Problem initializing and updating submodule Binary

[SophieGir]

I am trying to download CobraToolbox for the first time. This is the error I get when I try to run initCobraToolbox:

Checking if git is installed ... Done (version: 2.29.2).

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)...fatal: could not get a repository handle for submodule 'binary' Error using initCobraToolbox (line 209) The submodules could not be initialized.

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

(Note: You may replace [ ] with [X] to check the box)

[rmtfleming]

Hi Sophie, as it happens, I was working on the COBRA.binary submodule today and committed to master. However, that may not be the issue. Please can you try a fresh install again and init?

I just tried a fresh install $ git clone git@github.com:opencobra/cobratoolbox.git cobratoolbox

initCobraToolbox

and it worked with my configuration, attached.

generateSystemConfigReport

Regards,

Ronan

On Wed, 4 Nov 2020 at 19:01, SophieGir notifications@github.com wrote:

I am trying to download CobraToolbox for the first time. This is the error I get when I try to run initCobraToolbox:

Checking if git is installed ... Done (version: 2.29.2).

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)...fatal: could not get a repository handle for submodule 'binary' Error using initCobraToolbox (line 209) The submodules could not be initialized.

I hereby confirm that I have:

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

(Note: You may replace [ ] with [X] to check the box)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1650, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOUR3CDJNBL7UHJQ6ZDSOGQG7ANCNFSM4TKNQAPQ .

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

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 & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway.

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

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[SophieGir]

I tried that and it worked!

[SophieGir]

When I tried to run it again it doesn't work: same error message