initialization of cobratoolbox failed

Ravenclawer commented 3 years ago

Please include a short description of problem here I have tested the following to install the lastest cobratoolbox, and they all failed

using git to download cobratoolbox
download the latest release 3.2 and cd to the directory then initial
download the master zip and cd to the directory then initial they all result in the following message:

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)

Ravenclawer commented 3 years ago

I am quite desperate

rmtfleming commented 3 years ago

search for the problem in the google group

On Wed, 15 Sept 2021 at 15:04, robert zhang @.***> wrote:

I am quite desperate

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1800#issuecomment-920049376, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOSSOEQS2TNZA33W7A3UCCRYVANCNFSM5ECQ7KTQ . 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

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tpfau commented 3 years ago

Your toolbox seems to have a problem connecting to the internet. either your machine is not connected, or potentially some firewall is blocking the connection to github, making it impossible for the toolbox to download its submodels, which do contain the missing files that the function want to load. Could you test, whether you can ninitialize the submodules manually? (git submodule update --init) Also please check that curl works properly on your system (see the installation prerequisits here )

Ravenclawer commented 3 years ago

Thank you for the reply. My machine was connected to the internet, since I have used git to download all the relevant files to the directory I use git bash here and the code provided in the Github page of cobra toolbox. I have checked all the installation prerequisites and the curl works fine

tpfau commented 3 years ago

Could you try, whether curl can be called from within matlab? i.e. calling [status_curl, result_curl] = system('curl --version'); and checking the outputs status_curl (should be 0) and result_curl?

Ravenclawer commented 3 years ago

I have tried it in Matlab and the result is:

Ravenclawer commented 3 years ago

Is it possible that you may send me the cobra toolbox folder that has all the required components in it so that I don't need to have anything downloaded in Matlab to avoid any errors

rmtfleming commented 3 years ago

[status_curl, result_curl] = system('curl --version')

On Thu, 16 Sept 2021 at 09:25, robert zhang @.***> wrote:

Is it possible that you may send me the cobra toolbox folder that has all the required components in it so that I don't need to have anything downloaded in Matlab to avoid any errors

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

--

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.)

Ravenclawer commented 3 years ago

oh, thank you for reminding me, the correct result is this:

tpfau commented 3 years ago

Try running the following commands in your checked out Cobratoolbox repository: git submodule init git submodule update

After that everything should be there.

Ravenclawer commented 3 years ago

Should I open the cobra toolbox folder first and then use git bash here to open the git bash window. then paste these commands into the window to get it to work? I have just use the git command to download the cobra toolbox to a folder

tpfau commented 3 years ago

you'd have to go into the created cobratoolbox folder.

Ravenclawer commented 3 years ago

it seems something went wrong

tpfau commented 3 years ago

There seems to be some issue with your internet connection having hickups. I don't think a lot can be done there. You can try to manually check out the submodules into the corresponding toolbox repositories.

Ravenclawer commented 3 years ago

could you send me a complete Cobratoolbox folder or if I can use the previous version without updating any submodules?

rmtfleming commented 3 years ago

Hi Robert, no. You will need to proceed with the installation as per the detailed instructions. Regards, Ronan

On Thu, 16 Sept 2021 at 11:49, robert zhang @.***> wrote:

could you send me a complete Cobratoolbox folder or if I can use the previous version without updating any submodules?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1800#issuecomment-920792257, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEORL4ZDOVXM7Q3ZE4ELUCHDRZANCNFSM5ECQ7KTQ . 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.

--

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

The problem with providing a zip for the toolbox is that it's over 1 Gb. So that's not really an option. But maybe you could try to update the submodules again, if it's a connectivity issue you might get lucky. Alternatively: as mentioned, download the individual submodules and extract them into the respective folders.

