Hi guys,
I was trying to install cobra on Matlab 2016b, and i have installed GUROBI 7.02, which I think the GUROBI mex is no longer necessary. I cant install tomlab solver because that will cause 900 dollars...
When I followed the instructions on https://github.com/opencobra/cobratoolbox#the-cobra-toolbox---constraint-based-reconstruction-and-analysis-toolbox, and at the step of :
initCobraToolbox, Matlab shows the following error:
Adding all the COBRA Toolbox files ... Done.
-- Checking the installation of LP solvers --
Testing gurobi6 ... Passed. Testing gurobi5 ... Passed. Testing gurobi ... Warning: LP solver Gurobi not useable: gurobi_mex not in Matlab path In changeCobraSolver (line 161) In initCobraToolbox (line 79) Failed. Testing tomlab_cplex ... Warning: LP solver CPLEX through Tomlab not usable: tomRun.m not in Matlab path In changeCobraSolver (line 129) In initCobraToolbox (line 79) Failed. Testing glpk ... Passed. Testing mosek ... Warning: LP solver Mosek not usable: mosekopt.m not in Matlab path In changeCobraSolver (line 119) In initCobraToolbox (line 79) Failed. Testing cplex_direct ... Passed. Testing ibm_cplex ... Warning: LP solver CPLEX from IBM not usable: IBM CPLEX not installed or licence server not up In changeCobraSolver (line 147) In initCobraToolbox (line 79) Failed.
-- Checking the installation of MILP solvers --
Testing gurobi6 ... Passed. Testing gurobi5 ... Passed. Testing gurobi ... Warning: MILP solver Gurobi not useable: gurobi_mex not in Matlab path In changeCobraSolver (line 242) In initCobraToolbox (line 79) Failed. Testing tomlab_cplex ... Warning: MILP solver CPLEX through Tomlab not usable: tomRun.m not in Matlab path In changeCobraSolver (line 220) In initCobraToolbox (line 79) Failed. Testing glpk ... Passed. Testing cplex_direct ... Warning: MILP solver cplex_direct not supported by COBRA Toolbox In changeCobraSolver (line 256) In initCobraToolbox (line 79) Failed. Testing ibm_cplex ... Warning: MILP solver CPLEX from IBM not usable: IBM CPLEX not installed or licence server not up In changeCobraSolver (line 233) In initCobraToolbox (line 79) Failed.
-- Checking the installation of QP solvers --
Testing gurobi6 ... Passed. Testing gurobi5 ... Passed. Testing gurobi ... Warning: QP solver Gurobi not useable: gurobi_mex not in Matlab path In changeCobraSolver (line 296) In initCobraToolbox (line 79) Failed. Testing tomlab_cplex ... Warning: QP solver CPLEX through Tomlab not usable: tomRun.m not in Matlab path In changeCobraSolver (line 267) In initCobraToolbox (line 79) Failed. Testing qpng ... Warning: qpng solver has not been fully tested - results may not be correct In changeCobraSolver (line 277) In initCobraToolbox (line 79) Passed.
-- Checking the installation of MIQP solvers --
Testing gurobi6 ... Passed. Testing gurobi5 ... Passed. Testing tomlab_cplex ... Warning: MIQP solver CPLEX through Tomlab not usable: tomRun.m not in Matlab path In changeCobraSolver (line 320) In initCobraToolbox (line 79) Failed.
-- Checking the installation of NLP solvers --
Testing matlab ... Passed. Testing tomlab_snopt ... Warning: MIQP solver CPLEX through Tomlab not usable: tomRun.m not in Matlab path In changeCobraSolver (line 353) In initCobraToolbox (line 79) Failed. Define CB map output... CB map output: svg
Warning: TranslateSBML did not work with the test .xml file: Ecoli_core_ECOSAL.xml
In initCobraToolbox (line 147)
solverSummary =
LP MILP QP MIQP NLP
__ ____ __ ____ ___
lindo_old -1 -1 -1 -1 -1
lindo_new -1 -1 -1 -1 -1
glpk 1 1 -1 -1 -1
mosek 0 -1 -1 -1 -1
tomlab_cplex 0 0 0 0 -1
cplex_direct 1 0 -1 -1 -1
ibm_cplex 0 0 -1 -1 -1
lp_solve -1 -1 -1 -1 -1
pdco -1 -1 -1 -1 -1
gurobi 0 0 0 -1 -1
gurobi5 1 1 1 1 -1
gurobi6 1 1 1 1 -1
mps -1 -1 -1 -1 -1
quadMinos -1 -1 -1 -1 -1
dqqMinos -1 -1 -1 -1 -1
opti -1 -1 -1 -1 -1
matlab -1 -1 -1 -1 1
tomlab_snopt -1 -1 -1 -1 0
Legend: -1 = not applicable, 0 = solver not installed, 1 = solver installed.
LP solvers: 10 not applicable, 4 failed, 4 passed
- MILP solvers: 11 not applicable, 4 failed, 3 passed
- QP solvers: 14 not applicable, 2 failed, 2 passed
- MIQP solvers: 15 not applicable, 1 failed, 2 passed
NLP solvers: 16 not applicable, 1 failed, 1 passed
You can solve LP problems on this system, but some solvers may not be usable (see above summary). You can solve MILP problems on this system, but some solvers may not be usable (see above summary). You can solve QP problems on this system, but some solvers may not be usable (see above summary). You can solve MIQP problems on this system, but some solvers may not be usable (see above summary). You can solve NLP problems on this system, but some solvers may not be usable (see above summary).
More over, it looks like the cobra was not properly installed, as I dont see a cobra folder under Matlab folder as seen on tutorial (https://systemsbiology.usu.edu/documents/Cobra%20Toolbox%20-%202017.pdf), and instead, my Matlab folder looks empty.
Can I anyone advice on that? I would really appreciate that!
Best,
Wenhan
Given that Matlab is not used very much in the bioinformatics community and that your question is about Matlab, not bioinformatics, you may have better luck getting an answer on a Matlab-specific forum. Also since you probably paid for Matlab, you may have access to some sort of customer service. You can also ask the toolbox authors if you think the problem arises from their code.