******************************* * Welcome to SCT installation * *******************************  Checking OS type and version... Linux chatham 5.10.0-0.bpo.9-amd64 #1 SMP Debian 5.10.70-1~bpo10+1 (2021-10-10) x86_64 GNU/Linux Checking requirements... OK! SCT version ......... 5.6 Installation type ... package Operating system .... linux (unknown) Shell config ........ /home/valosek/.zshrc 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 not be sent. SCT will be installed here: [/home/valosek/sct_5.6]  Do you agree? [y]es/[n]o:  Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0):  WARNING: Directory already exists. Files will be overwritten. Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o:  Skipping copy of source files (source and destination folders are the same) Removing sct and isct softlink from /usr/local/lib/sct_v5.6.0/bin rm -rf /usr/local/lib/sct_v5.6.0/python mkdir -p /usr/local/lib/sct_v5.6.0/python Downloading Miniconda... wget -nv -O /tmp/tmp.YHwjlEamdU/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 2022-06-02 07:29:08 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [76607678/76607678] -> "/tmp/tmp.YHwjlEamdU/miniconda.sh" [1] Installing Miniconda... bash /tmp/tmp.YHwjlEamdU/miniconda.sh -p /usr/local/lib/sct_v5.6.0/python -b -f PREFIX=/usr/local/lib/sct_v5.6.0/python Unpacking payload ... 0%| | 0/40 [00:00 WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 4.13.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /usr/local/lib/sct_v5.6.0/python/envs/venv_sct added / updated specs: - python=3.7 The following packages will be downloaded: package | build ---------------------------|----------------- _openmp_mutex-5.1 | 1_gnu 21 KB ca-certificates-2022.4.26 | h06a4308_0 124 KB certifi-2022.5.18.1 | py37h06a4308_0 147 KB ld_impl_linux-64-2.38 | h1181459_1 654 KB libgcc-ng-11.2.0 | h1234567_1 5.3 MB libgomp-11.2.0 | h1234567_1 474 KB libstdcxx-ng-11.2.0 | h1234567_1 4.7 MB openssl-1.1.1o | h7f8727e_0 2.5 MB pip-21.2.2 | py37h06a4308_0 1.8 MB python-3.7.13 | h12debd9_0 46.2 MB setuptools-61.2.0 | py37h06a4308_0 1007 KB sqlite-3.38.3 | hc218d9a_0 1.0 MB tk-8.6.11 | h1ccaba5_1 3.0 MB xz-5.2.5 | h7f8727e_1 339 KB zlib-1.2.12 | h7f8727e_2 106 KB ------------------------------------------------------------ Total: 67.4 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu ca-certificates pkgs/main/linux-64::ca-certificates-2022.4.26-h06a4308_0 certifi pkgs/main/linux-64::certifi-2022.5.18.1-py37h06a4308_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2 openssl pkgs/main/linux-64::openssl-1.1.1o-h7f8727e_0 pip pkgs/main/linux-64::pip-21.2.2-py37h06a4308_0 python pkgs/main/linux-64::python-3.7.13-h12debd9_0 readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1 setuptools pkgs/main/linux-64::setuptools-61.2.0-py37h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.38.3-hc218d9a_0 tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_1 wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7f8727e_1 zlib pkgs/main/linux-64::zlib-1.2.12-h7f8727e_2 Downloading and Extracting Packages libgcc-ng-11.2.0 | 