Created
November 18, 2020 19:50
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Test install jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e
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[18/11/20 2:45:25] (base) alex@NeuroPoly-MacBook-Pro spinalcordtoolbox % ./install_sct | |
******************************* | |
* Welcome to SCT installation * | |
******************************* | |
Checking OS type and version... | |
Darwin NeuroPoly-MacBook-Pro.local 20.1.0 Darwin Kernel Version 20.1.0: Sat Oct 31 00:07:11 PDT 2020; root:xnu-7195.50.7~2/RELEASE_X86_64 x86_64 | |
ProductVersion: 11.0.1 | |
./install_sct: line 224: /Users/alex/.bash_profile: Permission denied | |
Checking requirements... | |
OK! | |
SCT version ......... dev | |
Installation type ... in-place | |
Operating system .... osx (11.0.1) | |
Shell config ........ /Users/alex/.zshrc | |
To improve user experience and fix bugs, the SCT development team is using a | |
report system to automatically receive crash reports and errors from users. | |
These reports are anonymous. | |
Do you agree to help us improve SCT? [y]es/[n]o: y | |
--> Crash reports will be sent to the SCT development team. Thank you! | |
SCT will be installed here: [/Users/alex/code/spinalcordtoolbox] | |
Do you agree? [y]es/[n]o: y | |
Skipping copy of source files (source and destination folders are the same) | |
Removing sct and isct softlink from /Users/alex/code/spinalcordtoolbox/bin | |
Installing conda... | |
rm -rf /Users/alex/code/spinalcordtoolbox/python | |
mkdir -p /Users/alex/code/spinalcordtoolbox/python | |
curl -o /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/tmp.LUBzgZ1Y/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh | |
% Total % Received % Xferd Average Speed Time Time Time Current | |
Dload Upload Total Spent Left Speed | |
100 53.2M 100 53.2M 0 0 44.6M 0 0:00:01 0:00:01 --:--:-- 44.6M | |
exit status is 0 | |
bash /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/tmp.LUBzgZ1Y/miniconda.sh -p /Users/alex/code/spinalcordtoolbox/python -b -f | |
PREFIX=/Users/alex/code/spinalcordtoolbox/python | |
Unpacking payload ... | |
Collecting package metadata (current_repodata.json): done | |
Solving environment: done | |
## Package Plan ## | |
environment location: /Users/alex/code/spinalcordtoolbox/python | |
added / updated specs: | |
- ca-certificates==2020.1.1=0 | |
- certifi==2020.4.5.1=py38_0 | |
- cffi==1.14.0=py38hc512035_1 | |
- chardet==3.0.4=py38_1003 | |
- conda-package-handling==1.6.1=py38h1de35cc_0 | |
- conda==4.8.3=py38_0 | |
- cryptography==2.9.2=py38ha12b0ac_0 | |
- idna==2.9=py_1 | |
- libcxx==10.0.0=1 | |
- libedit==3.1.20181209=hb402a30_0 | |
- libffi==3.3=h0a44026_1 | |
- ncurses==6.2=h0a44026_1 | |
- openssl==1.1.1g=h1de35cc_0 | |
- pip==20.0.2=py38_3 | |
- pycosat==0.6.3=py38h1de35cc_1 | |
- pycparser==2.20=py_0 | |
- pyopenssl==19.1.0=py38_0 | |
- pysocks==1.7.1=py38_0 | |
- python.app==2=py38_10 | |
- python==3.8.3=h26836e1_1 | |
- readline==8.0=h1de35cc_0 | |
- requests==2.23.0=py38_0 | |
- ruamel_yaml==0.15.87=py38h1de35cc_0 | |
- setuptools==46.4.0=py38_0 | |
- six==1.14.0=py38_0 | |
- sqlite==3.31.1=h5c1f38d_1 | |
- tk==8.6.8=ha441bb4_0 | |
- tqdm==4.46.0=py_0 | |
- urllib3==1.25.8=py38_0 | |
- wheel==0.34.2=py38_0 | |
- xz==5.2.5=h1de35cc_0 | |
- yaml==0.1.7=hc338f04_2 | |
- zlib==1.2.11=h1de35cc_3 | |
The following NEW packages will be INSTALLED: | |
ca-certificates pkgs/main/osx-64::ca-certificates-2020.1.1-0 | |
certifi pkgs/main/osx-64::certifi-2020.4.5.1-py38_0 | |
cffi pkgs/main/osx-64::cffi-1.14.0-py38hc512035_1 | |
chardet pkgs/main/osx-64::chardet-3.0.4-py38_1003 | |
conda pkgs/main/osx-64::conda-4.8.3-py38_0 | |
conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.6.1-py38h1de35cc_0 | |
cryptography pkgs/main/osx-64::cryptography-2.9.2-py38ha12b0ac_0 | |
idna pkgs/main/noarch::idna-2.9-py_1 | |
libcxx pkgs/main/osx-64::libcxx-10.0.0-1 | |
libedit pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0 | |
libffi pkgs/main/osx-64::libffi-3.3-h0a44026_1 | |
ncurses pkgs/main/osx-64::ncurses-6.2-h0a44026_1 | |
