Installation failed during installation of Keras

Abdullah_Althubaiti · February 28, 2020, 8:24am

Hi,
Would you be able to help us with installation? It failed during Keras installation.
We have tried to install Keras manually as in this website below, but it still did not work.

Regards,
Abdullah

\s4305056@cai-gajah:~/sct$ ./install_sct


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



Checking OS type and version...

Linux cai-gajah 4.15.0-88-generic #88-Ubuntu SMP Tue Feb 11 20:11:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...


OK!


SCT version ......... dev
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /data/home/s4305056/.bashrc

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

Do you agree to help us improve SCT? [y]es/[n]o: y

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


SCT will be installed here: [/data/home/s4305056/sct]

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

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


Removing sct and isct softlink from /data/home/s4305056/sct/bin


Installing conda...


rm -rf /data/home/s4305056/sct/python


mkdir -p /data/home/s4305056/sct/python


wget -O /tmp/tmp.TI5srwFtcv/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-02-28 16:53:30--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c94f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.200.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 71785000 (68M) [application/x-sh]
Saving to: '/tmp/tmp.TI5srwFtcv/miniconda.sh’

/tmp/tmp.TI5srwFtcv/mi 100%[===========================>]  68.46M  39.2MB/s    in 1.7s    

2020-02-28 16:53:31 (39.2 MB/s) - '/tmp/tmp.TI5srwFtcv/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.TI5srwFtcv/miniconda.sh -p /data/home/s4305056/sct/python -b -f

PREFIX=/data/home/s4305056/sct/python
Unpacking payload ...
Extracting : ruamel_yaml-0.15.46-py37h14c3975_0.conda:  46%|▍| 16/35 [00:40<08:17, 26.17s/iExtracting : six-1.12.0-py37_0.conda:  49%|███████▊        | 17/35 [00:40<07:50, 26.17s/it]Extracting : conda-package-handling-1.6.0-py37h7b6447c_0.conda:  54%|▌| 19/35 [00:40<06:58,Extracting : pyopenssl-19.0.0-py37_0.conda:  57%|█████▋    | 20/35 [00:40<06:32, 26.17s/it]Extracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2:  89%|▉| 31/35 [00:40<01:44, 26.17s/itExtracting : wheel-0.33.6-py37_0.tar.bz2:  91%|██████████▉ | 32/35 [00:40<01:18, 26.17s/it]Collecting package metadata (current_repodata.json): done                                  
Solving environment: done

## Package Plan ##

  environment location: /data/home/s4305056/sct/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: 4.8.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /data/home/s4305056/sct/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.1.1   |                0         125 KB
    certifi-2019.11.28         |           py36_0         153 KB
    ld_impl_linux-64-2.33.1    |       h53a641e_7         568 KB
    ncurses-6.2                |       he6710b0_0         1.1 MB
    openssl-1.1.1d             |       h7b6447c_4         2.5 MB
    pip-20.0.2                 |           py36_1         1.7 MB
    python-3.6.10              |       h0371630_0        29.7 MB
    setuptools-45.2.0          |           py36_0         520 KB
    sqlite-3.31.1              |       h7b6447c_0         1.1 MB
    wheel-0.34.2               |           py36_0          51 KB
    ------------------------------------------------------------
                                           Total:        37.5 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-2020.1.1-0
  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-6.2-he6710b0_0
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_4
  pip                pkgs/main/linux-64::pip-20.0.2-py36_1
  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-45.2.0-py36_0
  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.34.2-py36_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Proceed ([y]/n)? 

Downloading and Extracting Packages
sqlite-3.31.1        | 1.1 MB    | ################################################ | 100% 
ca-certificates-2020 | 125 KB    | ################################################ | 100% 
openssl-1.1.1d       | 2.5 MB    | ################################################ | 100% 
wheel-0.34.2         | 51 KB     | ################################################ | 100% 
python-3.6.10        | 29.7 MB   | ################################################ | 100% 
setuptools-45.2.0    | 520 KB    | ################################################ | 100% 
pip-20.0.2           | 1.7 MB    | ################################################ | 100% 
ncurses-6.2          | 1.1 MB    | ################################################ | 100% 
ld_impl_linux-64-2.3 | 568 KB    | ################################################ | 100% 
certifi-2019.11.28   | 153 KB    | ################################################ | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate


Installing Python dependencies...

