Skip to content

Instantly share code, notes, and snippets.

@alexfoias

alexfoias/install log - fc1879ea9aa2862c7c888d2454ae62bccde861d2

Created November 16, 2020 16:33
Show Gist options
  • Save alexfoias/1fe780d7847145a0295c0aa58fa0a96a to your computer and use it in GitHub Desktop.
Save alexfoias/1fe780d7847145a0295c0aa58fa0a96a to your computer and use it in GitHub Desktop.
Download ZIP
sct install Big sur
Raw
install log - fc1879ea9aa2862c7c888d2454ae62bccde861d2
[16/11/20 11:02:51] (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 132: ((: 0. < 12: syntax error: invalid arithmetic operator (error token is ". < 12")
./install_sct: line 223: /Users/alex/.bash_profile: Permission denied
Checking requirements...
OK!
SCT version ......... dev
Installation type ... in-place
Operating system .... osx (0.)
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)
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.xtW3NCe2/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 19.8M 0 0:00:02 0:00:02 --:--:-- 19.8M
exit status is 0
bash /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/tmp.xtW3NCe2/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
ca-certificates-2020 | 121 KB | ###################################################################################################################################################### | 100%
certifi-2020.6.20 | 155 KB | ###################################################################################################################################################### | 100%
setuptools-50.3.1 | 713 KB | ###################################################################################################################################################### | 100%
tk-8.6.10 | 3.0 MB | ###################################################################################################################################################### | 100%
libedit-3.1.20191231 | 96 KB | ###################################################################################################################################################### | 100%
wheel-0.35.1 | 38 KB | ###################################################################################################################################################### | 100%
libffi-3.3 | 44 KB | ###################################################################################################################################################### | 100%
sqlite-3.33.0 | 1.3 MB | ###################################################################################################################################################### | 100%
pip-20.2.4 | 1.8 MB | ###################################################################################################################################################### | 100%
openssl-1.1.1h | 2.2 MB | ###################################################################################################################################################### | 100%
python-3.6.12 | 16.9 MB | ###################################################################################################################################################### | 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
Collecting colored
Downloading colored-1.4.2.tar.gz (56 kB)
|████████████████████████████████| 56 kB 2.7 MB/s
Collecting dipy
Downloading dipy-1.3.0-cp36-cp36m-macosx_10_9_x86_64.whl (7.6 MB)
|████████████████████████████████| 7.6 MB 3.8 MB/s
Collecting futures
Downloading futures-3.1.1-py3-none-any.whl (2.8 kB)
Collecting h5py~=2.10.0
Downloading h5py-2.10.0-cp36-cp36m-macosx_10_6_intel.whl (3.0 MB)
|████████████████████████████████| 3.0 MB 37.9 MB/s
Collecting ivadomed==2.4.0
Downloading ivadomed-2.4.0-py3-none-any.whl (132 kB)
|████████████████████████████████| 132 kB 35.7 MB/s
Collecting Keras==2.1.5
Downloading Keras-2.1.5-py2.py3-none-any.whl (334 kB)
|████████████████████████████████| 334 kB 45.3 MB/s
Collecting matplotlib
Downloading matplotlib-3.3.3-cp36-cp36m-macosx_10_9_x86_64.whl (8.5 MB)
|████████████████████████████████| 8.5 MB 25.4 MB/s
Collecting nibabel
Downloading nibabel-3.2.0-py3-none-any.whl (3.3 MB)
|████████████████████████████████| 3.3 MB 31.5 MB/s
Collecting numpy
Downloading numpy-1.19.4-cp36-cp36m-macosx_10_9_x86_64.whl (15.3 MB)
|████████████████████████████████| 15.3 MB 21.4 MB/s
Collecting onnxruntime==1.4.0
