Hi,
I am trying to install SCT 4.2.2 under Ubuntu 16.04 using a proxy server to connect to internet.
I set up the proxy in the environment variables (http_proxy and https_proxy) and in the conda configuration file (~/.condarc).
When I run the installation code I got an error while downloading the data (e.g. https://www.neuro.polymtl.ca/_media/downloads/sct/20191029_PAM50.zip) that stop the installation script. However, if I try to download the same url from the same location using wget it does work. I am not sure if I can just download the data and copy them in the CTS data folder to complete the installation or not.
I pasted here the whole terminal output:
- Welcome to SCT installation *
Checking OS type and version…
Linux cervino-rm 4.4.0-112-generic #135-Ubuntu SMP Fri Jan 19 11:48:36 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Checking requirements…
OK!
SCT version … 4.2.2
Installation type … package
Operating system … linux (unknown)
Shell config … /home/dperuzzo/.bashrc
To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.
Do you agree to help us improve SCT? [y]es/[n]o: n
–> Crash reports will not be sent.
SCT will be installed here: [/home/dperuzzo/sct_4.2.2]
Do you agree? [y]es/[n]o: n
Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0):
/mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2
Copying source files from /mnt/store1/projects/atassia/ENIGMA_spinal_cord/spinalcordtoolbox-4.2.2 to /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2
…
Removing sct and isct softlink from /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/bin
Installing conda…
rm -rf /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python
mkdir -p /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python
wget -O /tmp/tmp.CNOrwXm3Nw/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
–2020-10-02 10:49:43-- https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Connecting to 10.7.0.253:80… connected.
Proxy request sent, awaiting response… 301 Moved Permanently
Location: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [following]
–2020-10-02 10:49:43-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Connecting to 10.7.0.253:80… connected.
Proxy request sent, awaiting response… 200 OK
Length: 93052469 (89M) [application/x-sh]
Saving to: ‘/tmp/tmp.CNOrwXm3Nw/miniconda.sh’
/tmp/tmp.CNOrwXm3Nw/miniconda.sh 100%[======================================================================>] 88.74M 38.6MB/s in 2.3s
2020-10-02 10:49:45 (38.6 MB/s) - ‘/tmp/tmp.CNOrwXm3Nw/miniconda.sh’ saved [93052469/93052469]
exit status is 0
bash /tmp/tmp.CNOrwXm3Nw/miniconda.sh -p /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python -b -f
PREFIX=/mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python
Unpacking payload …
Collecting package metadata (current_repodata.json): done
Solving environment: done
Package Plan
environment location: /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python
added / updated specs:
- _libgcc_mutex==0.1=main
- ca-certificates==2020.1.1=0
- certifi==2020.4.5.1=py38_0
- cffi==1.14.0=py38he30daa8_1
- chardet==3.0.4=py38_1003
- conda-package-handling==1.6.1=py38h7b6447c_0
- conda==4.8.3=py38_0
- cryptography==2.9.2=py38h1ba5d50_0
- idna==2.9=py_1
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.3=he6710b0_1
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1g=h7b6447c_0
- pip==20.0.2=py38_3
- pycosat==0.6.3=py38h7b6447c_1
- pycparser==2.20=py_0
- pyopenssl==19.1.0=py38_0
- pysocks==1.7.1=py38_0
- python==3.8.3=hcff3b4d_0
- readline==8.0=h7b6447c_0
- requests==2.23.0=py38_0
