initCobraToolbox

[kristycyw]

Please include a short description of problem here Hi, my cobra toolbox stopped working because it was an old version, upon installing a new version: Entering 'external/analysis/CnaCobraInterface' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/GeoCalcLib' error: invalid path 'aux/createLRSfile.m' error: invalid path 'aux/readLRSfile.m' fatal: run_command returned non-zero status for external/analysis/GeoCalcLib . Error using initCobraToolbox (line 233) The submodules could not be initialized.

I have checked the forum on google and there is someone with a similar issue but it is not solved. The the external/analysis/GeoCalcLib directrory is empty and is causing an issue with initialization. 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]

Did you download from here: https://github.com/opencobra/cobratoolbox.git or here https://github.com/opencobra/cobratoolbox/releases/tag/v3.33

On Thu, 18 Nov 2021 at 11:54, kristycyw @.***> wrote:

Please include a short description of problem here Hi, my cobra toolbox stopped working because it was an old version, upon installing a new version: Entering 'external/analysis/CnaCobraInterface' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/GeoCalcLib' error: invalid path 'aux/createLRSfile.m' error: invalid path 'aux/readLRSfile.m' fatal: run_command returned non-zero status for external/analysis/GeoCalcLib . Error using initCobraToolbox (line 233) The submodules could not be initialized.

I have checked the forum on google and there is someone with a similar issue but it is not solved. 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)

— 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/1874, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOXG3EYQIRBZZMSLJYTUMTSPRANCNFSM5IJNMFJA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

--

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.)

[kristycyw]

Hi Prof Flemming, I think the issue is the folder in GeoCalcLib is named 'aux' and this is not allowed, so the folders do not download onto windows devices "The specified device name is invalid" we are unable to name folders as con, aux, nul, etc. Microsoft MS-DOS had reserved these names for these system device drivers. I tried to manually download the GeoCalcLib folders and got this error

[kristycyw]

Sorry, I realised I did not answer the question adequately, I downloaded it via git bash: git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox This has never caused me issues till this version

[Moshkante]

@rmtfleming Hello, we are still having this issue with the latest update of the cobratoolbox (v 33.3). We used 'git clone https://github.com/opencobra/cobratoolbox.git' to install the tool and wish to use it with Cplex 129. We are currently getting the same issue as described above ( https://github.com/opencobra/cobratoolbox/issues/1874#issue-1057268546 ). We checked that setfield is only available under the following path: C:\Program Files\MATLAB\R2021b\toolbox\matlab\datatypes\setfield.m

What should we do to avoid this issue ? Many thanks in advance.

[rmtfleming]

Hi kristycyw, thanks a lot. I changed aux to io. Does that work now if you do: git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox Regards, Ronan

P.S Jeff, please post to the appropriate thread.

On Thu, 18 Nov 2021 at 15:13, Jeff Didier @.***> wrote:

@rmtfleming Hello, we are still having this issue with the latest update of the cobratoolbox (v 33.3). We used 'git clone https://github.com/opencobra/cobratoolbox.git' to install the tool and wish to use it with Cplex 129. We are currently getting the same issue as described above ( #1874 (comment) ). We checked that setfield is only available under the following path: C:\Program Files\MATLAB\R2021b\toolbox\matlab\datatypes\setfield.m

What should we do to avoid this issue ? Many thanks in advance.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

--

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.)

[kristycyw]

Hi Prof Flemming, Thank you it is now working, the remaining comment that it throws out at the end is- Warning: Name is nonexistent or not a directory: C:\Users\krist\cobratoolbox\src\analysis\thermo\vonBertalanffy\initVonBertalanffy.m

In path (line 109) In addpath (line 86) In initCobraToolbox (line 656)

However, it doesn't seem to be causing an issue. Thank you!

[rmtfleming]

Hi Kristy, thanks, that issue is not critical unless using vonBertalanffy, but I've repaired it and the fix will appear in the next master version. Regards Ronan

On Fri, 19 Nov 2021 at 02:51, kristycyw @.***> wrote:

Hi Prof Flemming, Thank you it is now working, the remaining comment that it throws out at the end is- Warning: Name is nonexistent or not a directory: C:\Users\krist\cobratoolbox\src\analysis\thermo\vonBertalanffy\initVonBertalanffy.m

In path (line 109) In addpath (line 86) In initCobraToolbox (line 656)

However, it doesn't seem to be causing an issue. Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1874#issuecomment-973679019, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOR4D55I2T4GOEGDAWLUMW3TZANCNFSM5IJNMFJA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

--

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.)

[Moshkante]

Dear @rmtfleming, please apologise for not opening a new thread, but this seemed to be the appropriate Thread as we received identical error message as described above by the issue-opener. Anyhow, thank you very much for the fix, as the latest version is now working properly on our windows machines. Regards