Error when using writeCbModel

[RieCo432]

I've been working with the COBRA Toolbox for almost a year now. Today, the writeCbModel function stopped working. I've tried reading and then saving various models I have been using for months and every time I try to save it, I get the following error:

Error using matlab.internal.math.uniqueCellstrHelper
Cell array input must be a cell array of character vectors.

Error in cell/unique (line 86)
    [varargout{1:nlhs}] = matlab.internal.math.uniqueCellstrHelper(A,[false true false true false]);

Error in getModelSubSystems (line 31)
        subSystems = unique(model.subSystems);

Error in writeSBML (line 453)
modelSubSystems = getModelSubSystems(model);

Error in writeCbModel (line 226)
        outmodel = writeSBML(model, fileName, input.compSymbols, input.compNames);

Error in enhance_iBsu1103v3 (line 152)
    outmodel = writeCbModel(model, 'format', 'sbml', 'filename', [filename '.xml']);

I have tried calling writeCbModel with the bare minimum of parameters (i.e. the model and a char array as a filename), but no luck.

I've had a look at the commit history for the source files that are involved in this, but there hasn't been any commits in about 3 weeks.

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

[RieCo432]

Turns out my model.subSystems was filled with empty char arrays. It worked fine after fixing that. Still wondering how that's never been an issue before though.

[rmtfleming]

What extra option would be needed here to make it fail gracefully? if all(charBool) subSystems = unique(model.subSystems); elseif all(cellBool) orderedSubs = cellfun(@(x) columnVector(x),model.subSystems,'UniformOUtput',false); subSystems = setdiff(vertcat(orderedSubs{:}),''); else subSystems = unique(model.subSystems); end

…

On Sun, 20 Nov 2022 at 19:18, Colin Ries ***@***.***> wrote: Turns out my model.subSystems was filled with empty char arrays. It worked fine after fixing that. Still wondering how that's never been an issue before though. — Reply to this email directly, view it on GitHub <#2071 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQMEOT7QQ3HIWDPKM4CCZ3WJJ2PJANCNFSM6AAAAAASFOVPQU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- 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 ---------------------------------------------------------------------------- Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming ---------------------------------------------------------------------------- (This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)