******************************* * Welcome to SCT installation * *******************************  Checking OS type and version... Linux ANW-72 4.18.0-240.1.1.el8_3.x86_64 #1 SMP Thu Nov 19 17:20:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Checking requirements... OK! SCT version ......... 5.7 Installation type ... package Operating system .... linux (unknown) Shell config ........ /home2/yvdwerf/.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: [/home2/yvdwerf/sct_5.7]  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:  Copying source files from /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/spinalcordtoolbox-5.7 to /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7 .............................................................................................................................................................................................................................................................................................................................................................................................................................................. rm -rf /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python mkdir -p /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python Downloading Miniconda... wget -nv -O /tmp/tmp.aTmyiiQQKO/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 2022-09-28 16:05:37 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [76607678/76607678] -> "/tmp/tmp.aTmyiiQQKO/miniconda.sh" [1] Installing Miniconda... bash /tmp/tmp.aTmyiiQQKO/miniconda.sh -p /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python -b -f PREFIX=/mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/python Unpacking payload ... 0%| | 0/40 [00:00 WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 22.9.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /mnt/anw-gold/NP/yvdwerf/data_ENIGMA_PD/projects/sct/sct_5.7/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-2022.07.19 | h06a4308_0 124 KB certifi-2022.9.14 | py37h06a4308_0 155 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 ncurses-6.3 | h5eee18b_3 781 KB openssl-1.1.1q | h7f8727e_0 2.5 MB pip-22.1.2 | py37h06a4308_0 2.4 MB python-3.7.13 | h12debd9_0 46.2 MB setuptools-63.4.1 | py37h06a4308_0 1.1 MB sqlite-3.39.2 | h5082296_0 1.1 MB tk-8.6.12 | h1ccaba5_0 3.0 MB xz-5.2.6 | h5eee18b_0 394 KB zlib-1.2.12 | h5eee18b_3 103 KB ------------------------------------------------------------ Total: 69.0 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-2022.07.19-h06a4308_0 certifi pkgs/main/linux-64::certifi-2022.9.14-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-h5eee18b_3 openssl pkgs/main/linux-64::openssl-1.1.1q-h7f8727e_0 pip pkgs/main/linux-64::pip-22.1.2-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-63.4.1-py37h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.39.2-h5082296_0 tk pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0 wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.6-h5eee18b_0 zlib pkgs/main/linux-64::zlib-1.2.12-h5eee18b_3 Downloading and Extracting Packages xz-5.2.6 | 394 KB | | 0% xz-5.2.6 | 394 KB | ########## | 100% xz-5.2.6 | 394 KB | ########## | 100% tk-8.6.12 | 3.0 MB | | 0% tk-8.6.12 | 3.0 MB | ########## | 100% tk-8.6.12 | 3.0 MB | ########## | 100% zlib-1.2.12 | 103 KB | | 0% zlib-1.2.12 | 103 KB | ########## | 100% zlib-1.2.12 | 103 KB | ########## | 100% sqlite-3.39.2 | 1.1 MB | | 0% sqlite-3.39.2 | 1.1 MB | ########## | 100% sqlite-3.39.2 | 1.1 MB | ########## | 100% _openmp_mutex-5.1 | 21 KB | | 0% _openmp_mutex-5.1 | 21 KB | ########## | 100% _openmp_mutex-5.1 | 21 KB | ########## | 100% libgomp-11.2.0 | 474 KB | | 0% libgomp-11.2.0 | 474 KB | ########## | 100% libgomp-11.2.0 | 474 KB | ########## | 100% ld_impl_linux-64-2.3 | 654 KB | | 0% ld_impl_linux-64-2.3 | 654 KB | ########## | 100% ld_impl_linux-64-2.3 | 654 KB | ########## | 100% openssl-1.1.1q | 2.5 MB | | 0% openssl-1.1.1q | 2.5 MB | ########## | 100% openssl-1.1.1q | 2.5 