******************************* * Welcome to SCT installation * *******************************  Checking OS type and version... Linux andromede 6.8.0-50-generic #51~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 21 12:03:03 UTC 2 x86_64 x86_64 x86_64 GNU/Linux Checking requirements... OK! SCT version ......... 5.8 Installation type ... package Operating system .... linux (unknown) Shell config ........ /root/.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 not be sent. SCT will be installed here: [/root/sct_5.8]  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 /mypath/src/spinalcordtoolbox-5.8 to /mypath/bin/x86_64/sct_v5.8_Mint .......................................................................................................................................................................................................................................................................................................................................................................................................................... rm -rf /mypath/bin/x86_64/sct_v5.8_Mint/python mkdir -p /mypath/bin/x86_64/sct_v5.8_Mint/python Downloading Miniconda... wget -nv -O /tmp/tmp.CMEzgyIm4c/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 2025-01-14 16:21:35 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [147784736/147784736] -> "/tmp/tmp.CMEzgyIm4c/miniconda.sh" [1] Installing Miniconda... bash /tmp/tmp.CMEzgyIm4c/miniconda.sh -p /mypath/bin/x86_64/sct_v5.8_Mint/python -b -f PREFIX=/mypath/bin/x86_64/sct_v5.8_Mint/python Unpacking payload ... Installing base environment... Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. Creating conda environment... Channels: - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct added / updated specs: - python=3.8 The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2024.12.31 | h06a4308_0 128 KB pip-24.2 | py38h06a4308_0 2.2 MB python-3.8.20 | he870216_0 23.8 MB setuptools-75.1.0 | py38h06a4308_0 1.7 MB wheel-0.44.0 | py38h06a4308_0 108 KB ------------------------------------------------------------ Total: 27.9 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-2024.12.31-h06a4308_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.40-h12ee557_0 libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1 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-6.4-h6a678d5_0 openssl pkgs/main/linux-64::openssl-3.0.15-h5eee18b_0 pip pkgs/main/linux-64::pip-24.2-py38h06a4308_0 python pkgs/main/linux-64::python-3.8.20-he870216_0 readline pkgs/main/linux-64::readline-8.2-h5eee18b_0 setuptools pkgs/main/linux-64::setuptools-75.1.0-py38h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0 tk pkgs/main/linux-64::tk-8.6.14-h39e8969_0 wheel pkgs/main/linux-64::wheel-0.44.0-py38h06a4308_0 xz pkgs/main/linux-64::xz-5.4.6-h5eee18b_1 zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1 Downloading and Extracting Packages: ...working... python-3.8.20 | 23.8 MB | | 0% pip-24.2 | 2.2 MB | | 0%  setuptools-75.1.0 | 1.7 MB | | 0%  ca-certificates-2024 | 128 KB | | 0%  wheel-0.44.0 | 108 KB | | 0%  python-3.8.20 | 23.8 MB | | 0% pip-24.2 | 2.2 MB | | 1%  setuptools-75.1.0 | 1.7 MB | | 1%  wheel-0.44.0 | 108 KB | #4 | 15%  ca-certificates-2024 | 128 KB | #2 | 12%  python-3.8.20 | 23.8 MB | 5 | 5% setuptools-75.1.0 | 1.7 MB | ##8 | 29%  pip-24.2 | 2.2 MB | ##9 | 30%  wheel-0.44.0 | 108 KB | ########## | 100%  wheel-0.44.0 | 108 KB | ########## | 100%  ca-certificates-2024 | 128 KB | ########## | 100%  ca-certificates-2024 | 128 KB | ########## | 100%  python-3.8.20 | 23.8 MB | ##2 | 22% setuptools-75.1.0 | 1.7 MB | ########## | 100%  setuptools-75.1.0 | 1.7 MB | ########## | 100%  python-3.8.20 | 23.8 MB | #####1 | 52% pip-24.2 | 2.2 MB | ########## | 100%  pip-24.2 | 2.2 MB | ########## | 100%  python-3.8.20 | 23.8 MB | ########7 | 87% python-3.8.20 | 23.8 MB | ########## | 100% ca-certificates-2024 | 128 KB | ########## | 100%  wheel-0.44.0 | 108 KB | ########## | 100%  pip-24.2 | 2.2 MB | ########## | 100%  setuptools-75.1.0 | 1.7 MB | ########## | 100%  python-3.8.20 | 23.8 MB | ########## | 100%     done 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 Validating that conda environment can be activated... Channels: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct added / updated specs: - libstdcxx-ng The following packages will be downloaded: package | build ---------------------------|----------------- _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge _openmp_mutex-4.5 | 2_gnu 23 KB conda-forge libgcc-14.2.0 | h77fa898_1 829 KB conda-forge libgcc-ng-14.2.0 | h69a702a_1 53 KB conda-forge libgomp-14.2.0 | h77fa898_1 450 KB conda-forge libstdcxx-14.2.0 | hc0a3c3a_1 3.7 MB conda-forge libstdcxx-ng-14.2.0 | h4852527_1 53 KB conda-forge openssl-3.4.0 | h7b32b05_1 2.8 MB conda-forge ------------------------------------------------------------ Total: 7.9 MB The following NEW packages will be INSTALLED: libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1 libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1 The following packages will be UPDATED: libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-14.2.0-h69a702a_1 libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-14.2.0-h77fa898_1 libstdcxx-ng pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-14.2.0-h4852527_1 openssl pkgs/main::openssl-3.0.15-h5eee18b_0 --> conda-forge::openssl-3.4.0-h7b32b05_1 The following packages will be SUPERSEDED by a higher-priority channel: _libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge _openmp_mutex pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu Downloading and Extracting Packages: ...working... libstdcxx-14.2.0 | 3.7 MB | | 0% openssl-3.4.0 | 2.8 MB | | 0%  libgcc-14.2.0 | 829 KB | | 0%  libgomp-14.2.0 | 450 KB | | 0%  libgcc-ng-14.2.0 | 53 KB | | 0%  libstdcxx-ng-14.2.0 | 53 KB | | 0%  _openmp_mutex-4.5 | 23 KB | | 0%  _libgcc_mutex-0.1 | 3 KB | | 0%  libgcc-14.2.0 | 829 KB | 1 | 2%  libgomp-14.2.0 | 450 KB | 3 | 4%  libstdcxx-14.2.0 | 3.7 MB | | 0% openssl-3.4.0 | 2.8 MB | | 1%  libgcc-ng-14.2.0 | 53 KB | ### | 30%  libstdcxx-14.2.0 | 3.7 MB | #3 | 13% openssl-3.4.0 | 2.8 MB | ####8 | 49%  libgcc-ng-14.2.0 | 53 KB | ########## | 100%  libgcc-ng-14.2.0 | 53 KB | ########## | 100%  libgcc-14.2.0 | 829 KB | ########## | 100%  libgcc-14.2.0 | 829 KB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | ###5 | 35% libgomp-14.2.0 | 450 KB | ########## | 100%  libgomp-14.2.0 | 450 KB | ########## | 100%  libstdcxx-ng-14.2.0 | 53 KB | ### | 30%  openssl-3.4.0 | 2.8 MB | ########## | 100%  openssl-3.4.0 | 2.8 MB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | ######9 | 69% _openmp_mutex-4.5 | 23 KB | ######9 | 69%  libstdcxx-ng-14.2.0 | 53 KB | ########## | 100%  _libgcc_mutex-0.1 | 3 KB | ########## | 100%  _openmp_mutex-4.5 | 23 KB | ########## | 100%  _libgcc_mutex-0.1 | 3 KB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | ########## | 100% libstdcxx-14.2.0 | 3.7 MB | ########## | 100% libgcc-ng-14.2.0 | 53 KB | ########## | 100%  libgomp-14.2.0 | 450 KB | ########## | 100%  libgcc-14.2.0 | 829 KB | ########## | 100%  _openmp_mutex-4.5 | 23 KB | ########## | 100%  _openmp_mutex-4.5 | 23 KB | ########## | 100%  _libgcc_mutex-0.1 | 3 KB | ########## | 100%  libstdcxx-ng-14.2.0 | 53 KB | ########## | 100%  libstdcxx-ng-14.2.0 | 53 KB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | ########## | 100% openssl-3.4.0 | 2.8 MB | ########## | 100%         done Preparing transaction: - \ | / - \ done Verifying transaction: / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done Executing transaction: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done Collecting pip!=21.2.*,<24.1 Using cached pip-24.0-py3-none-any.whl.metadata (3.6 kB) Using cached pip-24.0-py3-none-any.whl (2.1 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 24.2 Uninstalling pip-24.2: Successfully uninstalled pip-24.2 Successfully installed pip-24.0 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning. 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 Using cached certifi-2024.12.14-py3-none-any.whl.metadata (2.3 kB) Collecting absl-py==1.3.0 (from -r requirements-freeze.txt (line 1)) Using cached absl_py-1.3.0-py3-none-any.whl.metadata (2.3 kB) Collecting astor==0.8.1 (from -r requirements-freeze.txt (line 2)) Using cached astor-0.8.1-py2.py3-none-any.whl.metadata (4.2 kB) Collecting attrs==22.1.0 (from -r requirements-freeze.txt (line 3)) Using cached attrs-22.1.0-py2.py3-none-any.whl.metadata (11 kB) Collecting bids-validator==1.9.9 (from -r requirements-freeze.txt (line 4)) Using cached bids_validator-1.9.9-py2.py3-none-any.whl.metadata (38 kB) Collecting cachetools==5.2.0 (from -r requirements-freeze.txt (line 5)) Using cached cachetools-5.2.0-py3-none-any.whl.metadata (5.1 kB) Collecting certifi Using cached certifi-2022.9.24-py3-none-any.whl.metadata (2.9 kB) Collecting cffi==1.15.1 (from -r requirements-freeze.txt (line 7)) Using cached cffi-1.15.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.1 kB) Collecting charset-normalizer==2.1.1 (from -r requirements-freeze.txt (line 8)) Using cached https://download.pytorch.org/whl/charset_normalizer-2.1.1-py3-none-any.whl (39 kB) Collecting click==8.1.3 (from -r requirements-freeze.txt (line 9)) Using cached click-8.1.3-py3-none-any.whl.metadata (3.2 kB) Collecting colorama==0.4.6 (from -r requirements-freeze.txt (line 10)) Using cached https://download.pytorch.org/whl/colorama-0.4.6-py2.py3-none-any.whl (25 kB) Collecting coloredlogs==15.0.1 (from -r requirements-freeze.txt (line 11)) Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB) Collecting commonmark==0.9.1 (from -r requirements-freeze.txt (line 12)) Using cached commonmark-0.9.1-py2.py3-none-any.whl.metadata (5.7 kB) Collecting contourpy==1.0.6 (from -r requirements-freeze.txt (line 13)) Using cached contourpy-1.0.6-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB) Collecting coverage==6.5.0 (from -r requirements-freeze.txt (line 14)) Using cached coverage-6.5.