Ravenclawer commented 3 years ago

I have spent some time going to every failed links and downloaded the xxx-master zip files. after unzipping them, I put the content of these xxx-master folders in the failed directory provided together with the failed links. Could you please tell me if I am doing right? and how can I check that I have download the entire Conbratoolbox?

tpfau commented 3 years ago

If they are all extracted to the respective folders, than you should be able to run initCobraToolbox. It might still show some warnings, but it should finish.

Ravenclawer commented 3 years ago

I have download those failed repositories to the designated folders and it turned out the following message

Ravenclawer commented 3 years ago

it seems that it detect what i have download and copied contents but I don't know if it could read the content

Ravenclawer commented 3 years ago

I have noticed there is a code directory in what-i-have-to-download-myself file. should I put the content of the downloaded master to the directory first or just the content of the code directory to the directory

tpfau commented 3 years ago

Could you try: initCobraToolbox(0) And if that doesn't work in addition comment out lines 190-243 in initCobraToolbox (that's where the submodules are initialized).

Ravenclawer commented 3 years ago

I have recorded the process that I download the submodules. could you tell me if I am doing it right? Animation

Ravenclawer commented 3 years ago

i have tried

cd D:\Users\Desktop\cobratoolbox initCobraToolbox(0)

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

Checking if git is installed ... Done (version: 2.33.0). 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)... ***Local changes to submodules have been stashed. See https://git-scm.com/docs/git-stash. Entering 'external/analysis/CnaCobraInterface' warning: LF will be replaced by CRLF in CNAcna2cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in CNAcobra2cna.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in README.md. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in CNAcna2cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in CNAcobra2cna.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in README.md. The file will have its original line endings in your working directory Saved working directory and index state WIP on master: da27ffd Merge pull request #2 from tpfau/master Entering 'external/analysis/Volume-and-Sampling' warning: LF will be replaced by CRLF in .gitignore. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in README.md. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in expSampler.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/NearestSymmetricPositiveDefinite/html/nearestSPD_demo.html. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/NearestSymmetricPositiveDefinite/nearestSPD.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/NearestSymmetricPositiveDefinite/nearestSPD_demo.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/license.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_chkdata.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_presolve.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_run.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_solver.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/README. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/demo2d.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/draw_ellipse.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_chkdata_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_presolve_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_run_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_solver_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/testp1.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in gaussians/gaussianSampler.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in gaussians/getMuSigma.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in genSamples.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in genSamplesExp.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in getWidths.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in helper_functions/getCentroid.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in preprocessExp.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in .gitignore. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in README.md. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in expSampler.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/NearestSymmetricPositiveDefinite/html/nearestSPD_demo.html. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/NearestSymmetricPositiveDefinite/nearestSPD.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/NearestSymmetricPositiveDefinite/nearestSPD_demo.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/NearestSymmetricPositiveDefinite/license.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_chkdata.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_presolve.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_run.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/MVE_codes/mve_solver.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/README. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/demo2d.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/draw_ellipse.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_chkdata_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_presolve_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_run_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/mve_cobra/mve_solver_cobra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in external/mve11/testp1.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in gaussians/gaussianSampler.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in gaussians/getMuSigma.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in genSamples.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in genSamplesExp.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in getWidths.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in helper_functions/getCentroid.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in preprocessExp.m. The file will have its original line endings in your working directory Saved working directory and index state WIP on master: f9e9355 Merge pull request #6 from WegrzynAB/bug_preprocess Entering 'external/analysis/octave-networks-toolbox' warning: LF will be replaced by CRLF in BFS.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in DFS.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in DoddsWattsSabel.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in PriceModel.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in README. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in addEdgeWeights.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in adj2adjL.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in adj2edgeL.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in adj2inc.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in adj2simple.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in adj2str.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in adjL2adj.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in adjL2edgeL.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in algebraicConnectivity.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in aveNeighborDeg.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in avePathLength.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in averageDegree.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in buildSmaxGraph.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in canonicalNets.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in closeness.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in clustCoeff.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in cycle4nodes.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in cycles3.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in cycles4.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in degrees.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in diameter.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in dijkstra.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in distanceDistribution.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in dotMatrixPlot.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in drawCircGraph.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in edgeBetweenness.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in edgeL2adj.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in edgeL2adjL.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in edgeL2cyto.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in edgeL2simple.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in eigenCentrality.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in el2geom.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in exponentialGrowthModel.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in fabrikantModel.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in fiedlerVector.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in findAllShortestPaths.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in findConnComp.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in findConnCompI.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in forestFireModel.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in getEdges.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in getNodes.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in giantComponent.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in graphComplement.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in graphDual.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in graphEnergy.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in graphFromDegreeSequence.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in graphRadius.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in graphSpectrum.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in inc2adj.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in inc2edgeL.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isBipartite.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isComplete.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isConnected.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isDirected.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isEulerian.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isGraphic.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isRegular.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isSimple.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isSymmetric.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isTree.