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Marco Severgnini
Apr 19, 2019, 3:58:20 AM4/19/19
to COBRA Toolbox
Dear Support, I just installed COBRA toolbox on my server and I occurred in an error while running "initCobraToolbox" command.
After performing some of the checks, the command fails when trying to execute "getFilesInDir"
I had a look at Matlab code, but I wasn't able to understand what causes the fail
Here you can find what happened:
> Checking if git is installed ... Done (version: 1.8.3.).
> 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.
Error using cellstr (line 24)
S must be 2-D.
Error in cell/strcat (line 17)
varargin{i} = cellstr(varargin{i});
Error in getFilesInDir (line 143)
files = strcat(absPath, filesep, files);
Error in initCobraToolbox (line 222)
dirContent = getFilesInDir('type','all');The output of generateSystemConfigReport is reported below:
> ---------------------------------- SYSTEM CONFIGURATION REPORT ----------------------------------
_____ _____ _____ _____ _____ |
/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis
| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2019
| | | | | | | _ { | _ / | ___ | |
| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:
\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox
|
Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest you rename the function to
avoid a potential name conflict.
> In path (line 109)
In addpath (line 88)
In initCobraToolbox (line 108)
In generateSystemConfigReport (line 72)
Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest you rename the function to
avoid a potential name conflict.
> In path (line 109)
In addpath (line 88)
In initCobraToolbox (line 111)
In generateSystemConfigReport (line 72)
Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest you rename the function to
avoid a potential name conflict.
> In path (line 109)
In addpath (line 88)
In initCobraToolbox (line 114)
In generateSystemConfigReport (line 72)
> Checking if git is installed ... Done (version: 1.8.3.).
> 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.
----------------------------------------------------------------------------------------------------
MATLAB Version: 9.2.0.538062 (R2017a)
MATLAB License Number: 123456
Operating System: Linux 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64
Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
----------------------------------------------------------------------------------------------------
MATLAB Version 9.2 (R2017a)
Simulink Version 8.9 (R2017a)
Aerospace Blockset Version 3.19 (R2017a)
Aerospace Toolbox Version 2.19 (R2017a)
Antenna Toolbox Version 2.2 (R2017a)
Audio System Toolbox Version 1.2 (R2017a)
Automated Driving System Toolbox Version 1.0 (R2017a)
Bioinformatics Toolbox Version 4.8 (R2017a)
Communications System Toolbox Version 6.4 (R2017a)
Computer Vision System Toolbox Version 7.3 (R2017a)
Control System Toolbox Version 10.2 (R2017a)
Curve Fitting Toolbox Version 3.5.5 (R2017a)
DO Qualification Kit Version 3.3 (R2017a)
DSP System Toolbox Version 9.4 (R2017a)
Database Toolbox Version 7.1 (R2017a)
Datafeed Toolbox Version 5.5 (R2017a)
Econometrics Toolbox Version 4.0 (R2017a)
Embedded Coder Version 6.12 (R2017a)
Filter Design HDL Coder Version 3.1.1 (R2017a)
Financial Instruments Toolbox Version 2.5 (R2017a)
Financial Toolbox Version 5.9 (R2017a)
Fixed-Point Designer Version 5.4 (R2017a)
Fuzzy Logic Toolbox Version 2.2.25 (R2017a)
Global Optimization Toolbox Version 3.4.2 (R2017a)
HDL Coder Version 3.10 (R2017a)
HDL Verifier Version 5.2 (R2017a)
IEC Certification Kit Version 3.9 (R2017a)
Image Acquisition Toolbox Version 5.2 (R2017a)
Image Processing Toolbox Version 10.0 (R2017a)
Instrument Control Toolbox Version 3.11 (R2017a)
LTE System Toolbox Version 2.4 (R2017a)
MATLAB Coder Version 3.3 (R2017a)
MATLAB Compiler Version 6.4 (R2017a)
MATLAB Compiler SDK Version 6.3.1 (R2017a)
MATLAB Distributed Computing Server Version 6.10 (R2017a)
MATLAB Report Generator Version 5.2 (R2017a)
Mapping Toolbox Version 4.5 (R2017a)
Model Predictive Control Toolbox Version 5.2.2 (R2017a)
Neural Network Toolbox Version 10.0 (R2017a)
Optimization Toolbox Version 7.6 (R2017a)
Parallel Computing Toolbox Version 6.10 (R2017a)
Partial Differential Equation Toolbox Version 2.4 (R2017a)
Phased Array System Toolbox Version 3.4 (R2017a)