- ruamel_yaml==0.15.87=py38h7b6447c_0
- setuptools==46.4.0=py38_0
- six==1.14.0=py38_0
- sqlite==3.31.1=h62c20be_1
- tk==8.6.8=hbc83047_0
- tqdm==4.46.0=py_0
- urllib3==1.25.8=py38_0
- wheel==0.34.2=py38_0
- xz==5.2.5=h7b6447c_0
- yaml==0.1.7=had09818_2
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0
certifi pkgs/main/linux-64::certifi-2020.4.5.1-py38_0
cffi pkgs/main/linux-64::cffi-1.14.0-py38he30daa8_1
chardet pkgs/main/linux-64::chardet-3.0.4-py38_1003
conda pkgs/main/linux-64::conda-4.8.3-py38_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py38h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.9.2-py38h1ba5d50_0
idna pkgs/main/noarch::idna-2.9-py_1
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
pip pkgs/main/linux-64::pip-20.0.2-py38_3
pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py38_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py38_0
python pkgs/main/linux-64::python-3.8.3-hcff3b4d_0
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/linux-64::requests-2.23.0-py38_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-46.4.0-py38_0
six pkgs/main/linux-64::six-1.14.0-py38_0
sqlite pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py38_0
wheel pkgs/main/linux-64::wheel-0.34.2-py38_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_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: 4.8.5
Please update conda by running
$ conda update -n base -c defaults conda
Package Plan
environment location: /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python/envs/venv_sct
added / updated specs:
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 1_gnu 22 KB conda-forge
ca-certificates-2020.6.20 | hecda079_0 145 KB conda-forge
certifi-2020.6.20 | py36h9f0ad1d_0 151 KB conda-forge
ld_impl_linux-64-2.35 | h769bd43_9 617 KB conda-forge
libffi-3.2.1 | he1b5a44_1007 47 KB conda-forge
libgcc-ng-9.3.0 | h24d8f2e_16 7.8 MB conda-forge
libgomp-9.3.0 | h24d8f2e_16 378 KB conda-forge
libstdcxx-ng-9.3.0 | hdf63c60_16 4.0 MB conda-forge
ncurses-6.2 | he1b5a44_1 993 KB conda-forge
openssl-1.1.1h | h516909a_0 2.1 MB conda-forge
pip-20.2.3 | py_0 1.1 MB conda-forge
python-3.6.11 |h4d41432_2_cpython 34.2 MB conda-forge
python_abi-3.6 | 1_cp36m 4 KB conda-forge
readline-8.0 | he28a2e2_2 281 KB conda-forge
setuptools-49.6.0 | py36h9f0ad1d_1 934 KB conda-forge
sqlite-3.33.0 | h4cf870e_0 1.4 MB conda-forge
tk-8.6.10 | hed695b0_0 3.2 MB conda-forge
wheel-0.35.1 | pyh9f0ad1d_0 29 KB conda-forge
xz-5.2.5 | h516909a_1 343 KB conda-forge
zlib-1.2.11 | h516909a_1009 106 KB conda-forge
------------------------------------------------------------
Total: 57.9 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
certifi conda-forge/linux-64::certifi-2020.6.20-py36h9f0ad1d_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.35-h769bd43_9
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_16
libgomp conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_16
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_16
ncurses conda-forge/linux-64::ncurses-6.2-he1b5a44_1
openssl conda-forge/linux-64::openssl-1.1.1h-h516909a_0
pip conda-forge/noarch::pip-20.2.3-py_0
python conda-forge/linux-64::python-3.6.11-h4d41432_2_cpython
python_abi conda-forge/linux-64::python_abi-3.6-1_cp36m
readline conda-forge/linux-64::readline-8.0-he28a2e2_2
setuptools conda-forge/linux-64::setuptools-49.6.0-py36h9f0ad1d_1
sqlite conda-forge/linux-64::sqlite-3.33.0-h4cf870e_0
tk conda-forge/linux-64::tk-8.6.10-hed695b0_0
wheel conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1009
Proceed ([y]/n)?