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.8 kB) Collecting cryptography==38.0.4 (from -r requirements-freeze.txt (line 15)) Using cached cryptography-38.0.4-cp36-abi3-manylinux_2_28_x86_64.whl.metadata (5.3 kB) Collecting csv-diff==1.1 (from -r requirements-freeze.txt (line 16)) Using cached csv_diff-1.1-py3-none-any.whl.metadata (4.1 kB) Collecting cycler==0.11.0 (from -r requirements-freeze.txt (line 17)) Using cached cycler-0.11.0-py3-none-any.whl.metadata (785 bytes) Collecting Deprecated==1.2.13 (from -r requirements-freeze.txt (line 18)) Using cached Deprecated-1.2.13-py2.py3-none-any.whl.metadata (5.8 kB) Collecting dictdiffer==0.9.0 (from -r requirements-freeze.txt (line 19)) Using cached dictdiffer-0.9.0-py2.py3-none-any.whl.metadata (4.8 kB) Collecting dipy==1.5.0 (from -r requirements-freeze.txt (line 20)) Using cached dipy-1.5.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (3.9 kB) Collecting docker-pycreds==0.4.0 (from -r requirements-freeze.txt (line 21)) Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting docopt==0.6.2 (from -r requirements-freeze.txt (line 22)) Using cached docopt-0.6.2-py2.py3-none-any.whl Collecting exceptiongroup==1.0.4 (from -r requirements-freeze.txt (line 23)) Using cached exceptiongroup-1.0.4-py3-none-any.whl.metadata (6.1 kB) Collecting flatbuffers==22.11.23 (from -r requirements-freeze.txt (line 24)) Using cached flatbuffers-22.11.23-py2.py3-none-any.whl.metadata (851 bytes) Collecting fonttools==4.38.0 (from -r requirements-freeze.txt (line 25)) Using cached fonttools-4.38.0-py3-none-any.whl.metadata (138 kB) Collecting formulaic==0.3.4 (from -r requirements-freeze.txt (line 26)) Using cached formulaic-0.3.4-py3-none-any.whl.metadata (5.6 kB) Collecting gitdb==4.0.10 (from -r requirements-freeze.txt (line 27)) Using cached gitdb-4.0.10-py3-none-any.whl.metadata (1.1 kB) Collecting GitPython==3.1.29 (from -r requirements-freeze.txt (line 28)) Using cached GitPython-3.1.29-py3-none-any.whl.metadata (1.3 kB) Collecting google-auth==2.14.1 (from -r requirements-freeze.txt (line 29)) Using cached google_auth-2.14.1-py2.py3-none-any.whl.metadata (4.2 kB) Collecting google-auth-oauthlib==0.4.6 (from -r requirements-freeze.txt (line 30)) Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl.metadata (2.7 kB) Collecting grpcio==1.51.1 (from -r requirements-freeze.txt (line 31)) Using cached grpcio-1.51.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.8 kB) Collecting h5py==3.7.0 (from -r requirements-freeze.txt (line 32)) Using cached h5py-3.7.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (1.8 kB) Collecting humanfriendly==10.0 (from -r requirements-freeze.txt (line 33)) Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB) Collecting humanize==4.4.0 (from -r requirements-freeze.txt (line 34)) Using cached humanize-4.4.0-py3-none-any.whl.metadata (7.9 kB) Collecting idna==3.4 (from -r requirements-freeze.txt (line 35)) Using cached https://download.pytorch.org/whl/idna-3.4-py3-none-any.whl (61 kB) Collecting imageio==2.22.4 (from -r requirements-freeze.txt (line 36)) Using cached imageio-2.22.4-py3-none-any.whl.metadata (5.0 kB) Collecting importlib-metadata==5.1.0 (from -r requirements-freeze.txt (line 37)) Using cached importlib_metadata-5.1.0-py3-none-any.whl.metadata (4.9 kB) Collecting iniconfig==1.1.1 (from -r requirements-freeze.txt (line 38)) Using cached iniconfig-1.1.1-py2.py3-none-any.whl.metadata (2.4 kB) Collecting interface-meta==1.3.0 (from -r requirements-freeze.txt (line 39)) Using cached interface_meta-1.3.0-py3-none-any.whl.metadata (6.7 kB) Collecting ivadomed==2.9.8 (from -r requirements-freeze.txt (line 40)) Using cached ivadomed-2.9.8-py3-none-any.whl.metadata (6.6 kB) Collecting joblib==1.2.0 (from -r requirements-freeze.txt (line 41)) Using cached joblib-1.2.0-py3-none-any.whl.metadata (5.3 kB) Collecting kiwisolver==1.4.4 (from -r requirements-freeze.txt (line 42)) Using cached kiwisolver-1.4.4-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (6.3 kB) Collecting loguru==0.6.0 (from -r requirements-freeze.txt (line 43)) Using cached loguru-0.6.0-py3-none-any.whl.metadata (21 kB) Collecting lxml==4.9.1 (from -r requirements-freeze.txt (line 44)) Using cached lxml-4.9.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (3.3 kB) Collecting Markdown==3.4.1 (from -r requirements-freeze.txt (line 45)) Using cached Markdown-3.4.1-py3-none-any.whl.metadata (4.6 kB) Collecting MarkupSafe==2.1.1 (from -r requirements-freeze.txt (line 46)) Using cached MarkupSafe-2.1.