#39 How to completely uninstall?

[Does not Matter]

Hi,
so, how do I uninstall it? I removed the folder where the toolbox used to be, matlab's path contains no traces of the toolbox, the add-on manager shows no mention of it. Yet, everytime I start matlab, I get this:
Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/AccessModel Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/AccessModel/Test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Convenience Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Convenience/Test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/AlgebraicRule Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/AssignmentRule Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Compartment Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/CompartmentType Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/CompartmentVolumeRule Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Constraint Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Delay Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Event Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/EventAssignment Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/FunctionDefinition Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/InitialAssignment Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/KineticLaw Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/LocalParameter Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Model Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/ModifierSpeciesReference Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Parameter Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/ParameterRule Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Priority Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/RateRule Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Reaction Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Rule Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Species Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/SpeciesConcentrationRule Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/SpeciesReference Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/SpeciesType Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/StoichiometryMath Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Trigger Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/Unit Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/UnitDefinition Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/MATLAB_SBML_Structure_Functions/structFieldnames Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Simulation Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Simulation/Test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Test/test-data Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Validate_MATLAB_SBML_Structures Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/Validate_MATLAB_SBML_Structures/Test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures/FBCModel Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures/FBCSpecies Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures/FluxBound Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures/FluxObjective Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures/Objective Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures/structFieldnames Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/MATLAB_SBML_Structures/test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/Validate_MATLAB_SBML_Structures Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/Validate_MATLAB_SBML_Structures/test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/test Warning: Name is nonexistent or not a directory: /usr/share/SBMLToolbox/fbc_package/test/test-data

I cannot find the file that tires to do the above.

[Frank Bergmann]

I'm sorry for the inconvenience, the SBMLToolbox information is stored within the matlab path, which you can for example edit by executing pathtool. If you don't want to use the graphical user interface, you can use rmpathwhich will remove the path given as argument from MATLABs searchpath. Once you've made your changes run savepath for the changes to persist just in case.

[Michael Hucka]

Hello – I just wanted to circle back to this and ask if you were able to uninstall it. Please let us know.

[Does not Matter]

Hi,
thank you for the replies! I did check the path before I posted here, but couldn't find anything. Just to make sure I used pathtool and reviewed the path entries. There were many, so I did this:

matlab: savepath CurrentPath.m
shell: grep -i SBML CurrentPath.m

no results.

Perhaps it is interesting to note that I ran the install.m script inside of GNU Octave. I never actually installed it via matlab. Only as a side-effect did I get these messages in matlab.

I assume that the install script tries to find out whether it is being executed in octave or matlab and does different things, but perhaps it didn't quite guess right and put some files somewhere where matlabfinds them?

I checked as much as I could find online about matlab's startup procedure and couldn't find anything that contained mentions of SBMLToolbox (in any spelling). I also did a lot of grepping and find ~ -name '*.m' --exec [...] lines to try to find the above strings in any m file, no success.

If you have a guess which can make my search faster that would be appreciated, but if not: I can write up everything that I did in more detail (it will take some time as I have to go through everything again and script it). But I will do that if necessary.

Thanks again

[Frank Bergmann]

Further things to try:

• is there a MATLABPATH environment variable defined?
• since you mention octave, there could be octaverc files lying around with it
• there are some magic directories like ~/Documents/MATLAB that automatically get added (try calling userpath to figure out whether that could be an issue for you)
• also try and locate pathdef.m files maybe in /usr/share or therabouts
• maybe also run matlabroot and look for a file there.

sorry for the trouble,
i have not encountered any of this before. Please let us know how things go.

best
Frank