Collecting numpy
  Using cached numpy-1.18.1-cp36-cp36m-manylinux1_x86_64.whl (20.1 MB)
Installing collected packages: numpy
Successfully installed numpy-1.18.1

Using requirements-freeze.txt (release installation)

Processing /data/home/s4305056/.cache/pip/wheels/c3/af/84/3962a6af7b4ab336e951b7877dcfb758cf94548bb1771e0679/absl_py-0.9.0-py3-none-any.whl
Collecting astor==0.8.1
  Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting attrs==19.3.0
  Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting cachetools==4.0.0
  Using cached cachetools-4.0.0-py3-none-any.whl (10 kB)
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 cffi-1.13.2-cp36-cp36m-manylinux1_x86_64.whl (397 kB)
Collecting chardet==3.0.4
  Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting coverage==5.0
  Using cached coverage-5.0-cp36-cp36m-manylinux1_x86_64.whl (226 kB)
Collecting cryptography==2.8
  Using cached cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl (2.3 MB)
Collecting cycler==0.10.0
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting decorator==4.4.1
  Using cached decorator-4.4.1-py2.py3-none-any.whl (9.2 kB)
Collecting dipy==1.0.0
  Using cached dipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl (8.1 MB)
Collecting futures==3.1.1
  Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Processing /data/home/s4305056/.cache/pip/wheels/19/a7/b9/0740c7a3a7d1d348f04823339274b90de25fbcd217b2ee1fbe/gast-0.2.2-py3-none-any.whl
Collecting google-auth==1.10.0
  Using cached google_auth-1.10.0-py2.py3-none-any.whl (76 kB)
Collecting google-auth-oauthlib==0.4.1
  Using cached google_auth_oauthlib-0.4.1-py2.py3-none-any.whl (18 kB)
Collecting google-pasta==0.1.8
  Using cached google_pasta-0.1.8-py3-none-any.whl (57 kB)
Collecting grpcio==1.26.0
  Using cached grpcio-1.26.0-cp36-cp36m-manylinux2010_x86_64.whl (2.4 MB)
Collecting h5py==2.10.0
  Using cached h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Collecting idna==2.8
  Using cached idna-2.8-py2.py3-none-any.whl (58 kB)
Collecting imageio==2.6.1
  Using cached imageio-2.6.1-py3-none-any.whl (3.3 MB)
Collecting importlib-metadata==1.3.0
  Using cached importlib_metadata-1.3.0-py2.py3-none-any.whl (29 kB)
Collecting joblib==0.14.1
  Using cached joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Collecting Keras==2.3.1
  Using cached Keras-2.3.1-py2.py3-none-any.whl (377 kB)
Collecting Keras-Applications==1.0.8
  Using cached Keras_Applications-1.0.8-py3-none-any.whl (50 kB)
Collecting Keras-Preprocessing==1.1.0
  Using cached Keras_Preprocessing-1.1.0-py2.py3-none-any.whl (41 kB)
Collecting kiwisolver==1.1.0
  Using cached kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90 kB)
Collecting Markdown==3.1.1
  Using cached Markdown-3.1.1-py2.py3-none-any.whl (87 kB)
Collecting matplotlib==3.1.2
  Using cached matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1 MB)
Collecting more-itertools==8.0.2
  Using cached more_itertools-8.0.2-py3-none-any.whl (40 kB)
Collecting networkx==2.4
  Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting nibabel==3.0.0
  Using cached nibabel-3.0.0-py3-none-any.whl (3.3 MB)
Collecting numpy==1.17.4
  Using cached numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0 MB)
Collecting oauthlib==3.1.0
  Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB)
Processing /data/home/s4305056/.cache/pip/wheels/1f/6f/14/e0f4f6bceec756bbab45c392c4d5429a684b14d849464ebfbf/opt_einsum-3.1.0-py3-none-any.whl
Collecting packaging==19.2
  Using cached packaging-19.2-py2.py3-none-any.whl (30 kB)
Collecting pandas==0.25.3
  Using cached pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl (10.4 MB)
Collecting Pillow==6.2.1
  Using cached Pillow-6.2.1-cp36-cp36m-manylinux1_x86_64.whl (2.1 MB)
Collecting pluggy==0.13.1
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting protobuf==3.11.1
  Using cached protobuf-3.11.1-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB)
Processing /data/home/s4305056/.cache/pip/wheels/b2/b3/a3/551db06cebc9141c437c6b58aa751d3670471494e9f6d1428d/psutil-5.6.7-cp36-cp36m-linux_x86_64.whl
Collecting py==1.8.0
  Using cached py-1.8.0-py2.py3-none-any.whl (83 kB)
Collecting pyasn1==0.4.8
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting pyasn1-modules==0.2.7
