Last login: Sun Apr 7 18:29:46 on ttys000 The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://support.apple.com/kb/HT208050. (base) macbook-pro-de-mathilde:~ mathilde$ softwareupdate --install-rosetta I have read and agree to the terms of the software license agreement. A list of Apple SLAs may be found here: https://www.apple.com/legal/sla/ Type A and press return to agree: A 2024-04-07 18:56:14.445 softwareupdate[22498:1089240] Package Authoring Error: 042-78239: Package reference com.apple.pkg.RosettaUpdateAuto is missing installKBytes attribute Install of Rosetta 2 finished successfully (base) macbook-pro-de-mathilde:~ mathilde$ gcc --version Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.3.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin (base) macbook-pro-de-mathilde:~ mathilde$ sudo chown mathilde ~/.bash_profile Password: (base) macbook-pro-de-mathilde:~ mathilde$ ls Applications NetBeansProjects Desktop Pictures Documents Public Downloads README.md GIT_FLOW Sites GlassFish_Server anaconda3 Library first pandas notebook.ipynb MSS1 screen tp reseaux.pcapng Movies spinalcordtoolbox Music (base) macbook-pro-de-mathilde:~ mathilde$ ls -lah ~/ | grep bash_profile -rw-r--r-- 1 mathilde staff 989B 8 mar 10:36 .bash_profile -rw-r--r-- 1 root staff 603B 28 fév 00:33 .bash_profile.macports-saved_2024-03-08_at_10:36:05 -rw------- 1 mathilde staff 642B 8 mar 10:34 .bash_profile.save (base) macbook-pro-de-mathilde:~ mathilde$ git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox fatal: destination path 'spinalcordtoolbox' already exists and is not an empty directory. (base) macbook-pro-de-mathilde:~ mathilde$ cd spinalcordtoolbox (base) macbook-pro-de-mathilde:spinalcordtoolbox mathilde$ ./install_sct ******************************* * Welcome to SCT installation * ******************************* Checking OS type and version... Darwin macbook-pro-de-mathilde.home 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:30:27 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T8103 arm64 ProductVersion: 14.3 Checking requirements... OK! SCT version ......... 6.3.dev0 Installation type ... in-place Operating system .... osx ( 14.3) Shell config ........ /Users/mathilde/.bashrc SCT will be installed here: [/Users/mathilde/spinalcordtoolbox] Do you agree? [y]es/[n]o: y Skipping copy of source files (source and destination folders are the same) Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y Downloading Miniconda... curl -sS -o /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/tmp.ttKFnlcRkp/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh Installing Miniconda... bash /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/tmp.ttKFnlcRkp/miniconda.sh -p /Users/mathilde/spinalcordtoolbox/python -b -f PREFIX=/Users/mathilde/spinalcordtoolbox/python Unpacking payload ... Installing base environment... Downloading and Extracting Packages: ...working... done Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. Creating conda environment... Retrieving notices: ...working... done ERROR conda.notices.core:wrapper(116): Unable to open cache file: [Errno 13] Permission denied: '/Users/mathilde/Library/Caches/conda/notices/notices.cache' Channels: - defaults Platform: osx-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/mathilde/spinalcordtoolbox/python/envs/venv_sct added / updated specs: - python=3.9 The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2024.3.11 | hecd8cb5_0 128 KB pip-23.3.1 | py39hecd8cb5_0 2.6 MB python-3.9.19 | h5ee71fb_0 12.7 MB setuptools-68.2.2 | py39hecd8cb5_0 950 KB tzdata-2024a | h04d1e81_0 116 KB wheel-0.41.2 | py39hecd8cb5_0 109 KB xz-5.4.6 | h6c40b1e_0 373 KB ------------------------------------------------------------ Total: 16.9 MB The following NEW packages will be INSTALLED: ca-certificates pkgs/main/osx-64::ca-certificates-2024.3.11-hecd8cb5_0 libcxx pkgs/main/osx-64::libcxx-14.0.6-h9765a3e_0 libffi pkgs/main/osx-64::libffi-3.4.4-hecd8cb5_0 ncurses pkgs/main/osx-64::ncurses-6.4-hcec6c5f_0 openssl pkgs/main/osx-64::openssl-3.0.13-hca72f7f_0 pip pkgs/main/osx-64::pip-23.3.1-py39hecd8cb5_0 python pkgs/main/osx-64::python-3.9.19-h5ee71fb_0 readline pkgs/main/osx-64::readline-8.2-hca72f7f_0 setuptools pkgs/main/osx-64::setuptools-68.2.2-py39hecd8cb5_0 sqlite pkgs/main/osx-64::sqlite-3.41.2-h6c40b1e_0 tk pkgs/main/osx-64::tk-8.6.12-h5d9f67b_0 tzdata pkgs/main/noarch::tzdata-2024a-h04d1e81_0 wheel pkgs/main/osx-64::wheel-0.41.2-py39hecd8cb5_0 xz pkgs/main/osx-64::xz-5.4.6-h6c40b1e_0 zlib pkgs/main/osx-64::zlib-1.2.13-h4dc903c_0 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 /Users/mathilde/spinalcordtoolbox/python/envs/venv_sct # # To deactivate an active environment, use # # $ conda deactivate Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1) Collecting pip!=21.2.* Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB) Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 2.1 MB/s eta 0:00:00 Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 23.3.1 Uninstalling pip-23.3.1: Successfully uninstalled pip-23.3.1 Successfully installed pip-24.0 Installing Python dependencies... Using requirements.txt (git 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-2024.2.2-py3-none-any.whl.metadata (2.2 kB) Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7)) Downloading dipy-1.9.0-1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (9.0 kB) Collecting ivadomed (from -r requirements.txt (line 11)) Downloading ivadomed-2.9.10-py3-none-any.whl.metadata (6.4 kB) Collecting matplotlib (from -r requirements.txt (line 12)) Downloading matplotlib-3.8.4-cp39-cp39-macosx_10_12_x86_64.whl.metadata (5.8 kB) Collecting nibabel (from -r requirements.txt (line 21)) Downloading nibabel-5.2.1-py3-none-any.whl.metadata (8.8 kB) Collecting nilearn (from -r requirements.txt (line 22)) Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB) Collecting nnunetv2 (from -r requirements.txt (line 23)) Downloading nnunetv2-2.3.1.tar.gz (182 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 182.5/182.5 kB 1.6 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting numpy<1.24 (from -r requirements.txt (line 27)) Downloading numpy-1.23.5-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.3 kB) Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31)) Downloading onnxruntime-1.17.1-cp39-cp39-macosx_11_0_universal2.whl.metadata (4.2 kB) Collecting pandas (from -r requirements.txt (line 32)) Downloading pandas-2.2.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (19 kB) Collecting portalocker (from -r requirements.txt (line 33)) Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB) Collecting psutil (from -r requirements.txt (line 34)) Downloading psutil-5.9.8-cp36-abi3-macosx_10_9_x86_64.whl.metadata (21 kB) Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39)) Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-macosx_10_6_intel.whl.metadata (2.2 kB) Collecting pyqt5-sip<12.13.0 (from -r requirements.txt (line 41)) Downloading PyQt5_sip-12.12.2-cp39-cp39-macosx_10_9_universal2.whl.metadata (504 bytes) Collecting pytest (from -r requirements.txt (line 42)) Downloading pytest-8.1.1-py3-none-any.whl.metadata (7.6 kB) Collecting pytest-cov (from -r requirements.txt (line 43)) Downloading pytest_cov-5.0.0-py3-none-any.whl.metadata (27 kB) Collecting requests (from -r requirements.txt (line 44)) Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting requirements-parser (from -r requirements.txt (line 45)) Downloading requirements_parser-0.9.0-py3-none-any.whl.metadata (3.2 kB) Collecting scipy (from -r requirements.txt (line 46)) Downloading scipy-1.13.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 1.5 MB/s eta 0:00:00 Collecting scikit-image (from -r requirements.txt (line 47)) Downloading scikit_image-0.22.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (13 kB) Collecting scikit-learn (from -r requirements.txt (line 48)) Downloading scikit_learn-1.4.1.post1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (11 kB) Collecting xlwt (from -r requirements.txt (line 49)) Downloading xlwt-1.3.0-py2.py3-none-any.whl.metadata (3.5 kB) Collecting tqdm (from -r requirements.txt (line 50)) Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 1.2 MB/s eta 0:00:00 Collecting transforms3d (from -r requirements.txt (line 51)) Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB) Collecting urllib3 (from -r requirements.txt (line 52)) Downloading urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB) Collecting pytest_console_scripts (from -r requirements.txt (line 53)) Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB) Collecting pyyaml (from -r requirements.txt (line 54)) Downloading PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.1 kB) Collecting voxelmorph (from -r requirements.txt (line 55)) Downloading voxelmorph-0.2-py3-none-any.whl.metadata (660 bytes) Collecting wquantiles (from -r requirements.txt (line 56)) Downloading wquantiles-0.6-py3-none-any.whl.metadata (1.1 kB) Collecting xlsxwriter (from -r requirements.txt (line 59)) Downloading XlsxWriter-3.2.0-py3-none-any.whl.metadata (2.6 kB) Collecting monai[nibabel] (from -r requirements.txt (line 13)) Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB) Collecting h5py>=3.1.0 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7)) Downloading h5py-3.10.