TranslateSBML is installed but is not working properly.

[Sia Agarwal]

Hi, 

I quite new to everything so please give me some leeway for my lack of experience .

My log report is attached. I'm working on a mac with 2017a Matlab. When I try to initialise the cobra toolbox, I get the error: Warning:  > TranslateSBML is installed but is not working properly. 

For troubleshooting, Matlab suggests to run: TranslateSBML('/Users/s150890/Documents/UCL/Summer 2016_ GS/Modelling/cobratoolbox/test/models/Ec_iAF1260_flux1.xml');

When I do that, I get the error: 

Invalid MEX-file '/Users/s150890/Documents/UCL/Summer 2016_GS/Modelling/cobratoolbox/binary/maci64/bin/TranslateSBML.mexmaci64': '/Users/s150890/Documents/UCL/Summer 2016_GS/Modelling/cobratoolbox/binary/maci64/bin/TranslateSBML.mexmaci64' is not a valid shared library..

I'm not sure what to do, from a couple google searches, the problem may seem to be the 2017a version of Matlab but I'm not sure. Please let me know what you think. 

Thank you, 

Sia

[Sarah Keating]

Hi Sia

There is an issue with MATLAB 2017a on a mac !

If you take the files from here

https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface/libSBML-5.15.1-matlab2017a-macos-binaries.zip/download

and replace the TranslateSBML.mexmaci64 and OutputSBML.mexmaci64 in your
COBRA installation this should work.

Sarah

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[Sia Agarwal]

Hi Sarah, 

I wouldn't get it to work but I downloaded MATLAB2016a instead and that seemed to work. 

Thank you for your help, 

Sia

> <mailto:cobra-toolbox+unsub...@googlegroups.com>.

[Ronan M.T. Fleming]

Dear All,

the R2017b will be supported in future but the R2017a is not supported yet by many of the solvers so R2016b or earlier is advisable.

Regards,

Ronan

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[Sia Agarwal]

Hi Sarah, 

Installing MATLAB2016a worked for a while. But then I went on vacation, and it stopped working when I came back. I get a similar error now. 

Warning:  > TranslateSBML is installed but is not working properly. 

  >> TranslateSBML('/Users/s150890/Documents/UCL/Summer 2016_ GS/Modelling/cobratoolbox/test/models/Ec_iAF1260_flux1.xml');

   in order to debug.

So when I run that: 

>> TranslateSBML('/Users/s150890/Documents/UCL/Summer 2016_ GS/Modelling/cobratoolbox/test/models/Ec_iAF1260_flux1.xml');

Error using TranslateSBML

File ws does not exist on this path

What do you think the error could be? 

I even re-loaded the toolbox from github in case I had accidentally deleted something and it didn't work. 

Thanks, 

Sia

On Tuesday, July 11, 2017 at 10:06:24 AM UTC+1, Sarah Keating wrote:

> <mailto:cobra-toolbox+unsub...@googlegroups.com>.

[Thomas Pfau]

Hi,

This sounds odd. The best guess I have is that for some reason, the Toolbox did not download the sample xml File.
This should (in theory) be caught earlier, i.e. during loading of the models.

Could you check that the indicated file actually exists?

Best

Thomas

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[Sia Agarwal]

Hi Thomas, 

Sorry, I am still new to MatLab, is the sample xml called File? If so, I checked, it doesn't exist in the cobratoolbox folder.

Thank you, 

Sia

[Thomas Pfau]

Hi Sia,

The sample xml file should be:

test/models/Ec_iAF1260_flux1.xml

In the cobra toolbox folder.

Best

Thomas

[Sia Agarwal]

Hi Thomas, 

Yes, that is there. I can the same worry, and had checked before I posted this. Sorry, I hadn't understood what you were asking before. 

Thank you, 

Sia

[Laurent Heirendt]

Hi Sia,

In the configReport that you posted, TranslateSBML seems to be working.

May you post the exact commands after starting MATLAB that you are running that lead to the error?

