Open marcoxa opened 4 years ago
What is your call to fluxVariability? Could you post the line?
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
Hi,
any update on this?
All the best
Marco
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?
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 notifications@github.com 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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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]}
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 notifications@github.com 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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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
Hi
any progress on this one?
All the best
Marco
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 notifications@github.com wrote:
Hi
any progress on this one?
All the best
Marco
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Thanks. It is fixed.
One note. updateCobraToolbox
downloads git bash
even if it is already installed.
All the best
Marco
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 notifications@github.com 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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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 119The relevant code is in
C:\......\cobratoolbox\src\analysis\FVA\fluxVariability.m
The error is the call to
deal
. It is unclear to me where thefunParams
item is coming from.Any ideas about how to fix this?
Thanks
Marco
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