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.2 kB) Collecting matplotlib==3.6.2 (from -r requirements-freeze.txt (line 47)) Using cached matplotlib-3.6.2-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.8 kB) Collecting mpmath==1.2.1 (from -r requirements-freeze.txt (line 48)) Using cached https://download.pytorch.org/whl/mpmath-1.2.1-py3-none-any.whl (532 kB) Collecting networkx==2.8.8 (from -r requirements-freeze.txt (line 49)) Using cached networkx-2.8.8-py3-none-any.whl.metadata (5.1 kB) Collecting neurite==0.2 (from -r requirements-freeze.txt (line 50)) Using cached neurite-0.2-py3-none-any.whl.metadata (653 bytes) Collecting nibabel==3.2.2 (from -r requirements-freeze.txt (line 51)) Using cached nibabel-3.2.2-py3-none-any.whl.metadata (6.2 kB) Collecting nilearn==0.9.2 (from -r requirements-freeze.txt (line 52)) Using cached nilearn-0.9.2-py3-none-any.whl.metadata (6.7 kB) Collecting num2words==0.5.12 (from -r requirements-freeze.txt (line 53)) Using cached num2words-0.5.12-py3-none-any.whl.metadata (11 kB) Collecting numpy==1.23.5 (from -r requirements-freeze.txt (line 54)) Using cached numpy-1.23.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB) Collecting oauthlib==3.2.2 (from -r requirements-freeze.txt (line 55)) Using cached oauthlib-3.2.2-py3-none-any.whl.metadata (7.5 kB) Collecting onnxruntime==1.13.1 (from -r requirements-freeze.txt (line 56)) Using cached onnxruntime-1.13.1-cp38-cp38-manylinux_2_27_x86_64.whl.metadata (3.8 kB) Collecting packaging==21.3 (from -r requirements-freeze.txt (line 57)) Using cached packaging-21.3-py3-none-any.whl.metadata (15 kB) Collecting pandas==1.4.4 (from -r requirements-freeze.txt (line 58)) Using cached pandas-1.4.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB) Collecting pathtools==0.1.2 (from -r requirements-freeze.txt (line 59)) Using cached pathtools-0.1.2-py3-none-any.whl Collecting Pillow==9.3.0 (from -r requirements-freeze.txt (line 60)) Using cached Pillow-9.3.0-cp38-cp38-manylinux_2_28_x86_64.whl.metadata (9.2 kB) Collecting pluggy==1.0.0 (from -r requirements-freeze.txt (line 61)) Using cached pluggy-1.0.0-py2.py3-none-any.whl.metadata (4.3 kB) Collecting portalocker==2.6.0 (from -r requirements-freeze.txt (line 62)) Using cached portalocker-2.6.0-py2.py3-none-any.whl.metadata (6.8 kB) Collecting promise==2.3 (from -r requirements-freeze.txt (line 63)) Using cached promise-2.3-py3-none-any.whl Collecting protobuf==3.20.3 (from -r requirements-freeze.txt (line 64)) Using cached protobuf-3.20.3-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (679 bytes) Collecting psutil==5.9.4 (from -r requirements-freeze.txt (line 65)) Using cached psutil-5.9.4-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB) Collecting pyasn1==0.4.8 (from -r requirements-freeze.txt (line 66)) Using cached pyasn1-0.4.8-py2.py3-none-any.whl.metadata (1.5 kB) Collecting pyasn1-modules==0.2.8 (from -r requirements-freeze.txt (line 67)) Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl.metadata (1.9 kB) Collecting pybids==0.15.5 (from -r requirements-freeze.txt (line 68)) Using cached pybids-0.15.5-py3-none-any.whl.metadata (3.2 kB) Collecting pycparser==2.21 (from -r requirements-freeze.txt (line 69)) Using cached pycparser-2.21-py2.py3-none-any.whl.metadata (1.1 kB) Collecting Pygments==2.13.0 (from -r requirements-freeze.txt (line 70)) Using cached Pygments-2.13.0-py3-none-any.whl.metadata (1.6 kB) Collecting pyOpenSSL==22.1.0 (from -r requirements-freeze.txt (line 71)) Using cached pyOpenSSL-22.1.0-py3-none-any.whl.metadata (8.9 kB) Collecting pyparsing==2.4.7 (from -r requirements-freeze.txt (line 72)) Using cached pyparsing-2.4.7-py2.py3-none-any.whl.metadata (3.6 kB) Collecting PyQt5==5.14.2 (from -r requirements-freeze.txt (line 73)) Using cached PyQt5-5.14.2-5.14.2-cp35.cp36.cp37.cp38-abi3-manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting PyQt5-sip==12.11.0 (from -r requirements-freeze.txt (line 74)) Using cached PyQt5_sip-12.11.0-cp38-cp38-manylinux1_x86_64.whl.metadata (504 bytes) Collecting pystrum==0.2 (from -r requirements-freeze.txt (line 75)) Using cached pystrum-0.2-py3-none-any.whl.metadata (482 bytes) Collecting pytest==7.2.0 (from -r requirements-freeze.txt (line 76)) Using cached pytest-7.2.0-py3-none-any.whl.metadata (7.8 kB) Collecting pytest-console-scripts==1.3.1 (from -r requirements-freeze.txt (line 77)) Using cached pytest_console_scripts-1.3.1-py3-none-any.whl.metadata (9.7 kB) Collecting pytest-cov==4.0.0 (from -r requirements-freeze.txt (line 78)) Using cached pytest_cov-4.0.0-py3-none-any.whl.metadata (25 kB) Collecting python-dateutil==2.8.2 (from -r requirements-freeze.txt (line 79)) Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB) Collecting pytz==2022.6 (from -r requirements-freeze.txt (line 80)) Using cached pytz-2022.6-py2.py3-none-any.whl.metadata (21 kB) Collecting PyWavelets==1.4.1 (from -r requirements-freeze.txt (line 81)) Using cached PyWavelets-1.