Thanks,

Laurent 

[zaid ahmad]

I had a similar problem that continued after using the new Translate and Output SBML files. Is there anything else I should try?

[zaid ahmad]

I'm using MacOSX High Sierra (10.13) and Matlab R2017a. I'm attaching my configuration report and I used the new GitHub packages for Translate SBML and Output SBML from the download link above. 

[Thomas Pfau]

Hi,

There are known issues with Matlab 2017a and the libsbml matlab bindings, which, I think, are still not solved.
Currently we only support Matlab 2016b.

Best

Thomas

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[Laurent Heirendt]

Hi,

Do you have an option of downgrading to R2016b? As you are on Mac OS High Sierra, please note that there might be some issues: https://nl.mathworks.com/matlabcentral/answers/358261-why-do-my-matlab-files-appear-corrupt-on-macos-high-sierra

Best,

Laurent

On Thursday, October 5, 2017 at 6:22:09 AM UTC+2, Thomas Pfau wrote:

Hi,

There are known issues with Matlab 2017a and the libsbml matlab bindings, which, I think, are still not solved.
Currently we only support Matlab 2016b.

Best

Thomas

On 2017-10-05 05:29, zaid ahmad wrote:

I'm using MacOSX High Sierra (10.13) and Matlab R2017a. I'm attaching my configuration report and I used the new GitHub packages for Translate SBML and Output SBML from the download link above. 

On Wednesday, October 4, 2017 at 6:20:43 PM UTC-5, zaid ahmad wrote:

I had a similar problem that continued after using the new Translate and Output SBML files. Is there anything else I should try?

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[Sia Agarwal]

Hi Laurent, 

This is going to sound really strange but it works now. I'm not sure what happened. I re-started MatLab this morning and it seemed to work. That part of the code is no longer my issue. 

For you information I was running the initCobraToolbox command. 

Thank you all for your help, 

Sia

[zaid ahmad]

I did downgrade to R2016b and initCobraToolbox.m ran but it returned 6 error tests. I am attaching my system configuration report. 

On Thursday, October 5, 2017 at 1:09:09 AM UTC-5, Laurent Heirendt wrote:

Hi,

Do you have an option of downgrading to R2016b? As you are on Mac OS High Sierra, please note that there might be some issues: https://nl.mathworks.com/matlabcentral/answers/358261-why-do-my-matlab-files-appear-corrupt-on-macos-high-sierra

Best,

Laurent

On Thursday, October 5, 2017 at 6:22:09 AM UTC+2, Thomas Pfau wrote:

Hi,

There are known issues with Matlab 2017a and the libsbml matlab bindings, which, I think, are still not solved.
Currently we only support Matlab 2016b.

Best

Thomas

On 2017-10-05 05:29, zaid ahmad wrote:

I'm using MacOSX High Sierra (10.13) and Matlab R2017a. I'm attaching my configuration report and I used the new GitHub packages for Translate SBML and Output SBML from the download link above. 

On Wednesday, October 4, 2017 at 6:20:43 PM UTC-5, zaid ahmad wrote:

I had a similar problem that continued after using the new Translate and Output SBML files. Is there anything else I should try?

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[Laurent Heirendt]

Hi,

The COBRA Toolbox seems however correctly installed on your machine.

Out of curiosity, may you let me know which tests failed? This may be related to incompatible MEX files on your new macOS - nothing really to worry about for now.

Best,

Laurent

[zaid ahmad]

Here are the tests that failed/ were incomplete. 

 Name                                           Failed  Incomplete  Reason(s)

    ==============================================================================

     testReadSBML/testReadSBML                        X         X       Errored.

    ------------------------------------------------------------------------------

     testOptimizeCbModelNLP/testOptimizeCbModelNLP    X         X       Errored.

    ------------------------------------------------------------------------------

     testSolveCobraLP/testSolveCobraLP                X         X       Errored.

    ------------------------------------------------------------------------------

     testSolveCobraNLP/testSolveCobraNLP              X         X       Errored.

    ------------------------------------------------------------------------------

     testFitC13Data/testFitC13Data                    X         X       Errored.

    ------------------------------------------------------------------------------

     testTest4HumanFctExt/testTest4HumanFctExt        X         X       Errored.

    

 > 6 tests failed. 6 tests are incomplete.

When I tried running testReadSBML, it resulted in

testReadSBML

   Testing Abiotrophia_defectiva_ATCC_49176.xml ...

No model returned.

Reference to non-existent field 'annotation'.

Error in readSBML (line 34)

model.description.annotation = modelSBML.annotation;

Error in readCbModel (line 207)

        model = readSBML(fileName,defaultBound);

Error in testReadSBML (line 46)

    model = readCbModel(which(modelArr{i}));

I have libsbml 5.1.5.0 installed

[Laurent Heirendt]

Hi,

This is an issue with the MEX files on macOS High Sierra.

Thomas and Sarah, may you help out here?

Thanks,

Laurent

[Thomas Pfau]

Hmmm...

It's odd, that TranslateSBML doesn't simply fail but that it returns something seemingly "empty".
@Zaid, could you run
global CBTDIR
model = TranslateSBML([CBTDIR filesep 'test' filesep 'models' filesep 'Abiotrophia_defectiva_ATCC_49176.xml']);

And let us know what model is (i.e. if its not empty, send bus the matlab struct as a zip?)

I'm just curious and this could help Sarah in potential debugging efforts.

Best

Thomas

[zaid ahmad]

It did return an empty model.

model = TranslateSBML([CBTDIR filesep 'test' filesep 'models' filesep 'Abiotrophia_defectiva_ATCC_49176.xml'])

No model returned.

model = 

  0×0 empty struct array with no fields.

[Almut Heinken]

Dear all,

I also got an empty model as the output. However, when I replaced the file located in cobratoolbox/test/models with the newest version of Abiotrophia defectiva from https://vmh.uni.lu/#downloadview, it returns the model with the following output:
model =

  struct with fields:

               typecode: 'SBML_MODEL'
                 metaid: 'Abiotrophia_defectiva_ATCC_49176'
                  notes: '<notes>…'
             annotation: '<annotation>…'
                cvterms: [1×1 struct]
             SBML_level: 3
           SBML_version: 1
                   name: 'Abiotrophia defectiva ATCC 49176'
                     id: 'Abiotrophia_defectiva_ATCC_49176'
              timeUnits: ''
         substanceUnits: ''
            volumeUnits: ''
              areaUnits: ''
            lengthUnits: ''
            extentUnits: ''
       conversionFactor: ''
                sboTerm: -1
     functionDefinition: [1×0 struct]
         unitDefinition: [1×1 struct]
            compartment: [1×2 struct]
                species: [1×952 struct]
              parameter: [1×3 struct]
      initialAssignment: [1×0 struct]
                   rule: [1×0 struct]
             constraint: [1×0 struct]
               reaction: [1×1069 struct]
                  event: [1×0 struct]
            time_symbol: ''
           delay_symbol: ''
        avogadro_symbol: ''
             namespaces: [1×2 struct]
            fbc_version: 2
        fbc_geneProduct: [1×598 struct]
          fbc_objective: [1×1 struct]
    fbc_activeObjective: 'obj'
             fbc_strict: 1

So this problem seems to be due to the SBML file currently in Cobra Toolbox being an older version of SBML. I will replace it with the newer version.

Best

Almut

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[Thomas Pfau]

Hi Almut,

The toolbox does download this model (and thus it should be the latest version).
The only thing I can imagine is that at some point the model stored at that location was invalid.

@Zaid: Could you delete all Files in the test/models directory in your cobratoolbox folder and run initCobraToolbox again (and then run testReadSBML ?)

Sorry for the inconvenience.

Thomas

[zaid ahmad]

Hello Thomas,

   I reinstalled the toolbox, but there were still two tests that failed. I am attaching the report below as well as the tests that failed.