MB | ########## | 100% setuptools-63.4.1 | 1.1 MB | | 0% setuptools-63.4.1 | 1.1 MB | ########## | 100% setuptools-63.4.1 | 1.1 MB | ########## | 100% libstdcxx-ng-11.2.0 | 4.7 MB | | 0% libstdcxx-ng-11.2.0 | 4.7 MB | ########## | 100% libstdcxx-ng-11.2.0 | 4.7 MB | ########## | 100% ncurses-6.3 | 781 KB | | 0% ncurses-6.3 | 781 KB | ########## | 100% ncurses-6.3 | 781 KB | ########## | 100% ca-certificates-2022 | 124 KB | | 0% ca-certificates-2022 | 124 KB | ########## | 100% ca-certificates-2022 | 124 KB | ########## | 100% python-3.7.13 | 46.2 MB | | 0% python-3.7.13 | 46.2 MB | #4 | 15% python-3.7.13 | 46.2 MB | ###6 | 36% python-3.7.13 | 46.2 MB | #####6 | 57% python-3.7.13 | 46.2 MB | #######7 | 78% python-3.7.13 | 46.2 MB | #########7 | 97% python-3.7.13 | 46.2 MB | ########## | 100% pip-22.1.2 | 2.4 MB | | 0% pip-22.1.2 | 2.4 MB | ####6 | 46% pip-22.1.2 | 2.4 MB | ########## | 100% pip-22.1.2 | 2.4 MB | ########## | 100% certifi-2022.9.14 | 155 KB | | 0% certifi-2022.9.14 | 155 KB | ########## | 100% certifi-2022.9.14 | 155 KB | ########## | 100% libgcc-ng-11.2.0 | 5.3 MB | | 0% libgcc-ng-11.2.0 | 5.3 MB | ######5 | 65% libgcc-ng-11.2.0 | 5.3 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 Validating that conda environment can be activated... Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.7/site-packages (22.1.2) Collecting pip!=21.2.* Downloading pip-22.2.2-py3-none-any.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 13.7 MB/s eta 0:00:00 Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 22.1.2 Uninstalling pip-22.1.2: Successfully uninstalled pip-22.1.2 Successfully installed pip-22.2.2 Installing Python dependencies... Using requirements-freeze.txt (release installation) Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment Collecting certifi Downloading certifi-2022.9.24-py3-none-any.whl (161 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 161.1/161.1 kB 7.0 MB/s eta 0:00:00 Collecting absl-py==1.2.0 Downloading absl_py-1.2.0-py3-none-any.whl (123 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 123.4/123.4 kB 8.3 MB/s eta 0:00:00 Collecting astor==0.8.1 Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB) Collecting attrs==22.1.0 Downloading attrs-22.1.0-py2.py3-none-any.whl (58 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.8/58.8 kB 4.9 MB/s eta 0:00:00 Collecting bids-validator==1.9.7 Downloading bids_validator-1.9.7-py2.py3-none-any.whl (21 kB) Collecting cachetools==5.2.0 Downloading cachetools-5.2.0-py3-none-any.whl (9.3 kB) Collecting cffi==1.15.1 Downloading cffi-1.15.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (427 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 427.9/427.9 kB 18.6 MB/s eta 0:00:00 Collecting charset-normalizer==2.1.0 Downloading charset_normalizer-2.1.0-py3-none-any.whl (39 kB) Collecting click==8.1.3 Downloading click-8.1.3-py3-none-any.whl (96 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.6/96.6 kB 8.5 MB/s eta 0:00:00 Collecting coverage==6.4.2 Downloading coverage-6.4.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (209 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 209.1/209.1 kB 15.5 MB/s eta 0:00:00 Collecting cryptography==37.0.4 Downloading cryptography-37.0.4-cp36-abi3-manylinux_2_24_x86_64.whl (4.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 52.4 MB/s eta 0:00:00 Collecting csv-diff==1.1 Downloading csv_diff-1.1-py3-none-any.whl (12 kB) Collecting cycler==0.11.0 Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting Deprecated==1.2.13 Downloading Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB) Collecting dictdiffer==0.9.0 Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB) Collecting dipy==1.5.0 Downloading dipy-1.5.