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opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
https://opencobra.github.io/cobratoolbox
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cobra toolbox matlab installation #1635

Open bab135 opened 4 years ago

bab135 commented 4 years ago

Please include a short description of problem here initCobraToolbox

  _____   _____   _____   _____     _____     |
 /  ___| /  _  \ |  _  \ |  _  \   / ___ \    |   COnstraint-Based Reconstruction and Analysis
 | |     | | | | | |_| | | |_| |  | |___| |   |   The COBRA Toolbox - 2020
 | |     | | | | |  _  { |  _  /  |  ___  |   |
 | |___  | |_| | | |_| | | | \ \  | |   | |   |   Documentation:
 \_____| \_____/ |_____/ |_|  \_\ |_|   |_|   |   http://opencobra.github.io/cobratoolbox
                                              |

Checking if git is installed ... Done (version: 2.28.0). 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)...usage: git submodule [--quiet] [--cached] or: git submodule [--quiet] add [-b ] [-f|--force] [--name ] [--reference ] [--] [] or: git submodule [--quiet] status [--cached] [--recursive] [--] [...] or: git submodule [--quiet] init [--] [...] or: git submodule [--quiet] deinit [-f|--force] (--all| [--] ...) or: git submodule [--quiet] update [--init] [--remote] [-N|--no-fetch] [-f|--force] [--checkout|--merge|--rebase] [--[no-]recommend-shallow] [--reference ] [--recursive] [--[no-]single-branch] [--] [...] or: git submodule [--quiet] set-branch (--default|--branch ) [--] or: git submodule [--quiet] set-url [--] or: git submodule [--quiet] summary [--cached|--files] [--summary-limit ] [commit] [--] [...] or: git submodule [--quiet] foreach [--recursive] or: git submodule [--quiet] sync [--recursive] [--] [...] or: git submodule [--quiet] absorbgitdirs [--] [...] Warning: The submodules could not be reset. In initCobraToolbox (line 214) Done. Adding all the files of The COBRA Toolbox ... Done. Define CB map output... set to svg. Error using getDistributedModelFolder (line 37) 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 281) xmlTestFile = [getDistributedModelFolder(xmlTestModel) filesep xmlTestModel];

how to solve this issue? my matlab version is MATLAB R2020b I hereby confirm that I have:

(Note: You may replace [ ] with [X] to check the box)

rmtfleming commented 4 years ago

Update to the latest master version of the cobra toolbox and try again.

On Mon, 19 Oct 2020 at 14:00, bab135 notifications@github.com wrote:

Please include a short description of problem here initCobraToolbox

_____ / ___ / _ \ _ \ _ \ / ___ \ COnstraint-Based Reconstruction and Analysis _ _ ___ The COBRA Toolbox - 2020 _ { _ / ___ ___ _ _ \ \ Documentation: _____ _____/ _____/ _ _\ _ _ http://opencobra.github.io/cobratoolbox

Checking if git is installed ... Done (version: 2.28.0). 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)...usage: git submodule [--quiet] [--cached] or: git submodule [--quiet] add [-b ] [-f|--force] [--name ] [--reference ] [--] [] or: git submodule [--quiet] status [--cached] [--recursive] [--] [...] or: git submodule [--quiet] init [--] [...] or: git submodule [--quiet] deinit [-f|--force] (--all| [--] ...) or: git submodule [--quiet] update [--init] [--remote] [-N|--no-fetch] [-f|--force] [--checkout|--merge|--rebase] [--[no-]recommend-shallow] [--reference ] [--recursive] [--[no-]single-branch] [--] [...] or: git submodule [--quiet] set-branch (--default|--branch ) [--] or: git submodule [--quiet] set-url [--] or: git submodule [--quiet] summary [--cached|--files] [--summary-limit ] [commit] [--] [...] or: git submodule [--quiet] foreach [--recursive] or: git submodule [--quiet] sync [--recursive] [--] [...] or: git submodule [--quiet] absorbgitdirs [--] [...] Warning: The submodules could not be reset. In initCobraToolbox (line 214) Done. Adding all the files of The COBRA Toolbox ... Done. Define CB map output... set to svg. Error using getDistributedModelFolder (line 37) 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 281) xmlTestFile = [getDistributedModelFolder(xmlTestModel) filesep xmlTestModel];

how to solve this issue? my matlab version is MATLAB R2020b I hereby confirm that I have:

  • Tried to solve the issue on my own
  • Retried to run my code with the latest version of The COBRA Toolbox
  • Checked that a similar issue has not already been opened

(Note: You may replace [ ] with [X] to check the box)

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

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 & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway.

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