Downloading onnxruntime-1.4.0-cp36-cp36m-macosx_10_12_x86_64.whl (3.9 MB)
|████████████████████████████████| 3.9 MB 51.1 MB/s
Collecting pandas
Downloading pandas-1.1.4-cp36-cp36m-macosx_10_9_x86_64.whl (10.2 MB)
|████████████████████████████████| 10.2 MB 19.2 MB/s
Collecting psutil
Downloading psutil-5.7.3.tar.gz (465 kB)
|████████████████████████████████| 465 kB 37.6 MB/s
Collecting pyqt5==5.11.3
Downloading PyQt5-5.11.3-5.11.2_a-cp35.cp36.cp37.cp38-abi3-macosx_10_6_intel.whl (91.1 MB)
|████████████████████████████████| 91.1 MB 16.5 MB/s
Collecting pytest
Downloading pytest-6.1.2-py3-none-any.whl (272 kB)
|████████████████████████████████| 272 kB 64.1 MB/s
Collecting pytest-cov
Downloading pytest_cov-2.10.1-py2.py3-none-any.whl (19 kB)
Collecting raven
Downloading raven-6.10.0-py2.py3-none-any.whl (284 kB)
|████████████████████████████████| 284 kB 23.0 MB/s
Collecting requests
Downloading requests-2.25.0-py2.py3-none-any.whl (61 kB)
|████████████████████████████████| 61 kB 16.6 MB/s
Collecting requirements-parser
Downloading requirements-parser-0.2.0.tar.gz (6.3 kB)
Collecting scipy
Downloading scipy-1.5.4-cp36-cp36m-macosx_10_9_x86_64.whl (28.8 MB)
|████████████████████████████████| 28.8 MB 12.6 MB/s
Collecting scikit-image
Downloading scikit_image-0.17.2-cp36-cp36m-macosx_10_13_x86_64.whl (12.1 MB)
|████████████████████████████████| 12.1 MB 11.0 MB/s
Collecting scikit-learn
Downloading scikit_learn-0.23.2-cp36-cp36m-macosx_10_9_x86_64.whl (7.2 MB)
|████████████████████████████████| 7.2 MB 20.3 MB/s
Collecting tensorflow==1.5.0
Downloading tensorflow-1.5.0-cp36-cp36m-macosx_10_11_x86_64.whl (42.5 MB)
|████████████████████████████████| 42.5 MB 7.3 MB/s
Collecting torch==1.5.0
Downloading torch-1.5.0-cp36-none-macosx_10_9_x86_64.whl (80.5 MB)
|████████████████████████████████| 80.5 MB 9.8 MB/s
Collecting torchvision==0.6.0
Downloading torchvision-0.6.0-cp36-cp36m-macosx_10_9_x86_64.whl (436 kB)
|████████████████████████████████| 436 kB 44.6 MB/s
Collecting xlwt
Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
|████████████████████████████████| 99 kB 27.2 MB/s
Collecting tqdm
Downloading tqdm-4.52.0-py2.py3-none-any.whl (71 kB)
|████████████████████████████████| 71 kB 19.6 MB/s
Collecting transforms3d
Using cached transforms3d-0.3.1.tar.gz (62 kB)
Collecting urllib3[secure]
Downloading urllib3-1.26.2-py2.py3-none-any.whl (136 kB)
|████████████████████████████████| 136 kB 43.6 MB/s
Collecting pytest_console_scripts
Downloading pytest-console-scripts-1.0.0.tar.gz (12 kB)
Collecting pytest-xdist
Downloading pytest_xdist-2.1.0-py3-none-any.whl (36 kB)
Collecting six
Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting joblib
Using cached joblib-0.17.0-py3-none-any.whl (301 kB)
Collecting bids-neuropoly>=0.2
Downloading bids_neuropoly-0.2-py3-none-any.whl (3.1 kB)
Collecting pillow>=7.0.0
Downloading Pillow-8.0.1-cp36-cp36m-macosx_10_10_x86_64.whl (2.2 MB)
|████████████████████████████████| 2.2 MB 40.6 MB/s
Collecting tensorboard
Downloading tensorboard-2.4.0-py3-none-any.whl (10.6 MB)
|████████████████████████████████| 10.6 MB 49.7 MB/s
Collecting seaborn
Using cached seaborn-0.11.0-py3-none-any.whl (283 kB)
Collecting pyyaml
Using cached PyYAML-5.3.1.tar.gz (269 kB)
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.3.1-cp36-cp36m-macosx_10_9_x86_64.whl (61 kB)
|████████████████████████████████| 61 kB 20.6 MB/s
Collecting cycler>=0.10
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
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 packaging>=14.3
Using cached packaging-20.4-py2.py3-none-any.whl (37 kB)
Collecting protobuf
Downloading protobuf-3.14.0-cp36-cp36m-macosx_10_9_x86_64.whl (1.0 MB)
|████████████████████████████████| 1.0 MB 50.5 MB/s
Collecting pytz>=2017.2
Downloading pytz-2020.4-py2.py3-none-any.whl (509 kB)
|████████████████████████████████| 509 kB 33.7 MB/s
Collecting PyQt5_sip<4.20,>=4.19.11
Downloading PyQt5_sip-4.19.19-cp36-cp36m-macosx_10_6_intel.whl (52 kB)
|████████████████████████████████| 52 kB 2.4 MB/s
Collecting toml
Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
Collecting iniconfig
Downloading 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"
Downloading importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB)
Collecting attrs>=17.4.0
Downloading attrs-20.3.0-py2.py3-none-any.whl (49 kB)
|████████████████████████████████| 49 kB 18.2 MB/s
Collecting pluggy<1.0,>=0.12
Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting coverage>=4.4
Downloading coverage-5.3-cp36-cp36m-macosx_10_13_x86_64.whl (205 kB)
|████████████████████████████████| 205 kB 39.4 MB/s
Collecting chardet<4,>=3.0.2
Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB)
|████████████████████████████████| 133 kB 38.3 MB/s
Collecting idna<3,>=2.5
Downloading idna-2.10-py2.py3-none-any.whl (58 kB)
|████████████████████████████████| 58 kB 17.4 MB/s
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 networkx>=2.0
Using cached networkx-2.5-py3-none-any.whl (1.6 MB)
Collecting imageio>=2.3.0
Using cached imageio-2.9.0-py3-none-any.whl (3.3 MB)
Collecting tifffile>=2019.7.26
Downloading tifffile-2020.9.3-py3-none-any.whl (148 kB)
|████████████████████████████████| 148 kB 33.3 MB/s
Collecting PyWavelets>=1.1.1
Downloading PyWavelets-1.1.1-cp36-cp36m-macosx_10_9_x86_64.whl (4.3 MB)
|████████████████████████████████| 4.3 MB 36.2 MB/s
Collecting threadpoolctl>=2.0.0
Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Collecting tensorflow-tensorboard<1.6.0,>=1.5.0
Downloading tensorflow_tensorboard-1.5.1-py3-none-any.whl (3.0 MB)
|████████████████████████████████| 3.0 MB 28.7 MB/s
Collecting absl-py>=0.1.6
Downloading absl_py-0.11.0-py3-none-any.whl (127 kB)
|████████████████████████████████| 127 kB 33.8 MB/s
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 future
Using cached future-0.18.2.tar.gz (829 kB)
Collecting cryptography>=1.3.4; extra == "secure"
Downloading cryptography-3.2.1-cp35-abi3-macosx_10_10_x86_64.whl (1.8 MB)
|████████████████████████████████| 1.8 MB 43.1 MB/s
Collecting pyOpenSSL>=0.14; extra == "secure"
Downloading pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB)
|████████████████████████████████| 53 kB 6.1 MB/s
Collecting mock>=2.0.0
Downloading mock-4.0.2-py3-none-any.whl (28 kB)
Collecting execnet>=1.1
Downloading execnet-1.7.1-py2.py3-none-any.whl (39 kB)
Collecting pytest-forked
Downloading pytest_forked-1.3.0-py2.py3-none-any.whl (4.7 kB)
Collecting pybids>=0.6.5
Downloading pybids-0.12.4-py2.py3-none-any.whl (3.2 MB)
|████████████████████████████████| 3.2 MB 27.5 MB/s
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 werkzeug>=0.11.15
Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
|████████████████████████████████| 298 kB 52.2 MB/s
Collecting tensorboard-plugin-wit>=1.6.0
Downloading tensorboard_plugin_wit-1.7.0-py3-none-any.whl (779 kB)
|████████████████████████████████| 779 kB 57.9 MB/s
Collecting google-auth-oauthlib<0.5,>=0.4.1
Downloading google_auth_oauthlib-0.4.2-py2.py3-none-any.whl (18 kB)
Collecting grpcio>=1.24.3
Downloading grpcio-1.33.2-cp36-cp36m-macosx_10_9_x86_64.whl (3.4 MB)
|████████████████████████████████| 3.4 MB 44.3 MB/s
Collecting markdown>=2.6.8
Downloading Markdown-3.3.3-py3-none-any.whl (96 kB)
|████████████████████████████████| 96 kB 18.6 MB/s
Collecting google-auth<2,>=1.6.3
Downloading google_auth-1.23.0-py2.py3-none-any.whl (114 kB)
|████████████████████████████████| 114 kB 40.9 MB/s
Collecting zipp>=0.5
Downloading zipp-3.4.0-py3-none-any.whl (5.2 kB)
Collecting decorator>=4.3.0
Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting html5lib==0.9999999
Downloading html5lib-0.9999999.tar.gz (889 kB)
|████████████████████████████████| 889 kB 45.7 MB/s
Collecting bleach==1.5.0
Downloading bleach-1.5.0-py2.py3-none-any.whl (17 kB)
Collecting cffi!=1.11.3,>=1.8
Downloading cffi-1.14.3-2-cp36-cp36m-macosx_10_9_x86_64.whl (176 kB)
|████████████████████████████████| 176 kB 34.7 MB/s
Collecting apipkg>=1.4
Downloading apipkg-1.5-py2.py3-none-any.whl (4.9 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 click
Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Collecting patsy
Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Collecting sqlalchemy<1.4.0.dev0
Downloading SQLAlchemy-1.3.20-cp36-cp36m-macosx_10_14_x86_64.whl (1.2 MB)
|████████████████████████████████| 1.2 MB 33.6 MB/s
Collecting requests-oauthlib>=0.7.0
Downloading requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting pyasn1-modules>=0.2.1
Downloading pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
|████████████████████████████████| 155 kB 27.1 MB/s
Collecting rsa<5,>=3.1.4; python_version >= "3.5"
Downloading rsa-4.6-py3-none-any.whl (47 kB)
|████████████████████████████████| 47 kB 9.7 MB/s
Collecting cachetools<5.0,>=2.0.0
Downloading cachetools-4.1.1-py3-none-any.whl (10 kB)
