Problems with copasi on Debian 13 "Trixie"

[Marc Lefranc]

Dear all,

I am suddenly having a problem with launching CopasiUI on my computer, I
get a lot of errors which end by (after setting QT_DEBUG_PLUGINS=1,
complete log in attached file)

QLibraryPrivate::loadPlugin failed on
"/opt/COPASI/4.45.298/share/copasi/lib/plugins/platforms/libqxcb.so" :
"Cannot load library
/opt/COPASI/4.45.298/share/copasi/lib/plugins/platforms/libqxcb.so:
(/lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol:
FT_Done_MM_Var)"
This application failed to start because it could not find or load the
Qt platform plugin "xcb"
in "/opt/COPASI/4.45.298/share/copasi/lib/plugins".

Available platform plugins are: xcb.

Through googling, I could find a workaround that works: launching
Copasui with LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libfreetype.so.6 CopasiUI

However, all my basico-based Python scripts seem also to be broken. I
suspect a similar problem may be responsible and I do not know how to
solve them. What can I do ?

Thanks in advance,
best regards,
Marc

[Frank Bergmann]

It seems like the font library is no longer compatible with the Qt5 bundled with COPASI. I wonder if a Qt6 based snapshot would just work for you. If you would be willing to try this out i have a snapshot available here: 

https://heibox.uni-heidelberg.de/f/2f317120907d4c7db7e3/

This should have no influence on the python scripts. (That dont rely on Qt) Could you send me a list of errors, so i could have a look at it?

thank you

Frank

[Marc Lefranc]

Dear Frank, thank you for the snapshot, I will give it a try.

Regarding the scripts, this may indeed be due to something also related to the system update but not to Qt. 

It seems that the second time I call run_time_course but not the first, it fails thus:

Error while running the simulation: >EXCEPTION 2025-10-13T15:27:04<
  CTrajectoryMethod (25): Invalid state at time 'nan'.

Looks like time and state are filled with garbage. In Copasi UI, I can repeatedly run the time course task without problem.  Also the script worked before upgrading the machine to Debian 13. 

Best regards,
Marc

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[Marc Lefranc]

Hi again,

the snapshot does not have the problem, thanks.

Best

On 10/13/25 9:55 AM, Frank Bergmann wrote:

--

[Frank Bergmann]

Do you think it would be possible for you to send me the script / model privately? I'd be happy to debug, and ensure that this will continue to work as it did before. 

For whatever reasons NaNs were encountered during the simulation. That definitely should not happen, especially if it works with the GUI. 

If you want to o debug yourself, maybe you could set a breakpoint before the 2nd  run_time_course and instead call open_copasi(), this will open the model in the GUI, and you should be able to see what went wrong, or at least verify that the GUI behaves the same. 

best

Frank