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.5 kB) Collecting packaging>=21 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7)) Downloading packaging-24.0-py3-none-any.whl.metadata (3.2 kB) Collecting trx-python>=0.2.9 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7)) Downloading trx_python-0.2.9-py3-none-any.whl.metadata (2.7 kB) Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11)) Downloading csv_diff-1.1-py3-none-any.whl.metadata (4.1 kB) Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11)) Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB) Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11)) Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB) Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11)) Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB) Collecting onnx (from ivadomed->-r requirements.txt (line 11)) Downloading onnx-1.16.0-cp39-cp39-macosx_10_15_x86_64.whl.metadata (16 kB) Collecting pandas (from -r requirements.txt (line 32)) Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl.metadata (11 kB) Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11)) Downloading pybids-0.15.5-py3-none-any.whl.metadata (3.2 kB) Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11)) Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11)) Downloading tensorboard-2.16.2-py3-none-any.whl.metadata (1.6 kB) Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11)) Downloading torchio-0.19.6-py2.py3-none-any.whl.metadata (48 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 900.0 kB/s eta 0:00:00 Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11)) Downloading https://download.pytorch.org/whl/cpu/torch-2.2.2-cp39-none-macosx_10_9_x86_64.whl (151.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 151.0/151.0 MB 2.2 MB/s eta 0:00:00 Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 11)) Downloading https://download.pytorch.org/whl/cpu/torchvision-0.17.2-cp39-cp39-macosx_10_13_x86_64.whl (1.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 2.4 MB/s eta 0:00:00 Collecting wandb>=0.12.11 (from ivadomed->-r requirements.txt (line 11)) Downloading wandb-0.16.6-py3-none-any.whl.metadata (10 kB) Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 12)) Downloading contourpy-1.2.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (5.8 kB) Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 12)) Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib->-r requirements.txt (line 12)) Downloading fonttools-4.51.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (159 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 159.5/159.5 kB 2.7 MB/s eta 0:00:00 Collecting kiwisolver>=1.3.1 (from matplotlib->-r requirements.txt (line 12)) Downloading kiwisolver-1.4.5-cp39-cp39-macosx_10_9_x86_64.whl.metadata (6.4 kB) Collecting pillow>=8 (from matplotlib->-r requirements.txt (line 12)) Downloading pillow-10.3.0-cp39-cp39-macosx_10_10_x86_64.whl.metadata (9.2 kB) Collecting pyparsing>=2.3.1 (from matplotlib->-r requirements.txt (line 12)) Downloading pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB) Collecting python-dateutil>=2.7 (from matplotlib->-r requirements.txt (line 12)) Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting importlib-resources>=3.2.0 (from matplotlib->-r requirements.txt (line 12)) Downloading importlib_resources-6.4.0-py3-none-any.whl.metadata (3.9 kB) Collecting lxml (from nilearn->-r requirements.txt (line 22)) Downloading lxml-5.2.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (3.4 kB) Collecting acvl-utils<0.3,>=0.2 (from nnunetv2->-r requirements.txt (line 23)) Downloading acvl_utils-0.2.tar.gz (18 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting dynamic-network-architectures<0.4,>=0.2 (from nnunetv2->-r requirements.txt (line 23)) Downloading dynamic_network_architectures-0.3.1.tar.gz (20 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting dicom2nifti (from nnunetv2->-r requirements.txt (line 23)) Downloading dicom2nifti-2.4.10-py3-none-any.whl.metadata (1.3 kB) Collecting batchgenerators>=0.25 (from nnunetv2->-r requirements.txt (line 23)) Downloading batchgenerators-0.25.tar.gz (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.7/61.7 kB 2.2 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting SimpleITK>=2.2.1 (from nnunetv2->-r requirements.txt (line 23)) Downloading SimpleITK-2.3.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (7.9 kB) Collecting graphviz (from nnunetv2->-r requirements.txt (line 23)) Downloading graphviz-0.20.3-py3-none-any.whl.metadata (12 kB) Collecting tifffile (from nnunetv2->-r requirements.txt (line 23)) Downloading tifffile-2024.2.12-py3-none-any.whl.metadata (31 kB) Collecting imagecodecs (from nnunetv2->-r requirements.txt (line 23)) Downloading imagecodecs-2024.1.1-cp39-cp39-macosx_10_14_x86_64.whl.metadata (19 kB) Collecting yacs (from nnunetv2->-r requirements.txt (line 23)) Downloading yacs-0.1.8-py3-none-any.whl.metadata (639 bytes) Collecting coloredlogs (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31)) Downloading coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB) Collecting flatbuffers (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31)) Downloading flatbuffers-24.3.25-py2.py3-none-any.whl.metadata (850 bytes) Collecting protobuf (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31)) Downloading