unable to run optimizeCbModel with error of "unrecongnized field name "dual"

blai1989 commented 1 year ago

I changed to a new computer and reinstalled the cobratoolbox. The solver and so on were fine after checking with initCobraToolbox. Then I was trying to continue the work leftover for some FBA analysis, and the system returned with the following error message which I never met before:

                    Unrecognized field name "dual".

                    Error in optimizeCbModel (line 726)
                    if isempty(solution.dual)

Apart from the below, I also tried to solver the issue with some colleagues here next doors, but they also had no clue of why this happened.

May I please ask if you can help to give some advice to solve this problem?

Thanks very much!

Best regards, Bin

I hereby confirm that I have:

[x] Tried to solve the issue on my own
[x] Retried to run my code with the latest version of The COBRA Toolbox
[x] Checked that a similar issue has not already been opened

(Note: You may replace [ ] with [X] to check the box)

rmtfleming commented 1 year ago

What solver are you using? Try replacing that line with: if ~isfield(solution,'dual') || isempty(solution.dual) primalOnlyFlag=1; end

On Tue, 4 Oct 2022 at 14:43, blai @.***> wrote:

I changed to a new computer and reinstalled the cobratoolbox. The solver and so on were fine after checking with initCobraToolbox. Then I was trying to continue the work leftover for some FBA analysis, and the system returned with the following error message which I never met before:
                Unrecognized field name "dual".

                Error in optimizeCbModel (line 726)
                if isempty(solution.dual)
Apart from the below, I also tried to solver the issue with some colleagues here next doors, but they also had no clue of why this happened.

May I please ask if you can help to give some advice to solve this problem?

Thanks very much!

Best regards, Bin

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

(Note: You may replace [ ] with [X] to check the box)

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/2047, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOQPF7L5UJOMRQMCKE3WBQX6BANCNFSM6AAAAAAQ4S3LJQ . 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

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blai1989 commented 1 year ago

Dear Prof. Fleming,

Thanks very much! I am using Gurobi.

The problem is solved after I replace with the code you sent. Thanks very much again. That helps me a lot.

Cheers, Bin

Dr. Bin Lai BMBF junior research group leader of Biophotovoltaics Department of Solar Materials Helmholtz Centre for Environmental Research GmbH - UFZ

On Fri, Oct 7, 2022 at 10:11 AM Ronan M.T. Fleming @.***> wrote:

What solver are you using? Try replacing that line with: if ~isfield(solution,'dual') || isempty(solution.dual) primalOnlyFlag=1; end

On Tue, 4 Oct 2022 at 14:43, blai @.***> wrote:

I changed to a new computer and reinstalled the cobratoolbox. The solver and so on were fine after checking with initCobraToolbox. Then I was trying to continue the work leftover for some FBA analysis, and the system returned with the following error message which I never met before:

Unrecognized field name "dual".

Error in optimizeCbModel (line 726) if isempty(solution.dual)

Apart from the below, I also tried to solver the issue with some colleagues here next doors, but they also had no clue of why this happened.

May I please ask if you can help to give some advice to solve this problem?

Thanks very much!

Best regards, Bin

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

(Note: You may replace [ ] with [X] to check the box)

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/2047, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAQMEOQPF7L5UJOMRQMCKE3WBQX6BANCNFSM6AAAAAAQ4S3LJQ

. 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.)

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/2047#issuecomment-1271266467, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKTQF2RFLT3PTGVXIICHOA3WB7LMFANCNFSM6AAAAAAQ4S3LJQ . You are receiving this because you authored the thread.Message ID: @.***>

opencobra / cobratoolbox