openssl pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0 | |
pip pkgs/main/osx-64::pip-20.0.2-py38_3 | |
pycosat pkgs/main/osx-64::pycosat-0.6.3-py38h1de35cc_1 | |
pycparser pkgs/main/noarch::pycparser-2.20-py_0 | |
pyopenssl pkgs/main/osx-64::pyopenssl-19.1.0-py38_0 | |
pysocks pkgs/main/osx-64::pysocks-1.7.1-py38_0 | |
python pkgs/main/osx-64::python-3.8.3-h26836e1_1 | |
python.app pkgs/main/osx-64::python.app-2-py38_10 | |
readline pkgs/main/osx-64::readline-8.0-h1de35cc_0 | |
requests pkgs/main/osx-64::requests-2.23.0-py38_0 | |
ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.87-py38h1de35cc_0 | |
setuptools pkgs/main/osx-64::setuptools-46.4.0-py38_0 | |
six pkgs/main/osx-64::six-1.14.0-py38_0 | |
sqlite pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1 | |
tk pkgs/main/osx-64::tk-8.6.8-ha441bb4_0 | |
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0 | |
urllib3 pkgs/main/osx-64::urllib3-1.25.8-py38_0 | |
wheel pkgs/main/osx-64::wheel-0.34.2-py38_0 | |
xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0 | |
yaml pkgs/main/osx-64::yaml-0.1.7-hc338f04_2 | |
zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3 | |
Preparing transaction: done | |
Executing transaction: done | |
installation finished. | |
Collecting package metadata (current_repodata.json): done | |
Solving environment: done | |
==> WARNING: A newer version of conda exists. <== | |
current version: 4.8.3 | |
latest version: 4.9.2 | |
Please update conda by running | |
$ conda update -n base -c defaults conda | |
## Package Plan ## | |
environment location: /Users/alex/code/spinalcordtoolbox/python/envs/venv_sct | |
added / updated specs: | |
- python=3.6 | |
The following packages will be downloaded: | |
package | build | |
---------------------------|----------------- | |
ca-certificates-2020.10.14 | 0 121 KB | |
certifi-2020.6.20 | pyhd3eb1b0_3 155 KB | |
libedit-3.1.20191231 | h1de35cc_1 96 KB | |
libffi-3.3 | hb1e8313_2 44 KB | |
openssl-1.1.1h | haf1e3a3_0 2.2 MB | |
pip-20.2.4 | py36hecd8cb5_0 1.8 MB | |
python-3.6.12 | h26836e1_2 16.9 MB | |
setuptools-50.3.1 | py36hecd8cb5_1 713 KB | |
sqlite-3.33.0 | hffcf06c_0 1.3 MB | |
tk-8.6.10 | hb0a8c7a_0 3.0 MB | |
wheel-0.35.1 | pyhd3eb1b0_0 38 KB | |
------------------------------------------------------------ | |
Total: 26.2 MB | |
The following NEW packages will be INSTALLED: | |
ca-certificates pkgs/main/osx-64::ca-certificates-2020.10.14-0 | |
certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3 | |
libcxx pkgs/main/osx-64::libcxx-10.0.0-1 | |
libedit pkgs/main/osx-64::libedit-3.1.20191231-h1de35cc_1 | |
libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2 | |
ncurses pkgs/main/osx-64::ncurses-6.2-h0a44026_1 | |
openssl pkgs/main/osx-64::openssl-1.1.1h-haf1e3a3_0 | |
pip pkgs/main/osx-64::pip-20.2.4-py36hecd8cb5_0 | |
python pkgs/main/osx-64::python-3.6.12-h26836e1_2 | |
readline pkgs/main/osx-64::readline-8.0-h1de35cc_0 | |
setuptools pkgs/main/osx-64::setuptools-50.3.1-py36hecd8cb5_1 | |
sqlite pkgs/main/osx-64::sqlite-3.33.0-hffcf06c_0 | |
tk pkgs/main/osx-64::tk-8.6.10-hb0a8c7a_0 | |
wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0 | |
xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0 | |
zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3 | |
Proceed ([y]/n)? | |
Downloading and Extracting Packages | |
tk-8.6.10 | 3.0 MB | ################################################################################################################################# | 100% | |
python-3.6.12 | 16.9 MB | ################################################################################################################################# | 100% | |
ca-certificates-2020 | 121 KB | ################################################################################################################################# | 100% | |
certifi-2020.6.20 | 155 KB | ################################################################################################################################# | 100% | |
libffi-3.3 | 44 KB | ################################################################################################################################# | 100% | |
