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opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
https://opencobra.github.io/cobratoolbox
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problem initializing and updating problem #1795

Closed joel8484 closed 3 years ago

joel8484 commented 3 years ago

Hi I followed the installation of CobraToolbox as outlined. However the following error showed when runnint initCobraToolbox:

`>> initCobraToolbox

  _____   _____   _____   _____     _____     |
 /  ___| /  _  \ |  _  \ |  _  \   / ___ \    |   COnstraint-Based Reconstruction and Analysis
 | |     | | | | | |_| | | |_| |  | |___| |   |   The COBRA Toolbox - 2021
 | |     | | | | |  _  { |  _  /  |  ___  |   |
 | |___  | |_| | | |_| | | | \ \  | |   | |   |   Documentation:
 \_____| \_____/ |_____/ |_|  \_\ |_|   |_|   |   http://opencobra.github.io/cobratoolbox
                                              |

Checking if git is installed ... Done (version: 2.17.1). 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)...error: could not lock config file .git/config: Permission denied error: could not lock config file .git/config: Permission denied fatal: Failed to register url for submodule path 'binary' Error using initCobraToolbox (line 226) The submodules could not be initialized.`

Did anyone else face this issue? And is there a fix for this or any misstep by me which I am missing? Any help would be greatly appreciated. Thanks a lot.

Regards, Joel

rmtfleming commented 3 years ago

What access permissions are set to for the cobra toolbox installation folder?

error: could not lock config file .git/config: Permission denied

On Wed, 1 Sept 2021 at 12:13, joel8484 @.***> wrote:

Hi I followed the installation of CobraToolbox as outlined. However the following error showed when runnint initCobraToolbox:

`>> initCobraToolbox

_____ / ___ / _ \ _ \ _ \ / ___ \ COnstraint-Based Reconstruction and Analysis _ _ ___ The COBRA Toolbox - 2021 _ { _ / ___ ___ _ _ \ \ Documentation: _____ _____/ _____/ _ _\ _ _ http://opencobra.github.io/cobratoolbox

Checking if git is installed ... Done (version: 2.17.1). 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)...error: could not lock config file .git/config: Permission denied error: could not lock config file .git/config: Permission denied fatal: Failed to register url for submodule path 'binary' Error using initCobraToolbox (line 226) The submodules could not be initialized.`

Did anyone else face this issue? And is there a fix for this or any misstep by me which I am missing? Any help would be greatly appreciated. Thanks a lot.

Regards, Joel

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

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joel8484 commented 3 years ago

Hi Ronan,

Thanks for the reply.

I chechked and it showed as follows: drwxr-xr-x 13 root root 4096 Sep 1 04:28 cobratoolbox

Regards, Joel

rmtfleming commented 3 years ago

Permissions are too restrictive.

On Wed, 1 Sept 2021 at 12:23, joel8484 @.***> wrote:

Hi Ronan,

Thanks for the reply.

I chechked and it showed as follows: drwxr-xr-x 13 root root 4096 Sep 1 04:28 cobratoolbox

Regards, Joel

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1795#issuecomment-910188407, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOUTRMWMK3DTHKJCJRTT7YEJRANCNFSM5DGHKJHQ . 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.

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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.)

tpfau commented 3 years ago

Hi Joel,

The owner of your toolbox folder is root, and only root got read/write privileges. You'll either have to change the owner of the toolbox folder (chown username -R cobratoolbox) or change the permissions on the toolbox folder to also allow other users to read/write/execute files (chmod -R a+rwx cobratoolbox).

Best

Thomas

joel8484 commented 3 years ago

Thanks Thomas and Ronan for the comment; I think it ran well this time, the output is as follows:

initCobraToolbox

  _____   _____   _____   _____     _____     |
 /  ___| /  _  \ |  _  \ |  _  \   / ___ \    |   COnstraint-Based Reconstruction and Analysis
 | |     | | | | | |_| | | |_| |  | |___| |   |   The COBRA Toolbox - 2021
 | |     | | | | |  _  { |  _  /  |  ___  |   |
 | |___  | |_| | | |_| | | | \ \  | |   | |   |   Documentation:
 \_____| \_____/ |_____/ |_|  \_\ |_|   |_|   |   http://opencobra.github.io/cobratoolbox
                                              |

Checking if git is installed ... Done (version: 2.17.1). 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 ... Done. Define CB map output... set to svg. TranslateSBML is installed and working properly. Configuring solver environment variables ...

  • [---*] ILOG_CPLEX_PATH: /opt/ibm/ILOG/CPLEX_Studio129/cplex/matlab/x86-64_linux
  • [----] GUROBI_PATH: --> set this path manually after installing the solver ( see instructions )
  • [---*] TOMLAB_PATH: /opt/tomlab/
  • [-*--] MOSEK_PATH: /home/joe/RAVEN/mosek Done. Checking available solvers and solver interfaces ...Gurobi installed at this location? Licence file current? CPXPARAM_Output_WriteLevel 3 CPXPARAM_Output_CloneLog -1 Found incumbent of value 0.000000 after 0.00 sec. (0.00 ticks)

Root node processing (before b&c): Real time = 0.00 sec. (0.00 ticks) Parallel b&c, 32 threads: Real time = 0.00 sec. (0.00 ticks) Sync time (average) = 0.00 sec. Wait time (average) = 0.00 sec.

