Wrong error of pFBA

[Bhushan Dhamale]

I am testing a few of the functions of the COBRA toolbox from the Schellenberger et al, 2011, Nature Protocol paper examples.
When I run the pFBA function, I get the error message:

Error using optimizeCbModel (line 280)
The length of csense does not match the number of rows of model.S.
Error in pFBA>minimizeModelFlux_local (line 268)
MinimizedFlux = optimizeCbModel(modelIrrev,'min');
Error in pFBA (line 131)
[ MinimizedFlux,modelIrrevFM]= minimizeModelFlux_local(model,GeneOption);

However, when I check the model, the length of csense matches the number of rows in model.S.
What am I missing here? How do I get around this problem?

P.S. I am attaching the live script and HTML files for reference.

[Thomas Pfau]

Hi Bhushan,

There is a pull request which fixes this issue already submitted to the toolbox.
This unfortunately works in the test, since the test uses an outdated model hich is directly loaded (and not via readCbModel - which is also corrected in the PR).

I expect this to be merged within the next couple of days and it will then be incorporated into the master branch on the normal schedule (commonly once a week).

Best,

Thomas

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[Bhushan Dhamale]

Hello Thomas,
Thank you for the update.
I'll keep an eye out for it.

Best,
Bhushan

[Bhushan Dhamale]

Hello Thomas,
I have updated the toolbox an hour ago, but the error seems to persist. Is the fix for this issue merged into the master branch yet?

Best,
Bhushan

On Thursday, November 9, 2017 at 6:47:02 PM UTC+5:30, Thomas Pfau wrote:

[Thomas Pfau]

Hi Bushan,

No that pull is not yet on master. It is in the develop branch, so if you urgently need it you can checkout the develop branch and use the fixed code:

git checkout develop

The next regular merge is expected for the end of the week, at which point it should go into master.

Best

Thomas

[Bhushan Dhamale]

Hello Thomas,
I'll standby for the update.
Thank you.

Best,
Bhushan