Polyspace Bug Finder Version 2.3 (R2017a)
Polyspace Code Prover Version 9.7 (R2017a)
Powertrain Blockset Version 1.1 (R2017a)
RF Blockset Version 6.0 (R2017a)
RF Blockset Version 6.0 (R2017a)
RF Toolbox Version 3.2 (R2017a)
Risk Management Toolbox Version 1.1 (R2017a)
Robotics System Toolbox Version 1.4 (R2017a)
Robust Control Toolbox Version 6.3 (R2017a)
Signal Processing Toolbox Version 7.4 (R2017a)
SimBiology Version 5.6 (R2017a)
SimEvents Version 5.2 (R2017a)
Simscape Version 4.2 (R2017a)
Simscape Driveline Version 2.12 (R2017a)
Simscape Electronics Version 2.11 (R2017a)
Simscape Fluids Version 2.2 (R2017a)
Simscape Multibody Version 5.0 (R2017a)
Simscape Power Systems Version 6.7 (R2017a)
Simulink 3D Animation Version 7.7 (R2017a)
Simulink Code Inspector Version 3.0 (R2017a)
Simulink Coder Version 8.12 (R2017a)
Simulink Control Design Version 4.5 (R2017a)
Simulink Design Optimization Version 3.2 (R2017a)
Simulink Design Verifier Version 3.3 (R2017a)
Simulink Report Generator Version 5.2 (R2017a)
Simulink Test Version 2.2 (R2017a)
Simulink Verification and Validation Version 3.13 (R2017a)
Stateflow Version 8.9 (R2017a)
Statistics and Machine Learning Toolbox Version 11.1 (R2017a)
Symbolic Math Toolbox Version 7.2 (R2017a)
System Identification Toolbox Version 9.6 (R2017a)
Trading Toolbox Version 3.2 (R2017a)
Vision HDL Toolbox Version 1.4 (R2017a)
WLAN System Toolbox Version 1.3 (R2017a)
Wavelet Toolbox Version 4.18 (R2017a)
> Default shell : /bin/bash
> Version of shell : GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
> Architecture : GLNXA64
> MATLAB folder : /opt/MATLAB/R2017a
> COBRA Toolbox root : /opt/MATLAB/OtherToolbox/cobratoolbox
> git version : git version 1.8.3.1
> curl version : curl 7.29.0 (x86_64-redhat-linux-gnu)
> 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
/opt/MATLAB/OtherToolbox/cobratoolbox/COBRAconfigReport.logThank you very much for your support,
All the best,
Marco Severgnini
Marco Severgnini
May 3, 2019, 3:37:41 AM5/3/19
to COBRA Toolbox
Dear all, after a couple of weeks I haven't received any feedback about my question yet.
Can anyone help me in understanding what happened?
Thank you very much
Marco
Ronan M.T. Fleming
May 7, 2019, 6:35:46 AM5/7/19
to COBRA Toolbox
Maybe
Error in initCobraToolbox (line 222)
dirContent = getFilesInDir('type','all');
dirContent = getFilesInDir('type','all');
fails if you dont have the right permissions set for the folder?
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--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Marco Severgnini
May 7, 2019, 10:04:42 AM5/7/19
to COBRA Toolbox
Dear Ronan, I checked the path in which I installed COBRA toolbox and all the permissions were correctly set (i.e.: I can read the files and read/execute directories).
The problem, indeed seemed to be related to the fact that, when calling:
files = strcat(absPath, filesep, files); %line 143 in getFilesInDir
strcat command fails because it's attempting to concatenate absPath (length=1), filesep (length=1) and files (length=1707)
I succeded in hacking the code this way:
files=strcat(repmat({absPath},1,length(files)),repmat({filesep},1,length(files)),files);Moreover, I also occurred into an error when the script checks for Matlab version using verLessThan in changeCobraSolver and I had to build my own way to check whether Matlab version is >8.6. Just for information, I substituted
% LINE 428
if verLessThan('matlab', '9') && ~verLessThan('matlab', '8.6') % >2015b
warning('off', 'MATLAB:lang:badlyScopedReturnValue'); % take out warning message
endwith
matver=split(version,".");
matver=str2double(strcat(char(matver(1)),'.',char(matver(2))));
if matver < 8.6
warning('off', 'MATLAB:lang:badlyScopedReturnValue'); % take out warning message
end
The same substitution was made in isCompatible script (line 242)
I don't know if this is a real bug or something related only to my Matlba environment, but i would like to share my experience and how I succeeded (apparently) in overcoming the initialization issues.
Marco
Laurent Heirendt
May 13, 2019, 8:59:50 AM5/13/19
to COBRA Toolbox
Hi Marco,
Thanks for that: https://github.com/opencobra/cobratoolbox/pull/1472
Next time, feel free to contribute yourself: https://opencobra.github.io/cobratoolbox/latest/contributing.html
Best regards,
Laurent
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