5.3 MB | | 0% libgcc-ng-11.2.0 | 5.3 MB | 4 | 4% libgcc-ng-11.2.0 | 5.3 MB | #3 | 13% libgcc-ng-11.2.0 | 5.3 MB | ##1 | 22% libgcc-ng-11.2.0 | 5.3 MB | ###1 | 31% libgcc-ng-11.2.0 | 5.3 MB | #### | 41% libgcc-ng-11.2.0 | 5.3 MB | ##### | 50% libgcc-ng-11.2.0 | 5.3 MB | #####9 | 60% libgcc-ng-11.2.0 | 5.3 MB | ####### | 70% libgcc-ng-11.2.0 | 5.3 MB | ######## | 80% libgcc-ng-11.2.0 | 5.3 MB | ######### | 90% libgcc-ng-11.2.0 | 5.3 MB | ########## | 100% libgcc-ng-11.2.0 | 5.3 MB | ########## | 100% pip-21.2.2 | 1.8 MB | | 0% pip-21.2.2 | 1.8 MB | ## | 21% pip-21.2.2 | 1.8 MB | ####7 | 48% pip-21.2.2 | 1.8 MB | #######7 | 77% pip-21.2.2 | 1.8 MB | ########## | 100% python-3.7.13 | 46.2 MB | | 0% python-3.7.13 | 46.2 MB | | 1% python-3.7.13 | 46.2 MB | 2 | 2% python-3.7.13 | 46.2 MB | 3 | 3% python-3.7.13 | 46.2 MB | 4 | 4% python-3.7.13 | 46.2 MB | 5 | 6% python-3.7.13 | 46.2 MB | 6 | 7% python-3.7.13 | 46.2 MB | 7 | 8% python-3.7.13 | 46.2 MB | 8 | 9% python-3.7.13 | 46.2 MB | # | 10% python-3.7.13 | 46.2 MB | #1 | 11% python-3.7.13 | 46.2 MB | #2 | 12% python-3.7.13 | 46.2 MB | #3 | 14% python-3.7.13 | 46.2 MB | #4 | 15% python-3.7.13 | 46.2 MB | #5 | 16% python-3.7.13 | 46.2 MB | #6 | 17% python-3.7.13 | 46.2 MB | #8 | 18% python-3.7.13 | 46.2 MB | #9 | 19% python-3.7.13 | 46.2 MB | ## | 20% python-3.7.13 | 46.2 MB | ##1 | 22% python-3.7.13 | 46.2 MB | ##2 | 23% python-3.7.13 | 46.2 MB | ##3 | 24% python-3.7.13 | 46.2 MB | ##5 | 25% python-3.7.13 | 46.2 MB | ##6 | 26% python-3.7.13 | 46.2 MB | ##7 | 28% python-3.7.13 | 46.2 MB | ##8 | 29% python-3.7.13 | 46.2 MB | ##9 | 30% python-3.7.13 | 46.2 MB | ###1 | 31% python-3.7.13 | 46.2 MB | ###2 | 32% python-3.7.13 | 46.2 MB | ###3 | 33% python-3.7.13 | 46.2 MB | ###4 | 35% python-3.7.13 | 46.2 MB | ###5 | 36% python-3.7.13 | 46.2 MB | ###6 | 37% python-3.7.13 | 46.2 MB | ###8 | 38% python-3.7.13 | 46.2 MB | ###9 | 39% python-3.7.13 | 46.2 MB | #### | 40% python-3.7.13 | 46.2 MB | ####1 | 42% python-3.7.13 | 46.2 MB | ####2 | 43% python-3.7.13 | 46.2 MB | ####3 | 44% python-3.7.13 | 46.2 MB | ####5 | 45% python-3.7.13 | 46.2 MB | ####6 | 46% python-3.7.13 | 46.2 MB | ####7 | 47% python-3.7.13 | 46.2 MB | ####8 | 49% python-3.7.13 | 46.2 MB | ####9 | 50% python-3.7.13 | 46.2 MB | ##### | 51% python-3.7.13 | 46.2 MB | #####2 | 52% python-3.7.13 | 46.2 MB | #####3 | 53% python-3.7.13 | 46.2 MB | #####4 | 54% python-3.7.13 | 46.2 MB | #####5 | 56% python-3.7.13 | 46.2 MB | #####6 | 57% python-3.7.13 | 46.2 MB | #####7 | 58% python-3.7.13 | 46.2 MB | #####9 | 59% python-3.7.13 | 46.2 MB | ###### | 60% python-3.7.13 | 46.2 MB | ######1 | 62% python-3.7.13 | 46.2 MB | ######2 | 63% python-3.7.13 | 46.2 MB | ######4 | 64% python-3.7.13 | 46.2 MB | ######5 | 65% python-3.7.13 | 46.2 MB | ######6 | 66% python-3.7.13 | 46.2 MB | ######7 | 68% python-3.7.13 | 46.2 MB | ######8 | 69% python-3.7.13 | 46.2 MB | ######9 | 70% python-3.7.13 | 46.2 MB | #######1 | 71% python-3.7.13 | 46.2 MB | #######2 | 72% python-3.7.13 | 46.2 MB | #######3 | 73% python-3.7.13 | 46.2 MB | #######4 | 75% python-3.7.13 | 46.2 MB | #######5 | 76% python-3.7.13 | 46.2 MB | #######6 | 77% python-3.7.13 | 46.2 MB | #######8 | 78% python-3.7.13 | 46.2 MB | #######9 | 79% python-3.7.13 | 46.2 MB | ######## | 80% python-3.7.13 | 46.2 MB | ########1 | 81% python-3.7.13 | 46.2 MB | ########2 | 83% python-3.7.13 | 46.2 MB | ########3 | 84% python-3.7.13 | 46.2 MB | ########4 | 85% python-3.7.13 | 46.2 MB | ########5 | 86% python-3.7.13 | 46.2 MB | ########7 | 87% python-3.7.13 | 46.2 MB | ########8 | 88% python-3.7.13 | 46.2 MB | ########9 | 89% python-3.7.13 | 46.2 MB | ######### | 91% python-3.7.13 | 46.2 MB | #########1 | 92% python-3.7.13 | 46.2 MB | #########3 | 93% python-3.7.13 | 46.2 MB | #########4 | 94% python-3.7.13 | 46.2 MB | #########5 | 95% python-3.7.13 | 46.2 MB | #########6 | 97% python-3.7.13 | 46.2 MB | #########7 | 98% python-3.7.13 | 46.2 MB | #########8 | 99% python-3.7.13 | 46.2 MB | ########## | 100% zlib-1.2.12 | 106 KB | | 0% zlib-1.2.12 | 106 KB | ########## | 100% tk-8.6.11 | 3.0 MB | | 0% tk-8.6.11 | 3.0 MB | #4 | 15% tk-8.6.11 | 3.0 MB | ###2 | 33% tk-8.6.11 | 3.0 MB | #####1 | 52% tk-8.6.11 | 3.0 MB | ####### | 70% tk-8.6.11 | 3.0 MB | ########9 | 89% tk-8.6.11 | 3.0 MB | ########## | 100% setuptools-61.2.0 | 1007 KB | | 0% setuptools-61.2.0 | 1007 KB | ####6 | 46% setuptools-61.2.0 | 1007 KB | #########3 | 94% setuptools-61.2.0 | 1007 KB | ########## | 100% ca-certificates-2022 | 124 KB | | 0% ca-certificates-2022 | 124 KB | ########## | 100% openssl-1.1.1o | 2.5 MB | | 0% openssl-1.1.1o | 2.5 MB | #7 | 17% openssl-1.1.1o | 2.5 MB | ###9 | 40% openssl-1.1.1o | 2.5 MB | ######1 | 61% openssl-1.1.1o | 2.5 MB | ########2 | 82% openssl-1.1.1o | 2.5 MB | ########## | 100% xz-5.2.5 | 339 KB | | 0% xz-5.2.5 | 339 KB | ########## | 100% xz-5.2.5 | 339 KB | ########## | 100% sqlite-3.38.3 | 1.0 MB | | 0% sqlite-3.38.3 | 1.0 MB | ####1 | 41% sqlite-3.38.3 | 1.0 MB | #########6 | 97% sqlite-3.38.3 | 1.0 MB | ########## | 100% libgomp-11.2.0 | 474 KB | | 0% libgomp-11.2.0 | 474 KB | #########7 | 98% libgomp-11.2.0 | 474 KB | ########## | 100% ld_impl_linux-64-2.3 | 654 KB | | 0% ld_impl_linux-64-2.3 | 654 KB | ######3 | 64% ld_impl_linux-64-2.3 | 654 KB | ########## | 100% libstdcxx-ng-11.2.0 | 4.7 MB | | 0% libstdcxx-ng-11.2.0 | 4.7 MB | 9 | 9% libstdcxx-ng-11.2.0 | 4.7 MB | ## | 21% libstdcxx-ng-11.2.0 | 4.7 MB | ###1 | 31% libstdcxx-ng-11.2.0 | 4.7 MB | ####2 | 43% libstdcxx-ng-11.2.0 | 4.7 MB | #####4 | 54% libstdcxx-ng-11.2.0 | 4.7 MB | ######5 | 65% libstdcxx-ng-11.2.0 | 4.7 MB | #######6 | 77% libstdcxx-ng-11.2.0 | 4.7 MB | ########8 | 88% libstdcxx-ng-11.2.0 | 4.7 MB | #########9 | 100% libstdcxx-ng-11.2.0 | 4.7 MB | ########## | 100% _openmp_mutex-5.1 | 21 KB | | 0% _openmp_mutex-5.1 | 21 KB | ########## | 100% certifi-2022.5.18.1 | 147 KB | | 0% certifi-2022.5.18.1 | 147 KB | ########## | 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 Validating that conda environment can be activated... Collecting pip!=21.2.