Downloading and Extracting Packages
ld_impl_linux-64-2.3 | 617 KB | ######################################################################################################### | 100%
wheel-0.35.1 | 29 KB | ######################################################################################################### | 100%
readline-8.0 | 281 KB | ######################################################################################################### | 100%
tk-8.6.10 | 3.2 MB | ######################################################################################################### | 100%
python-3.6.11 | 34.2 MB | ######################################################################################################### | 100%
_libgcc_mutex-0.1 | 3 KB | ######################################################################################################### | 100%
xz-5.2.5 | 343 KB | ######################################################################################################### | 100%
setuptools-49.6.0 | 934 KB | ######################################################################################################### | 100%
sqlite-3.33.0 | 1.4 MB | ######################################################################################################### | 100%
zlib-1.2.11 | 106 KB | ######################################################################################################### | 100%
certifi-2020.6.20 | 151 KB | ######################################################################################################### | 100%
libgomp-9.3.0 | 378 KB | ######################################################################################################### | 100%
openssl-1.1.1h | 2.1 MB | ######################################################################################################### | 100%
ca-certificates-2020 | 145 KB | ######################################################################################################### | 100%
libstdcxx-ng-9.3.0 | 4.0 MB | ######################################################################################################### | 100%
pip-20.2.3 | 1.1 MB | ######################################################################################################### | 100%
python_abi-3.6 | 4 KB | ######################################################################################################### | 100%
libgcc-ng-9.3.0 | 7.8 MB | ######################################################################################################### | 100%
_openmp_mutex-4.5 | 22 KB | ######################################################################################################### | 100%
ncurses-6.2 | 993 KB | ######################################################################################################### | 100%
libffi-3.2.1 | 47 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…
Collecting numpy
Using cached numpy-1.19.2-cp36-cp36m-manylinux2010_x86_64.whl (14.5 MB)
Installing collected packages: numpy
Successfully installed numpy-1.19.2
Using requirements-freeze.txt (release installation)
Processing /home/dperuzzo/.cache/pip/wheels/c3/af/84/3962a6af7b4ab336e951b7877dcfb758cf94548bb1771e0679/absl_py-0.9.0-py3-none-any.whl
Collecting astor==0.8.1
Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting attrs==19.3.0
Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting cachetools==4.0.0
Using cached cachetools-4.0.0-py3-none-any.whl (10 kB)
Collecting certifi==2019.11.28
Using cached certifi-2019.11.28-py2.py3-none-any.whl (156 kB)
Collecting cffi==1.13.2
Using cached cffi-1.13.2-cp36-cp36m-manylinux1_x86_64.whl (397 kB)
Collecting chardet==3.0.4
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting coverage==5.0
Using cached coverage-5.0-cp36-cp36m-manylinux1_x86_64.whl (226 kB)
Collecting cryptography==2.8