Zaid

  Name                                       Failed  Incomplete  Reason(s)

    ==========================================================================

     testSolveCobraLP/testSolveCobraLP            X         X       Errored.

    --------------------------------------------------------------------------

     testTest4HumanFctExt/testTest4HumanFctExt    X         X       Errored.

[zaid ahmad]

I keep getting the SolveCobraLP error I think because there is something missing in the bin Minos folder but it is not there on github either. (qqFBA)

[Uri David Akavia]

Hello,

I'm having a similar problem on MATLAB 2017b on Mac Sierra 10.12.6 (16G29). This is a completely new Mac, so some things might not be configured correctly yet.

Trying to run installSBML fails with 

Checking for executables in 

/usr/local/lib

Executables not found

Trying to run

>installSBML('/users/uridavidakavia/Documents/MATLAB/fork-cobratoolbox/binary/maci64/bin/')

Fails with

TranslateSBML failed

Invalid MEX-file '/Users/uridavidakavia/Documents/MATLAB/fork-cobratoolbox/binary/maci64/bin/TranslateSBML.mexmaci64': dlopen(/Users/uridavidakavia/Documents/MATLAB/fork-cobratoolbox/binary/maci64/bin/TranslateSBML.mexmaci64, 6): Library not loaded: @loader_path/libmex.dylib

  Referenced from: /Users/uridavidakavia/Documents/MATLAB/fork-cobratoolbox/binary/maci64/bin/TranslateSBML.mexmaci64

  Reason: image not found.

Removing /users/uridavidakavia/Documents/MATLAB/fork-cobratoolbox/binary/maci64/bin/ from path ...

Success

Error using installSBML (line 77)

Executables were located at

/users/uridavidakavia/Documents/MATLAB/fork-cobratoolbox/binary/maci64/bin/ but

failed to execute

Please contact the libSBML team libsbm...@googlegroups.com for further

assistance

I tried loading the files you linked with no success.

Thank you,

Uri David

> <mailto:cobra-toolbox+unsub...@googlegroups.com>.

[Sarah Keating]

Hi Uri David

Is this the case when you use the binaries

https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface/libSBML-5.15.2-matlab2017a-macos-binaries.zip/download

This would suggest MATLAB2017b has yet another difference which we will
need to address :-(

Sarah

On 15/10/2017 10:55, Sarah Keating wrote:

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[Thomas Pfau]

Hi Sarah,

One question: Do the 2017a binaries work for older matlab versions on mac?
As we could then simply replace these binaries in our repository and (at
least) it would work up to 2017a.

Best

Thomas

[Frank T. Bergmann]

Hello Thomas, 

unfortunately the new binaries were necessary because Matlab2017a uses a different set of libraries. The new libsbml binaries were necessary to use the same set of libraries. As a result, the new bindings will only work with 2017a (and hopefully later versions), the existing libraries you had will work for all older matlab versions. So it is necessary to keep both of them around, and check at installation / runtime which one to use. 

Cheers

Frank

[Uri David Akavia]

Hi Sarah,

Yes, this is the case for the binaries. I was under the impression that 2017b Matlab on Mac was supported, as opposed to 2017a. Is there anyone who managed to install and run SBML on Matlab 2017b?

Can I help you guys debug it?

Thank you.

Yours,

Uri David

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[Frank T. Bergmann]

I still don't have access to 2017b, if libsbml is compiled against the same STL as matlab it just ought to work. To do that the correct cmake configuration options have to be specified ... for 2017a they were: 

MATLAB_ENG_LIBRARY:FILEPATH=/Applications/MATLAB_R2017a.app/bin/maci64/libeng.dylib

MATLAB_INCLUDE_DIR:PATH=/Applications/MATLAB_R2017a.app/extern/include

MATLAB_MEX_LIBRARY:FILEPATH=/Applications/MATLAB_R2017a.app/bin/maci64/libmex.dylib