pip-20.2.4 | 1.8 MB | ################################################################################################################################# | 100% | |
sqlite-3.33.0 | 1.3 MB | ################################################################################################################################# | 100% | |
setuptools-50.3.1 | 713 KB | ################################################################################################################################# | 100% | |
wheel-0.35.1 | 38 KB | ################################################################################################################################# | 100% | |
openssl-1.1.1h | 2.2 MB | ################################################################################################################################# | 100% | |
libedit-3.1.20191231 | 96 KB | ################################################################################################################################# | 100% | |
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 | |
Installing Python dependencies... | |
Using requirements.txt (git installation) | |
Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html | |
Ignoring torch: markers 'sys_platform != "darwin"' don't match your environment | |
Ignoring torchvision: markers 'sys_platform != "darwin"' don't match your environment | |
Processing /Users/alex/Library/Caches/pip/wheels/b7/be/ae/a98f7701429c3cfcebf4d2b537e48a1571549a4d8b55463a01/colored-1.4.2-py3-none-any.whl | |
Collecting dipy | |
Using cached dipy-1.3.0-cp36-cp36m-macosx_10_9_x86_64.whl (7.6 MB) | |
Collecting futures | |
Using cached futures-3.1.1-py3-none-any.whl (2.8 kB) | |
Collecting h5py~=2.10.0 | |
Using cached h5py-2.10.0-cp36-cp36m-macosx_10_6_intel.whl (3.0 MB) | |
Collecting ivadomed==2.4.0 | |
Using cached ivadomed-2.4.0-py3-none-any.whl (132 kB) | |
Collecting Keras==2.1.5 | |
Using cached Keras-2.1.5-py2.py3-none-any.whl (334 kB) | |
Collecting matplotlib | |
Using cached matplotlib-3.3.3-cp36-cp36m-macosx_10_9_x86_64.whl (8.5 MB) | |
Collecting nibabel | |
Using cached nibabel-3.2.0-py3-none-any.whl (3.3 MB) | |
Collecting numpy | |
Using cached numpy-1.19.4-cp36-cp36m-macosx_10_9_x86_64.whl (15.3 MB) | |
Collecting onnxruntime==1.4.0 | |
Using cached onnxruntime-1.4.0-cp36-cp36m-macosx_10_12_x86_64.whl (3.9 MB) | |
Collecting pandas | |
Using cached pandas-1.1.4-cp36-cp36m-macosx_10_9_x86_64.whl (10.2 MB) | |
Processing /Users/alex/Library/Caches/pip/wheels/fa/ad/67/90bbaacdcfe970960dd5158397f23a6579b51d853720d7856d/psutil-5.7.3-cp36-cp36m-macosx_10_9_x86_64.whl | |
Collecting pyqt5==5.11.3 | |
Using cached PyQt5-5.11.3-5.11.2_a-cp35.cp36.cp37.cp38-abi3-macosx_10_6_intel.whl (91.1 MB) | |
Collecting pytest | |
Using cached pytest-6.1.2-py3-none-any.whl (272 kB) | |
Collecting pytest-cov | |
Using cached pytest_cov-2.10.1-py2.py3-none-any.whl (19 kB) | |
Collecting raven | |
Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB) | |
Collecting requests | |
Using cached requests-2.25.0-py2.py3-none-any.whl (61 kB) | |
Processing /Users/alex/Library/Caches/pip/wheels/80/af/bd/32c202b632c3e9a1b482b33d37f5efd128137891a08f3c3bae/requirements_parser-0.2.0-py3-none-any.whl | |
Collecting scipy | |
Using cached scipy-1.5.4-cp36-cp36m-macosx_10_9_x86_64.whl (28.8 MB) | |
Collecting scikit-image | |
Using cached scikit_image-0.17.2-cp36-cp36m-macosx_10_13_x86_64.whl (12.1 MB) | |
Collecting scikit-learn | |
Using cached scikit_learn-0.23.2-cp36-cp36m-macosx_10_9_x86_64.whl (7.2 MB) | |
Collecting tensorflow==1.5.0 | |
Using cached tensorflow-1.5.0-cp36-cp36m-macosx_10_11_x86_64.whl (42.5 MB) | |
Collecting torch==1.5.0 | |
Using cached torch-1.5.0-cp36-none-macosx_10_9_x86_64.whl (80.5 MB) | |
Collecting torchvision==0.6.0 | |
Using cached torchvision-0.6.0-cp36-cp36m-macosx_10_9_x86_64.whl (436 kB) | |
Collecting xlwt | |
Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB) | |
Collecting tqdm | |
Using cached tqdm-4.52.0-py2.py3-none-any.whl (71 kB) | |