* Using cached pip-22.1.2-py3-none-any.whl (2.1 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 21.2.2 Uninstalling pip-21.2.2: Successfully uninstalled pip-21.2.2 Successfully installed pip-22.1.2 Installing Python dependencies... Using requirements-freeze.txt (release installation) Looking in links: https://download.pytorch.org/whl/torch/, https://download.pytorch.org/whl/torchvision/ Ignoring torch: markers 'sys_platform == "darwin"' don't match your environment Ignoring torchvision: markers 'sys_platform == "darwin"' don't match your environment Collecting certifi Using cached certifi-2022.5.18.1-py3-none-any.whl (155 kB) Collecting absl-py==1.0.0 Using cached absl_py-1.0.0-py3-none-any.whl (126 kB) Collecting astor==0.7.1 Using cached astor-0.7.1-py2.py3-none-any.whl (27 kB) Collecting attrs==21.4.0 Using cached attrs-21.4.0-py2.py3-none-any.whl (60 kB) Collecting bids-validator==1.9.3 Using cached bids_validator-1.9.3-py2.py3-none-any.whl (21 kB) Collecting certifi Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting cffi==1.15.0 Using cached cffi-1.15.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (427 kB) Collecting charset-normalizer==2.0.12 Using cached charset_normalizer-2.0.12-py3-none-any.whl (39 kB) Collecting click==8.1.3 Using cached click-8.1.3-py3-none-any.whl (96 kB) Collecting coverage==6.3.2 Using cached coverage-6.3.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (207 kB) Collecting cryptography==37.0.1 Using cached cryptography-37.0.1-cp36-abi3-manylinux_2_24_x86_64.whl (4.0 MB) Collecting csv-diff==1.1 Using cached csv_diff-1.1-py3-none-any.whl (12 kB) Collecting cycler==0.11.0 Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting Deprecated==1.2.13 Using cached Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB) Collecting dictdiffer==0.9.0 Using cached dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB) Collecting dipy==1.5.0 Using cached dipy-1.5.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.8 MB) Collecting docopt==0.6.2 Using cached docopt-0.6.2-py2.py3-none-any.whl Collecting fonttools==4.33.3 Using cached fonttools-4.33.3-py3-none-any.whl (930 kB) Collecting formulaic==0.3.3 Using cached formulaic-0.3.3-py3-none-any.whl (56 kB) Collecting future==0.18.2 Using cached future-0.18.2-py3-none-any.whl Collecting gast==0.2.2 Using cached gast-0.2.2-py3-none-any.whl Collecting google-pasta==0.2.0 Using cached google_pasta-0.2.0-py3-none-any.whl (57 kB) Collecting grpcio==1.44.0 Using cached grpcio-1.44.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB) Collecting h5py==2.10.0 Using cached h5py-2.10.0-cp37-cp37m-manylinux1_x86_64.whl (2.9 MB) Collecting humanize==4.0.0 Using cached humanize-4.0.0-py3-none-any.whl (97 kB) Collecting idna==3.3 Using cached idna-3.3-py3-none-any.whl (61 kB) Collecting imageio==2.18.0 Using cached imageio-2.18.0-py3-none-any.whl (3.4 MB) Collecting importlib-metadata==4.11.3 Using cached importlib_metadata-4.11.3-py3-none-any.whl (18 kB) Collecting iniconfig==1.1.1 Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting interface-meta==1.3.0 Using cached interface_meta-1.3.0-py3-none-any.whl (14 kB) Collecting ivadomed==2.9.5 Using cached ivadomed-2.9.5-py3-none-any.whl (223 kB) Collecting joblib==1.1.0 Using cached joblib-1.1.0-py2.py3-none-any.whl (306 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==1.1.2 Using cached Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB) Collecting kiwisolver==1.4.2 Using cached kiwisolver-1.4.