Using cached cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl (2.3 MB)
Collecting cycler==0.10.0
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting decorator==4.4.1
Using cached decorator-4.4.1-py2.py3-none-any.whl (9.2 kB)
Collecting dipy==1.0.0
Using cached dipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl (8.1 MB)
Collecting futures==3.1.1
Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Processing /home/dperuzzo/.cache/pip/wheels/19/a7/b9/0740c7a3a7d1d348f04823339274b90de25fbcd217b2ee1fbe/gast-0.2.2-py3-none-any.whl
Collecting google-auth==1.10.0
Using cached google_auth-1.10.0-py2.py3-none-any.whl (76 kB)
Collecting google-auth-oauthlib==0.4.1
Using cached google_auth_oauthlib-0.4.1-py2.py3-none-any.whl (18 kB)
Collecting google-pasta==0.1.8
Using cached google_pasta-0.1.8-py3-none-any.whl (57 kB)
Collecting grpcio==1.26.0
Using cached grpcio-1.26.0-cp36-cp36m-manylinux2010_x86_64.whl (2.4 MB)
Collecting h5py==2.10.0
Using cached h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Collecting idna==2.8
Using cached idna-2.8-py2.py3-none-any.whl (58 kB)
Collecting imageio==2.6.1
Using cached imageio-2.6.1-py3-none-any.whl (3.3 MB)
Collecting importlib-metadata==1.3.0
Using cached importlib_metadata-1.3.0-py2.py3-none-any.whl (29 kB)
Collecting joblib==0.14.1
Using cached joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Collecting Keras==2.3.1
Using cached Keras-2.3.1-py2.py3-none-any.whl (377 kB)
Collecting Keras-Applications==1.0.8
Using cached Keras_Applications-1.0.8-py3-none-any.whl (50 kB)
Collecting Keras-Preprocessing==1.1.0
Using cached Keras_Preprocessing-1.1.0-py2.py3-none-any.whl (41 kB)
Collecting kiwisolver==1.1.0
Using cached kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90 kB)
Collecting Markdown==3.1.1
Using cached Markdown-3.1.1-py2.py3-none-any.whl (87 kB)
Collecting matplotlib==3.1.2
Using cached matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1 MB)
Collecting more-itertools==8.0.2
Using cached more_itertools-8.0.2-py3-none-any.whl (40 kB)
Collecting networkx==2.4
Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting nibabel==3.0.0
Using cached nibabel-3.0.0-py3-none-any.whl (3.3 MB)
Collecting numpy==1.17.4
Using cached numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0 MB)
Collecting oauthlib==3.1.0
Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB)
Processing /home/dperuzzo/.cache/pip/wheels/1f/6f/14/e0f4f6bceec756bbab45c392c4d5429a684b14d849464ebfbf/opt_einsum-3.1.0-py3-none-any.whl
Collecting packaging==19.2
Using cached packaging-19.2-py2.py3-none-any.whl (30 kB)
Collecting pandas==0.25.3
Using cached pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl (10.4 MB)
Collecting Pillow==6.2.1
Using cached Pillow-6.2.1-cp36-cp36m-manylinux1_x86_64.whl (2.1 MB)
Collecting pluggy==0.13.1
Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting protobuf==3.11.1
Using cached protobuf-3.11.1-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB)
Processing /home/dperuzzo/.cache/pip/wheels/b2/b3/a3/551db06cebc9141c437c6b58aa751d3670471494e9f6d1428d/psutil-5.6.7-cp36-cp36m-linux_x86_64.whl
Collecting py==1.8.0
Using cached py-1.8.0-py2.py3-none-any.whl (83 kB)
Collecting pyasn1==0.4.8
Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting pyasn1-modules==0.2.7
Using cached pyasn1_modules-0.2.7-py2.py3-none-any.whl (131 kB)
Processing /home/dperuzzo/.cache/pip/wheels/c6/6b/83/2608afaa57ecfb0a66ac89191a8d9bad71c62ca55ee499c2d0/pycparser-2.19-py2.py3-none-any.whl
Collecting pyOpenSSL==19.1.0
Using cached pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB)
Collecting pyparsing==2.4.5
Using cached pyparsing-2.4.5-py2.py3-none-any.whl (67 kB)
Collecting PyQt5==5.11.3
Using cached PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8 MB)
Collecting PyQt5-sip==4.19.19
Using cached PyQt5_sip-4.19.19-cp36-cp36m-manylinux1_x86_64.whl (67 kB)
