Thomas Pfau

There seems to be some issue with your internet connection having hickups. I don't think a lot can be done there. You can try to manually check out the submodules...

The problem with providing a zip for the toolbox is that it's over 1 Gb. So that's not really an option. But maybe you could try to update the submodules...

If they are all extracted to the respective folders, than you should be able to run `initCobraToolbox`. It might still show some warnings, but it should finish.

Could you try: initCobraToolbox(0) And if that doesn't work in addition comment out lines 190-243 in initCobraToolbox (that's where the submodules are initialized).

What is your call to fluxVariability? Could you post the line?

This should work for all I can see. I currently can't test anything since I don't have a working Matlab copy, so I'm sorry about this. Since this seems to...

This is likely due to the runGapFill_example.m file using load instead of readCbModel, and the models having inconsistent fields in the .mat file. if you replace the line: model =...

Could you post the full error message along with the function call that caused the issue?

Did you initialize the toolbox before running gapFind via initCobraToolbox? And: do you have a working MILP solver installed?

What model are you using?