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.8/7.8 MB 51.9 MB/s eta 0:00:00 Collecting docker-pycreds==0.4.0 Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB) Collecting docopt==0.6.2 Downloading docopt-0.6.2.tar.gz (25 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting fonttools==4.34.4 Downloading fonttools-4.34.4-py3-none-any.whl (944 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 944.1/944.1 kB 39.6 MB/s eta 0:00:00 Collecting formulaic==0.3.4 Downloading formulaic-0.3.4-py3-none-any.whl (68 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.2/68.2 kB 5.8 MB/s eta 0:00:00 Collecting gitdb==4.0.9 Downloading gitdb-4.0.9-py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.1/63.1 kB 5.3 MB/s eta 0:00:00 Collecting GitPython==3.1.27 Downloading GitPython-3.1.27-py3-none-any.whl (181 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 181.2/181.2 kB 13.4 MB/s eta 0:00:00 Collecting google-auth==2.9.1 Downloading google_auth-2.9.1-py2.py3-none-any.whl (167 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 167.8/167.8 kB 13.7 MB/s eta 0:00:00 Collecting google-auth-oauthlib==0.4.6 Downloading google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB) Collecting grpcio==1.47.0 Downloading grpcio-1.47.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 51.6 MB/s eta 0:00:00 Collecting h5py==3.7.0 Downloading h5py-3.7.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 63.2 MB/s eta 0:00:00 Collecting humanize==4.2.3 Downloading humanize-4.2.3-py3-none-any.whl (102 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 102.6/102.6 kB 9.0 MB/s eta 0:00:00 Collecting idna==3.3 Downloading idna-3.3-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 5.7 MB/s eta 0:00:00 Collecting imageio==2.20.0 Downloading imageio-2.20.0-py3-none-any.whl (3.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 60.6 MB/s eta 0:00:00 Collecting importlib-metadata==4.12.0 Downloading importlib_metadata-4.12.0-py3-none-any.whl (21 kB) Collecting iniconfig==1.1.1 Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting interface-meta==1.3.0 Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB) Collecting ivadomed==2.9.6 Downloading ivadomed-2.9.6-py3-none-any.whl (225 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 225.4/225.4 kB 17.2 MB/s eta 0:00:00 Collecting joblib==1.1.0 Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 307.0/307.0 kB 16.3 MB/s eta 0:00:00 Collecting kiwisolver==1.4.4 Downloading kiwisolver-1.4.4-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 36.2 MB/s eta 0:00:00 Collecting loguru==0.6.0 Downloading loguru-0.6.0-py3-none-any.whl (58 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.3/58.3 kB 4.5 MB/s eta 0:00:00 Collecting lxml==4.9.1 Downloading lxml-4.9.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 64.5 MB/s eta 0:00:00 Collecting Markdown==3.4.1 Downloading Markdown-3.4.1-py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.3/93.3 kB 8.1 MB/s eta 0:00:00 Collecting MarkupSafe==2.1.1 Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting matplotlib==3.5.2 Downloading matplotlib-3.5.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 61.4 MB/s eta 0:00:00 Collecting networkx==2.6.3 Downloading networkx-2.6.3-py3-none-any.whl (1.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 43.0 MB/s eta 0:00:00 Collecting neurite==0.2 Downloading neurite-0.2-py3-none-any.whl (108 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 9.7 MB/s eta 0:00:00 Collecting nibabel==3.2.2 Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 50.8 MB/s eta 0:00:00 Collecting nilearn==0.9.1 Downloading nilearn-0.9.1-py3-none-any.whl (9.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.6/9.6 MB 54.3 MB/s eta 0:00:00 Collecting num2words==0.5.10 Downloading num2words-0.5.10-py3-none-any.whl (101 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 101.6/101.6 kB 8.6 MB/s eta 0:00:00 Collecting numpy==1.21.6 Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 54.7 MB/s eta 0:00:00 Collecting oauthlib==3.2.0 Downloading oauthlib-3.2.0-py3-none-any.whl (151 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 151.5/151.5 kB 12.1 MB/s eta 0:00:00 Collecting onnxruntime==1.7.0 Downloading onnxruntime-1.7.0-cp37-cp37m-manylinux2014_x86_64.whl (4.