protobuf-5.26.1-cp37-abi3-macosx_10_9_universal2.whl.metadata 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typer-0.12.1-py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 1.6 MB/s eta 0:00:00 Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 3.2 MB/s eta 0:00:00 Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 2.1 MB/s eta 0:00:00 Downloading smmap-5.0.1-py3-none-any.whl (24 kB) Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB) Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB) Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, docopt Building wheel for nnunetv2 (pyproject.toml): started Building wheel for nnunetv2 (pyproject.toml): finished with status 'done' Created wheel for nnunetv2: filename=nnunetv2-2.3.1-py3-none-any.whl size=243617 sha256=c8e796472e6d95fbccb05996c55cca6a411b52ea879da5604eb20968fa577126 Stored in directory: /Users/mathilde/Library/Caches/pip/wheels/a1/30/0f/6c41432250a748dee161be18f2f982042c1d5126903fffd936 Building wheel for acvl-utils (setup.py): started Building wheel for acvl-utils (setup.py): finished with status 'done' Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=d2b7b065922e03b961516a60ebeffdaf0ec30a744df8782da6eceecb8cc9d762 Stored in directory: /Users/mathilde/Library/Caches/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7 Building wheel for batchgenerators (setup.py): started Building wheel for batchgenerators (setup.py): finished with status 'done' Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=b51fef7b78257761c72f2a4126e034ab476dc01476655ec184cc1e710ffc58d3 Stored in directory: /Users/mathilde/Library/Caches/pip/wheels/41/e7/c9/91b1589e2a08ad83bdd96b0beb3a496effda855580ef698568 Building wheel for dynamic-network-architectures (setup.py): started Building wheel for dynamic-network-architectures (setup.py): finished with status 'done' Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.3.1-py3-none-any.whl size=30048 sha256=14cb128f7bd77e5387a6996aaa12b76e3b62c61e6903c842c86d11efd17af11c Stored in directory: /Users/mathilde/Library/Caches/pip/wheels/ec/59/c1/e65ad8b5ac7df95651f913251875b4cc8275644e0e28e82c63 Building wheel for pystrum (setup.py): started Building wheel for pystrum (setup.py): finished with status 'done' Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=f3a86a99469c6eaa775b2a39ccb086be000a4d063ceac921fb7a93d899864217 Stored in directory: /Users/mathilde/Library/Caches/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=fce016c434d57b0e697a1b0a726fa5b67652e91fc8f3b7fce2b0de02c7561b62 Stored in directory: /Users/mathilde/Library/Caches/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum docopt Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, pyqt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, ordered-set, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, click, charset-normalizer, certifi, bids-validator, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, tifffile, setuptools-scm, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, lazy_loader, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, deepdiff, csv-diff, contourpy, connected-components-3d, coloredlogs, trx-python, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dicom2nifti, wandb, typer, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, dipy, batchgenerators, pybids, neurite, acvl-utils, voxelmorph, torchio, nnunetv2, ivadomed Successfully installed Deprecated-1.2.14 GitPython-3.1.43 MarkupSafe-2.1.5 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.5 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 coloredlogs-15.0.1 connected-components-3d-3.13.0 contourpy-1.2.1 coverage-7.4.4 csv-diff-1.1 cycler-0.12.1 deepdiff-6.7.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.9.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.3.1 exceptiongroup-1.2.0 filelock-3.13.3 flatbuffers-24.3.25 fonttools-4.51.0 formulaic-0.3.4 fsspec-2024.3.1 future-1.0.0 gitdb-4.0.11 graphviz-0.20.3 grpcio-1.62.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.1.0 importlib-resources-6.4.0 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.10 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.4 linecache2-1.0.0 loguru-0.7.2 lxml-5.2.1 markdown-3.6 markdown-it-py-3.0.0 matplotlib-3.8.4 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-5.2.1 nilearn-0.10.3 nnunetv2-2.3.1 num2words-0.5.13 numpy-1.23.5 onnx-1.16.0 onnxruntime-1.17.1 ordered-set-4.1.0 packaging-24.0 pandas-1.5.3 pillow-10.3.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.3 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-3.1.2 pyqt5-5.12.3 pyqt5-sip-12.12.2 pystrum-0.4 pytest-8.1.1 pytest-cov-5.0.0 pytest_console_scripts-1.4.1 python-dateutil-2.9.0.post0 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.9.0 rich-13.7.1 scikit-image-0.22.0 scikit-learn-1.4.1.post1 scipy-1.13.0 seaborn-0.13.2 sentry-sdk-1.44.1 setproctitle-1.3.3 setuptools-68.2.2 setuptools-scm-8.0.4 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.2 tensorboard-data-server-0.7.2 threadpoolctl-3.4.