Collecting pycparser
Downloading pycparser-2.20-py2.py3-none-any.whl (112 kB)
|████████████████████████████████| 112 kB 20.0 MB/s
Collecting docopt>=0.6.2
Using cached docopt-0.6.2.tar.gz (25 kB)
Collecting oauthlib>=3.0.0
Downloading oauthlib-3.1.0-py2.py3-none-any.whl (147 kB)
|████████████████████████████████| 147 kB 28.1 MB/s
Collecting pyasn1<0.5.0,>=0.4.6
Downloading pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
|████████████████████████████████| 77 kB 15.5 MB/s
Building wheels for collected packages: colored, psutil, requirements-parser, transforms3d, pytest-console-scripts, pyyaml, future, html5lib, docopt
Building wheel for colored (setup.py) ... done
Created wheel for colored: filename=colored-1.4.2-py3-none-any.whl size=14002 sha256=6e5eaf5d38eb0fb653375e52847375a5f64b6c1f79a20e4e46cba0195d80cbfd
Stored in directory: /Users/alex/Library/Caches/pip/wheels/b7/be/ae/a98f7701429c3cfcebf4d2b537e48a1571549a4d8b55463a01
Building wheel for psutil (setup.py) ... done
Created wheel for psutil: filename=psutil-5.7.3-cp36-cp36m-macosx_10_9_x86_64.whl size=234596 sha256=c80213f523ae15abdb629b9778d5e5db1b948511edf30505fcaaa19eb35fd20d
Stored in directory: /Users/alex/Library/Caches/pip/wheels/fa/ad/67/90bbaacdcfe970960dd5158397f23a6579b51d853720d7856d
Building wheel for requirements-parser (setup.py) ... done
Created wheel for requirements-parser: filename=requirements_parser-0.2.0-py3-none-any.whl size=7656 sha256=fff427dcc4c4ab7c0f7e5e7d8e4e042aa2d05c084a3e8025e9650110382936f7
Stored in directory: /Users/alex/Library/Caches/pip/wheels/80/af/bd/32c202b632c3e9a1b482b33d37f5efd128137891a08f3c3bae
Building wheel for transforms3d (setup.py) ... done
Created wheel for transforms3d: filename=transforms3d-0.3.1-py3-none-any.whl size=59373 sha256=ff59e83af3da23247da0ce408d529df945a03702f20792eeb408521149529f3d
Stored in directory: /Users/alex/Library/Caches/pip/wheels/be/7a/eb/465e9bb085af816c4d504821d542cc0059cc3433f6e8edea3c
Building wheel for pytest-console-scripts (setup.py) ... done
Created wheel for pytest-console-scripts: filename=pytest_console_scripts-1.0.0-py3-none-any.whl size=7976 sha256=1fb394acf0878474ba3258748f41cd64391deb4ceebf31c7b47d21e42561cd85
Stored in directory: /Users/alex/Library/Caches/pip/wheels/d1/e3/94/26f2c05b0a648497c46b19eaa1fb7cc33f53f1e866ac0b74c2
Building wheel for pyyaml (setup.py) ... done
Created wheel for pyyaml: filename=PyYAML-5.3.1-cp36-cp36m-macosx_10_9_x86_64.whl size=44625 sha256=cab7b4df8ea0b05a532abbc78dafb769a2ee3cae7cd1b3d019d312d6bdd68f3b
Stored in directory: /Users/alex/Library/Caches/pip/wheels/e5/9d/ad/2ee53cf262cba1ffd8afe1487eef788ea3f260b7e6232a80fc
Building wheel for future (setup.py) ... done
Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=2f93f09a51a542be6774c3a5e426609ce24ea3f1a8714d8c94f83f7cd37edb31
Stored in directory: /Users/alex/Library/Caches/pip/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94
Building wheel for html5lib (setup.py) ... done
Created wheel for html5lib: filename=html5lib-0.9999999-py3-none-any.whl size=107219 sha256=5883b32c4b53620b7e3c9c7837470d5664049d7e775d75152b69819e5d03d5ad
Stored in directory: /Users/alex/Library/Caches/pip/wheels/90/1c/cb/a87fd097ff74648ecc468a703001f6c7c86d8a71d459e65c98
Building wheel for docopt (setup.py) ... done
Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13704 sha256=a61c904f0a5dd7fa0628b88383a4991236347b0c151fd080d4643f6afa1d55cd
Stored in directory: /Users/alex/Library/Caches/pip/wheels/3f/2a/fa/4d7a888e69774d5e6e855d190a8a51b357d77cc05eb1c097c9
Successfully built colored psutil requirements-parser transforms3d pytest-console-scripts pyyaml future html5lib docopt
Installing collected packages: colored, numpy, scipy, six, h5py, pyparsing, packaging, nibabel, tqdm, dipy, futures, pillow, decorator, networkx, imageio, tifffile, PyWavelets, kiwisolver, cycler, python-dateutil, matplotlib, scikit-image, pytz, pandas, joblib, toml, iniconfig, py, zipp, importlib-metadata, attrs, pluggy, pytest, bids-validator, docopt, num2words, click, patsy, sqlalchemy, pybids, bids-neuropoly, protobuf, onnxruntime, threadpoolctl, scikit-learn, future, torch, absl-py, werkzeug, tensorboard-plugin-wit, pyasn1, pyasn1-modules, rsa, cachetools, google-auth, oauthlib, chardet, idna, pycparser, cffi, cryptography, pyOpenSSL, urllib3, requests, requests-oauthlib, google-auth-oauthlib, grpcio, markdown, tensorboard, seaborn, torchvision, 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-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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 [00:02<00:00, 28.1MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110604.535727-j4eihup8)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110604.535727-j4eihup8