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.9 kB) Collecting PyYAML==6.0 (from -r requirements-freeze.txt (line 82)) Using cached PyYAML-6.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (2.0 kB) Collecting raven==6.10.0 (from -r requirements-freeze.txt (line 83)) Using cached raven-6.10.0-py2.py3-none-any.whl.metadata (2.9 kB) Collecting requests==2.28.1 (from -r requirements-freeze.txt (line 84)) Using cached https://download.pytorch.org/whl/requests-2.28.1-py3-none-any.whl (62 kB) Collecting requests-oauthlib==1.3.1 (from -r requirements-freeze.txt (line 85)) Using cached requests_oauthlib-1.3.1-py2.py3-none-any.whl.metadata (10 kB) Collecting requirements-parser==0.5.0 (from -r requirements-freeze.txt (line 86)) Using cached requirements_parser-0.5.0-py3-none-any.whl.metadata (3.1 kB) Collecting rich==12.6.0 (from -r requirements-freeze.txt (line 87)) Using cached rich-12.6.0-py3-none-any.whl.metadata (18 kB) Collecting rsa==4.9 (from -r requirements-freeze.txt (line 88)) Using cached rsa-4.9-py3-none-any.whl.metadata (4.2 kB) Collecting scikit-image==0.19.3 (from -r requirements-freeze.txt (line 89)) Using cached scikit_image-0.19.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.0 kB) Collecting scikit-learn==1.1.3 (from -r requirements-freeze.txt (line 90)) Using cached scikit_learn-1.1.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB) Collecting scipy==1.9.3 (from -r requirements-freeze.txt (line 91)) Using cached scipy-1.9.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (58 kB) Collecting seaborn==0.12.1 (from -r requirements-freeze.txt (line 92)) Using cached seaborn-0.12.1-py3-none-any.whl.metadata (5.4 kB) Collecting sentry-sdk==1.11.1 (from -r requirements-freeze.txt (line 93)) Using cached sentry_sdk-1.11.1-py2.py3-none-any.whl.metadata (8.2 kB) Collecting setproctitle==1.3.2 (from -r requirements-freeze.txt (line 94)) Using cached setproctitle-1.3.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.8 kB) Collecting shellingham==1.5.0 (from -r requirements-freeze.txt (line 95)) Using cached shellingham-1.5.0-py2.py3-none-any.whl.metadata (3.3 kB) Collecting shortuuid==1.0.11 (from -r requirements-freeze.txt (line 96)) Using cached shortuuid-1.0.11-py3-none-any.whl.metadata (6.1 kB) Collecting SimpleITK==2.2.0 (from -r requirements-freeze.txt (line 97)) Using cached SimpleITK-2.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.1 kB) Collecting six==1.16.0 (from -r requirements-freeze.txt (line 98)) Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting smmap==5.0.0 (from -r requirements-freeze.txt (line 99)) Using cached smmap-5.0.0-py3-none-any.whl.metadata (4.2 kB) Collecting SQLAlchemy==1.3.24 (from -r requirements-freeze.txt (line 100)) Using cached SQLAlchemy-1.3.24-cp38-cp38-manylinux2010_x86_64.whl.metadata (7.9 kB) Collecting sympy==1.11.1 (from -r requirements-freeze.txt (line 101)) Using cached https://download.pytorch.org/whl/sympy-1.11.1-py3-none-any.whl (6.5 MB) Collecting tensorboard==2.11.0 (from -r requirements-freeze.txt (line 102)) Using cached tensorboard-2.11.0-py3-none-any.whl.metadata (1.9 kB) Collecting tensorboard-data-server==0.6.1 (from -r requirements-freeze.txt (line 103)) Using cached tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl.metadata (1.1 kB) Collecting tensorboard-plugin-wit==1.8.1 (from -r requirements-freeze.txt (line 104)) Using cached tensorboard_plugin_wit-1.8.1-py3-none-any.whl.metadata (873 bytes) Collecting threadpoolctl==3.1.0 (from -r requirements-freeze.txt (line 105)) Using cached threadpoolctl-3.1.0-py3-none-any.whl.metadata (9.2 kB) Collecting tifffile==2022.10.10 (from -r requirements-freeze.txt (line 106)) Using cached tifffile-2022.10.10-py3-none-any.whl.metadata (28 kB) Collecting tomli==2.0.1 (from -r requirements-freeze.txt (line 107)) Using cached tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB) Collecting tqdm==4.64.1 (from -r requirements-freeze.txt (line 108)) Using cached https://download.pytorch.org/whl/tqdm-4.64.1-py2.py3-none-any.whl (78 kB) Collecting transforms3d==0.4.1 (from -r requirements-freeze.txt (line 109)) Using cached transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB) Collecting typer==0.7.0 (from -r requirements-freeze.txt (line 110)) Using cached typer-0.7.0-py3-none-any.whl.metadata (17 kB) Collecting types-setuptools==65.6.0.1 (from -r requirements-freeze.txt (line 111)) Using cached types_setuptools-65.6.0.1-py3-none-any.whl.metadata (1.2 kB) Collecting typing_extensions==4.4.0 (from -r requirements-freeze.txt (line 112)) Using cached https://download.pytorch.org/whl/typing_extensions-4.4.0-py3-none-any.whl (26 kB) Collecting urllib3==1.26.13 (from -r requirements-freeze.txt (line 113)) Using cached https://download.pytorch.org/whl/urllib3-1.26.13-py2.py3-none-any.whl (140 kB) Collecting urllib3-secure-extra==0.1.0 (from -r requirements-freeze.txt (line 114)) Using cached urllib3_secure_extra-0.1.0-py2.py3-none-any.whl.metadata (828 bytes) Collecting voxelmorph==0.2 (from -r requirements-freeze.txt (line 115)) Using cached voxelmorph-0.2-py3-none-any.whl.metadata (660 bytes) Collecting wandb==0.13.5 (from -r requirements-freeze.txt (line 116)) Using cached wandb-0.13.5-py2.py3-none-any.whl.metadata (7.4 kB) Collecting Werkzeug==2.2.2 (from -r requirements-freeze.txt (line 117)) Using cached Werkzeug-2.2.2-py3-none-any.whl.metadata (4.4 kB) Collecting wquantiles==0.6 (from -r requirements-freeze.txt (line 118)) Using cached wquantiles-0.6-py3-none-any.whl.metadata (1.1 kB) Collecting wrapt==1.14.1 (from -r requirements-freeze.txt (line 119)) Using cached wrapt-1.14.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB) Collecting xlwt==1.3.0 (from -r requirements-freeze.txt (line 120)) Using cached xlwt-1.3.0-py2.py3-none-any.whl.metadata (3.5 kB) Collecting zipp==3.11.0 (from -r requirements-freeze.txt (line 121)) Using cached zipp-3.11.0-py3-none-any.whl.metadata (3.7 kB) Collecting torchio>=0.18.68 (from ivadomed==2.9.8->-r requirements-freeze.txt (line 40)) Using cached torchio-0.20.1-py3-none-any.whl.metadata (50 kB) Collecting torch<=1.11.0,>=1.8.1 (from ivadomed==2.9.8->-r requirements-freeze.txt (line 40)) Using cached https://download.pytorch.org/whl/cpu/torch-1.11.0%2Bcpu-cp38-cp38-linux_x86_64.whl (169.2 MB) Collecting torchvision<=0.12.0,>=0.9.1 (from ivadomed==2.9.8->-r requirements-freeze.txt (line 40)) Using cached https://download.pytorch.org/whl/cpu/torchvision-0.12.0%2Bcpu-cp38-cp38-linux_x86_64.whl (14.7 MB) Collecting setuptools (from nibabel==3.2.2->-r requirements-freeze.txt (line 51)) Using cached setuptools-75.3.0-py3-none-any.whl.metadata (6.9 kB) Collecting wheel>=0.26 (from tensorboard==2.11.0->-r requirements-freeze.txt (line 102)) Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB) WARNING: The candidate selected for download or install is a yanked version: 'shellingham' candidate (version 1.5.0 at https://files.pythonhosted.org/packages/3d/1a/d31fce69c119df1fddab3706b63c53d363982c55d841d9c3839b12f15327/shellingham-1.5.0-py2.py3-none-any.whl (from https://pypi.org/simple/shellingham/) (requires-python:>=3.4)) Reason for being yanked: Incorrect package metadata Using cached certifi-2022.9.24-py3-none-any.whl (161 kB) Using cached absl_py-1.3.0-py3-none-any.whl (124 kB) Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB) Using cached attrs-22.1.0-py2.py3-none-any.whl (58 kB) Using cached bids_validator-1.9.9-py2.py3-none-any.whl (21 kB) Using cached cachetools-5.2.0-py3-none-any.whl (9.3 kB) Using cached cffi-1.15.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (442 kB) Using cached click-8.1.3-py3-none-any.whl (96 kB) Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) Using cached commonmark-0.9.1-py2.py3-none-any.whl (51 kB) Using cached contourpy-1.0.6-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (295 kB) Using cached coverage-6.5.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (214 kB) Using cached cryptography-38.0.4-cp36-abi3-manylinux_2_28_x86_64.whl (4.2 MB) Using cached csv_diff-1.1-py3-none-any.whl (12 kB) Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB) Using cached Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB) Using cached dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB) Using cached dipy-1.5.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB) Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB) Using cached exceptiongroup-1.0.4-py3-none-any.whl (14 kB) Using cached flatbuffers-22.11.23-py2.py3-none-any.whl (26 kB) Using cached fonttools-4.38.0-py3-none-any.whl (965 kB) Using cached formulaic-0.3.4-py3-none-any.whl (68 kB) Using cached gitdb-4.0.10-py3-none-any.whl (62 kB) Using cached GitPython-3.1.29-py3-none-any.whl (182 kB) Using cached google_auth-2.14.1-py2.py3-none-any.whl (175 kB) Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB) Using cached grpcio-1.51.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB) Using cached h5py-3.7.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB) Using cached humanize-4.4.0-py3-none-any.whl (106 kB) Using cached imageio-2.22.4-py3-none-any.whl (3.4 MB) Using cached 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Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB) Using cached Pygments-2.13.0-py3-none-any.whl (1.1 MB) Using cached pyOpenSSL-22.1.0-py3-none-any.whl (57 kB) Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Using cached PyQt5-5.14.2-5.14.2-cp35.cp36.cp37.cp38-abi3-manylinux2014_x86_64.whl (63.6 MB) Using cached PyQt5_sip-12.11.0-cp38-cp38-manylinux1_x86_64.whl (361 kB) Using cached pystrum-0.2-py3-none-any.whl (19 kB) Using cached pytest-7.2.0-py3-none-any.whl (316 kB) Using cached pytest_console_scripts-1.3.1-py3-none-any.whl (9.0 kB) Using cached pytest_cov-4.0.0-py3-none-any.whl (21 kB) Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Using cached pytz-2022.6-py2.py3-none-any.whl (498 kB) Using cached PyWavelets-1.