******************************* * Welcome to SCT installation * *******************************  Checking OS type and version... Linux vh 5.3.0-62-generic #56~18.04.1-Ubuntu SMP Wed Jun 24 16:17:03 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Checking requirements... OK! Full verbose! SCT version ......... 5.0.1 Installation type ... package Operating system .... linux (unknown) Shell config ........ /home/extop/.bashrc To improve user experience and fix bugs, the SCT development team is using a report system to automatically receive crash reports and errors from users. These reports are anonymous. Do you agree to help us improve SCT? [y]es/[n]o:  --> Crash reports will be sent to the SCT development team. Thank you! SCT will be installed here: [/home/extop/sct_5.0.1] Do you agree? [y]es/[n]o:  Copying source files from /home/extop/spinalcordtoolbox-5.0.1 to /home/extop/sct_5.0.1 .................................................................................................................................................................................................................................................................................................................................................................................................................. Removing sct and isct softlink from /home/extop/sct_5.0.1/bin Installing conda... rm -rf /home/extop/sct_5.0.1/python mkdir -p /home/extop/sct_5.0.1/python wget -O /tmp/tmp.MLMAXOTalx/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh exit status is 0 bash /tmp/tmp.MLMAXOTalx/miniconda.sh -p /home/extop/sct_5.0.1/python -b -f PREFIX=/home/extop/sct_5.0.1/python Unpacking payload ... Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/extop/sct_5.0.1/python added / updated specs: - _libgcc_mutex==0.1=main - brotlipy==0.7.0=py38h27cfd23_1003 - ca-certificates==2020.10.14=0 - certifi==2020.6.20=pyhd3eb1b0_3 - cffi==1.14.3=py38h261ae71_2 - chardet==3.0.4=py38h06a4308_1003 - conda-package-handling==1.7.2=py38h03888b9_0 - conda==4.9.2=py38h06a4308_0 - cryptography==3.2.1=py38h3c74f83_1 - idna==2.10=py_0 - ld_impl_linux-64==2.33.1=h53a641e_7 - libedit==3.1.20191231=h14c3975_1 - libffi==3.3=he6710b0_2 - libgcc-ng==9.1.0=hdf63c60_0 - libstdcxx-ng==9.1.0=hdf63c60_0 - ncurses==6.2=he6710b0_1 - openssl==1.1.1h=h7b6447c_0 - pip==20.2.4=py38h06a4308_0 - pycosat==0.6.3=py38h7b6447c_1 - pycparser==2.20=py_2 - pyopenssl==19.1.0=pyhd3eb1b0_1 - pysocks==1.7.1=py38h06a4308_0 - python==3.8.5=h7579374_1 - readline==8.0=h7b6447c_0 - requests==2.24.0=py_0 - ruamel_yaml==0.15.87=py38h7b6447c_1 - setuptools==50.3.1=py38h06a4308_1 - six==1.15.0=py38h06a4308_0 - sqlite==3.33.0=h62c20be_0 - tk==8.6.10=hbc83047_0 - tqdm==4.51.0=pyhd3eb1b0_0 - urllib3==1.25.11=py_0 - wheel==0.35.1=pyhd3eb1b0_0 - xz==5.2.5=h7b6447c_0 - yaml==0.2.5=h7b6447c_0 - zlib==1.2.11=h7b6447c_3 The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003 ca-certificates pkgs/main/linux-64::ca-certificates-2020.10.14-0 certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3 cffi pkgs/main/linux-64::cffi-1.14.3-py38h261ae71_2 chardet pkgs/main/linux-64::chardet-3.0.4-py38h06a4308_1003 conda pkgs/main/linux-64::conda-4.9.2-py38h06a4308_0 conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.2-py38h03888b9_0 cryptography pkgs/main/linux-64::cryptography-3.2.1-py38h3c74f83_1 idna