  Using cached pyasn1_modules-0.2.7-py2.py3-none-any.whl (131 kB)
Processing /data/home/s4305056/.cache/pip/wheels/c6/6b/83/2608afaa57ecfb0a66ac89191a8d9bad71c62ca55ee499c2d0/pycparser-2.19-py2.py3-none-any.whl
Collecting pyOpenSSL==19.1.0
  Using cached pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB)
Collecting pyparsing==2.4.5
  Using cached pyparsing-2.4.5-py2.py3-none-any.whl (67 kB)
Collecting PyQt5==5.11.3
  Using cached PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8 MB)
Collecting PyQt5-sip==4.19.19
  Using cached PyQt5_sip-4.19.19-cp36-cp36m-manylinux1_x86_64.whl (67 kB)
Collecting pytest==5.3.2
  Using cached pytest-5.3.2-py3-none-any.whl (234 kB)
Collecting pytest-cov==2.8.1
  Using cached pytest_cov-2.8.1-py2.py3-none-any.whl (18 kB)
Collecting python-dateutil==2.8.1
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pytz==2019.3
  Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting PyWavelets==1.1.1
  Using cached PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB)
Processing /data/home/s4305056/.cache/pip/wheels/af/4b/a6/d492db4435642aebd1df1cd3ed075815e75ad6665aa47f4d04/PyYAML-5.2-cp36-cp36m-linux_x86_64.whl
Collecting raven==6.10.0
  Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB)
Collecting requests==2.22.0
  Using cached requests-2.22.0-py2.py3-none-any.whl (57 kB)
Collecting requests-oauthlib==1.3.0
  Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting rsa==4.0
  Using cached rsa-4.0-py2.py3-none-any.whl (38 kB)
Collecting scikit-image==0.16.2
  Using cached scikit_image-0.16.2-cp36-cp36m-manylinux1_x86_64.whl (26.5 MB)
Collecting scikit-learn==0.22
  Using cached scikit_learn-0.22-cp36-cp36m-manylinux1_x86_64.whl (7.0 MB)
Collecting scipy==1.4.0
  Using cached scipy-1.4.0-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB)
Collecting six==1.13.0
  Using cached six-1.13.0-py2.py3-none-any.whl (10 kB)
Collecting tensorboard==2.0.2
  Using cached tensorboard-2.0.2-py3-none-any.whl (3.8 MB)
Collecting tensorflow==2.0.1
  Using cached tensorflow-2.0.1-cp36-cp36m-manylinux2010_x86_64.whl (86.3 MB)
Collecting tensorflow-estimator==2.0.1
  Using cached tensorflow_estimator-2.0.1-py2.py3-none-any.whl (449 kB)
Processing /data/home/s4305056/.cache/pip/wheels/93/2a/eb/e58dbcbc963549ee4f065ff80a59f274cc7210b6eab962acdc/termcolor-1.1.0-py3-none-any.whl
Collecting tqdm==4.40.2
  Using cached tqdm-4.40.2-py2.py3-none-any.whl (55 kB)
Processing /data/home/s4305056/.cache/pip/wheels/be/7a/eb/465e9bb085af816c4d504821d542cc0059cc3433f6e8edea3c/transforms3d-0.3.1-py3-none-any.whl
Collecting urllib3==1.25.7
  Using cached urllib3-1.25.7-py2.py3-none-any.whl (125 kB)
Collecting wcwidth==0.1.7
  Using cached wcwidth-0.1.7-py2.py3-none-any.whl (21 kB)
Collecting Werkzeug==0.16.0
  Using cached Werkzeug-0.16.0-py2.py3-none-any.whl (327 kB)
Processing /data/home/s4305056/.cache/pip/wheels/0d/85/48/15d7bfab92a2d0e87372224c1f628fc57db7447a663a58e86c/wrapt-1.11.2-cp36-cp36m-linux_x86_64.whl
Collecting xlrd==1.2.0
  Using cached xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
Collecting xlutils==2.0.0
  Using cached xlutils-2.0.0-py2.py3-none-any.whl (55 kB)
Collecting xlwt==1.3.0
  Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Collecting zipp==0.6.0
  Using cached zipp-0.6.0-py2.py3-none-any.whl (4.1 kB)
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)) (45.2.0.post20200210)
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)) (0.34.2)
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, urllib3, idna, requests, oauthlib, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, Keras-Applications, PyYAML, Keras-Preprocessing, Keras, kiwisolver, Markdown, python-dateutil, pyparsing, matplotlib, networkx, opt-einsum, packaging, pytz, pandas, pluggy, protobuf, psutil, py, pyOpenSSL, PyQt5-sip, PyQt5, wcwidth, pytest, pytest-cov, PyWavelets, raven, scikit-image, scikit-learn, Werkzeug, tensorboard, tensorflow-estimator, termcolor, wrapt, tensorflow, tqdm, transforms3d, xlrd, xlwt, xlutils
  Attempting uninstall: numpy
    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-2.0.1 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:///data/home/s4305056/sct
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 /data/home/s4305056/sct/bin


