Installing SCT 4.3 fails: pycache not empty

pelegrini · September 17, 2020, 3:11pm

Hi all,

Installation of SCT 4.3 suceeds on Linux CentOS 7 in my home account.

But it fails if I try to install it in another directory. The characteristic of this directory is that it is an NFS mount. Below is the installation backtrace

./install_sct

Welcome to SCT installation *

Checking OS type and version…

Linux imed137.lib.upmc.fr 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements…

OK!

SCT version … 4.3
Installation type … package
Operating system … linux (unknown)
Shell config … /home_local/pelegrin/.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: y

–> Crash reports will be sent to the SCT development team. Thank you!

SCT will be installed here: [/home_local/pelegrin/sct_4.3]

Do you agree? [y]es/[n]o: n

Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0):
/coconut/applis/bin/x86_64/sct_v4.3

Copying source files from /coconut/applis/bin/x86_64/spinalcordtoolbox-4.3 to /coconut/applis/bin/x86_64/sct_v4.3

…
Installing conda…

rm -rf /coconut/applis/bin/x86_64/sct_v4.3/python

mkdir -p /coconut/applis/bin/x86_64/sct_v4.3/python

wget -O /tmp/tmp.oEQQkEjON8/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

–2020-09-17 16:25:58-- https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Résolution de repo.continuum.io (repo.continuum.io)… 104.18.201.79, 104.18.200.79, 2606:4700::6812:c94f, …
Connexion vers repo.continuum.io (repo.continuum.io)|104.18.201.79|:443…connecté.
requête HTTP transmise, en attente de la réponse…301 Moved Permanently
Emplacement: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [suivant]
–2020-09-17 16:25:58-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Résolution de repo.anaconda.com (repo.anaconda.com)… 104.16.131.3, 104.16.130.3, 2606:4700::6810:8203, …
Connexion vers repo.anaconda.com (repo.anaconda.com)|104.16.131.3|:443…connecté.
requête HTTP transmise, en attente de la réponse…200 OK
Longueur: 93052469 (89M) [application/x-sh]
Sauvegarde en : «/tmp/tmp.oEQQkEjON8/miniconda.sh»

100%[===========================================================================================================>] 93 052 469 28,6MB/s ds 3,1s

2020-09-17 16:26:01 (28,6 MB/s) - «/tmp/tmp.oEQQkEjON8/miniconda.sh» sauvegardé [93052469/93052469]

exit status is 0

bash /tmp/tmp.oEQQkEjON8/miniconda.sh -p /coconut/applis/bin/x86_64/sct_v4.3/python -b -f

PREFIX=/coconut/applis/bin/x86_64/sct_v4.3/python
Unpacking payload …
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /coconut/applis/bin/x86_64/sct_v4.3/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: 4.8.4

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /coconut/applis/bin/x86_64/sct_v4.3/python/envs/venv_sct

added / updated specs:
- python=3.6

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
ca-certificates-2020.7.22  |                0         125 KB
certifi-2020.6.20          |           py36_0         156 KB
libedit-3.1.20191231       |       h14c3975_1         116 KB
libffi-3.3                 |       he6710b0_2          50 KB
pip-20.2.2                 |           py36_0         1.8 MB
python-3.6.12              |       hcff3b4d_2        29.7 MB
setuptools-49.6.0          |           py36_0         757 KB
sqlite-3.33.0              |       h62c20be_0         1.1 MB
tk-8.6.10                  |       hbc83047_0         3.0 MB
wheel-0.35.1               |             py_0          37 KB
------------------------------------------------------------
                                       Total:        36.8 MB

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-2020.7.22-0
certifi pkgs/main/linux-64::certifi-2020.6.20-py36_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
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-20.2.2-py36_0
python pkgs/main/linux-64::python-3.6.12-hcff3b4d_2
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-49.6.0-py36_0
sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0
wheel pkgs/main/noarch::wheel-0.35.1-py_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Proceed ([y]/n)?

Downloading and Extracting Packages
pip-20.2.2 | 1.8 MB | ########################################################################################################## | 100%
wheel-0.35.1 | 37 KB | ########################################################################################################## | 100%
python-3.6.12 | 29.7 MB | ########################################################################################################## | 100%
tk-8.6.10 | 3.0 MB | ########################################################################################################## | 100%
certifi-2020.6.20 | 156 KB | ########################################################################################################## | 100%
libffi-3.3 | 50 KB | ########################################################################################################## | 100%
libedit-3.1.20191231 | 116 KB | ########################################################################################################## | 100%
setuptools-49.6.0 | 757 KB | ########################################################################################################## | 100%
sqlite-3.33.0 | 1.1 MB | ########################################################################################################## | 100%
ca-certificates-2020 | 125 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)

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 /home_local/pelegrin/.cache/pip/wheels/c3/af/84/3962a6af7b4ab336e951b7877dcfb758cf94548bb1771e0679/absl_py-0.9.0-py3-none-any.whl
Collecting attrs==19.3.0
Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting bids-neuropoly==0.2
Using cached bids_neuropoly-0.2-py3-none-any.whl (3.1 kB)
Collecting bids-validator==1.5.2
Using cached bids_validator-1.5.2-py2.py3-none-any.whl (14 kB)
Collecting bleach==1.5.0
Using cached bleach-1.5.0-py2.py3-none-any.whl (17 kB)
Collecting cachetools==4.1.0
Using cached cachetools-4.1.0-py3-none-any.whl (10 kB)
Collecting certifi==2020.4.5.2
Using cached certifi-2020.4.5.2-py2.py3-none-any.whl (157 kB)
Collecting cffi==1.14.0
Using cached cffi-1.14.0-cp36-cp36m-manylinux1_x86_64.whl (399 kB)
Collecting chardet==3.0.4
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Processing /home_local/pelegrin/.cache/pip/wheels/b7/be/ae/a98f7701429c3cfcebf4d2b537e48a1571549a4d8b55463a01/colored-1.4.2-py3-none-any.whl
Collecting coverage==5.1
Using cached coverage-5.1-cp36-cp36m-manylinux1_x86_64.whl (227 kB)
Collecting cryptography==2.9.2
Using cached cryptography-2.9.2-cp35-abi3-manylinux2010_x86_64.whl (2.7 MB)
Collecting cycler==0.10.0
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting decorator==4.4.2
Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting dipy==1.1.1
Using cached dipy-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (8.1 MB)
Processing /home_local/pelegrin/.cache/pip/wheels/3f/2a/fa/4d7a888e69774d5e6e855d190a8a51b357d77cc05eb1c097c9/docopt-0.6.2-py2.py3-none-any.whl
Processing /home_local/pelegrin/.cache/pip/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94/future-0.18.2-py3-none-any.whl
Collecting futures==3.1.1
Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Collecting google-auth==1.17.0
Using cached google_auth-1.17.0-py2.py3-none-any.whl (90 kB)
Collecting google-auth-oauthlib==0.4.1
Using cached google_auth_oauthlib-0.4.1-py2.py3-none-any.whl (18 kB)
Collecting grpcio==1.29.0
Using cached grpcio-1.29.0-cp36-cp36m-manylinux2010_x86_64.whl (3.0 MB)
Collecting h5py==2.10.0
Using cached h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Processing /home_local/pelegrin/.cache/pip/wheels/90/1c/cb/a87fd097ff74648ecc468a703001f6c7c86d8a71d459e65c98/html5lib-0.9999999-py3-none-any.whl
Collecting idna==2.9
Using cached idna-2.9-py2.py3-none-any.whl (58 kB)
Collecting imageio==2.8.0
Using cached imageio-2.8.0-py3-none-any.whl (3.3 MB)
Collecting importlib-metadata==1.6.1
Using cached importlib_metadata-1.6.1-py2.py3-none-any.whl (31 kB)
Collecting ivadomed==1.2.1
Using cached ivadomed-1.2.1-py3-none-any.whl (68 kB)
Collecting joblib==0.15.1
Using cached joblib-0.15.1-py3-none-any.whl (298 kB)
Collecting Keras==2.1.5
Using cached Keras-2.1.5-py2.py3-none-any.whl (334 kB)
Collecting kiwisolver==1.2.0
Using cached kiwisolver-1.2.0-cp36-cp36m-manylinux1_x86_64.whl (88 kB)
Collecting Markdown==3.2.2
Using cached Markdown-3.2.2-py3-none-any.whl (88 kB)
Collecting matplotlib==3.2.1
Using cached matplotlib-3.2.1-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB)
Collecting more-itertools==8.3.0
Using cached more_itertools-8.3.0-py3-none-any.whl (44 kB)
Collecting networkx==2.4
Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting nibabel==3.1.0
Using cached nibabel-3.1.0-py3-none-any.whl (3.3 MB)
Collecting num2words==0.5.10
Using cached num2words-0.5.10-py3-none-any.whl (101 kB)
Collecting numpy==1.18.5
Using cached numpy-1.18.5-cp36-cp36m-manylinux1_x86_64.whl (20.1 MB)
Collecting oauthlib==3.1.0
Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB)
Collecting onnx==1.7.0
Using cached onnx-1.7.0-cp36-cp36m-manylinux1_x86_64.whl (7.4 MB)
Collecting onnxruntime==1.3.0
Using cached onnxruntime-1.3.0-cp36-cp36m-manylinux1_x86_64.whl (3.9 MB)
Collecting packaging==20.4
Using cached packaging-20.4-py2.py3-none-any.whl (37 kB)
Collecting pandas==1.0.4
Using cached pandas-1.0.4-cp36-cp36m-manylinux1_x86_64.whl (10.1 MB)
Collecting patsy==0.5.1
Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Collecting Pillow==7.1.2
Using cached Pillow-7.1.2-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==3.12.2
Using cached protobuf-3.12.2-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB)
Collecting py==1.8.1
Using cached py-1.8.1-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==0.2.8
Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
Collecting pybids==0.10.2
Using cached pybids-0.10.2-py2.py3-none-any.whl (3.1 MB)
Collecting pycparser==2.20
Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB)
Collecting pyOpenSSL==19.1.0
Using cached pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB)
Collecting pyparsing==2.4.7
Using cached pyparsing-2.4.7-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==5.4.3
Using cached pytest-5.4.3-py3-none-any.whl (248 kB)
Collecting pytest-cov==2.9.0
Using cached pytest_cov-2.9.0-py2.py3-none-any.whl (19 kB)
Collecting python-dateutil==2.8.1
Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pytz==2020.1
Using cached pytz-2020.1-py2.py3-none-any.whl (510 kB)
Collecting PyWavelets==1.1.1
Using cached PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB)
Processing /home_local/pelegrin/.cache/pip/wheels/e5/9d/ad/2ee53cf262cba1ffd8afe1487eef788ea3f260b7e6232a80fc/PyYAML-5.3.1-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==2.23.0
Using cached requests-2.23.0-py2.py3-none-any.whl (58 kB)
Collecting requests-oauthlib==1.3.0
Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Processing /home_local/pelegrin/.cache/pip/wheels/80/af/bd/32c202b632c3e9a1b482b33d37f5efd128137891a08f3c3bae/requirements_parser-0.2.0-py3-none-any.whl
Processing /home_local/pelegrin/.cache/pip/wheels/28/6c/d1/56076f8482025758c86414d5c9d1fb19748149bd15434861c3/rsa-4.2-py2.py3-none-any.whl
Collecting scikit-image==0.17.2
Using cached scikit_image-0.17.2-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB)
Collecting scikit-learn==0.23.1
Using cached scikit_learn-0.23.1-cp36-cp36m-manylinux1_x86_64.whl (6.8 MB)
Collecting scipy==1.4.1
Using cached scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB)
Collecting seaborn==0.10.1
Using cached seaborn-0.10.1-py3-none-any.whl (215 kB)
Collecting six==1.15.0
Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting SQLAlchemy==1.3.17
Using cached SQLAlchemy-1.3.17-cp36-cp36m-manylinux2010_x86_64.whl (1.2 MB)
Collecting tensorboard==2.2.2
Using cached tensorboard-2.2.2-py3-none-any.whl (3.0 MB)
Collecting tensorboard-plugin-wit==1.6.0.post3
Using cached tensorboard_plugin_wit-1.6.0.post3-py3-none-any.whl (777 kB)
Collecting tensorflow==1.5.0
Using cached tensorflow-1.5.0-cp36-cp36m-manylinux1_x86_64.whl (44.4 MB)
Collecting tensorflow-tensorboard==1.5.1
Using cached tensorflow_tensorboard-1.5.1-py3-none-any.whl (3.0 MB)
Collecting threadpoolctl==2.1.0
Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Collecting tifffile==2020.6.3
Using cached tifffile-2020.6.3-py3-none-any.whl (133 kB)
Collecting torch==1.5.0+cpu
Using cached https://download.pytorch.org/whl/cpu/torch-1.5.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (127.3 MB)
Collecting torchvision==0.6.0+cpu
Using cached https://download.pytorch.org/whl/cpu/torchvision-0.6.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (5.7 MB)
Collecting tqdm==4.46.1
Using cached tqdm-4.46.1-py2.py3-none-any.whl (63 kB)
Processing /home_local/pelegrin/.cache/pip/wheels/be/7a/eb/465e9bb085af816c4d504821d542cc0059cc3433f6e8edea3c/transforms3d-0.3.1-py3-none-any.whl
Collecting typing-extensions==3.7.4.2
Using cached typing_extensions-3.7.4.2-py3-none-any.whl (22 kB)
Collecting urllib3==1.25.9
Using cached urllib3-1.25.9-py2.py3-none-any.whl (126 kB)
Collecting wcwidth==0.2.4
Using cached wcwidth-0.2.4-py2.py3-none-any.whl (30 kB)
Collecting Werkzeug==1.0.1
Using cached Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
Collecting xlwt==1.3.0
Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Collecting zipp==3.1.0
Using cached zipp-3.1.0-py3-none-any.whl (4.9 kB)
Requirement already satisfied: setuptools>=40.3.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth==1.17.0->-r requirements-freeze.txt (line 19)) (49.6.0.post20200814)
Requirement already satisfied: wheel>=0.26; python_version >= “3” in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard==2.2.2->-r requirements-freeze.txt (line 73)) (0.35.1)
Installing collected packages: six, absl-py, attrs, pyparsing, packaging, numpy, nibabel, python-dateutil, pytz, pandas, patsy, scipy, docopt, num2words, SQLAlchemy, bids-validator, pybids, bids-neuropoly, html5lib, bleach, cachetools, certifi, pycparser, cffi, chardet, colored, coverage, cryptography, cycler, decorator, h5py, dipy, future, futures, pyasn1, pyasn1-modules, rsa, google-auth, idna, urllib3, requests, oauthlib, requests-oauthlib, google-auth-oauthlib, grpcio, Pillow, imageio, zipp, importlib-metadata, tqdm, Markdown, tensorboard-plugin-wit, Werkzeug, protobuf, tensorboard, kiwisolver, matplotlib, seaborn, torch, tifffile, PyWavelets, networkx, scikit-image, torchvision, typing-extensions, onnx, onnxruntime, py, wcwidth, pluggy, more-itertools, pytest, threadpoolctl, joblib, scikit-learn, ivadomed, PyYAML, Keras, pyOpenSSL, PyQt5-sip, PyQt5, pytest-cov, raven, requirements-parser, tensorflow-tensorboard, tensorflow, transforms3d, xlwt
Attempting uninstall: numpy
Found existing installation: numpy 1.19.2
Uninstalling numpy-1.19.2:
Successfully uninstalled numpy-1.19.2
ERROR: Could not install packages due to an EnvironmentError: [Errno 39] Le dossier n’est pas vide: ‘pycache’

ajora · September 17, 2020, 4:58pm

Hello,

I don’t think we test installations on NFS drives. Could you retry the installation with the verbose flag -> ./install_sct -v and post the output again? Maybe also try in a folder that isn’t at the root of the NFS mount (if it was before).

Regards,

pelegrini · September 18, 2020, 11:52am

Thank you for your reply

I cannot paste below the entire log of my new try in a different location (but still on the NFS mount), which resulted in a different error though :-/
It exceeds the allowed 32000 characters… But you can download it here
https://filesender.renater.fr/?s=download&token=50e132c0-7344-4500-a079-7bc4f7ae14bb

Maybe a workaround: since I am able to install the SCT in my home directory, is it possible to move the install directory to another location (preserving all links etc.)? I really need to put it on the NFS mount so that it is available to other users (I was able to do this until v.4.0.0 (incl.)).

ajora · September 18, 2020, 12:46pm

Hello,

Thank you for your patience. The provided log hints to an issue with the installation of numpy. Coincidentally we recently made a change related to this to mitigate an issue that occurred in some specific environments. I would like to know if what you are experiencing is a side-effect of this.

Could you try to run the installer again on the NFS, but this time comment the line 532 from the installation script:

pip install numpy -> #pip install numpy

It would be preferable to follow the officially supported installation methods. Copying the installation folder on drives shared by multiple systems may or may not work, it depends on what type of systems are using it, what libraries they have installed, etc.

Thanks,

pelegrini · September 18, 2020, 1:47pm

Thanks a lot again, the install script runs fine once line 532 is commented. You’ll find the log file here
https://filesender.renater.fr/?s=download&token=1312c18e-0fc6-449f-80aa-9757c510c6c6

I also ran sct_testing and here’s the output:

output of sct_testing

–
Spinal Cord Toolbox (4.3)

Trying URL: https://osf.io/yutrj/?action=download
Downloading: 20191031_sct_testing_data.zip
Status: 1%|\u2588 | 65.5k/6.78M [00:00<00:11, 589Status: 3%|\u2588\u2588\u2589 | 180k/6.78M [00:00<Status: 6%|\u2588\u2588\u2588\u2588\u2588\u2588 | 377Status: 12%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2589 Status: 27%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588Status: 55%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\Status: 86%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\uStatus: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 6.78M/6.78M [00:00<00:00, 8.86MB/s]
Creating temporary folder (/tmp/sct-20200918154129.685491-b8fpnup4)
Unzip data to: /tmp/sct-20200918154129.685491-b8fpnup4
Destination folder: /coconut/applis/src/spinalcordtoolbox-4.3
Checking if folder already exists…
Removing temporary folders…
Done!

Will run through the following tests:

sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
in parallel with 32 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template
Checking sct_deepseg_gm…[OK]
Checking sct_deepseg_lesion…[OK]
Checking sct_deepseg_sc…[OK]
Checking sct_analyze_lesion…[OK]
Checking sct_analyze_texture…[OK]
Checking sct_apply_transfo…[OK]
Checking sct_convert…[OK]
Checking sct_compute_ernst_angle…[OK]
Checking sct_compute_hausdorff_distance…[OK]
Checking sct_compute_mtr…[OK]
Checking sct_compute_mscc…[OK]
Checking sct_compute_snr…[OK]
Checking sct_concat_transfo…[OK]
Checking sct_create_mask…[OK]
Checking sct_crop_image…[OK]
Checking sct_dice_coefficient…[OK]
Checking sct_detect_pmj…[OK]
Checking sct_dmri_compute_dti…[OK]
Checking sct_dmri_concat_b0_and_dwi…[OK]
Checking sct_dmri_concat_bvals…[OK]
Checking sct_dmri_concat_bvecs…[OK]
Checking sct_dmri_create_noisemask…[OK]
Checking sct_dmri_compute_bvalue…[OK]
Checking sct_dmri_moco…[OK]
Checking sct_dmri_separate_b0_and_dwi…[OK]
Checking sct_dmri_transpose_bvecs…[OK]
Checking sct_extract_metric…[OK]
Checking sct_flatten_sagittal…[OK]
Checking sct_fmri_compute_tsnr…[OK]
Checking sct_fmri_moco…[OK]
Checking sct_get_centerline…[OK]
Checking sct_image…[OK]
Checking sct_label_utils…[OK]
Checking sct_label_vertebrae…[OK]
Checking sct_maths…[OK]
Checking sct_merge_images…[OK]
Checking sct_process_segmentation…[OK]
Checking sct_propseg…[OK]
Checking sct_qc…[OK]
Checking sct_register_multimodal…[OK]
Checking sct_register_to_template…[OK]
Checking sct_resample…[OK]
Checking sct_smooth_spinalcord…[OK]
Checking sct_straighten_spinalcord…[OK]
Checking sct_warp_template…[OK]
status: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
Finished! Elapsed time: 223s

Installing SCT 4.3 fails: __pycache__ not empty

Package Plan

Package Plan

To activate this environment, use

$ conda activate venv_sct

To deactivate an active environment, use

$ conda deactivate

Installing SCT 4.3 fails: pycache not empty