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB) Collecting loguru==0.6.0 Using cached loguru-0.6.0-py3-none-any.whl (58 kB) Collecting Markdown==3.3.6 Using cached Markdown-3.3.6-py3-none-any.whl (97 kB) Collecting matplotlib==3.5.1 Using cached matplotlib-3.5.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB) Collecting networkx==2.6.3 Using cached networkx-2.6.3-py3-none-any.whl (1.9 MB) Collecting nibabel==3.2.2 Using cached nibabel-3.2.2-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==1.18.5 Using cached numpy-1.18.5-cp37-cp37m-manylinux1_x86_64.whl (20.1 MB) Collecting onnxruntime==1.7.0 Using cached onnxruntime-1.7.0-cp37-cp37m-manylinux2014_x86_64.whl (4.1 MB) Collecting opt-einsum==3.3.0 Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB) Collecting packaging==21.3 Using cached packaging-21.3-py3-none-any.whl (40 kB) Collecting pandas==1.3.5 Using cached pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB) Collecting Pillow==9.1.0 Using cached Pillow-9.1.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB) Collecting pluggy==1.0.0 Using cached pluggy-1.0.0-py2.py3-none-any.whl (13 kB) Collecting portalocker==2.4.0 Using cached portalocker-2.4.0-py2.py3-none-any.whl (16 kB) Collecting protobuf==3.20.1 Using cached protobuf-3.20.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB) Collecting psutil==5.9.0 Using cached psutil-5.9.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (280 kB) Collecting py==1.11.0 Using cached py-1.11.0-py2.py3-none-any.whl (98 kB) Collecting pybids==0.15.1 Using cached pybids-0.15.1-py3-none-any.whl (3.2 MB) Collecting pycparser==2.21 Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB) Collecting pyOpenSSL==22.0.0 Using cached pyOpenSSL-22.0.0-py2.py3-none-any.whl (55 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-cp37-cp37m-manylinux1_x86_64.whl (67 kB) Collecting pytest==7.1.2 Using cached pytest-7.1.2-py3-none-any.whl (297 kB) Collecting pytest-console-scripts==1.3.1 Using cached pytest_console_scripts-1.3.1-py3-none-any.whl (9.0 kB) Collecting pytest-cov==3.0.0 Using cached pytest_cov-3.0.0-py3-none-any.whl (20 kB) Collecting python-dateutil==2.8.2 Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting pytz==2022.1 Using cached pytz-2022.1-py2.py3-none-any.whl (503 kB) Collecting PyWavelets==1.3.0 Using cached PyWavelets-1.3.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (6.4 MB) Collecting PyYAML==6.0 Using cached PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB) Collecting raven==6.10.0 Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB) Collecting requests==2.27.1 Using cached requests-2.27.1-py2.py3-none-any.whl (63 kB) Collecting requirements-parser==0.5.0 Using cached requirements_parser-0.5.0-py3-none-any.whl (18 kB) Collecting scikit-image==0.19.2 Using cached scikit_image-0.19.