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)

Folder /data/home/s4305056/sct/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 [00:10<00:00, 7.99MB/s]

Create temporary folder (/tmp/sct-20200228170355.247948-1yye36g9)...

Unzip data to: /tmp/sct-20200228170355.247948-1yye36g9

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

Remove temporary folders...
Done!


All requirements installed!


. /data/home/s4305056/sct/python/bin/activate /data/home/s4305056/sct/python


Installing data...


rm -rf /data/home/s4305056/sct/data


mkdir -p /data/home/s4305056/sct/data


cd /data/home/s4305056/sct/data


sct_download_data -d PAM50


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


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 [00:10, 6.60MB/s]                                                           

Create temporary folder (/tmp/sct-20200228170419.936900-txkco7l1)...

Unzip data to: /tmp/sct-20200228170419.936900-txkco7l1

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

Remove temporary folders...
Done!


sct_download_data -d gm_model


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


Trying URL: https://osf.io/ugscu/?action=download
Downloading 20160922_gm_model.zip...
Status: 100%|#########################################| 10.3M/10.3M [00:01<00:00, 6.47MB/s]

Create temporary folder (/tmp/sct-20200228170428.352300-uqrptp7m)...

Unzip data to: /tmp/sct-20200228170428.352300-uqrptp7m

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

Remove temporary folders...
Done!


sct_download_data -d optic_models


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


Trying URL: https://osf.io/g4fwn/?action=download
Downloading 20170413_optic_models.zip...
Status: 100%|#########################################| 17.7k/17.7k [00:00<00:00, 20.2MB/s]

Create temporary folder (/tmp/sct-20200228170440.803149-0tv013rt)...

