opencobra
Matlab installation error
Please include a short description of problem here One of our masters students just across this issue when trying to use the latest cobra on windows with matlab.
>> initCobraToolbox
_____ _____ _____ _____ _____ |
/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis
| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2019
| | | | | | | _ { | _ / | ___ | |
| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:
\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox
|
> Checking if git is installed ... Done (version: 2.22.0).
> 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)...Entering 'binary'
HEAD is now at d6ba736 Merge pull request #11 from opencobra/GLPKmacOS
error: unknown option `hard'
usage: git submodule--helper foreach [--quiet] [--recursive] [--] <command>
-q, --quiet Suppress output of entering each submodule command
--recursive Recurse into nested submodules
fatal: run_command returned non-zero status while recursing in the nested submodules of binary
.
Warning: The submodules could not be reset.
> In initCobraToolbox (line 213)
Done.
We managed to get the installer to work by adding some extra quotation marks to this line, i.e.:
[status_gitReset, result_gitReset] = system('git submodule foreach --recursive "git reset --hard"');
I hereby confirm that I have:
- [X] Tried to solve the issue on my own
- [X] Retried to run my code with the latest version of The COBRA Toolbox
- [X] Checked that a similar issue has not already been opened
(Note: You may replace [ ] with [X] to check the box)
@teddygroves, thanks for reporting this. What system are you using? Feel free to submit a PR.
I don't know exactly what system Andrei was using but fwiw I don't get the same issue on a mac with matlab 9.5.0.1033004
I just want to add that someone in our group encountered the same on a Windows laptop with Git 2.22 and Matlab 2017b. The solution by @teddygroves worked for us too!
Please include a short description of problem here One of our masters students just across this issue when trying to use the latest cobra on windows with matlab.
>> initCobraToolbox _____ _____ _____ _____ _____ | / ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis | | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2019 | | | | | | | _ { | _ / | ___ | | | |___ | |_| | | |_| | | | \ \ | | | | | Documentation: \_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox | > Checking if git is installed ... Done (version: 2.22.0). > 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)...Entering 'binary' HEAD is now at d6ba736 Merge pull request #11 from opencobra/GLPKmacOS error: unknown option `hard' usage: git submodule--helper foreach [--quiet] [--recursive] [--] <command> -q, --quiet Suppress output of entering each submodule command --recursive Recurse into nested submodules fatal: run_command returned non-zero status while recursing in the nested submodules of binary . Warning: The submodules could not be reset. > In initCobraToolbox (line 213) Done.We managed to get the installer to work by adding some extra quotation marks to this line, i.e.:
[status_gitReset, result_gitReset] = system('git submodule foreach --recursive "git reset --hard"');I hereby confirm that I have:
- [x] Tried to solve the issue on my own
- [x] Retried to run my code with the latest version of The COBRA Toolbox
- [x] Checked that a similar issue has not already been opened
(Note: You may replace [ ] with [X] to check the box)
Worked for me too ! Thanks a lot