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (13.5 MB) Collecting scikit-learn==1.0.2 Using cached scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB) Collecting scipy==1.7.3 Using cached scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB) Collecting seaborn==0.11.2 Using cached seaborn-0.11.2-py3-none-any.whl (292 kB) Collecting SimpleITK==2.1.1.2 Using cached SimpleITK-2.1.1.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (48.4 MB) Collecting six==1.16.0 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting SQLAlchemy==1.3.24 Using cached SQLAlchemy-1.3.24-cp37-cp37m-manylinux2010_x86_64.whl (1.3 MB) Collecting tensorboard==1.15.0 Using cached tensorboard-1.15.0-py3-none-any.whl (3.8 MB) Collecting tensorflow==1.15.5 Using cached tensorflow-1.15.5-cp37-cp37m-manylinux2010_x86_64.whl (110.5 MB) Collecting tensorflow-estimator==1.15.1 Using cached tensorflow_estimator-1.15.1-py2.py3-none-any.whl (503 kB) Collecting termcolor==1.1.0 Using cached termcolor-1.1.0-py3-none-any.whl Collecting threadpoolctl==3.1.0 Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting tifffile==2021.11.2 Using cached tifffile-2021.11.2-py3-none-any.whl (178 kB) Collecting tomli==2.0.1 Using cached tomli-2.0.1-py3-none-any.whl (12 kB) Collecting tqdm==4.64.0 Using cached tqdm-4.64.0-py2.py3-none-any.whl (78 kB) Collecting transforms3d==0.3.1 Using cached transforms3d-0.3.1-py3-none-any.whl Collecting types-setuptools==57.4.14 Using cached types_setuptools-57.4.14-py3-none-any.whl (27 kB) Collecting typing_extensions==4.2.0 Using cached typing_extensions-4.2.0-py3-none-any.whl (24 kB) Collecting urllib3==1.26.9 Using cached urllib3-1.26.9-py2.py3-none-any.whl (138 kB) Collecting Werkzeug==2.1.2 Using cached Werkzeug-2.1.2-py3-none-any.whl (224 kB) Collecting wquantiles==0.6 Using cached wquantiles-0.6-py3-none-any.whl (3.3 kB) Collecting wrapt==1.14.0 Using cached wrapt-1.14.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (75 kB) Collecting xlwt==1.3.0 Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB) Collecting zipp==3.8.0 Using cached zipp-3.8.0-py3-none-any.whl (5.4 kB) Collecting torch==1.5.0+cpu Using cached https://download.pytorch.org/whl/cpu/torch-1.5.0%2Bcpu-cp37-cp37m-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-cp37-cp37m-linux_x86_64.whl (5.7 MB) Collecting torchio>=0.18.68 Using cached torchio-0.18.77-py2.py3-none-any.whl (167 kB) Collecting setuptools Using cached setuptools-62.3.2-py3-none-any.whl (1.2 MB) Collecting coverage[toml]>=5.2.1 Using cached coverage-6.4-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (208 kB) Collecting wheel>=0.26 Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting coverage[toml]>=5.2.1 Using cached coverage-6.3.