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.9 MB) Using cached PyYAML-6.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (701 kB) Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB) Using cached requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB) Using cached requirements_parser-0.5.0-py3-none-any.whl (18 kB) Using cached rich-12.6.0-py3-none-any.whl (237 kB) Using cached rsa-4.9-py3-none-any.whl (34 kB) Using cached scikit_image-0.19.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.0 MB) Using cached scikit_learn-1.1.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (31.2 MB) Using cached scipy-1.9.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (33.8 MB) Using cached seaborn-0.12.1-py3-none-any.whl (288 kB) Using cached sentry_sdk-1.11.1-py2.py3-none-any.whl (168 kB) Using cached setproctitle-1.3.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (31 kB) Using cached shellingham-1.5.0-py2.py3-none-any.whl (9.3 kB) Using cached shortuuid-1.0.11-py3-none-any.whl (10 kB) Using cached SimpleITK-2.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (52.8 MB) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Using cached smmap-5.0.0-py3-none-any.whl (24 kB) Using cached SQLAlchemy-1.3.24-cp38-cp38-manylinux2010_x86_64.whl (1.3 MB) Using cached tensorboard-2.11.0-py3-none-any.whl (6.0 MB) Using cached tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl (4.9 MB) Using cached tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB) Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Using cached tifffile-2022.10.10-py3-none-any.whl (210 kB) Using cached tomli-2.0.1-py3-none-any.whl (12 kB) Using cached transforms3d-0.4.1-py3-none-any.whl (1.4 MB) Using cached typer-0.7.0-py3-none-any.whl (38 kB) Using cached types_setuptools-65.6.0.1-py3-none-any.whl (48 kB) Using cached urllib3_secure_extra-0.1.0-py2.py3-none-any.whl (1.4 kB) Using cached voxelmorph-0.2-py3-none-any.whl (54 kB) Using cached wandb-0.13.5-py2.py3-none-any.whl (1.9 MB) Using cached Werkzeug-2.2.2-py3-none-any.whl (232 kB) Using cached wquantiles-0.6-py3-none-any.whl (3.3 kB) Using cached wrapt-1.14.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (81 kB) Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB) Using cached zipp-3.11.0-py3-none-any.whl (6.6 kB) Using cached setuptools-75.3.0-py3-none-any.whl (1.3 MB) Using cached torchio-0.20.1-py3-none-any.whl (175 kB) Using cached wheel-0.45.1-py3-none-any.whl (72 kB) Installing collected packages: xlwt, urllib3-secure-extra, types-setuptools, tensorboard-plugin-wit, SimpleITK, raven, pytz, pyasn1, pathtools, mpmath, iniconfig, flatbuffers, docopt, dictdiffer, commonmark, bids-validator, zipp, wrapt, wheel, urllib3, typing_extensions, transforms3d, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, SQLAlchemy, smmap, six, shortuuid, shellingham, setuptools, setproctitle, rsa, requirements-parser, PyYAML, PyQt5-sip, pyparsing, Pygments, pycparser, pyasn1-modules, psutil, protobuf, portalocker, pluggy, Pillow, oauthlib, numpy, num2words, networkx, MarkupSafe, lxml, loguru, kiwisolver, joblib, interface-meta, idna, humanize, humanfriendly, grpcio, fonttools, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, cachetools, attrs, astor, absl-py, wquantiles, Werkzeug, typer, torch, tifffile, sentry-sdk, scipy, rich, requests, PyWavelets, python-dateutil, PyQt5, promise, packaging, importlib-metadata, imageio, h5py, google-auth, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, coloredlogs, cffi, torchvision, scikit-learn, scikit-image, requests-oauthlib, pytest, pandas, onnxruntime, nibabel, matplotlib, Markdown, GitPython, cryptography, wandb, torchio, seaborn, pytest-cov, pytest-console-scripts, pystrum, pyOpenSSL, nilearn, google-auth-oauthlib, formulaic, dipy, tensorboard, pybids, neurite, voxelmorph, ivadomed Successfully installed Deprecated-1.2.13 GitPython-3.1.29 Markdown-3.4.1 MarkupSafe-2.1.1 Pillow-9.3.0 PyQt5-5.14.2 PyQt5-sip-12.11.0 PyWavelets-1.4.1 PyYAML-6.0 Pygments-2.13.0 SQLAlchemy-1.3.24 SimpleITK-2.2.0 Werkzeug-2.2.2 absl-py-1.3.0 astor-0.8.1 attrs-22.1.0 bids-validator-1.9.9 cachetools-5.2.0 certifi-2022.9.24 cffi-1.15.1 charset-normalizer-2.1.1 click-8.1.3 colorama-0.4.6 coloredlogs-15.0.1 commonmark-0.9.1 contourpy-1.0.6 coverage-6.5.0 cryptography-38.0.4 csv-diff-1.1 cycler-0.11.0 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 exceptiongroup-1.0.4 flatbuffers-22.11.23 fonttools-4.38.0 formulaic-0.3.4 gitdb-4.0.10 google-auth-2.14.1 google-auth-oauthlib-0.4.6 grpcio-1.51.1 h5py-3.7.0 humanfriendly-10.0 humanize-4.4.0 idna-3.4 imageio-2.22.4 importlib-metadata-5.1.0 iniconfig-1.1.1 interface-meta-1.3.0 ivadomed-2.9.8 joblib-1.2.0 kiwisolver-1.4.4 loguru-0.6.0 lxml-4.9.1 matplotlib-3.6.2 mpmath-1.2.1 networkx-2.8.8 neurite-0.2 nibabel-3.2.2 nilearn-0.9.2 num2words-0.5.12 numpy-1.23.5 oauthlib-3.2.2 onnxruntime-1.13.1 packaging-21.3 pandas-1.4.4 pathtools-0.1.2 pluggy-1.0.0 portalocker-2.6.0 promise-2.3 protobuf-3.20.3 psutil-5.9.4 pyOpenSSL-22.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pybids-0.15.5 pycparser-2.21 pyparsing-2.4.7 pystrum-0.2 pytest-7.2.0 pytest-console-scripts-1.3.1 pytest-cov-4.0.0 python-dateutil-2.8.2 pytz-2022.6 raven-6.10.0 requests-2.28.1 requests-oauthlib-1.3.1 requirements-parser-0.5.0 rich-12.6.0 rsa-4.9 scikit-image-0.19.3 scikit-learn-1.1.3 scipy-1.9.3 seaborn-0.12.1 sentry-sdk-1.11.1 setproctitle-1.3.2 setuptools-75.1.0 shellingham-1.5.0 shortuuid-1.0.11 six-1.16.0 smmap-5.0.0 sympy-1.11.1 tensorboard-2.11.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 threadpoolctl-3.1.0 tifffile-2022.10.10 tomli-2.0.1 torch-1.11.0+cpu torchio-0.20.1 torchvision-0.12.0+cpu tqdm-4.64.1 transforms3d-0.4.1 typer-0.7.0 types-setuptools-65.6.0.1 typing_extensions-4.4.0 urllib3-1.26.13 urllib3-secure-extra-0.1.0 voxelmorph-0.2 wandb-0.13.5 wheel-0.44.0 wquantiles-0.6 wrapt-1.14.1 xlwt-1.3.0 zipp-3.11.0 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv [notice] A new release of pip is available: 24.0 -> 24.3.1 [notice] To update, run: pip install --upgrade pip Installing spinalcordtoolbox... Obtaining file:///mypath/bin/x86_64/sct_v5.8_Mint Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' error: subprocess-exited-with-error × python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [47 lines of output] running egg_info creating /tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info writing /tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info/PKG-INFO writing dependency_links to /tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info/dependency_links.txt writing entry points to /tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info/entry_points.txt writing requirements to /tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info/requires.txt writing top-level names to /tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info/top_level.txt writing manifest file '/tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info/SOURCES.txt' reading manifest file '/tmp/pip-pip-egg-info-mqj5ran0/spinalcordtoolbox.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'abstract.png' no previously-included directories found matching 'dev' no previously-included directories found matching 'scripts' no previously-included directories found matching 'testing' adding license file 'LICENSE' Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/mypath/bin/x86_64/sct_v5.8_Mint/setup.py", line 16, in setup( File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/__init__.py", line 117, in setup return distutils.core.setup(**attrs) File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 183, in setup return run_commands(dist) File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 199, in run_commands dist.run_commands() File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands self.run_command(cmd) File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/dist.py", line 999, in run_command super().run_command(command) File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 973, in run_command cmd_obj.run() File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/command/egg_info.py", line 312, in run self.find_sources() File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/command/egg_info.py", line 320, in find_sources mm.run() File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/command/egg_info.py", line 546, in run self.prune_file_list() File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/command/sdist.py", line 162, in prune_file_list super().prune_file_list() File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/_distutils/command/sdist.py", line 380, in prune_file_list base_dir = self.distribution.get_fullname() File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/_core_metadata.py", line 267, in get_fullname return _distribution_fullname(self.get_name(), self.get_version()) File "/mypath/bin/x86_64/sct_v5.8_Mint/python/envs/venv_sct/lib/python3.8/site-packages/setuptools/_core_metadata.py", line 285, in _distribution_fullname canonicalize_version(version, strip_trailing_zero=False), TypeError: canonicalize_version() got an unexpected keyword argument 'strip_trailing_zero' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details. [notice] A new release of pip is available: 24.0 -> 24.3.1 [notice] To update, run: pip install --upgrade pip Failed running pip install: 1 Installation failed! Please find the file "/mypath/src/spinalcordtoolbox-5.8/install_sct_log.txt", then upload it as a .txt attachment in a new topic on SCT's forum: --> http://forum.spinalcordmri.org/c/sct