Processing /Users/alex/Library/Caches/pip/wheels/be/7a/eb/465e9bb085af816c4d504821d542cc0059cc3433f6e8edea3c/transforms3d-0.3.1-py3-none-any.whl | |
Collecting urllib3[secure] | |
Using cached urllib3-1.26.2-py2.py3-none-any.whl (136 kB) | |
Processing /Users/alex/Library/Caches/pip/wheels/d1/e3/94/26f2c05b0a648497c46b19eaa1fb7cc33f53f1e866ac0b74c2/pytest_console_scripts-1.0.0-py3-none-any.whl | |
Collecting pytest-xdist | |
Using cached pytest_xdist-2.1.0-py3-none-any.whl (36 kB) | |
Collecting six | |
Using cached six-1.15.0-py2.py3-none-any.whl (10 kB) | |
Collecting seaborn | |
Using cached seaborn-0.11.0-py3-none-any.whl (283 kB) | |
Collecting joblib | |
Using cached joblib-0.17.0-py3-none-any.whl (301 kB) | |
Collecting pillow>=7.0.0 | |
Using cached Pillow-8.0.1-cp36-cp36m-macosx_10_10_x86_64.whl (2.2 MB) | |
Collecting bids-neuropoly>=0.2 | |
Using cached bids_neuropoly-0.2-py3-none-any.whl (3.1 kB) | |
Collecting tensorboard | |
Using cached tensorboard-2.4.0-py3-none-any.whl (10.6 MB) | |
Processing /Users/alex/Library/Caches/pip/wheels/e5/9d/ad/2ee53cf262cba1ffd8afe1487eef788ea3f260b7e6232a80fc/PyYAML-5.3.1-cp36-cp36m-macosx_10_9_x86_64.whl | |
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 | |
Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) | |
Collecting python-dateutil>=2.1 | |
Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) | |
Collecting kiwisolver>=1.0.1 | |
Using cached kiwisolver-1.3.1-cp36-cp36m-macosx_10_9_x86_64.whl (61 kB) | |
Collecting cycler>=0.10 | |
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) | |
Collecting packaging>=14.3 | |
Using cached packaging-20.4-py2.py3-none-any.whl (37 kB) | |
Collecting protobuf | |
Using cached protobuf-3.14.0-cp36-cp36m-macosx_10_9_x86_64.whl (1.0 MB) | |
Collecting pytz>=2017.2 | |
Using cached pytz-2020.4-py2.py3-none-any.whl (509 kB) | |
Collecting PyQt5_sip<4.20,>=4.19.11 | |
Using cached PyQt5_sip-4.19.19-cp36-cp36m-macosx_10_6_intel.whl (52 kB) | |
Collecting attrs>=17.4.0 | |
Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB) | |
Collecting toml | |
Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB) | |
Collecting iniconfig | |
Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) | |
Collecting py>=1.8.2 | |
Using cached py-1.9.0-py2.py3-none-any.whl (99 kB) | |
Collecting importlib-metadata>=0.12; python_version < "3.8" | |
Using cached importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB) | |
Collecting pluggy<1.0,>=0.12 | |
Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB) | |
Collecting coverage>=4.4 | |
Using cached coverage-5.3-cp36-cp36m-macosx_10_13_x86_64.whl (205 kB) | |
Collecting chardet<4,>=3.0.2 | |
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB) | |
Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests->-r requirements.txt (line 22)) (2020.6.20) | |
Collecting idna<3,>=2.5 | |
Using cached idna-2.10-py2.py3-none-any.whl (58 kB) | |
Collecting tifffile>=2019.7.26 | |
Using cached tifffile-2020.9.3-py3-none-any.whl (148 kB) | |
Collecting networkx>=2.0 | |
Using cached networkx-2.5-py3-none-any.whl (1.6 MB) | |
Collecting PyWavelets>=1.1.1 | |
Using cached PyWavelets-1.1.1-cp36-cp36m-macosx_10_9_x86_64.whl (4.3 MB) | |
Collecting imageio>=2.3.0 | |
Using cached imageio-2.9.0-py3-none-any.whl (3.3 MB) | |
Collecting threadpoolctl>=2.0.0 | |
Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB) | |
Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorflow==1.5.0->-r requirements.txt (line 27)) (0.35.1) | |
Collecting absl-py>=0.1.6 | |
Using cached absl_py-0.11.0-py3-none-any.whl (127 kB) | |
Collecting tensorflow-tensorboard<1.6.0,>=1.5.0 | |
Using cached tensorflow_tensorboard-1.5.1-py3-none-any.whl (3.0 MB) | |
Processing /Users/alex/Library/Caches/pip/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94/future-0.18.2-py3-none-any.whl | |
Collecting pyOpenSSL>=0.14; extra == "secure" | |
Using cached pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB) | |
Collecting cryptography>=1.3.4; extra == "secure" | |
Using cached cryptography-3.2.1-cp35-abi3-macosx_10_10_x86_64.whl (1.8 MB) | |
Collecting mock>=2.0.0 | |