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-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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 [00:05<00:00, 13.3MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110612.362844-9zuuw0es)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110612.362844-9zuuw0es
Removing temporary folders...
Done!
sct_download_data -d gm_model -o /Users/alex/code/spinalcordtoolbox/data/gm_model
--
Spinal Cord Toolbox (git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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, 17.0MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110615.404532-g95d5o34)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110615.404532-g95d5o34
Removing temporary folders...
Done!
sct_download_data -d optic_models -o /Users/alex/code/spinalcordtoolbox/data/optic_models
--
Spinal Cord Toolbox (git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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, 50.9MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110616.291205-b5fpimiw)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110616.291205-b5fpimiw
Removing temporary folders...
Done!
sct_download_data -d pmj_models -o /Users/alex/code/spinalcordtoolbox/data/pmj_models
--
Spinal Cord Toolbox (git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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, 34.8MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110617.166035-xcrkj2ct)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110617.166035-xcrkj2ct
Removing temporary folders...
Done!
sct_download_data -d deepseg_sc_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_sc_models
--
Spinal Cord Toolbox (git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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 [00:04<00:00, 12.5MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110622.758025-x3vgpuag)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110622.758025-x3vgpuag
Removing temporary folders...
Done!
sct_download_data -d deepseg_gm_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_gm_models
--
Spinal Cord Toolbox (git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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, 11.5MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110624.294869-iqkmed9o)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110624.294869-iqkmed9o
Removing temporary folders...
Done!
sct_download_data -d deepseg_lesion_models -o /Users/alex/code/spinalcordtoolbox/data/deepseg_lesion_models
--
Spinal Cord Toolbox (git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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 [00:01<00:00, 12.9MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110626.428071-fjesyssk)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110626.428071-fjesyssk
Removing temporary folders...
Done!
sct_download_data -d c2c3_disc_models -o /Users/alex/code/spinalcordtoolbox/data/c2c3_disc_models
--
Spinal Cord Toolbox (git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
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, 30.2MB/s]
Creating temporary folder (/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110627.406886-0px6lrno)
Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/sct-20201116110627.406886-0px6lrno
Removing temporary folders...
Done!
Status: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 18.0M/18.0M [00:01<00:00, 13.7MB/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-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2)
sct_check_dependencies
--
SCT info:
- version: git-master-fc1879ea9aa2862c7c888d2454ae62bccde861d2
- 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: 8029MB, Available: 5640MB
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....................[FAIL]
Open a new Terminal window to load environment variables, or run:
source /Users/alex/.zshrc
Installation finished successfully!
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment