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euba / BacArena

agent based modelling
GNU General Public License v3.0
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Explanation of warnings #151

Closed maringos closed 4 years ago

maringos commented 5 years ago

Dear All,

I would like to ask you to remind me of what the following warnings mean. I remember @jotech has explained them in person, but I cannot recall.

"Median lower bound for non-zero and non-Inf exchanges is:06"
Warning message:
In Organism(model = model, ...) :
  Many lower bounds of of the model seems to be set to non -infinity. Please be aware that they will be used as maximal uptake rates even when the available medium is more abundant! (set setAllExInf=TRUE to reset all exchanges to -INF)

Regards, Georgios

hites77 commented 4 years ago

I am getting the same issue for one of my genome model

jotech commented 4 years ago

https://github.com/jotech/gapseq/issues/43

jotech commented 4 years ago

the default behavior was changed to setAllExInf=TRUE from now on. The warning should not be occur anymore. For a discussion of the background please refer to https://github.com/jotech/gapseq/issues/43

also reopen issue if things are still unclear