Error in initCobraToolbox (line 212)

febedtu commented 2 years ago

Hi,

I have used older cobra toolbox versions fine for a while. However, after installing the latest version of cobra toolbox, following instructions (https://opencobra.github.io/cobratoolbox/latest/installation.html) with Matlab 2015b, initCobraToolbox reports the following:

 > Checking if git is installed ...  Done (version: 2.32.0).
 > Checking if the repository is tracked using git ...  Done.
 > Checking if curl is installed ...  Done.
 > Checking if remote can be reached ...  Done.
 > Initializing and updating submodules (this may take a while)...Undefined function 'contains' for input arguments of type 'char'.

Error in initCobraToolbox (line 212)
            if contains(result_gitSubmodule,'modified') || contains(result_gitSubmodule,'Untracked files')

Any idea what might cause this error?

rmtfleming commented 2 years ago

contains is a function that needs a newer version of matlab

On Mon, 11 Apr 2022 at 14:11, febedtu @.***> wrote:

Hi,

I have used older cobra toolbox versions fine for a while. However, after installing the latest version of cobra toolbox, following instructions ( https://opencobra.github.io/cobratoolbox/latest/installation.html) with Matlab 2015b, initCobraToolbox reports the following:

Checking if git is installed ... Done (version: 2.32.0). Checking if the repository is tracked using git ... Done. Checking if curl is installed ... Done. Checking if remote can be reached ... Done. Initializing and updating submodules (this may take a while)...Undefined function 'contains' for input arguments of type 'char'.

Error in initCobraToolbox (line 212) if contains(result_gitSubmodule,'modified') || contains(result_gitSubmodule,'Untracked files')

Any idea what might cause this error?

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

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febedtu commented 2 years ago

Alright, so there is no support for Matlab2015b? The documentation indicates support for >Matlab2014b.

febedtu commented 2 years ago

Is there support for Matlab2015b / a workaround for this issue, or did I misunderstand the documentation?

rmtfleming commented 2 years ago

Hi, feel free to contribute a PR with a workaround. Regards, Ronan

On Tue, 19 Apr 2022 at 10:17, febedtu @.***> wrote:

Is there support for Matlab2015b / a workaround for this issue, or did I misunderstand the documentation?

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

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bigsuicideparty commented 2 years ago

What is a PR? So there is no support for Matlab2015b? Which versions of Matlab are supported by COBRA Toolbox?

rmtfleming commented 2 years ago

PR = pull request https://opencobra.github.io/cobratoolbox/latest/contributing.html

https://uk.mathworks.com/help/matlab/ref/contains.html was Introduced in R2016b

On Wed, 20 Apr 2022 at 07:54, bigsuicideparty @.***> wrote:

What is a PR? So there is no support for Matlab2015b? Which versions of Matlab are supported COBRA Toolbox?

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

opencobra / cobratoolbox