pkgs/main/noarch::idna-2.10-py_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 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_1 openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0 pip pkgs/main/linux-64::pip-20.2.4-py38h06a4308_0 pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1 pycparser pkgs/main/noarch::pycparser-2.20-py_2 pyopenssl pkgs/main/noarch::pyopenssl-19.1.0-pyhd3eb1b0_1 pysocks pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0 python pkgs/main/linux-64::python-3.8.5-h7579374_1 readline pkgs/main/linux-64::readline-8.0-h7b6447c_0 requests pkgs/main/noarch::requests-2.24.0-py_0 ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_1 setuptools pkgs/main/linux-64::setuptools-50.3.1-py38h06a4308_1 six pkgs/main/linux-64::six-1.15.0-py38h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0 tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0 tqdm pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0 urllib3 pkgs/main/noarch::urllib3-1.25.11-py_0 wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/extop/sct_5.0.1/python/envs/venv_sct added / updated specs: - python=3.6 The following packages will be downloaded: package | build ---------------------------|----------------- certifi-2020.11.8 | py36h06a4308_0 147 KB pip-20.2.4 | py36h06a4308_0 1.8 MB python-3.6.12 | hcff3b4d_2 29.7 MB setuptools-50.3.1 | py36h06a4308_1 723 KB ------------------------------------------------------------ Total: 32.3 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-2020.10.14-0 certifi pkgs/main/linux-64::certifi-2020.11.8-py36h06a4308_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 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_1 openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0 pip pkgs/main/linux-64::pip-20.2.4-py36h06a4308_0 python pkgs/main/linux-64::python-3.6.12-hcff3b4d_2 readline pkgs/main/linux-64::readline-8.0-h7b6447c_0 setuptools pkgs/main/linux-64::setuptools-50.3.1-py36h06a4308_1 sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0 tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0 wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Proceed ([y]/n)? Downloading and Extracting Packages setuptools-50.3.1 | 723 KB | | 0% setuptools-50.3.1 | 723 KB | ########## | 100% setuptools-50.3.1 | 723 KB | ########## | 100% certifi-2020.11.8 | 147 KB | | 0% certifi-2020.11.8 | 147 KB | ########## | 100% python-3.6.12 | 29.7 MB | | 0% python-3.6.12 | 29.7 MB | 6 | 6% python-3.6.12 | 29.7 MB | #3 | 13% python-3.6.12 | 29.7 MB | ## | 20% python-3.6.12 | 29.7 MB | ##7 | 28% python-3.6.12 | 29.7 MB | ###4 | 35% python-3.6.12 | 29.7 MB | ####2 | 42% python-3.6.12 | 29.7 MB | ##### | 50% python-3.6.12 | 29.7 MB | #####7 | 57% python-3.6.12 | 29.7 MB | ######4 | 65% python-3.6.12 | 29.7 MB | #######2 | 73% python-3.6.12 | 29.7 MB | #######9 | 80% python-3.6.12 | 29.7 MB | ########7 | 87% python-3.6.12 | 29.7 MB | #########4 | 95% python-3.6.12 | 29.7 MB | ########## | 100% pip-20.2.4 | 1.8 MB | | 0% pip-20.2.4 | 1.8 MB | ########1 | 81% pip-20.2.4 | 1.8 MB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done # # To activate this environment, use # # $ conda activate venv_sct # # To deactivate an active environment, use # # $ conda deactivate Installing Python dependencies... Using requirements-freeze.txt (release installation) Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html Ignoring torch: markers 'sys_platform == "darwin"' don't match your environment Ignoring torchvision: markers 'sys_platform == "darwin"' don't match your environment Collecting absl-py==0.11.0 Using cached absl_py-0.11.0-py3-none-any.whl (127 kB) Collecting apipkg==1.5 Using cached apipkg-1.5-py2.py3-none-any.whl (4.9 kB) Collecting attrs==20.3.0 Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB) Collecting bids-neuropoly==0.2 Using cached bids_neuropoly-0.2-py3-none-any.whl (3.1 kB) Collecting bids-validator==1.5.7 Using cached bids_validator-1.5.7-py2.py3-none-any.whl (15 kB) Collecting bleach==1.5.0 Using cached bleach-1.5.0-py2.py3-none-any.whl (17 kB) Collecting cachetools==4.1.1 Using cached cachetools-4.1.1-py3-none-any.whl (10 kB) Requirement already satisfied: certifi==2020.11.8 in ./python/envs/venv_sct/lib/python3.6/site-packages (from -r requirements-freeze.txt (line 8)) (2020.11.8) Collecting cffi==1.14.3 Using cached cffi-1.14.3-cp36-cp36m-manylinux1_x86_64.whl (400 kB) Collecting chardet==3.0.4 Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting click==7.1.2 Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Processing /home/extop/.cache/pip/wheels/b7/be/ae/a98f7701429c3cfcebf4d2b537e48a1571549a4d8b55463a01/colored-1.4.2-py3-none-any.whl Collecting coverage==5.3 Using cached coverage-5.3-cp36-cp36m-manylinux1_x86_64.whl (229 kB) Collecting cryptography==3.2.1 Using cached cryptography-3.2.1-cp35-abi3-manylinux2010_x86_64.whl (2.6 MB) Collecting cycler==0.10.0 Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting decorator==4.4.2 Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting dipy==1.3.0 Using cached dipy-1.3.0-cp36-cp36m-manylinux2010_x86_64.whl (7.7 MB) Processing /home/extop/.cache/pip/wheels/3f/2a/fa/4d7a888e69774d5e6e855d190a8a51b357d77cc05eb1c097c9/docopt-0.6.2-py2.py3-none-any.whl Collecting execnet==1.7.1 Using cached execnet-1.7.1-py2.py3-none-any.whl (39 kB) Processing /home/extop/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e/future-0.18.2-cp36-none-any.whl Collecting futures==3.1.1 Using cached futures-3.1.1-py3-none-any.whl (2.8 kB) Collecting google-auth==1.23.0 Using cached google_auth-1.23.0-py2.py3-none-any.whl (114 kB) Collecting google-auth-oauthlib==0.4.2 Using cached google_auth_oauthlib-0.4.2-py2.py3-none-any.whl (18 kB) Collecting grpcio==1.33.2 Using cached grpcio-1.33.2-cp36-cp36m-manylinux2014_x86_64.whl (3.8 MB) Collecting h5py==2.10.0 Using cached h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB) Processing /home/extop/.cache/pip/wheels/90/1c/cb/a87fd097ff74648ecc468a703001f6c7c86d8a71d459e65c98/html5lib-0.9999999-py3-none-any.whl Collecting idna==2.10 Using cached idna-2.10-py2.py3-none-any.whl (58 kB) Collecting imageio==2.9.0 Using cached imageio-2.9.0-py3-none-any.whl (3.3 MB) Collecting importlib-metadata==2.0.0 Using cached importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB) Collecting iniconfig==1.1.1 Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting ivadomed==2.4.0 Using cached ivadomed-2.4.0-py3-none-any.whl (132 kB) Collecting joblib==0.17.0 Using cached joblib-0.17.0-py3-none-any.whl (301 kB) Collecting Keras==2.1.5 Using cached Keras-2.1.5-py2.py3-none-any.whl (334 kB) Collecting kiwisolver==1.3.1 Using cached kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB) Collecting Markdown==3.3.3 Using cached Markdown-3.3.3-py3-none-any.whl (96 kB) Collecting matplotlib==3.3.3 Using cached matplotlib-3.3.3-cp36-cp36m-manylinux1_x86_64.whl (11.6 MB) Collecting mock==4.0.2 Using cached mock-4.0.2-py3-none-any.whl (28 kB) Collecting networkx==2.5 Using cached networkx-2.5-py3-none-any.whl (1.6 MB) Collecting nibabel==3.2.0 Using cached nibabel-3.2.0-py3-none-any.whl (3.3 MB) Collecting num2words==0.5.10 Using cached num2words-0.5.10-py3-none-any.whl (101 kB) Collecting numpy==1.19.4 Using cached numpy-1.19.4-cp36-cp36m-manylinux2010_x86_64.whl (14.5 MB) Collecting oauthlib==3.1.0 Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB) Collecting onnxruntime==1.4.0 Using cached onnxruntime-1.4.0-cp36-cp36m-manylinux2010_x86_64.whl (4.4 MB) Collecting packaging==20.4 Using cached packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting pandas==1.1.4 Using cached pandas-1.1.4-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB) Collecting patsy==0.5.1 Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting Pillow==8.0.1 Using cached Pillow-8.0.1-cp36-cp36m-manylinux1_x86_64.whl (2.2 MB) Collecting pluggy==0.13.1 Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting protobuf==3.13.0 Using cached protobuf-3.13.0-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB) Processing /home/extop/.cache/pip/wheels/fa/ad/67/90bbaacdcfe970960dd5158397f23a6579b51d853720d7856d/psutil-5.7.3-cp36-cp36m-linux_x86_64.whl Collecting py==1.9.0 Using cached py-1.9.0-py2.py3-none-any.whl (99 kB) Collecting pyasn1==0.4.8 Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB) Collecting pyasn1-modules==0.2.8 Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB) Collecting pybids==0.12.4 Using cached pybids-0.12.4-py2.py3-none-any.whl (3.2 MB) Collecting pycparser==2.20 Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB) Collecting pyOpenSSL==19.1.0 Using cached pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB) Collecting pyparsing==2.4.7 Using cached pyparsing-2.4.7-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==6.1.2 Using cached pytest-6.1.2-py3-none-any.whl (272 kB) Processing /home/extop/.cache/pip/wheels/d1/e3/94/26f2c05b0a648497c46b19eaa1fb7cc33f53f1e866ac0b74c2/pytest_console_scripts-1.0.0-py3-none-any.whl Collecting pytest-cov==2.10.1 Using cached pytest_cov-2.10.1-py2.py3-none-any.whl (19 kB) Collecting pytest-forked==1.3.0 Using cached pytest_forked-1.3.0-py2.py3-none-any.whl (4.7 kB) Collecting pytest-xdist==2.1.0 Using cached pytest_xdist-2.1.0-py3-none-any.whl (36 kB) Collecting python-dateutil==2.8.1 Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting pytz==2020.4 Using cached pytz-2020.4-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 /home/extop/.cache/pip/wheels/a7/c1/ea/cf5bd31012e735dc1dfea3131a2d5eae7978b251083d6247bd/PyYAML-5.3.1-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==2.25.0 Using cached requests-2.25.0-py2.py3-none-any.whl (61 kB) Collecting requests-oauthlib==1.3.0 Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB) Processing /home/extop/.cache/pip/wheels/80/af/bd/32c202b632c3e9a1b482b33d37f5efd128137891a08f3c3bae/requirements_parser-0.2.0-py3-none-any.whl Collecting rsa==4.6 Using cached rsa-4.6-py3-none-any.whl (47 kB) Collecting scikit-image==0.17.2 Using cached scikit_image-0.17.2-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB) Collecting scikit-learn==0.23.2 Using cached