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 65.5 MB/s eta 0:00:00 Collecting packaging==21.3 Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 3.4 MB/s eta 0:00:00 Collecting pandas==1.3.5 Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 76.9 MB/s eta 0:00:00 Collecting pathtools==0.1.2 Downloading pathtools-0.1.2.tar.gz (11 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting Pillow==9.2.0 Downloading Pillow-9.2.0-cp37-cp37m-manylinux_2_28_x86_64.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 62.7 MB/s eta 0:00:00 Collecting pluggy==1.0.0 Downloading pluggy-1.0.0-py2.py3-none-any.whl (13 kB) Collecting portalocker==2.5.1 Downloading portalocker-2.5.1-py2.py3-none-any.whl (15 kB) Collecting promise==2.3 Downloading promise-2.3.tar.gz (19 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting protobuf==3.19.4 Downloading protobuf-3.19.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 45.7 MB/s eta 0:00:00 Collecting psutil==5.9.1 Downloading psutil-5.9.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (281 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 281.4/281.4 kB 19.4 MB/s eta 0:00:00 Collecting py==1.11.0 Downloading py-1.11.0-py2.py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.7/98.7 kB 8.5 MB/s eta 0:00:00 Collecting pyasn1==0.4.8 Downloading pyasn1-0.4.8-py2.py3-none-any.whl (77 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.1/77.1 kB 3.3 MB/s eta 0:00:00 Collecting pyasn1-modules==0.2.8 Downloading pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 12.5 MB/s eta 0:00:00 Collecting pybids==0.15.2 Downloading pybids-0.15.2-py3-none-any.whl (14.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 58.5 MB/s eta 0:00:00 Collecting pycparser==2.21 Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 kB 4.6 MB/s eta 0:00:00 Collecting pyOpenSSL==22.0.0 Downloading pyOpenSSL-22.0.0-py2.py3-none-any.whl (55 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.8/55.8 kB 4.5 MB/s eta 0:00:00 Collecting pyparsing==2.4.7 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 4.0 MB/s eta 0:00:00 Collecting PyQt5==5.11.3 Downloading PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.8/117.8 MB 11.9 MB/s eta 0:00:00 Collecting PyQt5_sip==4.19.19 Downloading PyQt5_sip-4.19.19-cp37-cp37m-manylinux1_x86_64.whl (67 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.4/67.4 kB 6.0 MB/s eta 0:00:00 Collecting pystrum==0.2 Downloading pystrum-0.2-py3-none-any.whl (19 kB) Collecting pytest==7.1.2 Downloading pytest-7.1.2-py3-none-any.whl (297 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 297.0/297.0 kB 18.9 MB/s eta 0:00:00 Collecting pytest-console-scripts==1.3.1 Downloading pytest_console_scripts-1.3.1-py3-none-any.whl (9.0 kB) Collecting pytest-cov==3.0.0 Downloading pytest_cov-3.0.0-py3-none-any.whl (20 kB) Collecting python-dateutil==2.8.2 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 19.4 MB/s eta 0:00:00 Collecting pytz==2022.1 Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 kB 131.4 MB/s eta 0:00:00 Collecting PyWavelets==1.3.0 Downloading 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 78.3 MB/s eta 0:00:00 Collecting PyYAML==6.0 Downloading PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 596.3/596.3 kB 89.1 MB/s eta 0:00:00 Collecting raven==6.10.0 Downloading raven-6.10.0-py2.py3-none-any.whl (284 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 284.3/284.3 kB 76.2 MB/s eta 0:00:00 Collecting requests==2.28.1 Downloading requests-2.28.1-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 54.2 MB/s eta 0:00:00 Collecting requests-oauthlib==1.3.1 Downloading requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB) Collecting requirements-parser==0.5.0 Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB) Collecting rsa==4.9 Downloading rsa-4.9-py3-none-any.whl (34 kB) Collecting scikit-image==0.19.3 Downloading scikit_image-0.19.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (13.