Using updated binary with MATLAB.devTools

[Uri David Akavia]

Hi All,

My travails with Matlab 2017b on Mac OS 13.1 (High Sierra) continue.

The binary version of SBML 5.15.2-matlab2017a-macos works on OS 13.1 and Matlab 2017b. Weirdly, the 5.15.1-2017a didn't work.

I tried installing the binary files in fork-cobratoolbox/binary/maci64/bin. Unfortunately, this marks binary as modified (with files waiting commit), and the general cobra toolbox as modified. At this point, MATLAB.devTools (understandably) don't update the fork anymore with changes committed to Git.

I can't use Matlab2017a because that can't set up Mex files for compilation, because it is confused by the OS 13.1 version of XCode (Xcode 9.1). Ditto for Matlab2016b. I need to compile MEX files to get fastFVA working with Cplex.

So far, I can't use gurobi, since OSX 13.1 seems to break it.,

Any suggestions on how to use the working translateSBML and outputSBML binaries, while still updating the fork automatically? 

Based on the way things have been behaving, I'm probably going to need to compile glpk  from scratch as well (glpk doesn't work with Matalb2017a), so the question repeats for glpk.

Thank you very much,

Uri David

[Laurent Heirendt]

Dear Uri David,

I am sorry to hear that you are facing these challenges. One of the reasons is that the compatibility of the COBRA Toolbox is not yet fully assured with the very latest version of MATLAB on the very latest operating system of macOS.

If you still want to update the fork using the MATLAB.devTools, I suggest to not leave the newly compiled binaries in the ~/fork-cobratoolbox/binary folder, but leave the binary folder untouched. I suggest to add the newly compiled SBML binaries to the newly compiled binaries of fastFVA, which are stored in the ~/fork-cobratoolbox/.tmp folder. The ~/fork-cobratoolbox/.tmp folder is actually added after the ~/fork-cobratoolbox/binary directory to the MATLAB path.

Please let me know if this works.

Best regards,

Laurent

[Uri David Akavia]

Dear Laurent,

That works great for SBML. Thank you!

I'm a bit confused by gplkmex - do I still have to download 4.48 on Mac?

Yours,

Uri David