scikit_learn-0.23.2-cp36-cp36m-manylinux1_x86_64.whl (6.8 MB) Collecting scipy==1.5.4 Using cached scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB) Collecting seaborn==0.11.0 Using cached seaborn-0.11.0-py3-none-any.whl (283 kB) Collecting six==1.15.0 Using cached six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting SQLAlchemy==1.3.20 Using cached SQLAlchemy-1.3.20-cp36-cp36m-manylinux2010_x86_64.whl (1.3 MB) Collecting tensorboard==2.4.0 Using cached tensorboard-2.4.0-py3-none-any.whl (10.6 MB) Collecting tensorboard-plugin-wit==1.7.0 Using cached tensorboard_plugin_wit-1.7.0-py3-none-any.whl (779 kB) Collecting tensorflow==1.5.0 Using cached tensorflow-1.5.0-cp36-cp36m-manylinux1_x86_64.whl (44.4 MB) Collecting tensorflow-tensorboard==1.5.1 Using cached tensorflow_tensorboard-1.5.1-py3-none-any.whl (3.0 MB) Collecting threadpoolctl==2.1.0 Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB) Collecting tifffile==2020.9.3 Using cached tifffile-2020.9.3-py3-none-any.whl (148 kB) Collecting toml==0.10.2 Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting tqdm==4.51.0 Using cached tqdm-4.51.0-py2.py3-none-any.whl (70 kB) Processing /home/extop/.cache/pip/wheels/3d/3c/84/28d36677f3c760c048bd02b5a547ea0c4027770cc9cdb9af1e/transforms3d-0.3.1-cp36-none-any.whl Collecting urllib3==1.26.2 Using cached urllib3-1.26.2-py2.py3-none-any.whl (136 kB) Collecting Werkzeug==1.0.1 Using cached Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB) Collecting xlwt==1.3.0 Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB) Collecting zipp==3.4.0 Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB) Collecting torch==1.5.0+cpu Using cached https://download.pytorch.org/whl/cpu/torch-1.5.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (127.3 MB) Collecting torchvision==0.6.0+cpu Using cached https://download.pytorch.org/whl/cpu/torchvision-0.6.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (5.7 MB) Requirement already satisfied: setuptools>=40.3.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth==1.23.0->-r requirements-freeze.txt (line 22)) (50.3.1.post20201107) Requirement already satisfied: wheel>=0.26; python_version >= "3" in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard==2.4.0->-r requirements-freeze.txt (line 80)) (0.35.1) Installing collected packages: six, absl-py, apipkg, attrs, numpy, patsy, SQLAlchemy, pytz, python-dateutil, pandas, docopt, num2words, scipy, click, pyparsing, packaging, nibabel, bids-validator, pybids, bids-neuropoly, html5lib, bleach, cachetools, pycparser, cffi, chardet, colored, coverage, cryptography, cycler, decorator, h5py, tqdm, dipy, execnet, future, futures, pyasn1, rsa, pyasn1-modules, google-auth, idna, urllib3, requests, oauthlib, requests-oauthlib, google-auth-oauthlib, grpcio, Pillow, imageio, zipp, importlib-metadata, iniconfig, PyWavelets, networkx, tifffile, kiwisolver, matplotlib, scikit-image, torch, torchvision, Werkzeug, Markdown, protobuf, tensorboard-plugin-wit, tensorboard, onnxruntime, joblib, threadpoolctl, scikit-learn, toml, pluggy, py, pytest, seaborn, ivadomed, PyYAML, Keras, mock, psutil, pyOpenSSL, PyQt5-sip, PyQt5, pytest-console-scripts, pytest-cov, pytest-forked, pytest-xdist, raven, requirements-parser, tensorflow-tensorboard, tensorflow, transforms3d, xlwt Successfully installed Keras-2.1.5 Markdown-3.3.3 Pillow-8.0.1 PyQt5-5.11.3 PyQt5-sip-4.19.19 PyWavelets-1.1.1 