Installation failed - problem with anaconda?

SCT
1

Hi,

I tried to install the newest sct-version (ubuntu 20.04, windows 10, 64bit) but the installation failed several times. I attached the error - message in a txt-file.
Do you have any idea how to solve the problem?

Looking forward to your answer!

Thanks,
Hanna.

2

Hi @Hanna

Thank you for reaching out and sorry you are experiencing difficulties in installing SCT. I cannot see your txt file, could you please attach it again?

Cheers,
Julien

3

error.txt (6.0 KB)

Thanks again,
Hanna

4

Hi @Hanna!

Based on your error, it looks like conda is having trouble connecting to the anaconda.com servers. Sometimes this can be caused by location/country. So, one possible solution is to use a third-party mirror as an alternative to anaconda.com.

To do this, I would recommend following the suggestions from this guide:

  1. Edit the file /home/hanna/.condarc and add the lines below. (If the file does not exist, create it first.)

    channels:
  - defaults
show_channel_urls: true
default_channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2
custom_channels:
  conda-forge: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  msys2: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  bioconda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  menpo: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  pytorch: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  simpleitk: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud

    These new channels should allow you to connect to the TUNA mirrors instead of anaconda.com.

  2. Re-run install_sct.

I hope this helps. :slightly_smiling_face:

Kind regards,
Joshua

5

Hi,
thank you for your answer but it does not work and the installation produces a similar error message.
I think it might be a problem with the combination of ubuntu 20.4 & wsl & conda --> I tried the installation on an older Ubuntu version on another computer and it worked (but I cannot use the computer for the analysis).
I’ll try to find a solution. (Rebooting of wsl/ubuntu did not solve the problem).

Kind regards,
Hanna.

6

You may also want to try the remaining combinations, too:

  • Other computer + Ubuntu 20.04
  • Same computer + Older Ubuntu

That way, you can isolate the problem, and determine if it is due to the Ubuntu version, or the computer itself.

Please let me know if you have any other questions or concerns, and I will be happy to help troubleshoot. :slightly_smiling_face:

Kind regards,
Joshua

7

Hi @Hanna,

I just wanted to let you know that we encountered this issue again, and this time we were able to determine the cause, as well as introduce a fix. You were correct – it was indeed because of Ubuntu 20.04 + WSL.

The fix was backported to SCT v5.4, which you can download here: https://github.com/spinalcordtoolbox/spinalcordtoolbox/releases/tag/5.4

Could you let me know if this version of SCT installs OK for you?

Kind regards,
Joshua

8

Hi Joshua,

I will try it and will give you a feedback.

Thanks,
Hanna

9

I have the same issue that i always failed when using any ‘conda …’ command
I have tried your suggestion and it really helps me
Thank you very much Joshua.
May God bless you~~

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