MATLAB_MX_LIBRARY:FILEPATH=/Applications/MATLAB_R2017a.app/bin/maci64/libmx.dylib

MATLAB_ROOT_PATH:PATH=/Applications/MATLAB_R2017a.app

WITH_MATLAB:BOOL=ON

WITH_MATLAB_BUILDSBML:BOOL=OFF

WITH_MATLAB_MEX:BOOL=OFF
CLANG_USE_STDLIB:BOOL=ON

assuming nothing else changes with 2017b, then those options should work. Should matlab have moved to the old STL, the last parameter has to be set to off. I'm afraid I won't be able to try this out until we have a version of 2017b available to us. 

best

Frank

[zaid ahmad]

On Matlab 2017b, translateSBML is installed but not working and on older versions such as 2016b, testSolveCobraLP, testIsCompatible, and. testTest4HumanFctExt are not working. There seems to be a file missing in the binaries that is called. 

[zaid ahmad]

Error using load

Unable to read file '/Users/zaidahmad/cobratoolbox/binary/maci64/bin/minos//qqFBA.sol'. No such

file or directory.

[Uri David Akavia]

Hello.

I tried compiling libsbml from scratch. The following commands failed 

$ ./configure --with-matlab=/Applications/MATLAB_R2017b.app/ --with-libxml CPPFLAGS=`xml2-config --cflags`

$ ./configure --with-matlab=/Applications/MATLAB_R2017b.app/ --with-libxml CPPFLAGS=`xml2-config --cflags` MATLAB_ENG_LIBRARY=/Applications/MATLAB_R2017b.app/bin/maci64/libeng.dylib MATLAB_INCLUDE_DIR=/Applications/MATLAB_R2017b.app/extern/include MATLAB_MEX_LIBRARY=/Applications/MATLAB_R2017b.app/bin/maci64/libmex.dylib MATLAB_MX_LIBRARY=/Applications/MATLAB_R2017b.app/bin/maci64/libmx.dylib MATLAB_ROOT_PATH=/Applications/MATLAB_R2017b.app WITH_MATLAB=ON WITH_MATLAB_MEX=OFF CLANG_USE_STDLIB=ON WITH_MATLAB_BUILDSBML=OFF

$ ./configure --with-matlab=/Applications/MATLAB_R2017b.app/ --with-libxml CPPFLAGS=`xml2-config --cflags` MATLAB_ENG_LIBRARY:FILEPATH=/Applications/MATLAB_R2017b.app/bin/maci64/libeng.dylib MATLAB_INCLUDE_DIR:PATH=/Applications/MATLAB_R2017b.app/extern/include MATLAB_MEX_LIBRARY:FILEPATH=/Applications/MATLAB_R2017b.app/bin/maci64/libmex.dylib MATLAB_MX_LIBRARY:FILEPATH=/Applications/MATLAB_R2017b.app/bin/maci64/libmx.dylib MATLAB_ROOT_PATH:PATH=/Applications/MATLAB_R2017b.app WITH_MATLAB:BOOL=ON WITH_MATLAB_BUILDSBML:BOOL=OFF

All commands have CPPFLAGS=`xml2-config --cflags`, otherwise libsbml complains it can't find libxml headers (which are installed, and are present in /usr/include/libxml2). This seems like some kind of bug in the configure script.

The third command fails by complaining that MATLAB_ENG_LIBRARY:FILEPATH is not a variable.

The second command fails, complaining (in matlab) that

Error using buildSBML>compile_mex (line 673)

Build failed

Error in buildSBML>build_unix (line 630)

    compile_mex(include, lib, matlab_octave);

Error in buildSBML (line 103)

      build_unix(matlab_octave, location, writeAccess, bit64);

The second command fails even if copy /Applications/MATLAB_R2017b.app/bin/maci64/mexopts.sh to the mexopts files already present in src/bindiings/matlab

It seems the only way to get this to compile is to modify the make files, which is beyond my ability to invest time. I think I'll be installing MATLAB2017a and work from there. If I've missed something, please let me know.