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in isWeighted.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in kminNeighbors.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in kneighbors.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in kregular.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in laplacianMatrix.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in leafEdges.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in leafNodes.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in license.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in linkDensity.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in loops3rev2.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in louvainCommunityFinding.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in masterEquationGrowthModel.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in minSpanTree.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in modularityMetric.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in multiEdges.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in nestedHierarchiesModel.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in newmanCommFast.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in newmanEigenvectorMethod.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in newmanGastner.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in newmanGirvan.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in nodeBetweenness.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in nodeBetweennessFaster.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in numConnComp.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in numConnTriples.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in numCycles.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in numEdges.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in numNodes.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in numStarMotifs.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in pdfCdfRank.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in pearson.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in pearsonW.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in preferentialAttachment.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in radialPlot.m. 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The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2015_fluxConcentrationDuality/iMM904/testRankFRSubset.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2015_fluxConcentrationDuality/paperFRexample.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/HighFiberDietAGORA.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/WesternDietAGORA.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/checkStoichFluxConsistency/checkRankFRMicrobiomedriver.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/checkStoichFluxConsistency/makeFR_AGORA_figures_and_table.m. 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The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/GlutenFreeDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/HighFatLowCarbDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/HighFiberDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/HighProteinDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/MediterraneanDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/Type2DiabetesDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/UnhealthyDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/VeganDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/VegetarianDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/startMgPipe.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_modelClassifier/modelClassifier.ipynb. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_modelClassifier/modelClassifier.md. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/efmviz_rcy3_ecoli.Rmd. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/efmviz_rcy3_human.Rmd. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/efmviz_style.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/EFMEnrichmentResults.xls. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/GSC-human.txt. 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The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2020_WholeBodyModelling/MethodSection3.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/demeter_run_reconstructions_batch.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/demeter_run_single_reconstruction.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Acetitomaculum_ruminis_DSM_5522.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Achromobacter_insuavis_AXX-A.RAST.fbamodel.sbml. 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The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Lactobacillus_jensenii_269-3.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Prevotella_bivia_DNF00320.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Pseudomonas_putida_OUS82.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Streptococcus_ratti_FA-1-DSM_20564.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleSpreadsheets/AAB_Ala.tsv. 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The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2013_Recon2/IEMCompendium.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2013_Recon2/README.md. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2013_Recon2/upRegulateModelGenes.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2015_fluxConcentrationDuality/checkGrowthBeforeAfter.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2015_fluxConcentrationDuality/checkRankFRdriver.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2015_fluxConcentrationDuality/iMM904/FR_iMM904_moieties.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2015_fluxConcentrationDuality/iMM904/testRankFRSubset.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2015_fluxConcentrationDuality/paperFRexample.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/HighFiberDietAGORA.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/WesternDietAGORA.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/checkStoichFluxConsistency/checkRankFRMicrobiomedriver.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/checkStoichFluxConsistency/makeFR_AGORA_figures_and_table.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2017_AGORA/checkStoichFluxConsistency/mergeFRresultBatchIntoFRresultsStructure.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_DecisionsTranscriptomicIntegration/Code_Preprocessing.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/examples/normCoverage.csv. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/AverageEuropeanDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/DACHDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/GlutenFreeDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/HighFatLowCarbDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/HighFiberDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/HighProteinDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/MediterraneanDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/Type2DiabetesDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/UnhealthyDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/VeganDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/input/VegetarianDiet.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_microbiomeModelingToolbox/startMgPipe.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_modelClassifier/modelClassifier.ipynb. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2018_modelClassifier/modelClassifier.md. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/efmviz_rcy3_ecoli.Rmd. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/efmviz_rcy3_human.Rmd. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/efmviz_style.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/EFMEnrichmentResults.xls. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/GSC-human.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/GSS-human.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/ecoli_EFM_18.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/ecoli_EFM_18woUbMet.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/ecoli_EFM_885.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/ecoli_EFM_885woUbMet.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/ecoli_EFM_percentage_65.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/ecolidataForMapping_EFM_18.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/ecolidataForMapping_EFM_885.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/human_EFM_83.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2019_efmviz/results/human_EFM_83woUbMet.xml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2020_WholeBodyModelling/Data/Recon3D_star/VMH_Metabolites.tsv. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2020_WholeBodyModelling/MethodSection3.html. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2020_WholeBodyModelling/MethodSection3.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/demeter_run_reconstructions_batch.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/demeter_run_single_reconstruction.m. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Acetitomaculum_ruminis_DSM_5522.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Achromobacter_insuavis_AXX-A.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Acinetobacter_pittii_TG6411.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Brevibacillus_laterosporus_GI-9.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Clostridioides_difficile_630.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Lactobacillus_brevis_EW.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Lactobacillus_jensenii_269-3.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Prevotella_bivia_DNF00320.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Pseudomonas_putida_OUS82.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleDraftReconstructions/Streptococcus_ratti_FA-1-DSM_20564.RAST.fbamodel.sbml. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/exampleSpreadsheets/AAB_Ala.tsv. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/input/ComplexMedium.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/input/MetaboliteTranslationTable.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in 2021_demeter/input/ReactionTranslationTable.txt. The file will have its original line endings in your working directory warning: LF will be replaced by CRLF in README.md. The file will have its original line endings in your working directory Saved working directory and index state WIP on master: 690f963 Merge pull request #76 from almut-heinken/demeter

