Failure of essential tasks under default solver

[JHL-452b]

Current behavior:

As we discussed in #820, if there is no problem with recently updated content, two bug in current metabolic tasks:

• Essential tasks failed under default solver(GLPK), but not with gurobi;
• Failed tasks could not get any feedback.

Proposed changes:

Modify the line 38 in the testMetabolicTasks function as below

setRavenSolver('gurobi')
% change the third parameter to `true` to printOutput.
verificationTaskReport=checkTasks(model,[],true,true,false,verificationTasks);

[edkerk]

Regarding the solver in #820 is suggested that RAVEN should automatically swap solvers. This would not be preferred behaviour of native RAVEN functions, to swap mid-function to a different solver that might not be installed on the user's computer. A better behaviour is indeed to set the preferred RAVEN solver before running testMetabolicTasks. However, that would make this task depend on gurobi, which again might not always be installed/functional.

Irrespective, this tasks shouldn't fail with glpk. I looked into the RAVEN code, and it seems like some glpk parameters are incorrectly set, which cause the FBA here to time out.

This is now solved in SysBioChalmers/RAVEN#539, which will soon end up in RAVEN 2.9.1 release.

The printOutput parameter should still be resolved in this repo.

[feiranl]

RAVEN 2.9.1 has released, the issue has been fixed.