Yours,

Uri David

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[Uri David Akavia]

Dear Sarah,

I downgraded to Matlab 2017a, downloaded SBML from https://newcontinuum.dl.sourceforge.net/project/sbml/libsbml/5.15.0/stable/Mac%20OS%20X/libSBML-5.15.0-libxml2-macos-sierra.dmg

And tried installing MATLAB sbml using the files that were linked. This also fails, see command and errors below.

Any suggestions?

Thank you,

Uri David

> installSBML('/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries')

Installing the libSBML interface.

* Doing preliminary checks of runtime environment ...

  - This appears to be MATLAB and not Octave.

Checking for executables in 

/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries

Executables found

Adding /Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries to path ...

Success

Attempting to execute functions

TranslateSBML failed

Invalid MEX-file '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64': Missing dependent shared libraries:

'/Users/skeating/working/buildmatlab/src/bindings/matlab/TranslateSBML.mexmaci64' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '__DefaultRuneLocale' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '__Unwind_Resume' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '___cxa_atexit' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '___error' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '___maskrune' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

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Missing symbol '_ftello' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_fwrite' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_localtime' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

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Missing symbol '_rand' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

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Missing symbol '_setlocale' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

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Missing symbol '_sinh' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_snprintf' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_sprintf' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_srand' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_stat$INODE64' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strcat' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strcmp' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strcpy' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strdup' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strlen' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strncat' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strncmp' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strncpy' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strstr' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strtod' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_strtol' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_tan' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_tanh' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_time' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_vsnprintf' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'

Missing symbol '_wcstombs' required by '/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries/TranslateSBML.mexmaci64'.

Removing /Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries from path ...

Success

Error using installSBML (line 77)

Executables were located at

/Users/uridavidakavia/Downloads/libSBML-5.15.1-matlab2017a-macos-binaries

but failed to execute

Please contact the libSBML team libsbm...@googlegroups.com for further

assistance

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[Ali]

Hi everyone,

Actually I found out when the xml file is in the current MATLAB directory, readCbModel can evoke it otherwise the error appears. So put the intended xml file in the current directory.

I hope it helps

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[Patrik]

Hi Ali,

I have this problem also, on a very recent download of COBRA toolbox (2 days ago), when starting with 'initCobraToolbox', and loading my model does not work, even if I move it to the current MATLAB directory.

''Warning:  > TranslateSBML is installed but is not working properly. 

> In initCobraToolbox at 293"

and after readCbModel:

"Error using readSBML (line 31)

Undefined function 'getStructure' for input arguments of type 'cell'.

Error in readCbModel (line 208)

        model = readSBML(fileName,defaultBound);"e

Help would be very much appreciated,

Thanks, Patrik

[Laurent Heirendt]

Hi Patrik,

Is this with the latest develop branch?

Best,

Laurent

[Patrik Jones]

Hi Laurent,

I don't know what a "develop branch" is (being a wet-lab biologist..), but I downloaded COBRA toolbox 2 days ago using the "$ git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox" command in Mac Terminal, after installing Xcode Command Line Tools on the same day.

Best regards, Patrik

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[Laurent Heirendt]

Hi Patrik,

Sorry about that :) There was recently an issue, so maybe this is fixed in the latest version (also referred to as the developer version). May you do the following in the terminal:

$ cd cobratoolbox
$ git checkout develop
$ git pull origin develop

Then, in MATLAB, do:

>> restoredefaultpath
>> clear all
>> initCobraToolbox

Also, if this doesn't work, may you post here the output of >> generateSystemConfigReport ?

Best,

Laurent

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[Patrik Jones]

Hi Laurent. No worries, thanks for helping :-)

The second command, 'git checkout develop', gave an error message:

"error: pathspec 'develop' did not match any file(s) known to git."