Unzip data to: /tmp/sct-20200228170440.803149-0tv013rt

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

Remove temporary folders...
Done!


sct_download_data -d pmj_models


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


Trying URL: https://osf.io/4gufr/?action=download
Downloading 20170922_pmj_models.zip...
Status: 100%|##########################################| 8.87k/8.87k [00:00<00:00, 870kB/s]

Create temporary folder (/tmp/sct-20200228170508.103870-ytsnvm70)...

Unzip data to: /tmp/sct-20200228170508.103870-ytsnvm70

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

Remove temporary folders...
Done!


sct_download_data -d deepseg_sc_models


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


Trying URL: https://osf.io/avf97/?action=download
Downloading 20180610_deepseg_sc_models.zip...
Status: 100%|#########################################| 58.7M/58.7M [00:06<00:00, 9.69MB/s]

Create temporary folder (/tmp/sct-20200228170517.878443-vy1jbh_0)...

Unzip data to: /tmp/sct-20200228170517.878443-vy1jbh_0

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

Remove temporary folders...
Done!


sct_download_data -d deepseg_gm_models


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


Trying URL: https://osf.io/b9y4x/?action=download
Downloading 20180205_deepseg_gm_models.zip...
Status: 100%|#########################################| 2.28M/2.28M [00:01<00:00, 1.90MB/s]

Create temporary folder (/tmp/sct-20200228170524.057653-f2b10c94)...

Unzip data to: /tmp/sct-20200228170524.057653-f2b10c94

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

Remove temporary folders...
Done!


sct_download_data -d deepseg_lesion_models


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


Trying URL: https://osf.io/eg7v9/?action=download
Downloading 20180613_deepseg_lesion_models.zip...
Status: 100%|#########################################| 16.0M/16.0M [00:03<00:00, 4.68MB/s]

Create temporary folder (/tmp/sct-20200228170531.207678-osd6og0p)...

Unzip data to: /tmp/sct-20200228170531.207678-osd6og0p

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

Remove temporary folders...
Done!


sct_download_data -d c2c3_disc_models


--
Spinal Cord Toolbox (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)


Trying URL: https://osf.io/t97ap/?action=download
Downloading 20190117_c2c3_disc_models.zip...
Status: 100%|#########################################| 8.94k/8.94k [00:00<00:00, 2.77MB/s]

Create temporary folder (/tmp/sct-20200228170535.145011-x1sf34vp)...

Unzip data to: /tmp/sct-20200228170535.145011-x1sf34vp

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 (git-master-af5e0a37b73df681fefb9880eb7d78262ba67205)

SCT info:
- version: git-master-af5e0a37b73df681fefb9880eb7d78262ba67205
- path: /data/home/s4305056/sct
OS: linux (Linux-4.15.0-88-generic-x86_64-with-debian-buster-sid)
CPU cores: Available: 8, Used by SCT: 8
RAM: MemTotal:       74215088 kB
total        used        free      shared  buff/cache   available
Mem:          72475        2267       62830         128        7377       69307
Swap:        511997           0      511997
Check Python executable.............................[OK]
  Using bundled python 3.6.10 |Anaconda, Inc.| (default, Jan  7 2020, 21:14:29) 
[GCC 7.3.0] at /data/home/s4305056/sct/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: line 678: 15664 Illegal instruction     (core dumped) sct_check_dependencies

Installation validation Failed!


Installation failed!

jcohenadad · February 28, 2020, 4:07pm

It is possible that your CPU does not support AVX. See related issue here. Could you run lscpu and copy/paste the output?

Nyoman_Kurniawan · February 29, 2020, 1:26am

Hi Julien, Below is the output of lscpu.
Thanks, Nyoman

Architecture:        x86_64
CPU op-mode(s):      32-bit, 64-bit
Byte Order:          Little Endian
CPU(s):              8
On-line CPU(s) list: 0-7
Thread(s) per core:  1
Core(s) per socket:  4
Socket(s):           2
NUMA node(s):        1
Vendor ID:           GenuineIntel
CPU family:          6
Model:               44
Model name:          Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
Stepping:            2
CPU MHz:             2102.760
BogoMIPS:            4788.05
Virtualisation:      VT-x
L1d cache:           32K
L1i cache:           32K
L2 cache:            256K
L3 cache:            12288K
NUMA node0 CPU(s):   0-7
Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pd
pe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm
2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_
l1d

jcohenadad · February 29, 2020, 1:53am

Thank you Nyoman,

Indeed, your CPU does not support AVX, which is required by tensorflow >1.6. Given that multiple users are in the same situation, we will look for a solution.
Stay tuned!

