x1ptqr8j)...

Unzip data to: /tmp/sct-20200123163329.021173-x1ptqr8j

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, 6.50MB/s]

Create temporary folder (/tmp/sct-20200123163331.186162-a0fj3aqb)...

Unzip data to: /tmp/sct-20200123163331.186162-a0fj3aqb

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, 16.5MB/s]

Create temporary folder (/tmp/sct-20200123163332.931403-w1map8bg)...

Unzip data to: /tmp/sct-20200123163332.931403-w1map8bg

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 [00:03<00:00, 14.8MB/s]

Create temporary folder (/tmp/sct-20200123163338.971279-eldcga_n)...

Unzip data to: /tmp/sct-20200123163338.971279-eldcga_n

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, 4.11MB/s]

Create temporary folder (/tmp/sct-20200123163342.744529-4l2k4qie)...

Unzip data to: /tmp/sct-20200123163342.744529-4l2k4qie

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, 12.2MB/s]

Create temporary folder (/tmp/sct-20200123163346.018499-myyh84fp)...

Unzip data to: /tmp/sct-20200123163346.018499-myyh84fp

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, 18.1MB/s]

Create temporary folder (/tmp/sct-20200123163348.161810-6hady_9r)...

Unzip data to: /tmp/sct-20200123163348.161810-6hady_9r

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: 8, Used by SCT: 8
RAM: MemTotal:       24512016 kB
total        used        free      shared  buff/cache   available
Mem:          23937         786       19981          20        3169       22787
Swap:         23999           0       23999
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........................../install_sct_test: line 673:  5437 Illegal instruction     (core dumped) sct_check_dependencies

Installation validation Failed!

Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):

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


Installation failed

vulcano:/autofs/space/alicudi_002/users/mscat/users/valeria/spinalcordtoolbox-4.2.1 $

jcohenadad · January 23, 2020, 9:44pm

your free RAM is still <2GB:

total        used        free      shared  buff/cache   available
Mem:          23937         786       19981          20        3169       22787