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.2 torchio-0.19.6 torchvision-0.17.2 tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 trx-python-0.2.9 typer-0.12.1 types-setuptools-69.2.0.20240317 typing-extensions-4.11.0 unittest2-1.1.0 urllib3-2.2.1 voxelmorph-0.2 wandb-0.16.6 werkzeug-3.0.2 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.2.0 xlwt-1.3.0 yacs-0.1.8 zipp-3.18.1 Installing spinalcordtoolbox... Obtaining file:///Users/mathilde/spinalcordtoolbox 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-6.3.dev0 Creating launchers for Python scripts... Installing binaries... sct_download_data -d binaries_osx -k -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d binaries_osx -k -- Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221018/spinalcordtoolbox-binaries_osx.tar.gz Downloading: spinalcordtoolbox-binaries_osx.tar.gz Status: 100%|██████████| 65.3M/65.3M [00:26<00:00, 2.48MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-09-25_install-data_0jo9d_d8) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-09-25_install-data_0jo9d_d8 Copying data to: /Users/mathilde/spinalcordtoolbox/bin Removing temporary folders... Done! All requirements installed! Installing data... mkdir -p /Users/mathilde/spinalcordtoolbox/data sct_download_data -d PAM50 -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d PAM50 -- Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20240215/PAM50-r20240215.zip Downloading: PAM50-r20240215.zip Status: 100%|██████████| 104M/104M [00:41<00:00, 2.51MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-08_install-data_rc6xocua) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-08_install-data_rc6xocua Copying data to: /Users/mathilde/spinalcordtoolbox/data/PAM50 Removing temporary folders... Done! sct_download_data -d deepseg_sc_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepseg_sc_models -- Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip Downloading: 20220325_deepseg_sc_models_onnx.zip Status: 100%|██████████| 19.5M/19.5M [00:07<00:00, 2.54MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-18_install-data_b3b1wcdl) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-18_install-data_b3b1wcdl Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepseg_sc_models Removing temporary folders... Done! sct_download_data -d deepseg_gm_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepseg_gm_models -- Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip Downloading: 20220325_deepseg_gm_models_onnx.zip Status: 100%|██████████| 2.24M/2.24M [00:00<00:00, 2.50MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-20_install-data_epk01cfz) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-20_install-data_epk01cfz Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepseg_gm_models Removing temporary folders... Done! sct_download_data -d deepseg_lesion_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepseg_lesion_models -- Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip Downloading: 20220325_deepseg_lesion_models_onnx.zip Status: 100%|██████████| 5.35M/5.35M [00:02<00:00, 2.67MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-23_install-data_j15g1181) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-10-23_install-data_j15g1181 Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepseg_lesion_models Removing temporary folders... Done! sct_download_data -d deepreg_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepreg_models -- Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip Downloading: models.zip Status: 100%|██████████| 158M/158M [01:03<00:00, 2.50MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-11-28_install-data_chgu8dne) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-11-28_install-data_chgu8dne Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepreg_models Removing temporary folders... Done! sct_download_data -d PAM50_normalized_metrics -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d PAM50_normalized_metrics -- Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip Downloading: PAM50-normalized-metrics-r20230222.zip Status: 6.92MB [00:02, 2.53MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-11-33_install-data_ad7l4p8i) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-07_19-11-33_install-data_ad7l4p8i Copying data to: /Users/mathilde/spinalcordtoolbox/data/PAM50_normalized_metrics Removing temporary folders... Done! Status: 100%|██████████| 18.0M/18.0M [00:07<00:00, 2.52MB/s] ./install_sct: line 286: /Users/mathilde/.bashrc: Permission denied Installation failed! Please find the file "/Users/mathilde/spinalcordtoolbox/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 (base) macbook-pro-de-mathilde:spinalcordtoolbox mathilde$