Julien

jcohenadad · February 29, 2020, 2:54am

Nyoman, could you please try the following and copy/paste the Terminal output:

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

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

sct_testing

Nyoman_Kurniawan · March 2, 2020, 2:07am

Hi Julien,
I still have some errors during installation for pyqt. I have tried to install both Qt4 and 5 but it did not help (?), although at the end it said installation was successful

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: 

Validate installation...


--
Spinal Cord Toolbox (git-jca/2562-tensorflow-1.5-1850497098eed76fe47028263b52f845030a6480)

SCT info:
- version: git-jca/2562-tensorflow-1.5-1850497098eed76fe47028263b52f845030a6480
- path: /data/home/uqnkurn1/sct-tf1.5
OS: linux (Linux-4.15.0-88-generic-x86_64-with-debian-buster-sid)
CPU cores: Available: 8, Used by SCT: 8
RAM: MemTotal:       74215088 kB
total        used        free      shared  buff/cache   available
Mem:          72475        2753       46321         224       23400       68726
Swap:        511997           0      511997
Check Python executable.............................[OK]
  Using bundled python 3.6.10 |Anaconda, Inc.| (default, Jan  7 2020, 21:14:29) 
[GCC 7.3.0] at /data/home/uqnkurn1/sct-tf1.5/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.18.1)
Check if cryptography is installed..................[OK] (2.8)
Check if dipy is installed..........................[OK] (1.1.1)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.1.5) is installed.................[OK]
Check if matplotlib is installed....................[OK] (3.1.3)
Check if nibabel is installed.......................[OK] (3.0.1)
Check if pandas is installed........................[OK] (1.0.1)
Check if psutil is installed........................[OK] (5.7.0)
Check if pyqt5 (5.11.3) is installed................[OK]
Check if pytest is installed........................[OK] (5.3.5)
Check if pytest-cov is installed....................[OK] (2.8.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.23.0)
Check if scipy is installed.........................[OK] (1.4.1)
Check if scikit-image is installed..................[OK] (0.16.2)
Check if scikit-learn is installed..................[OK] (0.22.2)
Check if tensorflow (1.5.0) is installed............[OK]
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.43.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.8)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if DISPLAY variable is set....................[OK]
Check if figure can be opened with PyQt.............libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
[OK]


Open a new Terminal window to load environment variables, or run:
source /data/home/uqnkurn1/.bashrc


Installation finished successfully!

Nyoman_Kurniawan · March 2, 2020, 2:09am

Below is the output for sct_testing.

Regards,
nyoman

uqnkurn1@cai-gajah:~/sct-tf1.5$ sct_testing

--
Spinal Cord Toolbox (git-master-d8d887c155dec9450da37a5ee4f02de3cf6cdca5)


Trying URL: https://osf.io/yutrj/?action=download
Downloading 20191031_sct_testing_data.zip...
Status: 100%|##################################################################################################################################################################| 6.78M/6.78M [00:01<00:00, 5.70MB/s]

Create temporary folder (/tmp/sct-20200302120150.022681-zmm0yavn)...

Unzip data to: /tmp/sct-20200302120150.022681-zmm0yavn

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

Remove temporary folders...
Done!

