#363 5.8.0 macosx dmg requires R framework

libSBML-5.8.0
closed
nobody
None
2014-10-13
2013-10-23
No

I'm attempting to use libsbml-5.8.0-libxml2-macosx-mountainlion.dmg for an installation which requires 5.8.0 on osx 10.8.5. I get the error below which seems to indicate that libSBML expects R to be installed. Was this library compiled to expect the R bindings? Why R 2.15 - looks ancient to me?

I am able to move around this issue, if I put in the right R 2.15 installation files. Please offer other possible solutions as requiring my users to install R seems tragic.

Library not loaded: /Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib
Referenced from: /usr/local/lib/libSBML.so
Reason: image not found

Discussion

  • Sarah Keating

    Sarah Keating - 2014-10-13
    • status: open --> closed
    • Priority: -->
     
  • Sarah Keating

    Sarah Keating - 2014-10-13

    Closing this as it is a year old and hopefully sorted.

     
  • Frank Bergmann

    Frank Bergmann - 2015-01-20

    NOTICE NOTICE NOTICE
    The comments associated with this ticket were lost in late 2014.
    The SBML Team manually recovered the comments. The text is appended below.
    NOTICE NOTICE NOTICE


    Comment By: Frank Bergmann (fbergmann)
    Date: 2013-10-23 06:05

    Hello Michal,

    I'm afraid I'm not sure how that file got there. However, the libsbml installer would not have put it there. It would place .dylib files there. So perhaps you could remove existing files first:

    sudo rm -rf /usr/local/include/sbml
    sudo rm /usr/local/lib/libsbml*
    sudo rm /usr/local/libSBML*
    

    And try the installation again. This will place a libsbml.dylib file there that only requires libbz2, libz, libxml2 from the OSX installation.

    Please let me know whether this helps.


    Comment By: Michal Galdzicki (mgaldzic)
    Date: 2013-10-23 08:47

    Frank,
    thanks for the quick reply.
    Please note that I'm using Lucian's Antimony, it relies on "libSBML.so"
    When this lib goes missing Antimony cries ;( see [1] below for ref. I've
    cc'd Lucian here

    Also, since posting my original issue, I have built a clean libSBML for osx
    locally (no universal). The build does not produce libSBML.so. However,
    Antimony does not take a .dylib instead of the libSBML.so

    Let me know if you have a suggestion for me in trying to get around the
    issue if you're planning a fix.

    Here is what I did, as requested.

    sudo rm -rf /usr/local/include/sbmlsudo rm /usr/local/lib/libsbmlsudo rm /usr/local/libSBML

    Improvised - I gather you want to rm, the offending file, so:
    sudo rm /usr/local/libSBML*

    $ ls /usr/local/lib/libSBML
    ls: /usr/local/lib/libSBML
    : No such file or directory

    Downloaded stable 5.8.0 from
    http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/stable/Mac%20OS%20X/libsbml-5.8.0-libxml2-macosx-mountainlion.dmg/download

    Installed: libsbml-5.8.0-libxml2-macosx-mountainlion.dmg

    Result:

    $ ls -l /usr/local/lib/libSBML*
    -rwxr-xr-x 1 mgaldzic staff 14016576 Feb 27 2013
    /usr/local/lib/libSBML.so

    It's like a ghost from last winter! libSBML.so is back

    thanks,
    mike

    [1] import libantimony
    ImportError:
    dlopen(/Applications/Spyder.app/Contents/Resources/lib/python2.7/_libantimony.so,
    2): Library not loaded: libSBML.so
    Referenced from:
    /Applications/Spyder.app/Contents/Resources/lib/python2.7//_libantimony.so
    Reason: image not found


    Comment By: Frank Bergmann (fbergmann)
    Date: 2013-10-23 08:56

    Hello Michal,

    My bad, ok there are indeed R bindings installed (libSBML.so), which perhaps should go to a different folder. However, as far as antimony is concerned, it would be better if it linked against the libsbml c/c++ bindings libsbml.dylib (or its versioned variants: libsbml.5.dylib or libsbml.5.8.0.dylib) or libsbml-static.a.

    While we prepare a new release for you, please delete the R bindings from the folder, and perhaps re-install antimony, so it will pick up the correct one.

     

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