InitCobratoolbox() command keeps running for a longtime

[john irudayaraj]

Hi,

   I am facing some problem while running the initCobratoolbox() command, it gets stuck or keeps running for a long time at the 'Initializing and updating submodules' step. When i terminate the process using Ctrl+C i can see that it is stuck line 201 of the initCobratoolbox() which is as follows:

[status_gitSubmodule, result_gitSubmodule] = system(['git submodule update --init --remote --no-fetch ' depthFlag]);

I tried updating my git but it didn't fix the problem. I would greatly appreciate your help.

John Hendry

Postdoc

Penn state

[Amirhossein Masroor]

Hey

Try initCobraToolbox(false) see if it runs properly. The false means that it won't update cobea. If it works your cobra is installed properly. If not, I would reinstall

Best regards

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[Ronan M.T. Fleming]

Hi,
in addition to Amirhossein's suggestion, please check you satisfy the
requirements: https://opencobra.github.io/cobratoolbox/stable/installation.html#system-requirements

What is the output of generateSystemConfigReport?

Regards,

Ronan

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[John Irudayaraj]

Dear Amirhossein and Dr. Fleming,

         Thanks for getting back to me. I did try initCobraToolbox(false) but it did not work since that does not skip the line 201 that i have copy pasted earlier. Whenever i use changecobrasolver command it goes to initcobratoolbox and gets stuck at line 201. I removed my existing cobra toolbox and downloaded the compressed archive of cobra toolbox and installed it offline and it fixed the issue. (Note that offline installation skipped the update submodule step.) But I don't know if it would create any problem in the future. 

Dr. Fleming,

      I tried running generateSystemConfigReport it get stuck at initCobraToolbox (line 546: updateCobraToolbox(true)) and if i go offline it skips that step and works fine. I am using mac with high sierra and my matlab version is 2017b. My git version is 2.17 and I also tried git version 2.26. 

Regards

John

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[Charles Swofford]

I am also having the exact same issue!

On Tuesday, March 24, 2020 at 10:38:00 AM UTC-4, john irudayaraj wrote:

Dear Amirhossein and Dr. Fleming,

         Thanks for getting back to me. I did try initCobraToolbox(false) but it did not work since that does not skip the line 201 that i have copy pasted earlier. Whenever i use changecobrasolver command it goes to initcobratoolbox and gets stuck at line 201. I removed my existing cobra toolbox and downloaded the compressed archive of cobra toolbox and installed it offline and it fixed the issue. (Note that offline installation skipped the update submodule step.) But I don't know if it would create any problem in the future. 

Dr. Fleming,

      I tried running generateSystemConfigReport it get stuck at initCobraToolbox (line 546: updateCobraToolbox(true)) and if i go offline it skips that step and works fine. I am using mac with high sierra and my matlab version is 2017b. My git version is 2.17 and I also tried git version 2.26. 

Regards

John

On Tue, Mar 24, 2020 at 6:45 AM Ronan M.T. Fleming <ronan.m...@gmail.com> wrote:

Hi,
in addition to Amirhossein's suggestion, please check you satisfy the
requirements: https://opencobra.github.io/cobratoolbox/stable/installation.html#system-requirements

What is the output of generateSystemConfigReport?

Regards,

Ronan

On Tue, 24 Mar 2020 at 08:07, Amirhossein Masroor
<amirhosse...@gmail.com> wrote:
>
> Hey
> Try initCobraToolbox(false) see if it runs properly. The false means that it won't update cobea. If it works your cobra is installed properly. If not, I would reinstall
> Best regards
>
> On Tue, Mar 24, 2020, 8:25 AM john irudayaraj <joh...@gmail.com> wrote:
>>
>> Hi,
>>    I am facing some problem while running the initCobratoolbox() command, it gets stuck or keeps running for a long time at the 'Initializing and updating submodules' step. When i terminate the process using Ctrl+C i can see that it is stuck line 201 of the initCobratoolbox() which is as follows:
>>
>> [status_gitSubmodule, result_gitSubmodule] = system(['git submodule update --init --remote --no-fetch ' depthFlag]);
>>
>> I tried updating my git but it didn't fix the problem. I would greatly appreciate your help.
>>
>> John Hendry
>> Postdoc
>> Penn state
>>
>> --
>>
>> ---
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>> To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/d0556802-b4f0-4dfe-a47a-65b6ce2a3eed%40googlegroups.com.
>
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[Ronan M.T. Fleming]

Hi,
this should be fixed in the develop branch now:
https://github.com/opencobra/cobratoolbox/tree/develop
I have initiated a pull request to merge recent changes with master.
https://github.com/opencobra/cobratoolbox/pull/1579
Once several key checks have passed, it should be possible to update
the master version.
Regards,
Ronan

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[Charles Swofford]

Thank you for looking into this Ronan!  I tried to run initCobraToolbox this morning and am still having the same issue.  When should we expect that the master version has been updated?

[Ronan M.T. Fleming]

Hi Charles,

once all the platform tests are passing here:
https://github.com/opencobra/cobratoolbox/pull/1579
Currently 4 are pending and 30 are passed.

There is a workaround in the mean time
https://github.com/opencobra/cobratoolbox/issues/1584
After checking out the repo, but before running matlab, do one of the following:

git submodule update --init --remote --no-fetch

Regards,

Ronan

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