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 8 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template
Checking **sct_deepseg_gm.............................[FAIL]**
   
   ====================================================================================================
   sct_deepseg_gm -i t2s/t2s_uncropped.nii.gz -o output.nii.gz -qc testing-qc
   ====================================================================================================
   
   
   --
   Spinal Cord Toolbox (git-master-d8d887c155dec9450da37a5ee4f02de3cf6cdca5)
   
   Illegal instruction (core dumped)
Checking **sct_deepseg_lesion.........................[FAIL]**
   
   ====================================================================================================
   sct_deepseg_lesion -i t2/t2.nii.gz -c t2
   ====================================================================================================
   
   
   --
   Spinal Cord Toolbox (git-master-d8d887c155dec9450da37a5ee4f02de3cf6cdca5)
   
   Illegal instruction (core dumped)
Checking **sct_deepseg_sc.............................[FAIL]**
   
   ====================================================================================================
   sct_deepseg_sc -i t2/t2.nii.gz -c t2 -igt t2/t2_seg_manual.nii.gz -qc testing-qc
   ====================================================================================================
   
   
   --
   Spinal Cord Toolbox (git-master-d8d887c155dec9450da37a5ee4f02de3cf6cdca5)
   
   Illegal instruction (core dumped)
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_convert................................[OK]
Checking sct_compute_ernst_angle....................[OK]
Checking sct_compute_hausdorff_distance.............[OK]
Checking sct_compute_mtr............................[OK]
Checking sct_compute_mscc...........................[OK]
Checking sct_compute_snr............................[OK]
Checking sct_concat_transfo.........................[OK]
Checking sct_create_mask............................[OK]
Checking sct_crop_image.............................[OK]
Checking sct_dice_coefficient.......................[OK]
Checking sct_detect_pmj.............................[OK]
Checking sct_dmri_compute_dti.......................[OK]
Checking sct_dmri_concat_b0_and_dwi.................[OK]
Checking sct_dmri_concat_bvals......................[OK]
Checking sct_dmri_concat_bvecs......................[OK]
Checking sct_dmri_create_noisemask..................[OK]
Checking sct_dmri_compute_bvalue....................[OK]
Checking sct_dmri_moco..............................[OK]
Checking sct_dmri_separate_b0_and_dwi...............[OK]
Checking sct_dmri_transpose_bvecs...................[OK]
Checking sct_extract_metric.........................[OK]
Checking sct_flatten_sagittal.......................[OK]
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_image..................................[OK]
Checking sct_label_utils............................[OK]
Checking sct_label_vertebrae........................[OK]
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[OK]
Checking sct_process_segmentation...................[OK]
Checking sct_propseg................................[OK]
Checking sct_qc.....................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_register_to_template...................[OK]
Checking sct_resample...............................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_warp_template..........................[OK]
status: [1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
Failures: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
Finished! Elapsed time: 153s

jcohenadad · March 2, 2020, 2:37am

Hi @Nyoman_Kurniawan,

You did not run sct_testing with the correct SCT installation (you probably did not restart a new terminal after having installed SCT from the specific branch). Version you were running for sct_testing:

git-master-d8d887c155dec9450da37a5ee4f02de3cf6cdca5

While the SCT install I asked you to do was:

git-jca/2562-tensorflow-1.5-1850497098eed76fe47028263b52f845030a6480

Could you please:

open a new Terminal
run: sct_check_dependencies
run: sct_testing
send me the entire terminal output

Regarding the issue with PyQT: we are looking into this, but you could still use SCT (only not with viewer initializations).

thanks!
julien

Nyoman_Kurniawan · March 2, 2020, 3:00am

Whoops! Sorry for that.
The two outputs are looking fine now?

Regards,
nyoman

uqnkurn1@cai-gajah:~$ sct_check_dependencies

--
Spinal Cord Toolbox (git-jca/2562-tensorflow-1.5-1850497098eed76fe47028263b52f845030a6480)