fatal: destination path 'D:/Users/Desktop/cobratoolbox/binary' already exists and is not an empty directory. fatal: clone of 'https://github.com/opencobra/COBRA.binary.git' into submodule path 'D:/Users/Desktop/cobratoolbox/binary' failed Failed to clone 'binary'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/external/analysis/PolytopeSamplerMatlab' already exists and is not an empty directory. fatal: clone of 'https://github.com/ConstrainedSampler/PolytopeSamplerMatlab' into submodule path 'D:/Users/Desktop/cobratoolbox/external/analysis/PolytopeSamplerMatlab' failed Failed to clone 'external/analysis/PolytopeSamplerMatlab'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/external/analysis/gaimc' already exists and is not an empty directory. fatal: clone of 'https://github.com/dgleich/gaimc.git' into submodule path 'D:/Users/Desktop/cobratoolbox/external/analysis/gaimc' failed Failed to clone 'external/analysis/gaimc'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/external/base/samplers/looplessFluxSampler' already exists and is not an empty directory. fatal: clone of 'https://github.com/rmtfleming/looplessFluxSampler' into submodule path 'D:/Users/Desktop/cobratoolbox/external/base/samplers/looplessFluxSampler' failed Failed to clone 'external/base/samplers/looplessFluxSampler'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/external/base/solvers/lusol' already exists and is not an empty directory. fatal: clone of 'https://github.com/nwh/lusol.git' into submodule path 'D:/Users/Desktop/cobratoolbox/external/base/solvers/lusol' failed Failed to clone 'external/base/solvers/lusol'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/external/base/solvers/pdco' already exists and is not an empty directory. fatal: clone of 'https://github.com/mxsaunders/pdco.git' into submodule path 'D:/Users/Desktop/cobratoolbox/external/base/solvers/pdco' failed Failed to clone 'external/base/solvers/pdco'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/external/base/utilities/Smith-Decomposition' already exists and is not an empty directory. fatal: clone of 'https://github.com/nbfigueroa/Smith-Decomposition.git' into submodule path 'D:/Users/Desktop/cobratoolbox/external/base/utilities/Smith-Decomposition' failed Failed to clone 'external/base/utilities/Smith-Decomposition'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/external/base/utilities/condalab' already exists and is not an empty directory. fatal: clone of 'https://github.com/sg-s/condalab' into submodule path 'D:/Users/Desktop/cobratoolbox/external/base/utilities/condalab' failed Failed to clone 'external/base/utilities/condalab'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/test/models' already exists and is not an empty directory. fatal: clone of 'https://github.com/opencobra/COBRA.models' into submodule path 'D:/Users/Desktop/cobratoolbox/test/models' failed Failed to clone 'test/models'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/tutorials' already exists and is not an empty directory. fatal: clone of 'https://github.com/opencobra/COBRA.tutorials.git' into submodule path 'D:/Users/Desktop/cobratoolbox/tutorials' failed Failed to clone 'tutorials'. Retry scheduled fatal: destination path 'D:/Users/Desktop/cobratoolbox/binary' already exists and is not an empty directory. fatal: clone of 'https://github.com/opencobra/COBRA.binary.git' into submodule path 'D:/Users/Desktop/cobratoolbox/binary' failed Failed to clone 'binary' a second time, aborting 错误使用 initCobraToolbox (line 226) The submodules could not be initialized.

