rsbml load error on Mac
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resuper ▴ 10
@resuper-10715
Last seen 5.5 years ago

Not sure if this is appropriate to post here, but this is a solution to a problem I encountered with rsbml, which I figured others could potentially face. Maybe it seems like a simple fix for others, but I would have benefited from a post like this. I'm using a Mac (OS X El Capitan), fyi.

 

I installed the rsbml R package, and tried to load it, but received the following error (I removed some filepath info):

 

> library("rsbml", lib.loc="~/Library/R/3.2/library")
Error : .onLoad failed in loadNamespace() for 'rsbml', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '.../Library/R/3.2/library/rsbml/libs/rsbml.so':
  dlopen(.../Library/R/3.2/library/rsbml/libs/rsbml.so, 6): Library not loaded: /usr/local/lib/libsbml.5.dylib
  Referenced from: .../Library/R/3.2/library/rsbml/libs/rsbml.so
  Reason: image not found
Error: package or namespace load failed for ‘rsbml’

 

My problem originated from how I installed libSBML. I went to the SBML Sourceforge page to download the latest stable version of libSBML (5.13.0 at this time). I navigated to the "R Interface" folder, downloaded the libSBML_5.13.0.tar.gz file, and installed in R via the package installer GUI (as explained on the SBML installation instructions for R). DO NOT DO THIS.

Instead of going to the "R Interface" folder, choose instead the "Mac OS X" folder. I realize this probably seems very obvious to others, but it wasn't to me. Download the appropriate file for your operating system ("libsbml-5.13.0-libxml2-macosx-elcapitan.dmg" in my case), open it, and double click the .pkg file to start the installer. This will install libSBML properly, and put the DLL file in the location that rsbml looks at.

That's it. Once you're done with that, rsbml should load without a problem.

R sbml rsbml mac os x • 598 views
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Thanks for this. Yes, the SBML "R Interface" is not the same as rsbml.

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Thank you very much, I would have probably gone on with this for a long time before figuring it out!

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