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Collecting execnet>=1.1 | |
Using cached execnet-1.7.1-py2.py3-none-any.whl (39 kB) | |
Collecting pytest-forked | |
Using cached pytest_forked-1.3.0-py2.py3-none-any.whl (4.7 kB) | |
Collecting pybids>=0.6.5 | |
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Collecting tensorboard-plugin-wit>=1.6.0 | |
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Collecting google-auth<2,>=1.6.3 | |
Using cached google_auth-1.23.0-py2.py3-none-any.whl (114 kB) | |
Collecting markdown>=2.6.8 | |
Using cached Markdown-3.3.3-py3-none-any.whl (96 kB) | |
Requirement already satisfied: setuptools>=41.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard->ivadomed==2.4.0->-r requirements.txt (line 7)) (50.3.1.post20201107) | |
Collecting grpcio>=1.24.3 | |
Using cached grpcio-1.33.2-cp36-cp36m-macosx_10_9_x86_64.whl (3.4 MB) | |
Collecting google-auth-oauthlib<0.5,>=0.4.1 | |
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Using cached Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB) | |
Collecting zipp>=0.5 | |
Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB) | |
Collecting decorator>=4.3.0 | |
Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) | |
Processing /Users/alex/Library/Caches/pip/wheels/90/1c/cb/a87fd097ff74648ecc468a703001f6c7c86d8a71d459e65c98/html5lib-0.9999999-py3-none-any.whl | |
Collecting bleach==1.5.0 | |
Using cached bleach-1.5.0-py2.py3-none-any.whl (17 kB) | |
Collecting cffi!=1.11.3,>=1.8 | |
Using cached cffi-1.14.3-2-cp36-cp36m-macosx_10_9_x86_64.whl (176 kB) | |
Collecting apipkg>=1.4 | |
Using cached apipkg-1.5-py2.py3-none-any.whl (4.9 kB) | |
Collecting patsy | |
Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB) | |
Collecting click | |
Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) | |
Collecting bids-validator | |
Using cached bids_validator-1.5.7-py2.py3-none-any.whl (15 kB) | |
Collecting num2words | |
Using cached num2words-0.5.10-py3-none-any.whl (101 kB) | |
Collecting sqlalchemy<1.4.0.dev0 | |
Using cached SQLAlchemy-1.3.20-cp36-cp36m-macosx_10_14_x86_64.whl (1.2 MB) | |
Collecting pyasn1-modules>=0.2.1 | |
Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB) | |
Collecting rsa<5,>=3.1.4; python_version >= "3.5" | |
Using cached rsa-4.6-py3-none-any.whl (47 kB) | |
Collecting cachetools<5.0,>=2.0.0 | |
Using cached cachetools-4.1.1-py3-none-any.whl (10 kB) | |
Collecting requests-oauthlib>=0.7.0 | |
Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB) | |
Collecting pycparser | |
Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB) | |
Processing /Users/alex/Library/Caches/pip/wheels/3f/2a/fa/4d7a888e69774d5e6e855d190a8a51b357d77cc05eb1c097c9/docopt-0.6.2-py2.py3-none-any.whl | |
Collecting pyasn1<0.5.0,>=0.4.6 | |
Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB) | |
Collecting oauthlib>=3.0.0 | |
Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB) | |
Installing collected packages: colored, numpy, scipy, pyparsing, six, packaging, nibabel, h5py, tqdm, dipy, futures, python-dateutil, kiwisolver, pillow, cycler, matplotlib, pytz, pandas, seaborn, future, torch, torchvision, joblib, tifffile, decorator, networkx, PyWavelets, imageio, scikit-image, attrs, toml, iniconfig, py, zipp, importlib-metadata, pluggy, pytest, patsy, click, bids-validator, docopt, num2words, sqlalchemy, pybids, bids-neuropoly, protobuf, onnxruntime, threadpoolctl, scikit-learn, absl-py, tensorboard-plugin-wit, pycparser, cffi, cryptography, pyOpenSSL, idna, urllib3, chardet, requests, pyasn1, pyasn1-modules, rsa, cachetools, google-auth, markdown, grpcio, oauthlib, requests-oauthlib, google-auth-oauthlib, werkzeug, tensorboard, ivadomed, pyyaml, Keras, psutil, PyQt5-sip, pyqt5, coverage, pytest-cov, raven, requirements-parser, html5lib, bleach, tensorflow-tensorboard, tensorflow, xlwt, transforms3d, mock, pytest-console-scripts, apipkg, execnet, pytest-forked, pytest-xdist | |