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (207 kB) Installing collected packages: xlwt, types-setuptools, transforms3d, termcolor, tensorflow-estimator, SimpleITK, raven, pytz, PyQt5_sip, iniconfig, docopt, dictdiffer, certifi, bids-validator, zipp, wrapt, wheel, Werkzeug, urllib3, typing_extensions, tqdm, tomli, threadpoolctl, SQLAlchemy, six, setuptools, requirements-parser, PyYAML, PyQt5, pyparsing, pycparser, py, psutil, protobuf, portalocker, Pillow, numpy, num2words, networkx, loguru, joblib, interface-meta, idna, gast, future, fonttools, cycler, coverage, charset-normalizer, attrs, astor, wquantiles, torch, tifffile, scipy, requests, PyWavelets, python-dateutil, packaging, opt-einsum, onnxruntime, kiwisolver, Keras-Preprocessing, importlib-metadata, imageio, h5py, grpcio, google-pasta, Deprecated, cffi, absl-py, torchvision, scikit-learn, scikit-image, pluggy, pandas, nibabel, matplotlib, Markdown, Keras-Applications, humanize, cryptography, click, torchio, tensorboard, seaborn, pytest, pyOpenSSL, Keras, formulaic, dipy, csv-diff, tensorflow, pytest-cov, pytest-console-scripts, pybids, ivadomed Successfully installed Deprecated-1.2.13 Keras-2.3.1 Keras-Applications-1.0.8 Keras-Preprocessing-1.1.2 Markdown-3.3.6 Pillow-9.1.0 PyQt5-5.11.3 PyQt5_sip-4.19.19 PyWavelets-1.3.0 PyYAML-6.0 SQLAlchemy-1.3.24 SimpleITK-2.1.1.2 Werkzeug-2.1.2 absl-py-1.0.0 astor-0.7.1 attrs-21.4.0 bids-validator-1.9.3 certifi-2022.5.18.1 cffi-1.15.0 charset-normalizer-2.0.12 click-8.1.3 coverage-6.3.2 cryptography-37.0.1 csv-diff-1.1 cycler-0.11.0 dictdiffer-0.9.0 dipy-1.5.0 docopt-0.6.2 fonttools-4.33.3 formulaic-0.3.3 future-0.18.2 gast-0.2.2 google-pasta-0.2.0 grpcio-1.44.0 h5py-2.10.0 humanize-4.0.0 idna-3.3 imageio-2.18.0 importlib-metadata-4.11.3 iniconfig-1.1.1 interface-meta-1.3.0 ivadomed-2.9.5 joblib-1.1.0 kiwisolver-1.4.2 loguru-0.6.0 matplotlib-3.5.1 networkx-2.6.3 nibabel-3.2.2 num2words-0.5.10 numpy-1.18.5 onnxruntime-1.7.0 opt-einsum-3.3.0 packaging-21.3 pandas-1.3.5 pluggy-1.0.0 portalocker-2.4.0 protobuf-3.20.1 psutil-5.9.0 py-1.11.0 pyOpenSSL-22.0.0 pybids-0.15.1 pycparser-2.21 pyparsing-2.4.7 pytest-7.1.2 pytest-console-scripts-1.3.1 pytest-cov-3.0.0 python-dateutil-2.8.2 pytz-2022.1 raven-6.10.0 requests-2.27.1 requirements-parser-0.5.0 scikit-image-0.19.2 scikit-learn-1.0.2 scipy-1.7.3 seaborn-0.11.2 setuptools-62.3.2 six-1.16.0 tensorboard-1.15.0 tensorflow-1.15.5 tensorflow-estimator-1.15.1 termcolor-1.1.0 threadpoolctl-3.1.0 tifffile-2021.11.2 tomli-2.0.1 torch-1.5.0+cpu torchio-0.18.77 torchvision-0.6.0+cpu tqdm-4.64.0 transforms3d-0.3.1 types-setuptools-57.4.14 typing_extensions-4.2.0 urllib3-1.26.9 wheel-0.37.1 wquantiles-0.6 wrapt-1.14.0 xlwt-1.3.0 zipp-3.8.0 Installing spinalcordtoolbox... Obtaining file:///usr/local/lib/sct_v5.6.0 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Installing collected packages: spinalcordtoolbox Running setup.py develop for spinalcordtoolbox Successfully installed spinalcordtoolbox-5.6 AVX is supported on this Linux machine. Keeping default TensorFlow... Creating launchers for Python scripts... Installing binaries... sct_download_data -d binaries_linux -k -- Spinal Cord Toolbox (git-HEAD-45b1c1759f991332697b4120160303e963f7a3c7) sct_download_data -d binaries_linux -k -- Trying URL: https://osf.io/cs6zt/?action=download Downloading: 20200801_sct_binaries_linux.tar.gz Status: 0%| | 0.00/78.2M [00:00 http://forum.spinalcordmri.org/c/sct