And, the third command seemed OK (downloading 595 MB) until it returned the following:

"From https://github.com/opencobra/cobratoolbox

 * branch              develop    -> FETCH_HEAD

fatal: refusing to merge unrelated histories"

I still carried out your suggested three commands (restoreDefaultpath/clear all/initCT) for MATLAB, however, the same issue "Warning:  > TranslateSBML is installed but is not working properly. 

> In initCobraToolbox at 293

  In generateSystemConfigReport at 72" was still persisting..

One thing I noted, however, was that this problem does not occur when I use my desktop Mac Pro. The main difference (it too has the latest cobra toolbox downloaded 1-2 weeks ago) is that it uses Matlab 2015a, whilst on my laptop (where the problem is) I have 2014b.. I will see if I can obtain a later version of Matlab for the laptop.

Meanwhile, I attach the COBRAconfigReport.log file from the laptop.

Thanks, Patrik

[Laurent Heirendt]

Hi Patrik,

Ok, so you didn't have the 'develop' branch cloned, hence the error. I forgot to mention that before running these commands, you have to clone the COBRA Toolbox without '--depth=1'.

The same error that we had a few days ago is exactly because of the MATLAB version R2014b, but it should be fixed by now.

Eventually, it is easiest for you to simply upgrade your MATLAB version. This error does not occur on versions R2016b or R2017b, which I recommend you to use.

Best,

Laurent

[Patrik Jones]

Hi Laurent,

I didn't quite understand what I should do with respect to '--depth=1'..?

I managed to update to R2017b but it unfortunately made no difference to solving the TranslateSBML problem.. still installed but "..not working properly".

Thanks, Patrik

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[Thomas Pfau]

Hi Patrik,

Could you try to update your toolbox and give it another shot?
For some very very odd reason, after we updated the binaries on a submodule, it seems as if that version is always  checked out regardless on what should actually be checked out.

This is causing the use of TranslateSBML/OutputSBML from version 5.17 on git revisions which should normally still use 5.16, and the newer (5.17) binaries need some files which are not part of the 5.16 version. This should be fixed on the latest master version though.

Sorry for this being quite technical, but I don't have a better explanation. In essence: If you update your cobra toolbox to the latest version, it should work.

Best

Thomas

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[Patrik Jones]

Hi Thomas,

Thanks for your help. I re-installed cobra toolbox and yes, the translateSBML problem was now gone! Great.

However, now, it did not seem to recognize any standard solvers.. 

   

Given that Gurobi is installed (7.5.2) and license recently renewed, (clicking on Gurobi seems to be fine) I tried to change this manually:

changeCobraSolver('gurobi','LP') 

 > Solver gurobi is installed but not working properly.

ans =

  logical

   0

and the same for glpk..

>> changeCobraSolver('glpk','LP')

 > Solver glpk is installed but not working properly.

ans =

  logical

   0

Despite the "summary of available solvers" listing both Gurobi and glpk with a '1'. Using solution=optimizeCbModel(model,'max') the solver 'pdco' was indicated, and I did get a reasonable f-value.

I will keep on trying, getting closer.

Thanks, Patrik

[Laurent Heirendt]

Hi Patrik,

May you run:

>> restoredefaultpath
>> clear all
>> initCobraToolbox
>> generateSystemConfigReport

and then post the output (your configuration report) here so that we can debug?

Thanks,

Laurent

Thanks, Patrik

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[Patrik]

Hi Laurent,

Thanks for not giving up :-)

Attached is the configreport

Thanks, Patrik

Thanks, Patrik

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[Thomas Pfau]

Hi Patrik,

You mention, that you have gurobi 7.5.2 on your system, but it seems, that the toolbox tries to access a gurobi 8 version.
I'm not entirely sure about the gurobi licensing system, but if you have a license for 7.5.2 it might not work for the 8.0 version.
Now, the toolbox will try to use the latest installed version of the solvers (but does not check the licenses). So what could happen (at least for gutobi) is that the Toolbox sees a gurobi 8. Adds it, and notices, that it does not work.
However, it will currently NOT try to look for other versions, as we assume, that only one solver version is installed for all solvers.