Collecting pytest==5.3.2
Using cached pytest-5.3.2-py3-none-any.whl (234 kB)
Collecting pytest-cov==2.8.1
Using cached pytest_cov-2.8.1-py2.py3-none-any.whl (18 kB)
Collecting python-dateutil==2.8.1
Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pytz==2019.3
Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting PyWavelets==1.1.1
Using cached PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB)
Processing /home/dperuzzo/.cache/pip/wheels/af/4b/a6/d492db4435642aebd1df1cd3ed075815e75ad6665aa47f4d04/PyYAML-5.2-cp36-cp36m-linux_x86_64.whl
Collecting raven==6.10.0
Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB)
Collecting requests==2.22.0
Using cached requests-2.22.0-py2.py3-none-any.whl (57 kB)
Collecting requests-oauthlib==1.3.0
Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting rsa==4.0
Using cached rsa-4.0-py2.py3-none-any.whl (38 kB)
Collecting scikit-image==0.16.2
Using cached scikit_image-0.16.2-cp36-cp36m-manylinux1_x86_64.whl (26.5 MB)
Collecting scikit-learn==0.22
Using cached scikit_learn-0.22-cp36-cp36m-manylinux1_x86_64.whl (7.0 MB)
Collecting scipy==1.4.0
Using cached scipy-1.4.0-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB)
Collecting six==1.13.0
Using cached six-1.13.0-py2.py3-none-any.whl (10 kB)
Collecting tensorboard==2.0.2
Using cached tensorboard-2.0.2-py3-none-any.whl (3.8 MB)
Collecting tensorflow==2.0.1
Using cached tensorflow-2.0.1-cp36-cp36m-manylinux2010_x86_64.whl (86.3 MB)
Collecting tensorflow-estimator==2.0.1
Using cached tensorflow_estimator-2.0.1-py2.py3-none-any.whl (449 kB)
Processing /home/dperuzzo/.cache/pip/wheels/93/2a/eb/e58dbcbc963549ee4f065ff80a59f274cc7210b6eab962acdc/termcolor-1.1.0-py3-none-any.whl
Collecting tqdm==4.40.2
Using cached tqdm-4.40.2-py2.py3-none-any.whl (55 kB)
Processing /home/dperuzzo/.cache/pip/wheels/be/7a/eb/465e9bb085af816c4d504821d542cc0059cc3433f6e8edea3c/transforms3d-0.3.1-py3-none-any.whl
Collecting urllib3==1.25.7
Using cached urllib3-1.25.7-py2.py3-none-any.whl (125 kB)
Collecting wcwidth==0.1.7
Using cached wcwidth-0.1.7-py2.py3-none-any.whl (21 kB)
Collecting Werkzeug==0.16.0
Using cached Werkzeug-0.16.0-py2.py3-none-any.whl (327 kB)
Processing /home/dperuzzo/.cache/pip/wheels/0d/85/48/15d7bfab92a2d0e87372224c1f628fc57db7447a663a58e86c/wrapt-1.11.2-cp36-cp36m-linux_x86_64.whl
Collecting xlrd==1.2.0
Using cached xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
Collecting xlutils==2.0.0
Using cached xlutils-2.0.0-py2.py3-none-any.whl (55 kB)
Collecting xlwt==1.3.0
Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Collecting zipp==0.6.0
Using cached zipp-0.6.0-py2.py3-none-any.whl (4.1 kB)
Requirement already satisfied: setuptools>=40.3.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth==1.10.0->-r requirements-freeze.txt (line 15)) (49.6.0.post20200917)
Requirement already satisfied: wheel>=0.26; python_version >= “3” in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard==2.0.2->-r requirements-freeze.txt (line 64)) (0.35.1)
Installing collected packages: six, absl-py, astor, attrs, cachetools, certifi, pycparser, cffi, chardet, coverage, cryptography, cycler, decorator, numpy, h5py, nibabel, scipy, dipy, futures, gast, pyasn1, rsa, pyasn1-modules, google-auth, oauthlib, idna, urllib3, requests, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, PyYAML, Keras-Preprocessing, Keras-Applications, Keras, kiwisolver, Markdown, python-dateutil, pyparsing, matplotlib, networkx, opt-einsum, packaging, pytz, pandas, pluggy, protobuf, psutil, py, pyOpenSSL, PyQt5-sip, PyQt5, wcwidth, pytest, pytest-cov, PyWavelets, raven, scikit-image, scikit-learn, Werkzeug, tensorboard, termcolor, wrapt, tensorflow-estimator, tensorflow, tqdm, transforms3d, xlrd, xlwt, xlutils
Attempting uninstall: certifi
Found existing installation: certifi 2020.6.20
Uninstalling certifi-2020.6.20:
