******************************* * Welcome to SCT installation * *******************************  Checking OS type and version... Linux ptb-03240175.irisa.fr 6.11.6-200.fc40.x86_64 #1 SMP PREEMPT_DYNAMIC Fri Nov 1 16:09:34 UTC 2024 x86_64 GNU/Linux Checking requirements... OK! Source files not present. Downloading source files (@ 6.1) to /tmp/tmp.qclaEclPQ7/spinalcordtoolbox. Clonage dans '/tmp/tmp.qclaEclPQ7/spinalcordtoolbox'... Note : basculement sur '3e7dc3db4a67a39fc41fa2bfb7dd0539f3a49d0c'. Vous êtes dans l'état « HEAD détachée ». Vous pouvez visiter, faire des modifications expérimentales et les valider. Il vous suffit de faire un autre basculement pour abandonner les commits que vous faites dans cet état sans impacter les autres branches Si vous voulez créer une nouvelle branche pour conserver les commits que vous créez, il vous suffit d'utiliser l'option -c de la commande switch comme ceci : git switch -c Ou annuler cette opération avec : git switch - Désactivez ce conseil en renseignant la variable de configuration advice.detachedHead à false SCT version ......... 6.1 Installation type ... package Operating system .... linux (unknown) Shell config ........ /home/mliffran/.bashrc SCT will be installed here: [/home/mliffran/sct_6.1]  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. Copying source files from /tmp/tmp.qclaEclPQ7/spinalcordtoolbox to /home/mliffran/Documents/Software/SCT/sct_6.1 .............................................................................................................................................................................................................................................................................................................................................................................................................................. Removing sct and isct softlink from /home/mliffran/Documents/Software/SCT/sct_6.1/bin rm -rf /home/mliffran/Documents/Software/SCT/sct_6.1/python mkdir -p /home/mliffran/Documents/Software/SCT/sct_6.1/python Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o:  Downloading Miniconda... wget -nv -O /tmp/tmp.qclaEclPQ7/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh Installing Miniconda... bash /tmp/tmp.qclaEclPQ7/miniconda.sh -p /home/mliffran/Documents/Software/SCT/sct_6.1/python -b -f PREFIX=/home/mliffran/Documents/Software/SCT/sct_6.1/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: /home/mliffran/Documents/Software/SCT/sct_6.1/python/envs/venv_sct added / updated specs: - python=3.9 The following packages will be downloaded: package | build ---------------------------|----------------- pip-24.2 | py39h06a4308_0 2.2 MB python-3.9.20 | he870216_1 25.1 MB setuptools-75.1.0 | py39h06a4308_0 1.7 MB wheel-0.44.0 | py39h06a4308_0 108 KB ------------------------------------------------------------ Total: 29.1 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-2024.9.24-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-py39h06a4308_0 python pkgs/main/linux-64::python-3.9.20-he870216_1 readline pkgs/main/linux-64::readline-8.2-h5eee18b_0 setuptools pkgs/main/linux-64::setuptools-75.1.0-py39h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0 tk pkgs/main/linux-64::tk-8.6.14-h39e8969_0 tzdata pkgs/main/noarch::tzdata-2024b-h04d1e81_0 wheel pkgs/main/linux-64::wheel-0.44.0-py39h06a4308_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... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done # # To activate this environment, use # # $ conda activate /home/mliffran/Documents/Software/SCT/sct_6.1/python/envs/venv_sct # # To deactivate an active environment, use # # $ conda deactivate Channels: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/mliffran/Documents/Software/SCT/sct_6.1/python/envs/venv_sct added / updated specs: - libstdcxx-ng The following packages will be downloaded: package | build ---------------------------|----------------- 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 | hb9d3cd8_0 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-hb9d3cd8_0 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... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done # All requested packages already installed. Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (24.2) Collecting pip!=21.2.* Using cached pip-24.3.1-py3-none-any.whl.metadata (3.7 kB) Using cached pip-24.3.1-py3-none-any.whl (1.8 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-24.3.1 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-2024.8.30-py3-none-any.whl.metadata (2.2 kB) Collecting absl-py==2.0.0 (from -r requirements-freeze.txt (line 1)) Using cached absl_py-2.0.0-py3-none-any.whl.metadata (2.3 kB) Collecting appdirs==1.4.4 (from -r requirements-freeze.txt (line 2)) Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) Collecting astor==0.8.1 (from -r requirements-freeze.txt (line 3)) Using cached astor-0.8.1-py2.py3-none-any.whl.metadata (4.2 kB) Collecting bids-validator==1.13.1 (from -r requirements-freeze.txt (line 4)) Using cached bids_validator-1.13.1-py2.py3-none-any.whl.metadata (38 kB) Collecting cachetools==5.3.2 (from -r requirements-freeze.txt (line 5)) Using cached cachetools-5.3.2-py3-none-any.whl.metadata (5.2 kB) Collecting certifi Using cached certifi-2023.7.22-py3-none-any.whl.metadata (2.2 kB) Collecting charset-normalizer==3.3.2 (from -r requirements-freeze.txt (line 7)) Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting click==8.1.7 (from -r requirements-freeze.txt (line 8)) Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting colorama==0.4.6 (from -r requirements-freeze.txt (line 9)) 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 10)) Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB) Collecting contourpy==1.2.0 (from -r requirements-freeze.txt (line 11)) Using cached contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Collecting coverage==7.3.2 (from -r requirements-freeze.txt (line 12)) Using cached coverage-7.3.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.1 kB) Collecting csv-diff==1.1 (from -r requirements-freeze.txt (line 13)) Using cached csv_diff-1.1-py3-none-any.whl.metadata (4.1 kB) Collecting cycler==0.12.1 (from -r requirements-freeze.txt (line 14)) Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting Deprecated==1.2.14 (from -r requirements-freeze.txt (line 15)) Using cached Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB) Collecting dictdiffer==0.9.0 (from -r requirements-freeze.txt (line 16)) 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 17)) Using cached dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (3.9 kB) WARNING: Ignoring version 1.5.0 of dipy since it has invalid metadata: Requested dipy==1.5.0 from https://files.pythonhosted.org/packages/4d/ff/933d40f73187c3e1996e833d8fe20c0863130e8d881e09bba14449a42e85/dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from -r requirements-freeze.txt (line 17)) has invalid metadata: Expected matching RIGHT_PARENTHESIS for LEFT_PARENTHESIS, after version specifier fury (>=0.8.0scikit-learn) ; extra == 'all' ~~~~~~~~^ Please use pip<24.1 if you need to use this version. ERROR: Ignored the following versions that require a different python version: 1.3.1 Requires-Python >=3.10 ERROR: Could not find a version that satisfies the requirement dipy==1.5.0 (from versions: 0.5.0, 0.6.0, 0.7.0, 0.7.1, 0.8.0, 0.9.1, 0.9.2, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.14.0, 0.15.0, 0.16.0, 1.0.0, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.4.1, 1.5.0, 1.6.0, 1.7.0, 1.8.0, 1.9.0) ERROR: No matching distribution found for dipy==1.5.0 Failed running pip install: 1 Installation failed! Please find the file "/home/mliffran/Documents/Software/SCT/sct_6.1/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