You could try the following:

>> restoredefaultpath
>> clear all
>> setenv('GUROBI_PATH','<path/to/your/gurobi/installation>')
>> initCobraToolbox
>> generateSystemConfigReport

where you replace '<path/to/your/gurobi/installation>'  by your actual installation folder for gurobi.

If this works, I would suggest to either remove the 800 version from your system, or set the GUROBI_PATH environment variable.

As for glpk: I assume this is an incompatability between the glpk binaries and some macOS components. But just to check this could you do the following:

>> initCobraToolbox
>> global CBT_LP_SOLVER
>> CBT_LP_SOLVER = 'glpk';
>> model = getDistributedModel('ecoli_core_model.mat');
>> sol = optimizeCbModel(model)

This should produce an error. Coudl you report that error?

Best

Thomas

On 2018-05-30 00:05, Patrik wrote:

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[Patrik Jones]

Hi Thomas,

This was solved now but perhaps the below might be helpful for others in a similar situation. 

Regarding GUROBI, given that my license apparently was v. 8, I installed version 8 of the app. When I then clicked on Gurobi 8.0.0.app the terminal interface says "Version number is 8.0, license is for version 7.0 - license file '/Users/patrikjones/gurobi.lic'". This is weird since when I go to my account at www.gurobi.com it says clearly that I have a license for version 8, whilst viewing the license it says version 7 !?!# (license file and screenshot from gurobi.com below)

"# License ID 244786

# Gurobi license for Imperial College

ORGANIZATION=Imperial College

TYPE=ACADEMIC

HOSTNAME=dyn3162-215.wlan.ic.ac.uk

HOSTID=8a34c8e

USERNAME=patrikjones

EXPIRATION=2019-05-25

VERSION=7

KEY=KGS6VTRZ"

Still, when I went back having re-installed Gurobi 7.52, CBT insisted I had v. 8 present. Consequently, I deleted all Gurobi filesn (app + folder) apart from the license and downloaded Gurobi 7.52 fresh. Once installed, finally optimizeCbModel started using 'gurobi', and the answer was as expected. Hence, solved.

Regarding GLPK, I followed your instructions and obtained the following:

>> global CBT_LP_SOLVER

>> CBT_LP_SOLVER = 'glpk';

>> model = getDistributedModel('ecoli_core_model.mat');

>> sol = optimizeCbModel(model)

Invalid MEX-file

'/Users/patrikjones/cobratoolbox/binary/maci64/bin/glpkcc.mexmaci64':

dlopen(/Users/patrikjones/cobratoolbox/binary/maci64/bin/glpkcc.mexmaci64, 6):

Library not loaded: @loader_path/libmex.dylib

  Referenced from:

  /Users/patrikjones/cobratoolbox/binary/maci64/bin/glpkcc.mexmaci64

  Reason: image not found.

Error in glpk (line 508)

[xopt, fmin, status, extra] = glpkcc(c, a, b, lb, ub, ctype, vartype, sense,

param);

Error in solveCobraLP>solveGlpk (line 1851)

[x,f,origStat,extra] = glpk(c,A,b,lb,ub,csense,[],osense,params);

Error in solveCobraLP (line 582)

        [x, f, y, w, stat, origStat] = solveGlpk(c, A, b, lb, ub, csense,

        osense, param);

Error in optimizeCbModel (line 346)

    solution = solveCobraLP(LPproblem);

Many, many thanks for your help, much appreciated.

Patrik

[Uri David Akavia]

Hi Thomas,

This is something about Mac OS Sierra and onwards. The way that GLPK works for me is download this link (https://github.com/blegat/glpkmex/blob/master/glpkcc.mexmaci64), place it in cobratoolbox/.tmp

I don't know how to improve/debug glpkmex in the distribution. I'd be happy to discuss and do it with guidance. The other alternative is to add this to the installation instructions, maybe?

Uri David 

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