SCT info:
- version: git-jca/2562-tensorflow-1.5-1850497098eed76fe47028263b52f845030a6480
- path: /data/home/uqnkurn1/sct-tf1.5
OS: linux (Linux-4.15.0-88-generic-x86_64-with-debian-buster-sid)
CPU cores: Available: 8, Used by SCT: 8
RAM: MemTotal:       74215088 kB
total        used        free      shared  buff/cache   available
Mem:          72475        2773       46371         224       23330       68706
Swap:        511997           0      511997
Check Python executable.............................[OK]
  Using bundled python 3.6.10 |Anaconda, Inc.| (default, Jan  7 2020, 21:14:29) 
[GCC 7.3.0] at /data/home/uqnkurn1/sct-tf1.5/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.18.1)
Check if cryptography is installed..................[OK] (2.8)
Check if dipy is installed..........................[OK] (1.1.1)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.1.5) is installed.................[OK]
Check if matplotlib is installed....................[OK] (3.1.3)
Check if nibabel is installed.......................[OK] (3.0.1)
Check if pandas is installed........................[OK] (1.0.1)
Check if psutil is installed........................[OK] (5.7.0)
Check if pyqt5 (5.11.3) is installed................[OK]
Check if pytest is installed........................[OK] (5.3.5)
Check if pytest-cov is installed....................[OK] (2.8.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.23.0)
Check if scipy is installed.........................[OK] (1.4.1)
Check if scikit-image is installed..................[OK] (0.16.2)
Check if scikit-learn is installed..................[OK] (0.22.2)
Check if tensorflow (1.5.0) is installed............[OK]
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.43.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.8)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if DISPLAY variable is set....................[OK]
Check if figure can be opened with PyQt.............libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
[OK]

uqnkurn1@cai-gajah:~$ sct_testing

--
Spinal Cord Toolbox (git-jca/2562-tensorflow-1.5-1850497098eed76fe47028263b52f845030a6480)


Trying URL: https://osf.io/yutrj/?action=download
Downloading 20191031_sct_testing_data.zip...
Status: 100%|#####################################################################################################################################################################| 6.78M/6.78M [00:00<00:00, 6.94MB/s]

Create temporary folder (/tmp/sct-20200302125235.917131-roaaaygr)...

Unzip data to: /tmp/sct-20200302125235.917131-roaaaygr

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

Remove temporary folders...
Done!

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 8 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template
Checking sct_deepseg_gm.............................[OK]
Checking sct_deepseg_lesion.........................[OK]
Checking sct_deepseg_sc.............................[OK]
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_convert................................[OK]
Checking sct_compute_ernst_angle....................[OK]
Checking sct_compute_hausdorff_distance.............[OK]
Checking sct_compute_mtr............................[OK]
Checking sct_compute_mscc...........................[OK]
Checking sct_compute_snr............................[OK]
Checking sct_concat_transfo.........................[OK]
Checking sct_create_mask............................[OK]
Checking sct_crop_image.............................[OK]
Checking sct_dice_coefficient.......................[OK]
Checking sct_detect_pmj.............................[OK]
Checking sct_dmri_compute_dti.......................[OK]
Checking sct_dmri_concat_b0_and_dwi.................[OK]
Checking sct_dmri_concat_bvals......................[OK]
Checking sct_dmri_concat_bvecs......................[OK]
Checking sct_dmri_create_noisemask..................[OK]
Checking sct_dmri_compute_bvalue....................[OK]
Checking sct_dmri_moco..............................[OK]
Checking sct_dmri_separate_b0_and_dwi...............[OK]
Checking sct_dmri_transpose_bvecs...................[OK]
Checking sct_extract_metric.........................[OK]
Checking sct_flatten_sagittal.......................[OK]
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_image..................................[OK]
Checking sct_label_utils............................[OK]
Checking sct_label_vertebrae........................[OK]
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[OK]
Checking sct_process_segmentation...................[OK]
Checking sct_propseg................................[OK]
Checking sct_qc.....................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_register_to_template...................[OK]
Checking sct_resample...............................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_warp_template..........................[OK]
status: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
Finished! Elapsed time: 194s

jcohenadad · March 2, 2020, 4:21am

All good

jcohenadad · March 4, 2020, 10:57pm

@Nyoman_Kurniawan Just to let you know that the fix has now been implemented into SCT’s master branch (see pull request), and will be available in SCT’s next stable release.