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Zhao Yunpeng
May 29, 2019, 3:56:41 AM5/29/19
to COBRA Toolbox
Hello,
I have basic questions regarding uFBA.
I'm trying the uFBA test with the "tutorial_uFBA.mlx" and "sample_data.mat". And I did the analysis according to the tutorials step by step.
When inputting the command "uFBAoutput = buildUFBAmodel(model, uFBAvariables)", the analysis fails. The error I get is:
Warning: Sinks with very low bounds required for model to simulate.
> In buildUFBAmodel (line 599)
> Solver gurobi is installed but not working properly.
The assignment cannot be performed because the number of elements on the left and right sides is different.
Error buildUFBAmodel (line 612)
tmpModel.ub(length(model.c) + 1:end)=tmpSol.x(length(model.c) + 1:end) * lambda;
Could you help me to solve this problem?
Thanks,
Yunpeng Zhao
The output of generateSystemConfigReport is reported below:
> ---------------------------------- SYSTEM CONFIGURATION REPORT ----------------------------------
_____ _____ _____ _____ _____ |
/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis
| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2019
| | | | | | | _ { | _ / | ___ | |
| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:
\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox
|
> Checking if git is installed ... Done (version: 2.21.0).
> Checking if the repository is tracked using git ... Done.
> Checking if curl is installed ... Done.
> Checking if remote can be reached ... Done.
> Initializing and updating submodules (this may take a while)... Done.
> 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_Studio129\cplex\matlab\x64_win64
- [---*] GUROBI_PATH: C:\gurobi811\win64\matlab
- [----] TOMLAB_PATH: --> set this path manually after installing the solver ( see instructions )
- [---*] MOSEK_PATH: C:\Program Files\Mosek\9.0\
Done.
> Checking available solvers and solver interfaces ... rcode: 1008
rmsg: 'License cannot be located. The default search path is ';C:\Users\dell\mosek\mosek.lic;'.'
rcodestr: 'MSK_RES_ERR_MISSING_LICENSE_FILE'
Done.
> Setting default solvers ... Done.
> Saving the MATLAB path ... Done.
- The MATLAB path was saved in the default location.
> Summary of available solvers and solver interfaces
Support LP MILP QP MIQP NLP
----------------------------------------------------------------------
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 1 - 1 - -
matlab active 1 - - - 1
cplex_direct active 0 0 0 - -
dqqMinos active 0 - - - -
pdco active 1 - 1 - -
quadMinos active 0 - - - -
qpng passive - - 1 - -
tomlab_snopt passive - - - - 0
lp_solve legacy 1 - - - -
----------------------------------------------------------------------
Total - 7 3 5 2 1
+ Legend: - = not applicable, 0 = solver not compatible or not installed, 1 = solver installed.
> You can solve LP problems using: 'ibm_cplex' - 'glpk' - 'mosek' - 'matlab' - 'pdco'
> You can solve MILP problems using: 'ibm_cplex' - 'glpk'
> You can solve QP problems using: 'ibm_cplex' - 'mosek' - 'pdco' - 'qpng'
> You can solve MIQP problems using: 'ibm_cplex'
> You can solve NLP problems using: 'matlab'
> Checking for available updates ...
> The COBRA Toolbox is up-to-date.
------------------------------------------------------------------------------------------------
MATLAB Version: 9.5.0.944444 (R2018b)
MATLAB License Number: 40504596
Operating System: Microsoft Windows 10 Version 10.0 (Build 17134)
Java Version: Java 1.8.0_152-b16 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
------------------------------------------------------------------------------------------------
MATLAB Version 9.5 (R2018b)
Simulink Version 9.2 (R2018b)
5G Toolbox Version 1.0 (R2018b)
Aerospace Blockset Version 4.0 (R2018b)
Aerospace Toolbox Version 3.0 (R2018b)
Antenna Toolbox Version 3.2 (R2018b)
Audio System Toolbox Version 1.5 (R2018b)
Automated Driving System Toolbox Version 1.3 (R2018b)
Bioinformatics Toolbox Version 4.11 (R2018b)
Communications Toolbox Version 7.0 (R2018b)
Computer Vision System Toolbox Version 8.2 (R2018b)
Control System Toolbox Version 10.5 (R2018b)
