uFBA : error when testing it (testuFBA)

[CcileMoul1]

Hi everyone,

I recently installed CobraToolbox as well as Gurobi version 9.50 in order to use uFBA. However, when I run the test function testuFBA, I have the following message

Each model.subSystems{x} is a character array, and this format is retained.

 > changeCobraSolver: Gurobi interface added to MATLAB path.

 > changeCobraSolver: Gurobi interface added to MATLAB path.

 > changeCobraSolver: Gurobi interface added to MATLAB path.

 > changeCobraSolver: Gurobi interface added to MATLAB path.

 > changeCobraSolver: Gurobi interface added to MATLAB path.

 > changeCobraSolver: Gurobi interface added to MATLAB path.
Error using testuFBA (line 99)
Solution incorrect to 2 decimals.

Line 99 is

assert(sol.f > 0.225 & sol.f < 0.235, 'Solution incorrect to 2 decimals.')

with sol.f = 0.1431 on my computer.

I'm quite confused by this results and I don't know what to conclude. Do I have a "wrong" solver ? If it's a solver problem, how to trust the results as it seems they might change according to the solver or its version (I don't know if 0.1431 is far from 0.225/0.235 in the context of the test). If it's not a solver problem, where does this difference come from ?

Thanks for your help

I hereby confirm that I have:

• [X] Tried to solve the issue on my own
• [X] Retried to run my code with the latest version of The COBRA Toolbox
• [X] Checked that a similar issue has not already been opened

[rmtfleming]

Hi Cecile,

I get almost the same solution. Perhaps Aarash can provide a pointer as to the issue?

Regards,

Ronan

sol =

struct with fields:

origStatText: []
           f: 0.1442
          f0: 0
          f1: 0
          f2: 0
           v: [232×1 double]
           y: [432×1 double]
           w: [232×1 double]
           s: [432×1 double]
      solver: 'gurobi'
   algorithm: 'default'
        stat: 1
    origStat: 'OPTIMAL'
        time: 0.0046
       basis: [1×1 struct]
      vars_v: []
           x: [232×1 double]

On Sun, 23 Jan 2022 at 19:02, Cécile Moulin @.***> wrote:

Hi everyone,

I recently installed CobraToolbox as well as Gurobi version 9.50 in order to use uFBA. However, when I run the test function testuFBA, I have the following message

Each model.subSystems{x} is a character array, and this format is retained.

changeCobraSolver: Gurobi interface added to MATLAB path.

changeCobraSolver: Gurobi interface added to MATLAB path.

changeCobraSolver: Gurobi interface added to MATLAB path.

changeCobraSolver: Gurobi interface added to MATLAB path.

changeCobraSolver: Gurobi interface added to MATLAB path.

changeCobraSolver: Gurobi interface added to MATLAB path. Error using testuFBA (line 99) Solution incorrect to 2 decimals.

Line 99 is

assert(sol.f > 0.225 & sol.f < 0.235, 'Solution incorrect to 2 decimals.')

with sol.f = 0.1431 on my computer.

I'm quite confused by this results and I don't know what to conclude. Do I have a "wrong" solver ? If it's a solver problem, how to trust the results as it seems they might change according to the solver or its version (I don't know if 0.1431 is far from 0.225/0.235 in the context of the test). If it's not a solver problem, where does this difference come from ?

Thanks for your help

I hereby confirm that I have:

• Tried to solve the issue on my own
• Retried to run my code with the latest version of The COBRA Toolbox
• Checked that a similar issue has not already been opened

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

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