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.5/13.5 MB 77.7 MB/s eta 0:00:00 Collecting scikit-learn==1.0.2 Downloading scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.8/24.8 MB 68.9 MB/s eta 0:00:00 Collecting scipy==1.7.3 Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.1/38.1 MB 55.3 MB/s eta 0:00:00 Collecting seaborn==0.11.2 Downloading seaborn-0.11.2-py3-none-any.whl (292 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 292.8/292.8 kB 94.0 MB/s eta 0:00:00 Collecting sentry-sdk==1.9.0 Downloading sentry_sdk-1.9.0-py2.py3-none-any.whl (156 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 156.6/156.6 kB 101.0 MB/s eta 0:00:00 Collecting setproctitle==1.3.0 Downloading setproctitle-1.3.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (30 kB) Collecting shortuuid==1.0.9 Downloading shortuuid-1.0.9-py3-none-any.whl (9.4 kB) Collecting SimpleITK==2.1.1.2 Downloading SimpleITK-2.1.1.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (48.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.4/48.4 MB 48.2 MB/s eta 0:00:00 Collecting six==1.16.0 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting smmap==5.0.0 Downloading smmap-5.0.0-py3-none-any.whl (24 kB) Collecting SQLAlchemy==1.3.24 Downloading SQLAlchemy-1.3.24-cp37-cp37m-manylinux2010_x86_64.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 86.8 MB/s eta 0:00:00 Collecting tensorboard==2.9.1 Downloading tensorboard-2.9.1-py3-none-any.whl (5.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.8/5.8 MB 95.4 MB/s eta 0:00:00 Collecting tensorboard-data-server==0.6.1 Downloading tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl (4.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 80.2 MB/s eta 0:00:00 Collecting tensorboard-plugin-wit==1.8.1 Downloading tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 781.3/781.3 kB 133.0 MB/s eta 0:00:00 Collecting threadpoolctl==3.1.0 Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting tifffile==2021.11.2 Downloading tifffile-2021.11.2-py3-none-any.whl (178 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.9/178.9 kB 96.5 MB/s eta 0:00:00 Collecting tomli==2.0.1 Downloading 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 Downloading transforms3d-0.3.1.tar.gz (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 44.1 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting types-setuptools==63.2.2 Downloading types_setuptools-63.2.2-py3-none-any.whl (50 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.2/50.2 kB 36.6 MB/s eta 0:00:00 Collecting typing_extensions==4.3.0 Downloading typing_extensions-4.3.0-py3-none-any.whl (25 kB) Collecting urllib3==1.26.11 Downloading urllib3-1.26.11-py2.py3-none-any.whl (139 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.9/139.9 kB 88.3 MB/s eta 0:00:00 Collecting voxelmorph==0.2 Downloading voxelmorph-0.2-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 47.5 MB/s eta 0:00:00 Collecting wandb==0.12.21 Downloading wandb-0.12.21-py2.py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 75.7 MB/s eta 0:00:00 Collecting Werkzeug==2.2.1 Downloading Werkzeug-2.2.1-py3-none-any.whl (232 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 232.4/232.4 kB 114.6 MB/s eta 0:00:00 Collecting wquantiles==0.6 Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB) Collecting wrapt==1.14.1 Downloading wrapt-1.14.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (75 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 75.2/75.2 kB 61.7 MB/s eta 0:00:00 Collecting xlwt==1.3.0 Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 78.2 MB/s eta 0:00:00 Collecting zipp==3.8.1 Downloading zipp-3.8.1-py3-none-any.whl (5.6 kB) Collecting torchvision~=0.9.1 Downloading https://download.pytorch.org/whl/cpu/torchvision-0.9.1%2Bcpu-cp37-cp37m-linux_x86_64.whl (13.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.3/13.3 MB 59.0 MB/s eta 0:00:00 Collecting torch~=1.8.1 Downloading https://download.pytorch.org/whl/cpu/torch-1.8.1%2Bcpu-cp37-cp37m-linux_x86_64.whl (169.