"optimizeCbModel" glpkcc problem

[Andres Pinzon]

Dear all,
This is my CobraToolBox session:

======================================
>>clear all;
>>close all;
>>initCobraToolbox();
LP solver set to glpk successful
MILP solver set to glpk successful
QP solver set to qpng successful
MIQP solver set failed
CB map output set to svg successful
>>lmr2=readCbModel('lmr2',1000,'SimPheny');

#... AND HERE COMES THE PROBLEM....

>>solution = optimizeCbModel(lmr2,'max',0);
??? Undefined function or method 'glpkcc' for input
arguments of type 'struct'.

Error in ==> glpk at 508
[xopt, fmin, status, extra] = glpkcc(c, a, b, lb, ub,
ctype, vartype, sense, param);

Error in ==> solveCobraLP>solveGlpk at 502
[x,f,origStat,extra] =
glpk(c,A,b,lb,ub,csense,[],osense,params);

Error in ==> solveCobraLP at 159
[x,f,y,w,stat,origStat] =
solveGlpk(c,A,b,lb,ub,csense,osense,params);

Error in ==> optimizeCbModel at 155
solution = solveCobraLP(LPproblem);
=====================================

Perhaps this is a silly question but this is the first time I ran into
this kind of problem and I am not
sure what it means. I've used the simpheny format before and it "used
to behave" :)

Machine running it:
-OSX 10.5.8
-MatLab 7.8.0 (R2009a)
-Cobra 2.0.4
-libsbml-5.4.1

Any hint will be apperciated.

Best Regards,

--
Andrés Pinzón

[Ronan Fleming]

1)
To obtain a free Academic License for Gurobi, please follow these
steps: http://www.gurobi.com/products/licensing-and-pricing/academic-licensing

2)
>> edit glpk.m
% Matlab MEX interface for the GLPK library
%
% [xopt, fmin, status, extra] = glpk (c, a, b, lb, ub, ctype, vartype,
% sense, param)
%
% Solve an LP/MILP problem using the GNU GLPK library. Given three
% arguments, glpk solves the following standard LP:
%
% min C'*x subject to A*x <= b
%
% but may also solve problems of the form
%
% [ min | max ] C'*x
% subject to
% A*x [ "=" | "<=" | ">=" ] b
% x >= LB
% x <= UB
%
% Input arguments:
% c = A column array containing the objective function coefficients.
%
% A = A matrix containing the constraints coefficients.
%
% b = A column array containing the right-hand side value for each constraint
% in the constraint matrix.
%
% lb = An array containing the lower bound on each of the variables. If
% lb is not supplied (or an empty array) the default lower bound
for the variables is
% minus infinite.
%
% ub = An array containing the upper bound on each of the variables. If
% ub is not supplied (or an empty array) the default upper bound
is assumed to be
% infinite.
%
% ctype = An array of characters containing the sense of each constraint in the
% constraint matrix. Each element of the array may be one of the
% following values
% 'F' Free (unbounded) variable (the constraint is ignored).
% 'U' Variable with upper bound ( A(i,:)*x <= b(i)).
% 'S' Fixed Variable (A(i,:)*x = b(i)).
% 'L' Variable with lower bound (A(i,:)*x >= b(i)).
% 'D' Double-bounded variable (A(i,:)*x >= -b(i) and
A(i,:)*x <= b(i)).
%
% vartype = A column array containing the types of the variables.
% 'C' Continuous variable.
% 'I' Integer variable
% 'B' Binary variable
%
% sense = If sense is 1, the problem is a minimization. If sense is
% -1, the problem is a maximization. The default value is 1.
%
% param = A structure containing the following parameters used to define the
% behavior of solver. Missing elements in the structure take on default
% values, so you only need to set the elements that you wish to change
% from the default.

--
--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
-----------------------------------------------------------------
Currently on an EMBO Short-Term Fellowship visit to:
Netherlands Metabolomic Center,
University of Leiden,
Netherlands.
Gorlaeus Laboratories,
Einsteinweg 55,
2333 CC Leiden,
Room Number HB-726.
-----------------------------------------------------------------
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Dept. Biochemistry & Molecular Biology,
Faculty of Medicine,
University of Iceland,
&
Center for Systems Biology,
University of Iceland,
Sturlugata 8,
101 Reykjavik,
Iceland.
http://www.hi.is/~rfleming
http://systemsbiology.hi.is/
Ph:  +354 618 6245
Skype: ronan.fleming
-----------------------------------------------------------------

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[Andres Pinzon]

Thank you for such a quick reply.

Andrés Pinzón