Error in initialization of Cobra Toolbox

K Mlm

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Sep 12, 2018, 8:04:49 AM9/12/18

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Hello everybody,

I have followed the steps for the Cobra Toolbox installation (https://opencobra.github.io/cobratoolbox/latest/installation.html#test-the-installation). Still I have a error message on Matlab when I try to initialize it. I obtain: "

initCobraToolbox

_____ _____ _____ _____ _____ |

/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis

| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2018

| | | | | | | _ { | _ / | ___ | |

| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:

\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox

|

> Checking if git is installed ... Done (version: 2.14.3).

> 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)... Done.

> Adding all the files of The COBRA Toolbox ... Warning: Name is nonexistent or not a

directory:

/Users/khadijamhallem/Downloads/cobratoolbox-master/binary/maci64/bin/postSierra

> In path (line 109)

In addpath (line 96)

In adaptMacPath (line 36)

In initCobraToolbox (line 247)

Warning:

"/Users/khadijamhallem/Downloads/cobratoolbox-master/binary/maci64/bin/preSierra"

not found in path.

> In rmpath (line 75)

In adaptMacPath (line 37)

In initCobraToolbox (line 247)

Done.

> Define CB map output... set to svg.

Error using getDistributedModelFolder

(line 36)

Requested Model not present in the model

directory.\n This is either due to the

model not being downloaded, or not being

part of the distributed models.

Error in initCobraToolbox (line 280)

xmlTestFile =

[getDistributedModelFolder(xmlTestModel)

filesep xmlTestModel];

Could anyone help me please? I do not understand what I have made badly.

Thank in advance,

Khadija

Laurent Heirendt

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Sep 12, 2018, 10:01:12 AM9/12/18

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Hi,

It seems as if there are some issues with your path. May you try:

>> restoredefaultpath;
>> initCobraToolbox

If that does not work, may you attach the systemConfigReport?

Thanks,

Laurent

K Mlm

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Sep 12, 2018, 12:27:34 PM9/12/18

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Thank you Laurent. I have tried following your advices but it did not work. How can I find a systemConfigReport?

Thanks,

Khadija

Laurent Heirendt

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Sep 13, 2018, 9:16:25 AM9/13/18

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Hi,

May you run:

>> generateSystemConfigReport

Then, attach the report to this conversation.

May you also run the following commands from within the cobratoolbox directory and let me know the output?

>> system('git status')
>> system('git submodule update --init')
>> system('git status')
>> initCobraToolbox

Best regards,

Laurent

K Mlm

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Sep 13, 2018, 11:59:36 AM9/13/18

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Hello Laurent,

Here is what I obtain:

generateSystemConfigReport

> ---------------------------------- SYSTEM CONFIGURATION REPORT ----------------------------------

_____ _____ _____ _____ _____ |

/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis

| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2018

| | | | | | | _ { | _ / | ___ | |

| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:

\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox

|

> Checking if git is installed ... Done (version: 2.14.3).

> 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)... Done.

> Adding all the files of The COBRA Toolbox ... Warning: Name is nonexistent or not a

directory:

/Users/khadijamhallem/Downloads/cobratoolbox-master/binary/maci64/bin/postSierra

> In path (line 109)

In addpath (line 96)

In adaptMacPath (line 36)

In initCobraToolbox (line 247)

In generateSystemConfigReport (line 72)

Warning:

"/Users/khadijamhallem/Downloads/cobratoolbox-master/binary/maci64/bin/preSierra"

not found in path.

> In rmpath (line 75)

In adaptMacPath (line 37)

In initCobraToolbox (line 247)

In generateSystemConfigReport (line 72)

Done.

> Define CB map output... set to svg.

-----------------------------------------------------------------------------------------------------

MATLAB Version: 9.4.0.813654 (R2018a)

MATLAB License Number: DEMO

Operating System: Mac OS X Version: 10.12.6 Build: 16G1510

Java Version: Java 1.8.0_144-b01 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

-----------------------------------------------------------------------------------------------------

MATLAB Version 9.4 (R2018a)

Simulink Version 9.1 (R2018a)

Bioinformatics Toolbox Version 4.10 (R2018a)

Communications System Toolbox Version 6.6 (R2018a)

Computer Vision System Toolbox Version 8.1 (R2018a)

Control System Toolbox Version 10.4 (R2018a)

Curve Fitting Toolbox Version 3.5.7 (R2018a)

DSP System Toolbox Version 9.6 (R2018a)

Database Toolbox Version 8.1 (R2018a)

Datafeed Toolbox Version 5.7 (R2018a)

Econometrics Toolbox Version 5.0 (R2018a)

Financial Instruments Toolbox Version 2.7 (R2018a)

Financial Toolbox Version 5.11 (R2018a)

Global Optimization Toolbox Version 3.4.4 (R2018a)

Image Acquisition Toolbox Version 5.4 (R2018a)

Image Processing Toolbox Version 10.2 (R2018a)

Instrument Control Toolbox Version 3.13 (R2018a)

Neural Network Toolbox Version 11.1 (R2018a)