Total (root+branch&cut) = 0.00 sec. (0.00 ticks) Error 2100: Cannot open file /opt/tomlab/tomlab.lic for reading. Set environment variable TOMLAB_LICENSE_FILE to the full path of your license file or name it tomlab.lic and put it in your tomlab installation directory. GLPK Simplex Optimizer, v4.42 1 row, 2 columns, 1 non-zero Preprocessing... ~ 0: obj = 0.000000000e+00 infeas = 0.000e+00 OPTIMAL SOLUTION FOUND BY LP PREPROCESSOR

[glpk] Primal optimality condition in solveCobraLP satisfied.

pdco.m Version pdco5 of 15 Jun 2018 Primal-dual barrier method to minimize a convex function subject to linear constraints Ax + r = b, bl <= x <= bu

Michael Saunders SOL and ICME, Stanford University Contributors: Byunggyoo Kim (SOL), Chris Maes (ICME) Santiago Akle (ICME), Matt Zahr (ICME) Aekaansh Verma (ME)

The objective is linear The matrix A is an explicit sparse matrix

m = 1 n = 2 nnz(A) = 1 max |b | = 0 max |x0| = 1.0e+00 xsize = 1.0e+00 max |y0| = 1 max |z0| = 1.0e+00 zsize = 1.0e+00

x0min = 1 featol = 1.0e-06 d1max = 1.0e-04 z0min = 1 opttol = 1.0e-06 d2max = 5.0e-04 mu0 = 1.0e-01 steptol = 0.99 bigcenter= 1000

LSMR/MINRES: atol1 = 1.0e-10 atol2 = 1.0e-15 btol = 0.0e+00 conlim = 1.0e+12 itnlim = 10 show = 0

Method = 2 (1 or 11=chol 2 or 12=QR 3 or 13=LSMR 4 or 14=MINRES 21=SQD(LU) 22=SQD(MA57)) Eliminating dy before dx

Bounds: [0,inf] [-inf,0] Finite bl Finite bu Two bnds Fixed Free 0 0 0 0 0 2 0 [0, bu] [bl, 0] excluding fixed variables 0 0

Itn mu stepx stepz Pinf Dinf Cinf Objective nf center QR 0 -6.6 -99.0 -Inf 1.2500000e-07 1.0 1 -1.0 1.000 1.000 -99.0 -99.0 -Inf 0.0000000e+00 1 1.0 1 2 -3.0 1.000 1.000 -99.0 -99.0 -Inf 0.0000000e+00 1 1.0 3 -5.0 1.000 1.000 -99.0 -99.0 -Inf 0.0000000e+00 1 1.0 4 -7.0 1.000 1.000 -99.0 -99.0 -Inf 0.0000000e+00 1 1.0 Converged

max |x| = 0.000 max |y| = 0.000 max |z| = 0.000 scaled max |x| = 0.000 max |y| = 0.000 max |z| = 0.000 unscaled max |x| and max |z| exclude fixed variables PDitns = 4 QRitns = 0 cputime = 0.2

Distribution of vector x z [ 1, 10 ) 0 2 [ 0.1, 1 ) 0 0 [ 0.01, 0.1 ) 0 0 [ 0.001, 0.01 ) 0 0 [ 0.0001, 0.001 ) 0 0 [ 1e-05, 0.0001 ) 0 0 [ 1e-06, 1e-05 ) 0 0 [ 1e-07, 1e-06 ) 0 0 [ 1e-08, 1e-07 ) 0 0 [ 0, 1e-08 ) 2 0 Elapsed time is 0.166244 seconds.

[pdco] Primal optimality condition in solveCobraLP satisfied. [pdco] Dual optimality condition in solveCobraLP satisfied.

[cplexlp] Primal optimality condition in solveCobraLP satisfied. [cplexlp] Dual optimality condition in solveCobraLP satisfied. Error: License information is corrupt. If the license file was recently changed or reinstalled, do "clear mex" and try again. Done. Setting default solvers ... Done. Saving the MATLAB path ... Done.

  • The MATLAB path was saved as ~/pathdef.m.

Summary of available solvers and solver interfaces

        Support        LP    MILP      QP    MIQP     NLP      EP
------------------------------------------------------------------------------
gurobi          active              0       0       0       0       -       -
ibm_cplex       active              1       1       1       1       -       -
tomlab_cplex    active              1       1       1       1       -       -
glpk            active              1       1       -       -       -       -
mosek           active              0       -       0       -       -       0
matlab          active              0       -       -       -       0       -
pdco            active              1       -       1       -       -       1
quadMinos       active              0       -       -       -       -       -
dqqMinos        active              0       -       0       -       -       -
cplex_direct    active              1       1       1       -       -       -
cplexlp         active              1       -       -       -       -       -
qpng            passive             -       -       1       -       -       -
tomlab_snopt    passive             -       -       -       -       1       -
lp_solve        legacy              1       -       -       -       -       -
------------------------------------------------------------------------------
Total           -                   7       4       5       2       1       1

Do you have any further suggestions?

(Sorry its the first time I'm on MATLAB and using CobraToolbox, hence I am still learning and am causing troubles with all these queries.)

Kind Regards, Joel