Issue installing sct 7.0 on linux

SCT
1

Dear SCT team,

I’m trying to install the lastest version of SCT on my Linux. Currently, I have an old version of SCT, the 4.2.

It seems that the installation failed during the miniforge part. On my linux, I already have a miniconda environment.

I attach the log install_sct_log.txt (2.6 KB)

Any help would be appreciate !!

Thanks,

Emilie

2

Dear @Emilie_Poirion,

Thank you for your question! We would be happy to help. :slight_smile:

The error is as follows:

GnuTLS: Error in the pull function.
Incapable d’établir une connexion SSL.

curl: (35) OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to github.com:443

This error suggests that there is something wrong with your computer’s network, because the wget and curl commands are unable to access the website http://github.com (where the Miniforge installer is located).

There are many possible causes of this error. Sometimes resolving it is as simple as retrying, or restarting your computer.

If that doesn’t work, then resolving it fully will likely involve some trial and error. To make things easier, instead of retrying the SCT installer in your terminal every single time, you can instead run the following test command:

curl -o Miniforge.zip -L https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

I would recommend trying the fixes from the link I shared above, then retrying the curl command, and repeating. Once this curl command succeeds, it should be safe to proceed with the SCT installer.

Kind regards,
Joshua

3

Dear Joshua,

Thanks for your quick answer. I’ve tried many solutions and it seems that the problem comes from my linux version, Debian 10, that is too old to support communication process with Git.

Kind regards,

Emilie

4

Dear Emilie,

This is surprising to me! Because, SCT runs tests daily for Debian 10 to make sure that SCT installs successfully on this OS: Tests · spinalcordtoolbox/spinalcordtoolbox@3e3d36f · GitHub

Could you please try the following command instead?

curl -vvv --trace-config ssl,tcp -o Miniforge.zip -L https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh &> output.txt

This will produce a file called output.txt in your working directory, which will contain some logs that I can use to help debug. Could you then upload this file to the forum?

Thank you kindly,
Joshua