Error in function fluxVariability.

[marcoxa]

Please include a short description of problem here

Hi I am running the latest COBRA (just installed) on Matlab 2020b (on a W10 machine). I am calling directly fluxVariability with one argument (in a LiveScript), but the call generates an error, on line 119

Error using deal (line 37)
The number of outputs should match the number of inputs.

Error in fluxVariability (line 119)
    advind, threads, heuristics, useMtFVA] = deal(funParams{:});

The relevant code is in C:\......\cobratoolbox\src\analysis\FVA\fluxVariability.m

% solverParams not outputted as a function parameter since it is individually handled and embedded in solverVarargin
[optPercentage, osenseStr, rxnNameList, printLevel, allowLoops, method, ...
    advind, threads, heuristics, useMtFVA] = deal(funParams{:});

The error is the call to deal. It is unclear to me where the funParams item is coming from.

Any ideas about how to fix this?

Thanks

Marco

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[tpfau]

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

[marcoxa]

Hi,

here is the call

[f_min, f_MAX] = fluxVariability(ENGRO);

ENGRO is obtained from a call to

ENGRO = readCbModel('Engro.xml')

which seems to return a correct model, AFAIU.

All the best

Marco

[marcoxa]

Hi,

any update on this?

All the best

Marco

[tpfau]

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 be in issue with input parsing and the inputs are fine for all I can say, I would have to test things. @rmtfleming Could you test whether there are any issues with such a simple fluxVariability call?

[rmtfleming]

Hi Marco, put a breakpoint at L118

[optPercentage, osenseStr, rxnNameList, printLevel, allowLoops, method, ...

advind, threads, heuristics, useMtFVA] = deal(funParams{:});

then reply with the output of running funParams at the command line. funParams is being generated on L115. What is your call to fluxVariability.m ?

Regards,

Ronan

On Sun, 25 Oct 2020 at 17:46, Thomas Pfau [email protected] wrote:

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 be in issue with input parsing and the inputs are fine for all I can say, I would have to test things. @rmtfleming https://github.com/rmtfleming Could you test whether there are any issues with such a simple fluxVariability call?

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

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 & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway.

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

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[marcoxa]

Hi Ronan

this is what I get following your instructions...

funParams =

  1×11 cell array

    {[100]}    {'max'}    {84×1 cell}    {[0]}    {[1]}    {'2-norm'}    {1×1 struct}    {[0]}    {0×0 double}    {0×0 double}    {[0]}

[rmtfleming]

Hi Marco,

there are 11 parameters there but there should only be 10.

What is your call to fluxVariability.m ? What are the options you specify?

Regards,

Ronan

On Mon, 26 Oct 2020 at 22:44, Marco Antoniotti [email protected] wrote:

Hi Ronan

this is what I get following your instructions...

funParams =

1×11 cell array

{[100]}    {'max'}    {84×1 cell}    {[0]}    {[1]}    {'2-norm'}    {1×1 struct}    {[0]}    {0×0 double}    {0×0 double}    {[0]}

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

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 & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway.

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

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[marcoxa]

Hi Ronan

the call to fluxVariability is shown in the message above. There is only one parameter passed in that is the result of parsing a SBML file via readCbModel.

Marco

[marcoxa]

Hi

any progress on this one?

All the best

Marco

[rmtfleming]

Hi Marco, I think this has been fixed. Run updateCobraToolbox then run testFVA to see. Regards, Ronan

On Mon, 9 Nov 2020 at 18:05, Marco Antoniotti [email protected] wrote:

Hi

any progress on this one?

All the best

Marco

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

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 & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway.

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.)

[marcoxa]

Thanks. It is fixed.

One note. updateCobraToolbox downloads git bash even if it is already installed.

All the best

Marco

[rmtfleming]

Hi Marco, if you look into the code I think you will see that it should only update git bash, not reinstall it. https://github.com/opencobra/cobratoolbox/blob/457d6a5feab5dabb1b5a838e2e1412b3f0d41060/src/base/install/updateCobraToolbox.m#L20 Regards, Ronan

On Tue, 10 Nov 2020 at 17:34, Marco Antoniotti [email protected] wrote:

Thanks. It is fixed.

One note. updateCobraToolbox downloads git bash even if it is already installed.

All the best

Marco

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

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 & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway.

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.)