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Warnings with unknown origins

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Andrei Kramer
Andrei Kramer 2021년 6월 8일
이동: Walter Roberson 2022년 9월 8일
Hi,
In the past, I once installed a toolbox called "SBMLToolbox", I immedieately uninstalled it on the same day (it isn't an official toolbox like the optimization toolbox, it's not in the APP menu). But some warnings persist after removal, even after upgrading to a newer version of MATLAB (2019b to 2021a). Every time I start matlab I get a wall of warnings similar to:
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
I cannot find the origin of these warnings (which file is trying to source these paths). I have tried this, on the command line:
IFS=$'\n' F=(`find ~/.matlab -type f`)
for f in "${F[@]}"; do grep SBMLToolbox "${f}" ; done
which resulted in nothing. So, if
~/.matlab
contains nothing related to this Toolbox, what can? The APP menu has no mention of this Toolbox (I didn't expect it to).
I also ran the command above for my ~/.local folder, no text file contains any mention of SBMLToolbox and the Command Window (in matlab) desn't show the origin of the warnings. How do I determine that? Is there a trace method for warnings?
Unfortunately, I don't remember much of that day, almost a year ago, when I installed that cursed SBMLToolbox. I just lived with those warnings since then. But, I really want them gone.

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FRANCISCO Curado
FRANCISCO Curado 2022년 9월 8일
이동: Walter Roberson 2022년 9월 8일
Short answer:
If you do not have the toolbox just delete or rename the file /etc/profile.d/SBMLToolbox.sh (without the .sh extension) and logout or reboot your system. It should solve the problem.
Longer answer:
I had the same problem before in Matlab and more recently a similar problem in Octave (apparently as the remainings of a previous installation). The problem is caused by the shell script located in /etc/profile.d/SBMLToolbox.sh which is executed whenever a bash login shell is entered (e.g. when logging in from the console or over ssh).
This is related with the Systems Biology Markup Language (SBML) Toolbox which is a free, open-source MATLAB/Octave toolbox that provides both MATLAB and Octave users with functions for reading, writing and manipulation data expressed in the Systems Biology Markup Language (https://sourceforge.net/projects/sbml/files/SBMLToolbox/4.1.0/).
I have tried it on Octave and if you take a look at the file /etc/profile.d/SBMLToolbox.sh you will find there a series of commands for adding PATHs starting with the string TB="/usr/share/SBMLToolbox" to the environment variables $OCTAVE_PATH and $MATLABPATH used by Octave and Matlab, respectively. This should be the reason of those warnings.

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