Optimization Toolbox Version 8.1 (R2018a)

Parallel Computing Toolbox Version 6.12 (R2018a)

Signal Processing Toolbox Version 8.0 (R2018a)

SimBiology Version 5.8 (R2018a)

Simulink Control Design Version 5.1 (R2018a)

Stateflow Version 9.1 (R2018a)

Statistics and Machine Learning Toolbox Version 11.3 (R2018a)

Symbolic Math Toolbox Version 8.1 (R2018a)

System Identification Toolbox Version 9.8 (R2018a)

> Default shell : /bin/bash

> Version of shell : GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin16)

> Architecture : MACI64

> MATLAB folder : /Applications/MATLAB_R2018a.app

> COBRA Toolbox root : /Users/khadijamhallem/Downloads/cobratoolbox-master

> git version : git version 2.14.3 (Apple Git-98)

> curl version : curl 7.54.0 (x86_64-apple-darwin16.0)

> CBT_LP_SOLVER :

> CBT_MILP_SOLVER :

> CBT_QP_SOLVER :

> CBT_MIQP_SOLVER :

> CBT_NLP_SOLVER :

> GUROBI_PATH :

> ILOG_CPLEX_PATH :

> TOMLAB_PATH :

> MOSEK_PATH :

> ----------------------------------- END OF CONFIGURATION REPORT -----------------------------------

> Please send the report located in

/Users/khadijamhallem/Downloads/cobratoolbox-master/COBRAconfigReport.log

to the developers or post it in the forum:

AND THEN, following your advices:

system('git status')

system('git submodule update --init')

system('git status')

initCobraToolbox

On branch master

No commits yet

Untracked files:

(use "git add <file>..." to include in what will be committed)

.artenolis.yml

.artenolis/

.gitattributes

.github/

.gitignore

.gitmodules

LICENSE.md

README.rst

codecov.yml

docs/

external/

initCobraToolbox.m

src/

test/

nothing added to commit but untracked files present (use "git add" to track)

ans =

0

ans =

0

On branch master

No commits yet

Untracked files:

(use "git add <file>..." to include in what will be committed)

.artenolis.yml

.artenolis/

.gitattributes

.github/

.gitignore

.gitmodules

LICENSE.md

README.rst

codecov.yml

docs/

external/

initCobraToolbox.m

src/

test/

nothing added to commit but untracked files present (use "git add" to track)

ans =

0

Anne Richelle

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Sep 14, 2018, 4:49:22 AM9/14/18

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Interestingly, I had the same problem when I wanted to install the latest version on a new computer.

Khadija, could you check if the following directory is empty:

:\cobratoolbox\test\models

This is the issue I had, the folder was empty while normally it should be a repository of xml and mat models.

@Laurent, the download of the "model" folder content does not occur (download as zip or cloning cobra does not change)

K Mlm

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Sep 17, 2018, 11:02:37 AM9/17/18

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@Anne Richelle, thank you for your answer. Indeed, the directory :\cobratoolbox\test\models is empty. Should I download one more time cobra toolbox to complete it by the repository of xml and mat models?

Thanks in advance,

Khadija

Ps: Hope you are well ;)

Message has been deleted

Supreeta V

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Sep 21, 2018, 8:28:47 AM9/21/18

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@Anne Richelle @K MIm @Laurent Heirendt I'm also having the same issues, the test/models folder is empty so initCobraToolbox is not working. Did you happen to resolve the issue?

Laurent Heirendt

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Sep 21, 2018, 10:28:09 AM9/21/18

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Hi,

There seems to be a local installation/configuration issue.

Did you clone the COBRA Toolbox or did you download the zip archive?

May you try downloading the full version of the COBRA Toolbox from here? https://prince.lcsb.uni.lu/releases/theCOBRAToolbox.zip

Best,

Laurent

Supreeta V

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Sep 24, 2018, 6:58:31 AM9/24/18

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Thanks Laurent, the full version zip archive from your link works.

Previously, neither cloning the git or downloading the zip from https://github.com/opencobra/cobratoolbox/archive/master.zip worked for me.

K Mlm

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Sep 24, 2018, 10:18:57 AM9/24/18

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Thanks to all of you, it has finally worked! Excited to get familiar with this :)

Teresa

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Apr 27, 2020, 3:37:13 AM4/27/20

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Hi all,

I had some problems using GitHub, thats why I downloaded the cobratoolbox from this link https://github.com/opencobra/cobratoolbox.

However I have now the same problem as described here and my folder cobratoolbox-master/test/models is empty and therefore I get an error while initialisation of the toolbox.

The link from Laurent is obviously not available any more.

Is there an idea from someone how to handle this problem?

Thank you for your help.

Teresa

Ronan M.T. Fleming

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Apr 27, 2020, 7:21:51 AM4/27/20

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Hi Teresa,
please start again and follow each one of the installation steps
https://opencobra.github.io/cobratoolbox/stable/installation.html
then if it does not work provide the response of a call to:
generateSystemConfigReport()
Regards,
Ronan

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