Successfully installed Keras-2.1.5 PyQt5-sip-4.19.19 PyWavelets-1.1.1 absl-py-0.11.0 apipkg-1.5 attrs-20.3.0 bids-neuropoly-0.2 bids-validator-1.5.7 bleach-1.5.0 cachetools-4.1.1 cffi-1.14.3 chardet-3.0.4 click-7.1.2 colored-1.4.2 coverage-5.3 cryptography-3.2.1 cycler-0.10.0 decorator-4.4.2 dipy-1.3.0 docopt-0.6.2 execnet-1.7.1 future-0.18.2 futures-3.1.1 google-auth-1.23.0 google-auth-oauthlib-0.4.2 grpcio-1.33.2 h5py-2.10.0 html5lib-0.9999999 idna-2.10 imageio-2.9.0 importlib-metadata-2.0.0 iniconfig-1.1.1 ivadomed-2.4.0 joblib-0.17.0 kiwisolver-1.3.1 markdown-3.3.3 matplotlib-3.3.3 mock-4.0.2 networkx-2.5 nibabel-3.2.0 num2words-0.5.10 numpy-1.19.4 oauthlib-3.1.0 onnxruntime-1.4.0 packaging-20.4 pandas-1.1.4 patsy-0.5.1 pillow-8.0.1 pluggy-0.13.1 protobuf-3.14.0 psutil-5.7.3 py-1.9.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pybids-0.12.4 pycparser-2.20 pyparsing-2.4.7 pyqt5-5.11.3 pytest-6.1.2 pytest-console-scripts-1.0.0 pytest-cov-2.10.1 pytest-forked-1.3.0 pytest-xdist-2.1.0 python-dateutil-2.8.1 pytz-2020.4 pyyaml-5.3.1 raven-6.10.0 requests-2.25.0 requests-oauthlib-1.3.0 requirements-parser-0.2.0 rsa-4.6 scikit-image-0.17.2 scikit-learn-0.23.2 scipy-1.5.4 seaborn-0.11.0 six-1.15.0 sqlalchemy-1.3.20 tensorboard-2.4.0 tensorboard-plugin-wit-1.7.0 tensorflow-1.5.0 tensorflow-tensorboard-1.5.1 threadpoolctl-2.1.0 tifffile-2020.9.3 toml-0.10.2 torch-1.5.0 torchvision-0.6.0 tqdm-4.52.0 transforms3d-0.3.1 urllib3-1.26.2 werkzeug-1.0.1 xlwt-1.3.0 zipp-3.4.0 | |
Obtaining file:///Users/alex/code/spinalcordtoolbox | |
Installing collected packages: spinalcordtoolbox | |
Running setup.py develop for spinalcordtoolbox | |
Successfully installed spinalcordtoolbox | |
Creating launchers for Python scripts... | |
Installing binaries... | |
sct_download_data -d binaries_osx -o /Users/alex/code/spinalcordtoolbox/bin -k | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d binaries_osx -o /Users/alex/code/spinalcordtoolbox/bin -k | |
-- | |
Trying URL: https://osf.io/874cy?action=download | |
Downloading: 20200801_sct_binaries_osx.tar.gz | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 60.8M/60.8M [00:01<00:00, 50.4MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144736.440863-lco4k70t) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144736.440863-lco4k70t | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_ComposeMultiTransform” | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_antsApplyTransforms” | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_antsRegistration” | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_antsSliceRegularizedRegistration” | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_dice_coefficient” | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_propseg” | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_spine_detect” | |
Updating existing “/Users/alex/code/spinalcordtoolbox/bin/isct_train_svm” | |
Removing temporary folders... | |
Done! | |
All requirements installed! | |
Installing data... | |
rm -rf /Users/alex/code/spinalcordtoolbox/data | |
mkdir -p /Users/alex/code/spinalcordtoolbox/data | |
sct_download_data -d PAM50 -o /Users/alex/code/spinalcordtoolbox/data/PAM50 | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d PAM50 -o /Users/alex/code/spinalcordtoolbox/data/PAM50 | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/PAM50” | |
Trying URL: https://github.com/sct-data/PAM50/releases/download/r20201104/PAM50-r20201104.zip | |
Downloading: PAM50-r20201104.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 70.9M/70.9M [00:01<00:00, 50.7MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144740.573530-s_5_2375) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144740.573530-s_5_2375 | |
Removing temporary folders... | |
Done! | |
sct_download_data -d gm_model -o /Users/alex/code/spinalcordtoolbox/data/gm_model | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d gm_model -o /Users/alex/code/spinalcordtoolbox/data/gm_model | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/gm_model” | |
Trying URL: https://osf.io/ugscu/?action=download | |
Downloading: 20160922_gm_model.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10.3M/10.3M [00:00<00:00, 35.0MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144743.461329-dhpahwt3) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144743.461329-dhpahwt3 | |