Successfully uninstalled certifi-2020.6.20
Attempting uninstall: numpy
Found existing installation: numpy 1.19.2
Uninstalling numpy-1.19.2:
Successfully uninstalled numpy-1.19.2
Successfully installed Keras-2.3.1 Keras-Applications-1.0.8 Keras-Preprocessing-1.1.0 Markdown-3.1.1 Pillow-6.2.1 PyQt5-5.11.3 PyQt5-sip-4.19.19 PyWavelets-1.1.1 PyYAML-5.2 Werkzeug-0.16.0 absl-py-0.9.0 astor-0.8.1 attrs-19.3.0 cachetools-4.0.0 certifi-2019.11.28 cffi-1.13.2 chardet-3.0.4 coverage-5.0 cryptography-2.8 cycler-0.10.0 decorator-4.4.1 dipy-1.0.0 futures-3.1.1 gast-0.2.2 google-auth-1.10.0 google-auth-oauthlib-0.4.1 google-pasta-0.1.8 grpcio-1.26.0 h5py-2.10.0 idna-2.8 imageio-2.6.1 importlib-metadata-1.3.0 joblib-0.14.1 kiwisolver-1.1.0 matplotlib-3.1.2 more-itertools-8.0.2 networkx-2.4 nibabel-3.0.0 numpy-1.17.4 oauthlib-3.1.0 opt-einsum-3.1.0 packaging-19.2 pandas-0.25.3 pluggy-0.13.1 protobuf-3.11.1 psutil-5.6.7 py-1.8.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.7 pycparser-2.19 pyparsing-2.4.5 pytest-5.3.2 pytest-cov-2.8.1 python-dateutil-2.8.1 pytz-2019.3 raven-6.10.0 requests-2.22.0 requests-oauthlib-1.3.0 rsa-4.0 scikit-image-0.16.2 scikit-learn-0.22 scipy-1.4.0 six-1.13.0 tensorboard-2.0.2 tensorflow-2.0.1 tensorflow-estimator-2.0.1 termcolor-1.1.0 tqdm-4.40.2 transforms3d-0.3.1 urllib3-1.25.7 wcwidth-0.1.7 wrapt-1.11.2 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0 zipp-0.6.0
Obtaining file:///mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2
Installing collected packages: spinalcordtoolbox
Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox
Creating launchers for Python scripts…
Make shell scripts executable…
Creating symbolic links for Shell scripts…
Installing binaries…
sct_download_data -d binaries_debian -o /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/bin
–
Spinal Cord Toolbox (4.2.2)
Folder /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/bin has been created.
Trying URL: https://osf.io/bt58d/?action=download
Downloading 20190930_sct_binaries_linux.tar.gz…
Status: 100%|##################################################################################################| 81.1M/81.1M [00:02<00:00, 29.1MB/s]
Create temporary folder (/tmp/sct-20201002105056.510042-9ig2r420)…
Unzip data to: /tmp/sct-20201002105056.510042-9ig2r420
Check if folder already exists on the destination path…
Remove temporary folders…
Done!
All requirements installed!
. /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python/bin/activate /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/python
Installing data…
rm -rf /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/data
mkdir -p /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/data
cd /mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/data
sct_download_data -d PAM50
–
Spinal Cord Toolbox (4.2.2)
Trying URL: https://osf.io/u79sr/?pid=6zbyf/?action=download
Unexpected: link doesn’t provide a filename
Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20191029_PAM50.zip
Unexpected: link doesn’t provide a filename
Download error
Create temporary folder (/tmp/sct-20201002105100.407639-oq5wqhhb)…
Unzip data to: /tmp/sct-20201002105100.407639-oq5wqhhb
Traceback (most recent call last):
File “/mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/scripts/sct_download_data.py”, line 248, in
res = main()
File “/mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/scripts/sct_download_data.py”, line 140, in main
unzip(tmp_file, dest_tmp_folder, verbose)
File “/mnt/store1/projects/atassia/ENIGMA_spinal_cord/sct_v4.2.2/scripts/sct_download_data.py”, line 174, in unzip
if compressed.endswith(‘zip’):
AttributeError: ‘NoneType’ object has no attribute ‘endswith’
ERROR: Command failed.
Installation failed!
Please copy the historic of this Terminal (starting with the command install_sct) and paste it in a new created topic on SCT’s forum: