When trying to install SCT in my computer I get the following error:
*******************************
* Welcome to SCT installation *
*******************************
Checking OS type and version...
Linux beatrix 3.16.0-10-amd64 #1 SMP Debian 3.16.81-1 (2020-01-17) x86_64 GNU/Linux
Checking requirements...
OK!
SCT version ......... 5.3.0
Installation type ... package
Operating system .... linux (unknown)
Shell config ........ /home/rosella/.bashrc
Then everything is ok until sct_check_dependencies:
–
Spinal Cord Toolbox (5.3.0)
sct_check_dependencies
--
SCT info:
- version: 5.3.0
- path: /home/rosella/sct_5.3.0
OS: linux (Linux-3.16.0-10-amd64-x86_64-with-debian-8.11)
CPU cores: Available: 40, Used by ITK functions: 40
RAM: Total: 258243MB, Used: 11427MB, Available: 245879MB
Check Python executable.............................[OK]
Using bundled python 3.6.13 |Anaconda, Inc.| (default, Feb 23 2021, 21:15:04)
[GCC 7.3.0] at /home/rosella/sct_5.3.0/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] (1.4.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.1.5) is installed.................[OK] (2.1.5)
Check if ivadomed is installed......................Generating new fontManager, this may take some time...
[OK] (2.7.4)
Check if matplotlib is installed....................[OK] (3.3.4)
Check if nibabel is installed.......................[OK] (3.2.1)
Check if numpy is installed.........................[OK] (1.19.5)
Check if onnxruntime (1.4.0) is installed.........../home/rosella/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/onnxruntime/capi/_pybind_state.py:14: UserWarning: Cannot load onnxruntime.capi. Error: 'dlopen: cannot load any more object with static TLS'.
warnings.warn("Cannot load onnxruntime.capi. Error: '{0}'.".format(str(e)))
[FAIL]
cannot import name 'get_all_providers'
Check if pandas is installed........................[OK] (1.1.5)
Check if psutil is installed........................[OK] (5.8.0)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (6.2.3)
Check if pytest-cov is installed....................[OK] (__version__ = '2.11.1')
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.25.1)
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..................[FAIL]
dlopen: cannot load any more object with static TLS
It seems that scikit-image has not been built correctly.
Your install of scikit-image appears to be broken.
Try re-installing the package following the instructions at:
https://scikit-image.org/docs/stable/install.html
Check if scikit-learn is installed..................[FAIL]
dlopen: cannot load any more object with static TLS
___________________________________________________________________________
Contents of /home/rosella/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/sklearn/__check_build:
setup.py __pycache__ __init__.py
_check_build.cpython-36m-x86_64-linux-gnu.so
___________________________________________________________________________
It seems that scikit-learn has not been built correctly.
If you have installed scikit-learn from source, please do not forget
to build the package before using it: run `python setup.py install` or
`make` in the source directory.
If you have used an installer, please check that it is suited for your
Python version, your operating system and your platform.
Check if tensorflow (1.5.0) is installed............[OK] (1.5.0)
Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu)
Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.60.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.26.4)
Check if pytest_console_scripts is installed........[OK]
Check if wquantiles is installed....................[OK] (0.4)
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.............Traceback (most recent call last):
File "/home/rosella/sct_5.3.0/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 347, in <module>
main(sys.argv[1:])
File "/home/rosella/sct_5.3.0/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 327, in main
from PyQt5.QtWidgets import QApplication, QLabel
ImportError: dlopen: cannot load any more object with static TLS
Installation validation Failed!
Installation failed!
My OS features are:
Distributor ID: Debian
Description: Debian GNU/Linux 8.11 (jessie)
Release: 8.11
Codename: jessie
I have Python 3.8.5 installed through conda package
thanks a lot
Rosella