Ravenclawer commented 3 years ago

This is like a paradox, if I rely on the git to update the submodules for me, it could't connect to those git repositories. if i download those files from the git repositories and put them into the designated folders. the Matlab just telling me that there are files already exist and still send the warning message.

Ravenclawer commented 3 years ago

I have tried to download all the submodules manually but there are still some problems after initiation and test of the Cobratoolbox

after running initCobraToolbox command, the following warning appeared

Warning: The name does not exist or is not a directory: D:\Users\Desktop\cobratest\cobratoolbox\src\analysis\thermo\vonBertalanffy\initVonBertalanffy.m 警告: 名称不存在或不是目录: D:\Users\Desktop\cobratest\cobratoolbox\src\analysis\thermo\vonBertalanffy\initVonBertalanffy.m

In path (line 109) In addpath (line 86) In initCobraToolbox (line 640) In testAll (line 68)

after running testall command in Matlab the following warning frequently appeared

Warning: The escape character'\U' is invalid. See'doc sprintf' for supported special characters. 警告: 转义字符 '\U' 无效。有关支持的特殊字符，请参阅 'doc sprintf'。

In runTestSuite (line 80) In testAll (line 177)

Ravenclawer commented 3 years ago

the test result showed that there is something wrong with line 242 testBiomassPrecursorCheck.m: 警告: 转义字符 '\U' 无效。有关支持的特殊字符，请参阅 'doc sprintf'。

In testAll (line 242) 引用了不存在的字段 'Edges'。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 未定义与 'struct' 类型的输入参数相对应的函数 'LP9'。出错 testAll (line 242) 函数或变量 'param' 无法识别。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 joinModelsPairwiseFromList 输出参数太多。出错 testAll (line 242) 错误使用 joinModelsPairwiseFromList 输出参数太多。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 函数或变量 'excludeSolvers' 无法识别。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 引用了不存在的字段 'SConsistentMetBool'。出错 testAll (line 242) 调用 "getRankLUSOL" 时，未对输出参数 "rankA" (可能还包括其他参数)赋值。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 未找到具有匹配签名的构造函数 'org.apache.poi.xssf.usermodel.XSSFWorkbook'。出错 testAll (line 242) 未找到具有匹配签名的构造函数 'org.apache.poi.xssf.usermodel.XSSFWorkbook'。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 gurobi Gurobi error 10003: Element 0 of a double array is Nan. 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 未找到具有匹配签名的构造函数 'org.apache.poi.xssf.usermodel.XSSFWorkbook'。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 索引超出数组元素的数目(0)。出错 testAll (line 242) 错误使用 regexprep 所有元胞都必须为字符行向量。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 此类型的变量不支持使用花括号进行索引。出错 testAll (line 242) 错误使用 <a href="matlab:matlab.internal.language.introspective.errorDocCallback('testPaint4Net', 'D:

