Installing SCT-7.0; Undefined symbol in ../site-packages/PyQt5/QtCore.so

SCT
1

Using the install script gives a undefined symbol error for shared object QtCore.so:

> ./install_sct-7.0_linux.sh

Check if pyqt5 (5.12.3) is installed................[FAIL]
An error occured while importing module pyqt5 -> /u3/SCT/sct_7.0/python/envs/venv_sct/lib/python3.9/site-packages/PyQt5/QtCore.so: undefined symbol: _ZdlPvm, version Qt_5
Full traceback: Traceback (most recent call last):
File "/u3/SCT/sct_6.5.dev0/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 364, in main
module = module_import(module_name, suppress_stderr)
File "/u3/SCT/sct_6.5.dev0/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 107, in module_import
module = importlib.import_module(module_name)
File "/u3/SCT/sct_7.0/python/envs/venv_sct/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 666, in _load_unlocked
File "", line 565, in module_from_spec
File "", line 1173, in create_module
File "", line 228, in _call_with_frames_removed
ImportError: /u3/SCT/sct_7.0/python/envs/venv_sct/lib/python3.9/site-packages/PyQt5/QtCore.so: undefined symbol: _ZdlPvm, version Qt_5

What could be the problem and how to fix it? I’m running the latest LTS version of UBUNTU-24.04.

Thank you for your help.

Jack van Asten.
(Radboud University Nijmegen, Netherlands).

2

Dear @Jack_van_Asten,

Thanks much for reporting this error! We’d be happy to help. :slight_smile:

The first thing I notice is that in the error log, there is mention of a secondary SCT installation (/u3/SCT/sct_6.5.dev0/ in addition to /u3/SCT/sct_7.0/). It appears that when the installer script executes the command “sct_check_dependencies”, what actually gets run is the sct_check_dependencies script from the old sct_6.5.dev0/ installation. This is strange!

Just to double-check a few things:

  • Could you try running the following command, which will show the location of the script?
    command -v sct_check_dependencies
  • Then, could you try running the command:
    sct_check_dependencies
    This is the same command that failed during the installation. But, we’re just running it outside of the ./install_sct-7.0-linux.sh context to see if the error persists.
  • If the error still occurs, could you try temporarily renaming the folder sct_6.5.dev0 to something else? (This is just a test to see if temporarily removing the sct_6.5.dev0 folder will change how the 7.0 scripts run.)

Thank you kindly for your patience and understanding while we resolve this issue.

Kind regards,
Joshua

3

Hi Joshua,

Thank you very much for your quick response!

The former SCT version is still intact indeed:

which sct_check_dependencies
/u3/SCT/sct_6.5.dev0/bin/sct_check_dependencies
env |grep SCT_DIR
SCT_DIR=/u3/SCT/sct_6.5.dev0

I will run the install script install_sct-7.0_linux_into_u3_SCT.sh again with an empty environment variable SCT_DIR and changed former sct directory (to /u3/SCT/sct_6.5.dev0_).

I changed the install script slightly, to install SCT into a location that is accessible to several users at several servers.

Regards Jack.

4

Dear Joshua,

Unfortunately, the installation of SCT-7.0 still fails for the PyQt5 package. Again with the same ‘undefined symbol: _ZdlPvm’ error. See the attached ‘install_sct_log.txt’ file. We need this package to be able to re-label certain vertebra segmentations, in a comfortable manner.

By the way, to be able to install SCT in a custom directory, I changed this:

diff install_sct-7.0_linux.sh install_sct-7.0_linux_into_u3_SCT.sh
484c484,486
<   SCT_DIR="$HOME/sct_$SCT_VERSION"
---
>   #JvA:20241121; Install in custom directory.
>   #SCT_DIR="$HOME/sct_$SCT_VERSION"
>   SCT_DIR="/u3/SCT/sct_$SCT_VERSION"

Maybe, this would be a nice extra option to the installation script? To offer the possibility of a custom installation directory?

Thanks again in advance for your help.

Kind regards,
Jack van Asten.
(Radboud University Nijmegen, the Netherlands).

5

Maybe, this would be a nice extra option to the installation script? To offer the possibility of a custom installation directory?

Out of curiosity, are you running the script with the option -y? I ask because, if -y is not provided, then the script should prompt for the option to change the installation directory:

image
image693×397 32.3 KB

Please let me know if you don’t see this prompt!

See the attached ‘install_sct_log.txt’ file.

My apologies, but I don’t see any attachments. Perhaps I’m missing something, but would you be able to reupload this file?

Thanks much! :slight_smile:

6

Dear Joshua,

Thank you for your response.

I hope you can now receive the sct installation log file (apparently, the ‘upload’ button did not work):
install_sct_log.txt.gz (21.1 KB)
This is the log file, in which the Qt5 package error ‘undefined symbol: _ZdlPvm’ occurs.

I made some progress though, because I managed to install the toolbox on another Linux server (younger hardware, but same OS, UBUNTU-24.04.2 LTS) without any errors.

So, I guess the error message correlates with contradictory python versions? I would not expect this because the sct has it’s own python environment installed, isn’t it?

The command,
ldd /u3/SCT/sct_7.0/python/envs/venv_sct/lib/python3.9/site-packages/PyQt5/QtWidgets.so
shows no missing libraries. Do you maybe have another way to sought this out?

Last but not least, I owe you an apology because the installation scripts indeed offers the possibility to install SCT in a custom subdirectory. I completely overlooked that.

Again many thanks for your help.

Regards,
Jack van Asten.
(Radboud University Nijmegen, the Netherlands.

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