MatLab crashing

[Vitor Geniselli]

Hello everyone,

I'm new to the COBRA Toolbox and have been trying for some days to run the simulations from the tutorial but without success.

My last installation check (by using the "testAll" function) reported that 2 tests were given errors "testBiomassPrecursorCheck" and "testMtFVA", which limited my application of the toolbox but I was still able to execute some basic functions. However, all of a sudden MatLab started crashing every time I initiate the toolbox. 

I don't know what is causing this crashing issue, which seems to be a compatibility problem. I also suppose that the previous errors in testAll could be related to the same cause. I've already tried to re-install both COBRA, solvers, compilers, MatLab, but without success.

I'm running the code on Windows 10, MatLab R2021b, IBM CPLEX 12.10, Gurobi 9.1.1, Mosek 9.2.

Is anyone having the same problem or had any similar difficulties in the past and know how to fix it?

Please find attached a print of my command window.

Thanks 

[Tim Hensen]

Hi Vitor,

Thank you for bringing up this problem. I also experienced MATLAB crashing when initialising the CobraToolbox. Going back to MATLAB 2020b solved the issue for me. However, a fix should be found for newer MATLAB versions. According my crash log, a mex file in CPLEX is trying to access restricted files in Windows, making MATLAB crash. Interestingly, the problem is not always reproducible for me. I am not sure why.

I was running MATLAB 2022a with cplex 12.10 on a Windows 10 system. I am on the latest CobraToolbox version. I added a log file with a bit more in-depth information about the crash logs. Feel free to look for solutions. I will also try to find a fix.

Best,
Tim

Op vrijdag 29 juli 2022 om 02:56:05 UTC+1 schreef vitorge...@gmail.com:

[Vitor Geniselli]

Hi Tim,

Thank you very much for your answer. Installing MatLab 2020b solved the crashing issue and right now I am able to execute some functions.

Unfortunately, I'm still having errors in executing the functions BiomassPrecursorCheck and mtFVA.

>> testBiomassPrecursorCheck
Cofactors in the biomass reaction that CAN be synthesized:
G  -> H
Cofactors in the biomass reaction that CAN be synthesized:
G  -> H
Cofactors in the biomass reaction that CANNOT be synthesized:
G  -> H
Each model.subSystems{x} is a character array, and this format is retained.
Cofactors in the biomass reaction that CAN be synthesized:
atp[c]  -> adp[c]
nad[c]  -> nadh[c]
nadph[c]  -> nadp[c]
accoa[c]  -> coa[c]
Cofactors in the biomass reaction that CANNOT be synthesized:
metTest1[c]  -> metTest2[c]

Atom mappings found for 4 model reactions.
Generating atom transition network for reactions with atom mappings.

Cofactors in the biomass reaction that CAN be synthesized:
thbpt[c]  -> dhbpt[c]
Reference to non-existent field 'Edges'.

Error in identifyConservedMoieties (line 168)
rxnAtomMappedBool = ismember(model.rxns,dATM.Edges.Rxn); % True for reactions included in dATM

Error in biomassPrecursorCheck (line 121)
        EMV = identifyConservedMoieties(model, ATN);

Error in testBiomassPrecursorCheck (line 164)
[missingMets, presentMets, coupledMets, missingCofs, presentCofs] = biomassPrecursorCheck(model, 1, 1, ATN);

>> testMtFVA

 > changeCobraSolver: IBM ILOG CPLEX interface added to MATLAB path.
 > isCompatible: The solver compatibility cannot be verified with MATLAB R2020b.
Each model.subSystems{x} is a character array, and this format is retained.
   Testing flux variability analysis using mtFVA
    Testing flux variability for the following reactions:
  Columns 1 through 14

    {'PGI'}    {'PFK'}    {'FBP'}    {'FBA'}    {'TPI'}    {'GAPD'}    {'PGK'}    {'PGM'}    {'ENO'}    {'PYK'}    {'PPS'}    {'G6PDH2r'}    {'PGL'}    {'GND'}

  Columns 15 through 19

    {'RPI'}    {'RPE'}    {'TKT1'}    {'TKT2'}    {'TALA'}

Compiling JAVA classes.
'javac' is not recognized as an internal or external command,
operable program or batch file.
Error using mtFVA (line 42)
Cannot call JAVA compiler; please check if 'javac' is available on your system.

Error in fluxVariability (line 498)
        [fvalb, fvaub]= mtFVA(LPproblem, [columnVector(Order(~maxSolved)); columnVector(-Order(~minSolved))], solverVarargin.LP{1});

Error in testMtFVA (line 31)
    [minFluxS2, maxFluxS2] = fluxVariability(model, 90, 'max', rxnNames, 0, true, 'FBA', struct(), 0, 1, j, 1);
 

Did anyone have similar problems with these functions?

All the best,

Vitor