TranslateSBML due to hard coded path in TranslateSBML.mexmaci64

[pcm32]

[Please include a short description of problem here]

When executing TranslateSBML with one of the test models (Ec_iAF1260_flux1.xml) it produces an error for what it seems to be a hard coded path to a library:

Trial>> TranslateSBML('/Users/pmoreno/Development/cobratoolbox/test/models/Ec_iAF1260_flux1.xml')
Invalid MEX-file '/Users/pmoreno/Development/cobratoolbox/binary/maci64/bin/TranslateSBML.mexmaci64': Missing
dependent shared libraries:
'/Users/skeating/working/buildmatlab/src/bindings/matlab/TranslateSBML.mexmaci64' required by
'/Users/pmoreno/Development/cobratoolbox/binary/maci64/bin/TranslateSBML.mexmaci64'

This is on the latest version of Matlab R2017a (9.2.0.556344) for macOS. I guess that you need to recompile that mexmaci64 binary, but I don't use matlab often to know how to do this.

I hereby confirm that I have:

• [x] Tried to solve the issue on my own
• [x] Retried to run my code with the latest version of The COBRA Toolbox
• [x] Checked that a similar issue has not already been opened

[pcm32]

An update on this... if I do a symlink from the missing path to the one I actually have, it seems to be working...

No, sorry, took ages, gave an horrible malloc error, and didn't work, but error was different.

[rmtfleming]

Hi Pablo, TranslateSBML is maintained by our SBML colleagues.

Hi Sarah, this looks like something you might be able to help with.

Regards, Ronan

On 25 June 2017 at 08:50, Pablo Moreno notifications@github.com wrote:

An update on this... if I do a symlink from the missing path to the one I actually have, it seems to work... but of course this is not a proper fix for this. Thanks!

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[syarra]

@pcm32, this issue has already been filed a couple of months ago on the libSBML issue tracker It hasn't been fixed yet. However, the mex-files are working properly on R2016b. If you can downgrade to R2016b, you will be safe!

[pcm32]

Thanks @syarra and @rmtfleming! I was only using a trial of Matlab (so would only get latest version I guess) while on a workshop from Maike Aurich, and got the error, so I'd thought I'd report it. I'm more of a python guy when it comes to COBRA ;-).

[syarra]

Some binaries for using SBML on MATLAB R2017a on macOS are provided here thanks to Sarah Keating.