Removing temporary folders... | |
Done! | |
sct_download_data -d optic_models -o /Users/alex/code/spinalcordtoolbox/data/optic_models | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d optic_models -o /Users/alex/code/spinalcordtoolbox/data/optic_models | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/optic_models” | |
Trying URL: https://github.com/sct-data/optic_models/releases/download/r20170413/20170413_optic_models.zip | |
Downloading: 20170413_optic_models.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17.7k/17.7k [00:00<00:00, 47.2MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144744.521876-85ywd37p) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144744.521876-85ywd37p | |
Removing temporary folders... | |
Done! | |
sct_download_data -d pmj_models -o /Users/alex/code/spinalcordtoolbox/data/pmj_models | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d pmj_models -o /Users/alex/code/spinalcordtoolbox/data/pmj_models | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/pmj_models” | |
Trying URL: https://github.com/sct-data/pmj_models/releases/download/r20170922/20170922_pmj_models.zip | |
Downloading: 20170922_pmj_models.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8.87k/8.87k [00:00<00:00, 21.5MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144745.454200-lsf_zdja) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144745.454200-lsf_zdja | |
Removing temporary folders... | |
Done! | |
sct_download_data -d deepseg_sc_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_sc_models | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d deepseg_sc_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_sc_models | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/deepseg_sc_models” | |
Trying URL: https://github.com/sct-data/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip | |
Downloading: 20180610_deepseg_sc_models.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 58.7M/58.7M [00:01<00:00, 49.3MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144747.620006-xyumxfno) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144747.620006-xyumxfno | |
Removing temporary folders... | |
Done! | |
sct_download_data -d deepseg_gm_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_gm_models | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d deepseg_gm_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_gm_models | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/deepseg_gm_models” | |
Trying URL: https://github.com/sct-data/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip | |
Downloading: 20180205_deepseg_gm_models.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.28M/2.28M [00:00<00:00, 12.4MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144749.234474-_lenvktw) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144749.234474-_lenvktw | |
Removing temporary folders... | |
Done! | |
sct_download_data -d deepseg_lesion_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_lesion_models | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d deepseg_lesion_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_lesion_models | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/deepseg_lesion_models” | |
Trying URL: https://github.com/sct-data/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip | |
Downloading: 20180613_deepseg_lesion_models.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 16.0M/16.0M [00:00<00:00, 36.9MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144750.679295-7b0a45f6) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144750.679295-7b0a45f6 | |
Removing temporary folders... | |
Done! | |
sct_download_data -d c2c3_disc_models -o /Users/alex/code/spinalcordtoolbox/data/c2c3_disc_models | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_download_data -d c2c3_disc_models -o /Users/alex/code/spinalcordtoolbox/data/c2c3_disc_models | |
-- | |
Removing existing destination folder “/Users/alex/code/spinalcordtoolbox/data/c2c3_disc_models” | |