The exit code is 1.

rmtfleming commented 3 years ago

Hi, update to the master version of the cobra toolbox, make sure git and curl are installed, then try again. Regards, Ronan

On Tue, 5 Oct 2021 at 10:35, robert zhang @.***> wrote:

the test result showed that there is something wrong with line 242 testBiomassPrecursorCheck.m: 警告: 转义字符 '\U' 无效。有关支持的特殊字符，请参阅 'doc sprintf'。

In testAll (line 242) 引用了不存在的字段 'Edges'。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 未定义与 'struct' 类型的输入参数相对应的函数 'LP9'。出错 testAll (line 242) 函数或变量 'param' 无法识别。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 joinModelsPairwiseFromList 输出参数太多。出错 testAll (line 242) 错误使用 joinModelsPairwiseFromList 输出参数太多。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 函数或变量 'excludeSolvers' 无法识别。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 引用了不存在的字段 'SConsistentMetBool'。出错 testAll (line 242) 调用 "getRankLUSOL" 时，未对输出参数 "rankA" (可能还包括其他参数)赋值。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 未找到具有匹配签名的构造函数 'org.apache.poi.xssf.usermodel.XSSFWorkbook'。出错 testAll (line 242) 未找到具有匹配签名的构造函数 'org.apache.poi.xssf.usermodel.XSSFWorkbook'。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 gurobi Gurobi error 10003: Element 0 of a double array is Nan. 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 未找到具有匹配签名的构造函数 'org.apache.poi.xssf.usermodel.XSSFWorkbook'。出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 错误使用 cplexmex Reduce problem size 出错 testAll (line 242) 索引超出数组元素的数目(0)。出错 testAll (line 242) 错误使用 regexprep 所有元胞都必须为字符行向量。出错 testAll (line 242) 错误使用 testAll (line 242) 错误使用 testAll (line 242) 此类型的变量不支持使用花括号进行索引。出错 testAll (line 242) 错误使用 <a href="matlab:matlab.internal.language.introspective.errorDocCallback('testPaint4Net', 'D:

The exit code is 1.

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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

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Ravenclawer commented 3 years ago

Thank you for replying to me. sorry for that I don't understand what you mean about "update to the master version of the cobora toolbox" . I am not familiar with the git. Did you mean which one of the following method:

download zip
download release
using git command in git bash or any other command/methods that could help me to update to the master version of the cobra toolbox

Ravenclawer commented 3 years ago

Could you please tell me which Matlab version you are using now, I have installed 2020a but I am in doubt of my Matlab version that caused the problem so I have uninstalled it now and plan to switch to another version and try to install cobra toolbox again

rmtfleming commented 3 years ago

Hi Robert, you need to have git and curl installed for the installation to complete successfully. My version is below. Regards, Ronan

https://opencobra.github.io/cobratoolbox/stable/installation.html#can-i-check-if-everything-is-properly-set-up-before-i-start

version

ans =

'9.10.0.1602886 (R2021a)'

On Wed, 6 Oct 2021 at 05:23, robert zhang @.***> wrote:

Could you please tell me which Matlab version you are using now, I have installed 2020a but I am in doubt of my Matlab version that caused the problem so I have uninstalled it now and plan to switch to another version and try to install cobra toolbox again

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opencobra / cobratoolbox