Curve Fitting Toolbox Version 3.5.8 (R2018b)
DSP System Toolbox Version 9.7 (R2018b)
Data Acquisition Toolbox Version 3.14 (R2018b)
Database Toolbox Version 9.0 (R2018b)
Datafeed Toolbox Version 5.8 (R2018b)
Deep Learning Toolbox Version 12.0 (R2018b)
Econometrics Toolbox Version 5.1 (R2018b)
Embedded Coder Version 7.1 (R2018b)
Filter Design HDL Coder Version 3.1.4 (R2018b)
Financial Instruments Toolbox Version 2.8 (R2018b)
Financial Toolbox Version 5.12 (R2018b)
Fixed-Point Designer Version 6.2 (R2018b)
Fuzzy Logic Toolbox Version 2.4 (R2018b)
GPU Coder Version 1.2 (R2018b)
Global Optimization Toolbox Version 4.0 (R2018b)
HDL Coder Version 3.13 (R2018b)
HDL Verifier Version 5.5 (R2018b)
Image Acquisition Toolbox Version 5.5 (R2018b)
Image Processing Toolbox Version 10.3 (R2018b)
Instrument Control Toolbox Version 3.14 (R2018b)
LTE HDL Toolbox Version 1.2 (R2018b)
LTE Toolbox Version 3.0 (R2018b)
MATLAB Coder Version 4.1 (R2018b)
MATLAB Compiler Version 7.0 (R2018b)
MATLAB Compiler SDK Version 6.6 (R2018b)
MATLAB Report Generator Version 5.5 (R2018b)
Mapping Toolbox Version 4.7 (R2018b)
Model Predictive Control Toolbox Version 6.2 (R2018b)
Model-Based Calibration Toolbox Version 5.5 (R2018b)
OPC Toolbox Version 4.0.6 (R2018b)
Optimization Toolbox Version 8.2 (R2018b)
Parallel Computing Toolbox Version 6.13 (R2018b)
Partial Differential Equation Toolbox Version 3.1 (R2018b)
Phased Array System Toolbox Version 4.0 (R2018b)
Polyspace Bug Finder Version 2.6 (R2018b)
Polyspace Code Prover Version 9.10 (R2018b)
Powertrain Blockset Version 1.4 (R2018b)
Predictive Maintenance Toolbox Version 1.1 (R2018b)
RF Blockset Version 7.1 (R2018b)
RF Toolbox Version 3.5 (R2018b)
Risk Management Toolbox Version 1.4 (R2018b)
Robotics System Toolbox Version 2.1 (R2018b)
Robust Control Toolbox Version 6.5 (R2018b)
Sensor Fusion and Tracking Toolbox Version 1.0 (R2018b)
Signal Processing Toolbox Version 8.1 (R2018b)
SimBiology Version 5.8.1 (R2018b)
SimEvents Version 5.5 (R2018b)
Simscape Version 4.5 (R2018b)
Simscape Driveline Version 2.15 (R2018b)
Simscape Electrical Version 7.0 (R2018b)
Simscape Fluids Version 2.5 (R2018b)
Simscape Multibody Version 6.0 (R2018b)
Simulink 3D Animation Version 8.1 (R2018b)
Simulink Check Version 4.2 (R2018b)
Simulink Code Inspector Version 3.3 (R2018b)
Simulink Coder Version 9.0 (R2018b)
Simulink Control Design Version 5.2 (R2018b)
Simulink Coverage Version 4.2 (R2018b)
Simulink Design Optimization Version 3.5 (R2018b)
Simulink Design Verifier Version 4.0 (R2018b)
Simulink Desktop Real-Time Version 5.7 (R2018b)
Simulink PLC Coder Version 2.6 (R2018b)
Simulink Real-Time Version 6.9 (R2018b)
Simulink Report Generator Version 5.5 (R2018b)
Simulink Requirements Version 1.2 (R2018b)
Simulink Test Version 2.5 (R2018b)
Spreadsheet Link Version 3.4 (R2018b)
Stateflow Version 9.2 (R2018b)
Statistics and Machine Learning Toolbox Version 11.4 (R2018b)
Symbolic Math Toolbox Version 8.2 (R2018b)
System Identification Toolbox Version 9.9 (R2018b)
Text Analytics Toolbox Version 1.2 (R2018b)
Trading Toolbox Version 3.5 (R2018b)
Vehicle Dynamics Blockset Version 1.1 (R2018b)
Vehicle Network Toolbox Version 4.1 (R2018b)
Vision HDL Toolbox Version 1.7 (R2018b)
WLAN Toolbox Version 2.0 (R2018b)
Wavelet Toolbox Version 5.1 (R2018b)
> Default shell :
> Version of shell : '--version' It is not an internal or external command, nor is it a runnable program or batch file.
> Architecture : PCWIN64
> MATLAB folder : C:\Program Files\MATLAB\R2018b
> COBRA Toolbox root : C:\Program Files\cobratoolbox
> git version : git version 2.21.0.windows.1
> curl version : curl 7.55.1 (Windows)
> CBT_LP_SOLVER : glpk
> CBT_MILP_SOLVER : glpk
> CBT_QP_SOLVER : qpng
> CBT_MIQP_SOLVER : ibm_cplex
> CBT_NLP_SOLVER : matlab
> GUROBI_PATH : C:\gurobi811\win64\matlab
> ILOG_CPLEX_PATH : C:\Program Files\ibm\ILOG\CPLEX_Studio129\cplex\matlab\x64_win64
> TOMLAB_PATH :
> MOSEK_PATH : C:\Program Files\Mosek\9.0\
> ----------------------------------- END OF CONFIGURATION REPORT -----------------------------------
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