Trying URL: https://github.com/sct-data/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip | |
Downloading: 20190117_c2c3_disc_models.zip | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8.94k/8.94k [00:00<00:00, 32.4MB/s] | |
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144751.684535-2is_7j1w) | |
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201118144751.684535-2is_7j1w | |
Removing temporary folders... | |
Done! | |
Status: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 18.0M/18.0M [00:00<00:00, 36.8MB/s] | |
In case an old version SCT is already installed (4.0.0-beta.1 or before), remove 'sct_env' declaration in RC file | |
Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y | |
Validate installation... | |
-- | |
Spinal Cord Toolbox (git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e) | |
sct_check_dependencies | |
-- | |
SCT info: | |
- version: git-jn/3048-big-sur-version-parsing-9b30b2a2fd751a4cbb2c24677e1e9eb5fc39f51e | |
- path: /Users/alex/code/spinalcordtoolbox | |
OS: osx (Darwin-20.1.0-x86_64-i386-64bit) | |
CPU cores: Available: 12, Used by ITK functions: 12 | |
RAM: Total: 16384MB, Used: 8988MB, Available: 7199MB | |
Check Python executable.............................[OK] | |
Using bundled python 3.6.12 |Anaconda, Inc.| (default, Sep 8 2020, 17:50:39) | |
[GCC Clang 10.0.0 ] at /Users/alex/code/spinalcordtoolbox/python/envs/venv_sct/bin/python | |
Check if data are installed.........................[OK] | |
Check if colored is installed.......................[OK] (1.4.2) | |
Check if dipy is installed..........................[OK] (1.3.0) | |
Check if futures is installed.......................[OK] | |
Check if h5py is installed..........................[OK] (2.10.0) | |
Check if ivadomed (2.4.0) is installed..............[OK] (2.4.0) | |
Check if Keras (2.1.5) is installed.................[OK] (2.1.5) | |
Check if matplotlib is installed....................[OK] (3.3.3) | |
Check if nibabel is installed.......................[OK] (3.2.0) | |
Check if numpy is installed.........................[OK] (1.19.4) | |
Check if onnxruntime (1.4.0) is installed...........[OK] (1.4.0) | |
Check if pandas is installed........................[OK] (1.1.4) | |
Check if psutil is installed........................[OK] (5.7.3) | |
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3) | |
Check if pytest is installed........................[OK] (6.1.2) | |
Check if pytest-cov is installed....................[OK] (__version__ = '2.10.1') | |
Check if raven is installed.........................[OK] | |
Check if requests is installed......................[OK] (2.25.0) | |
Check if requirements-parser is installed...........[OK] (0.2.0) | |
Check if scipy is installed.........................[OK] (1.5.4) | |
Check if scikit-image is installed..................[OK] (0.17.2) | |
Check if scikit-learn is installed..................[OK] (0.23.2) | |
Check if tensorflow (1.5.0) is installed............[OK] (1.5.0) | |
Check if torch (1.5.0) is installed.................[OK] (1.5.0) | |
Check if torchvision (0.6.0) is installed...........[OK] (0.6.0) | |
Check if xlwt is installed..........................[OK] (1.3.0) | |
Check if tqdm is installed..........................[OK] (4.52.0) | |
Check if transforms3d is installed..................[OK] (0.3.1) | |
Check if urllib3 is installed.......................[OK] (1.26.2) | |
Check if pytest_console_scripts is installed........[OK] | |
Check if pytest-xdist is installed..................[OK] (2.1.0) | |
Check if spinalcordtoolbox is installed.............[OK] | |
Check ANTs compatibility with OS ...................[OK] | |
Check PropSeg compatibility with OS ................[OK] | |
Check if DISPLAY variable is set....................[OK] | |
Check if figure can be opened with PyQt.............[OK] | |
Open a new Terminal window to load environment variables, or run: | |
source /Users/alex/.zshrc | |
Installation finished successfully! | |
[18/11/20 2:48:42] (base) alex@NeuroPoly-MacBook-Pro spinalcordtoolbox % |
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