Initialization error after update

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Bhushan Dhamale

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Jan 23, 2018, 7:17:56 AM1/23/18
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After updating COBRA Toolbox today, I have encountered the following:

1. On starting MATLAB, I get:

Warning: Name is nonexistent or not a directory:

/home/bhushan/softwares/MATLAB/R2017b/toolbox/matlab/cobratoolbox/external/libSBML-5.15.3-matlab


2. On initializing the COBRA Toolbox using initCobraToolbox, I get the error:

Error using initCobraToolbox (line 188)

The submodules could not be initialized.



How do I fix these errors?


P.S. Every time I update the toolbox through the terminal, I get new errors in the initialization script. They are mostly easy to fix, and I do the same.

However, this time around, I am unable to fix the error. How do I get rid of this cycle?

I am also attaching the script output for reference.

init_error.pdf

Laurent Heirendt

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Jan 23, 2018, 8:44:37 AM1/23/18
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Hi,

The update function of the COBRA Toolbox might throw errors when there are too many updates or major changes to be performed (including binaries) that cannot be handled properly by git.

Do you mind cloning the COBRA Toolbox again, and restoring your MATLAB path (>> restoredefaultpath followed by >> initCobraToolbox)?

Best,

Laurent

Bhushan Dhamale

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Jan 24, 2018, 4:26:05 AM1/24/18
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Hi Laurent,
I recloned COBRA Toolbox and executed restordefaultpath and initCobraToolbox.
The error however persists.

Bhushan Dhamale

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Jan 24, 2018, 11:15:06 AM1/24/18
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Hi Laurent,
As a temporary crude fix, I commented out lines 183 to 189. This prevented the error from popping up.
I also added the path to the libSBML-15.6-matlab directory from Environment--->Set Path.

Would this fix negatively affect my results?


On Tuesday, January 23, 2018 at 7:14:37 PM UTC+5:30, Laurent Heirendt wrote:

Thomas Pfau

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Jan 25, 2018, 12:41:18 AM1/25/18
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Hello Bhushan,

Did you delete the cobra toolbox directory before you recloned?
What I would do is the following:

start matlab. Run:

restoredefaultpath

savepath

Go to a shell (outside matlab). Run:

rm -rf /home/bhushan/softwares/MATLAB/R2017b/toolbox/matlab/cobratoolbox/

cd /home/bhushan/softwares/MATLAB/R2017b/toolbox/matlab/

git clone g...@github.com:opencobra/cobratoolbox.git cobratoolbox

Go back to matlab

cd /home/bhushan/softwares/MATLAB/R2017b/toolbox/matlab/cobratoolbox

initCobraToolbox

This should make sure, that no remnants of the old toolbox remain and that you work with a clean new clone.
Commenting out the submodules can lead to some things not working properly, so I would not recommend it.

Best

Thomas

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Bhushan Dhamale

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Jan 25, 2018, 3:58:45 AM1/25/18
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Hello Thomas,
Thank you for the detailed reply. I really appreciate it.
And to answer your previous query, yes, I had indeed deleted the COBRA Toolbox directory before recloning.

I have followed your instructions.
When I try to run


I get
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

How might I fix this?

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Thomas Pfau

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Jan 25, 2018, 5:31:19 AM1/25/18
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Hi Bhushan,

Please try:

git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox
Best,

Thomas


On 2018-01-25 09:58, Bhushan Dhamale wrote:
Hello Thomas,
Thank you for the detailed reply. I really appreciate it.
And to answer your previous query, yes, I had indeed deleted the COBRA Toolbox directory before recloning.
That is actually odd.

Bhushan Dhamale

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Jan 29, 2018, 4:28:57 AM1/29/18
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Hello Thomas,
I was able to install the COBRA Toolbox by using 
git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox

The error however persisted. So, I have edited out the --depth 1 from line 184. The toolbox is initializing fine now.
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