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opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
https://opencobra.github.io/cobratoolbox
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Error in generateMexFastFVA depends on CPLEX1210 and MATLAB R2021a #1794

Open tarzicha opened 3 years ago

tarzicha commented 3 years ago

Adding all the files of The COBRA Toolbox ... Done. Define CB map output... set to svg. TranslateSBML is installed and working properly. Configuring solver environment variables ...

  • [*---] ILOG_CPLEX_PATH: C:\Program Files\ibm\ILOG\CPLEX_Studio1210\cplex\matlab\x64_win64
  • [---*] GUROBI_PATH: C:\gurobi911\win64\matlab
  • [----] TOMLAB_PATH: --> set this path manually after installing the solver ( see instructions )
  • [----] MOSEK_PATH: --> set this path manually after installing the solver ( see instructions ) Done. Checking available solvers and solver interfaces ...Version identifier: 12.10.0.0 | 2019-11-26 | 843d4de2ae Summary of available solvers and solver interfaces
                Support           LP     MILP      QP    MIQP     NLP      EP
------------------------------------------------------------------------------
gurobi          active              1       1       1       1       -       -
ibm_cplex       active              1       1       1       1       -       -
tomlab_cplex    active              0       0       0       0       -       -
glpk            active              1       1       -       -       -       -
mosek           active              0       -       0       -       -       0
matlab          active              0       -       -       -       0       -
pdco            active              1       -       1       -       -       1
quadMinos       active              0       -       -       -       -       -
dqqMinos        active              0       -       0       -       -       -
cplex_direct    active              0       0       0       -       -       -
cplexlp         active              1       -       -       -       -       -
qpng            passive             -       -       1       -       -       -
tomlab_snopt    passive             -       -       -       -       0       -
lp_solve        legacy              1       -       -       -       -       -
------------------------------------------------------------------------------
Total           -                   6       3       4       2       0       1

Error in generateMexFastFVA (line 148) eval(['mex ' cmd]);

I hereby confirm that I have:

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rmtfleming commented 3 years ago

This issue has already been identified and the requirement for a coding solution explained in the cobra toolbox google group. Someone needs to step up to the plate and implement the update of the code required.

On Mon, 30 Aug 2021 at 13:20, tarzicha @.***> wrote:

Adding all the files of The COBRA Toolbox ... Done. Define CB map output... set to svg. TranslateSBML is installed and working properly. Configuring solver environment variables ...

  • [*---] ILOG_CPLEX_PATH: C:\Program Files\ibm\ILOG\CPLEX_Studio1210\cplex\matlab\x64_win64
  • [---*] GUROBI_PATH: C:\gurobi911\win64\matlab
  • [----] TOMLAB_PATH: --> set this path manually after installing the solver ( see instructions )
  • [----] MOSEK_PATH: --> set this path manually after installing the solver ( see instructions ) Done.

Checking available solvers and solver interfaces ...Version identifier: 12.10.0.0 | 2019-11-26 | 843d4de2ae Summary of available solvers and solver interfaces

          Support           LP     MILP      QP    MIQP     NLP      EP

gurobi active 1 1 1 1 - - ibm_cplex active 1 1 1 1 - - tomlab_cplex active 0 0 0 0 - - glpk active 1 1 - - - - mosek active 0 - 0 - - 0 matlab active 0 - - - 0 - pdco active 1 - 1 - - 1 quadMinos active 0 - - - - - dqqMinos active 0 - 0 - - - cplex_direct active 0 0 0 - - - cplexlp active 1 - - - - - qpng passive - - 1 - - - tomlab_snopt passive - - - - 0 - lp_solve legacy 1 - - - - -

Total - 6 3 4 2 0 1

  • Legend: - = not applicable, 0 = solver not compatible or not installed, 1 = solver installed.

You can solve LP problems using: 'ibm_cplex' - 'glpk' - 'pdco' - 'cplexlp' You can solve MILP problems using: 'ibm_cplex' - 'glpk' You can solve QP problems using: 'ibm_cplex' - 'pdco' You can solve MIQP problems using: 'ibm_cplex' You can solve NLP problems using: You can solve EP problems using: 'pdco'

Checking for available updates ... gitBash is installed (version: 2.13.3). gitBash is up-to-date (version: 2.13.3). remote.origin.url = https://github.com/opencobra/cobratoolbox.git . currentBranch = master. The COBRA Toolbox is up-to-date. generateMexFastFVA The solver compatibility is not tested with MATLAB R2021a. Warning: As the ibm_cplex interface is not compatible, the generated MEX file might not be compatible. In generateMexFastFVA (line 34) The version of CPLEX is 1210. MEX configured to use 'MinGW64 Compiler (C)' for C language compilation. Building with 'MinGW64 Compiler (C)'. Error using mex gcc: error: -fexceptions: No such file or directory

Error in generateMexFastFVA (line 148) eval(['mex ' cmd]);

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)

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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 & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

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