PyYAML-5.3.1 SQLAlchemy-1.3.20 Werkzeug-1.0.1 absl-py-0.11.0 apipkg-1.5 attrs-20.3.0 bids-neuropoly-0.2 bids-validator-1.5.7 bleach-1.5.0 cachetools-4.1.1 cffi-1.14.3 chardet-3.0.4 click-7.1.2 colored-1.4.2 coverage-5.3 cryptography-3.2.1 cycler-0.10.0 decorator-4.4.2 dipy-1.3.0 docopt-0.6.2 execnet-1.7.1 future-0.18.2 futures-3.1.1 google-auth-1.23.0 google-auth-oauthlib-0.4.2 grpcio-1.33.2 h5py-2.10.0 html5lib-0.9999999 idna-2.10 imageio-2.9.0 importlib-metadata-2.0.0 iniconfig-1.1.1 ivadomed-2.4.0 joblib-0.17.0 kiwisolver-1.3.1 matplotlib-3.3.3 mock-4.0.2 networkx-2.5 nibabel-3.2.0 num2words-0.5.10 numpy-1.19.4 oauthlib-3.1.0 onnxruntime-1.4.0 packaging-20.4 pandas-1.1.4 patsy-0.5.1 pluggy-0.13.1 protobuf-3.13.0 psutil-5.7.3 py-1.9.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pybids-0.12.4 pycparser-2.20 pyparsing-2.4.7 pytest-6.1.2 pytest-console-scripts-1.0.0 pytest-cov-2.10.1 pytest-forked-1.3.0 pytest-xdist-2.1.0 python-dateutil-2.8.1 pytz-2020.4 raven-6.10.0 requests-2.25.0 requests-oauthlib-1.3.0 requirements-parser-0.2.0 rsa-4.6 scikit-image-0.17.2 scikit-learn-0.23.2 scipy-1.5.4 seaborn-0.11.0 six-1.15.0 tensorboard-2.4.0 tensorboard-plugin-wit-1.7.0 tensorflow-1.5.0 tensorflow-tensorboard-1.5.1 threadpoolctl-2.1.0 tifffile-2020.9.3 toml-0.10.2 torch-1.5.0+cpu torchvision-0.6.0+cpu tqdm-4.51.0 transforms3d-0.3.1 urllib3-1.26.2 xlwt-1.3.0 zipp-3.4.0 Obtaining file:///home/extop/sct_5.0.1 Installing collected packages: spinalcordtoolbox Running setup.py develop for spinalcordtoolbox Successfully installed spinalcordtoolbox Creating launchers for Python scripts... Installing binaries... sct_download_data -d binaries_linux -o /home/extop/sct_5.0.1/bin -k -- Spinal Cord Toolbox (5.0.1) sct_download_data -d binaries_linux -o /home/extop/sct_5.0.1/bin -k -- Trying URL: https://osf.io/cs6zt/?action=download Downloading: 20200801_sct_binaries_linux.tar.gz Creating temporary folder (/tmp/sct-20201127073755.943910-s4zpc1qy) Unzip data to: /tmp/sct-20201127073755.943910-s4zpc1qy Updating existing “/home/extop/sct_5.0.1/bin/isct_ComposeMultiTransform” Updating existing “/home/extop/sct_5.0.1/bin/isct_antsApplyTransforms” Updating existing “/home/extop/sct_5.0.1/bin/isct_antsRegistration” Updating existing “/home/extop/sct_5.0.1/bin/isct_antsSliceRegularizedRegistration” Updating existing “/home/extop/sct_5.0.1/bin/isct_dice_coefficient” Updating existing “/home/extop/sct_5.0.1/bin/isct_propseg” Updating existing “/home/extop/sct_5.0.1/bin/isct_spine_detect” Updating existing “/home/extop/sct_5.0.1/bin/isct_train_svm” Removing temporary folders... Done! All requirements installed! Installing data... rm -rf /home/extop/sct_5.0.1/data mkdir -p /home/extop/sct_5.0.1/data sct_download_data -d PAM50 -o /home/extop/sct_5.0.1/data/PAM50 -- Spinal Cord Toolbox (5.0.1) sct_download_data -d PAM50 -o /home/extop/sct_5.0.1/data/PAM50 -- Removing existing destination folder “/home/extop/sct_5.0.1/data/PAM50” Trying URL: https://github.com/sct-data/PAM50/releases/download/r20201104/PAM50-r20201104.zip Downloading: PAM50-r20201104.zip Creating temporary folder (/tmp/sct-20201127074000.657320-8b_1v9s1) Unzip data to: /tmp/sct-20201127074000.657320-8b_1v9s1 Removing temporary folders... Done! sct_download_data -d gm_model -o /home/extop/sct_5.0.1/data/gm_model -- Spinal Cord Toolbox (5.0.1) sct_download_data -d gm_model -o /home/extop/sct_5.0.1/data/gm_model -- Removing existing destination folder “/home/extop/sct_5.0.1/data/gm_model” Trying URL: https://osf.io/ugscu/?action=download Downloading: 20160922_gm_model.zip Creating temporary folder (/tmp/sct-20201127074005.407267-461he8m0) Unzip data to: /tmp/sct-20201127074005.407267-461he8m0 Removing temporary folders... Done! sct_download_data -d optic_models -o /home/extop/sct_5.0.1/data/optic_models -- Spinal Cord Toolbox (5.0.1) sct_download_data -d optic_models -o /home/extop/sct_5.0.1/data/optic_models -- Removing existing destination folder “/home/extop/sct_5.0.1/data/optic_models” Trying URL: https://github.com/sct-data/optic_models/releases/download/r20170413/20170413_optic_models.zip Downloading: 20170413_optic_models.zip Creating temporary folder (/tmp/sct-20201127074006.691518-37avc12k) Unzip data to: /tmp/sct-20201127074006.691518-37avc12k Removing temporary folders... Done! sct_download_data -d pmj_models -o /home/extop/sct_5.0.1/data/pmj_models -- Spinal Cord Toolbox (5.0.1) sct_download_data -d pmj_models -o /home/extop/sct_5.0.1/data/pmj_models -- Removing existing destination folder “/home/extop/sct_5.0.1/data/pmj_models” Trying URL: https://github.com/sct-data/pmj_models/releases/download/r20170922/20170922_pmj_models.zip Downloading: 20170922_pmj_models.zip Creating temporary folder (/tmp/sct-20201127074007.770720-mlfp72_6) Unzip data to: /tmp/sct-20201127074007.770720-mlfp72_6 Removing temporary folders... Done! sct_download_data -d deepseg_sc_models -o /home/extop/sct_5.0.1/data/deepseg_sc_models -- Spinal Cord Toolbox (5.0.1) sct_download_data -d deepseg_sc_models -o /home/extop/sct_5.0.1/data/deepseg_sc_models -- Removing existing destination folder “/home/extop/sct_5.0.1/data/deepseg_sc_models” Trying URL: https://github.com/sct-data/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip Downloading: 20180610_deepseg_sc_models.zip Creating temporary folder (/tmp/sct-20201127074145.386646-po3sqker) Unzip data to: /tmp/sct-20201127074145.386646-po3sqker Removing temporary folders... Done! sct_download_data -d deepseg_gm_models -o /home/extop/sct_5.0.1/data/deepseg_gm_models -- Spinal Cord Toolbox (5.0.1) sct_download_data -d deepseg_gm_models -o /home/extop/sct_5.0.1/data/deepseg_gm_models -- Removing existing destination folder “/home/extop/sct_5.0.1/data/deepseg_gm_models” Trying URL: https://github.com/sct-data/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip Downloading: 20180205_deepseg_gm_models.zip Creating temporary folder (/tmp/sct-20201127074150.793983-5gd_ztp5) Unzip data to: /tmp/sct-20201127074150.793983-5gd_ztp5 Removing temporary folders... Done! sct_download_data -d deepseg_lesion_models -o /home/extop/sct_5.0.1/data/deepseg_lesion_models -- Spinal Cord Toolbox (5.0.1) sct_download_data -d deepseg_lesion_models -o /home/extop/sct_5.0.1/data/deepseg_lesion_models -- Removing existing destination folder “/home/extop/sct_5.0.1/data/deepseg_lesion_models” Trying URL: https://github.com/sct-data/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip Downloading: 20180613_deepseg_lesion_models.zip Creating temporary folder (/tmp/sct-20201127074216.620272-0oh5cbr9) Unzip data to: /tmp/sct-20201127074216.620272-0oh5cbr9 Removing temporary folders... Done! sct_download_data -d c2c3_disc_models -o /home/extop/sct_5.0.1/data/c2c3_disc_models -- Spinal Cord Toolbox (5.0.1) sct_download_data -d c2c3_disc_models -o /home/extop/sct_5.0.1/data/c2c3_disc_models -- Removing existing destination folder “/home/extop/sct_5.0.1/data/c2c3_disc_models” Trying URL: https://github.com/sct-data/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip Downloading: 20190117_c2c3_disc_models.zip Creating temporary folder (/tmp/sct-20201127074217.875875-3n21t40b) Unzip data to: /tmp/sct-20201127074217.875875-3n21t40b Removing 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:  Validate installation... -- Spinal Cord Toolbox (5.0.1) sct_check_dependencies -- SCT info: - version: 5.0.1 - path: /home/extop/sct_5.0.1 OS: linux (Linux-5.3.0-62-generic-x86_64-with-debian-buster-sid) CPU cores: Available: 12, Used by ITK functions: 12 RAM: Total: 128511MB, Used: 18772MB, Available: 108278MB Check Python executable.............................[OK] Using bundled python 3.6.12 |Anaconda, Inc.| (default, Sep 8 2020, 23:10:56) [GCC 7.3.0] at /home/extop/sct_5.0.1/python/envs/venv_sct/bin/python Check if data are installed.........................[OK] Check if colored is installed.......................[OK] (1.4.2) Check if dipy is installed..........................[OK] (1.3.0) Check if futures is installed.......................[OK] Check if h5py is installed..........................[OK] (2.10.0) Check if ivadomed (2.4.0) is installed..............[OK] (2.4.0) Check if Keras (2.1.5) is installed.................[OK] (2.1.5) Check if matplotlib is installed....................[OK] (3.3.3) Check if nibabel is installed.......................[OK] (3.2.0) Check if numpy is installed.........................[OK] (1.19.4) Check if onnxruntime (1.4.0) is installed...........[OK] (1.4.0) Check if pandas is installed........................[OK] (1.1.4) Check if psutil is installed........................[OK] (5.7.3) Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3) Check if pytest is installed........................[OK] (6.1.2) Check if pytest-cov is installed....................[OK] (__version__ = '2.10.1') Check if raven is installed.........................[OK] Check if requests is installed......................[OK] (2.25.0) Check if requirements-parser is installed...........[OK] (0.2.0) Check if scipy is installed.........................[OK] (1.5.4) Check if scikit-image is installed..................[OK] (0.17.2) Check if scikit-learn is installed..................[OK] (0.23.2) Check if tensorflow (1.5.0) is installed............[OK] (1.5.0) Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu) Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu) Check if xlwt is installed..........................[OK] (1.3.0) Check if tqdm is installed..........................[OK] (4.51.0) Check if transforms3d is installed..................[OK] (0.3.1) Check if urllib3 is installed.......................[OK] (1.26.2) Check if pytest_console_scripts is installed........[OK] Check if pytest-xdist is installed..................[OK] (2.1.0) Check if spinalcordtoolbox is installed.............[OK] Check ANTs compatibility with OS ...................[OK] Check PropSeg compatibility with OS ................[OK] Check if DISPLAY variable is set....................[OK] Check if figure can be opened with PyQt.............[OK] Open a new Terminal window to load environment variables, or run: source /home/extop/.bashrc Installation finished successfully!