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 169.1/169.1 MB 25.6 MB/s eta 0:00:00 Collecting torchio>=0.18.68 Downloading torchio-0.18.84-py2.py3-none-any.whl (172 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 172.0/172.0 kB 106.6 MB/s eta 0:00:00 Collecting setuptools Downloading setuptools-65.4.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 83.2 MB/s eta 0:00:00 Collecting coverage[toml]>=5.2.1 Downloading coverage-6.4.4-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (209 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 209.3/209.3 kB 118.7 MB/s eta 0:00:00 Collecting wheel>=0.26 Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting coverage[toml]>=5.2.1 Downloading coverage-6.4.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (209 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 209.4/209.4 kB 117.8 MB/s eta 0:00:00 Building wheels for collected packages: docopt, pathtools, promise, transforms3d WARNING: Building wheel for docopt failed: [Errno 28] No space left on device: '/mnt/home2/yvdwerf/.cache/pip/wheels/72' WARNING: Building wheel for pathtools failed: [Errno 28] No space left on device: '/mnt/home2/yvdwerf/.cache/pip/wheels/3e' WARNING: Building wheel for promise failed: [Errno 28] No space left on device: '/mnt/home2/yvdwerf/.cache/pip/wheels/29' WARNING: Building wheel for transforms3d failed: [Errno 28] No space left on device: '/mnt/home2/yvdwerf/.cache/pip/wheels/b5' Failed to build docopt pathtools promise transforms3d Installing collected packages: xlwt, types-setuptools, transforms3d, tensorboard-plugin-wit, SimpleITK, raven, pytz, PyQt5_sip, pyasn1, pathtools, iniconfig, docopt, dictdiffer, bids-validator, zipp, wrapt, wheel, urllib3, typing_extensions, tqdm, tomli, threadpoolctl, tensorboard-data-server, SQLAlchemy, smmap, six, shortuuid, setuptools, setproctitle, rsa, requirements-parser, PyYAML, PyQt5, pyparsing, pycparser, pyasn1-modules, py, psutil, protobuf, portalocker, Pillow, oauthlib, numpy, num2words, networkx, MarkupSafe, lxml, loguru, joblib, interface-meta, idna, fonttools, cycler, coverage, charset-normalizer, certifi, cachetools, attrs, astor, absl-py, wquantiles, Werkzeug, torch, tifffile, sentry-sdk, scipy, requests, PyWavelets, python-dateutil, promise, packaging, onnxruntime, kiwisolver, importlib-metadata, imageio, h5py, grpcio, google-auth, gitdb, docker-pycreds, Deprecated, cffi, torchvision, scikit-learn, scikit-image, requests-oauthlib, pluggy, pandas, nibabel, matplotlib, Markdown, humanize, GitPython, cryptography, click, wandb, torchio, seaborn, pytest, pystrum, pyOpenSSL, nilearn, google-auth-oauthlib, formulaic, dipy, csv-diff, tensorboard, pytest-cov, pytest-console-scripts, pybids, neurite, voxelmorph, ivadomed Running setup.py install for transforms3d: started Running setup.py install for transforms3d: finished with status 'done' DEPRECATION: transforms3d was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. A possible replacement is to fix the wheel build issue reported above. Discussion can be found at https://github.com/pypa/pip/issues/8368 Running setup.py install for pathtools: started Running setup.py install for pathtools: finished with status 'done' DEPRECATION: pathtools was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. A possible replacement is to fix the wheel build issue reported above. Discussion can be found at https://github.com/pypa/pip/issues/8368 Running setup.py install for docopt: started Running setup.py install for docopt: finished with status 'done' DEPRECATION: docopt was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. A possible replacement is to fix the wheel build issue reported above. Discussion can be found at https://github.com/pypa/pip/issues/8368 Running setup.py install for promise: started Running setup.py install for promise: finished with status 'done' DEPRECATION: promise was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. A possible replacement is to fix the wheel build issue reported above. Discussion can be found at https://github.com/pypa/pip/issues/8368