[BioC] difficulty loading rsbml

Paul Shannon pshannon at systemsbiology.org
Sun Feb 6 05:23:19 CET 2011


The specific error is see (text below) suggests that libsbml is not being found.  ASTNode appears to be a symbol in libsbml

  biocLite ('rbsml')
  installing /usr/local/lib/libsbml.4.2.0.dylib
  export DYLD_LIBRARY_PATH=/usr/local/lib
  R
  > library (rsbml)

I get this error message:

Error : .onLoad failed in loadNamespace() for 'rsbml', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so':
  dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so, 6): Symbol not found: _ASTNode_addChild
  Referenced from: /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so
  Expected in: dynamic lookup

Error: package/namespace load failed for 'rsbml'

rsbml.so is where it is supposed to be:

  /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64:
     -rwxr-xr-x  1 pshannon  admin  95328 Oct 19 22:08 rsbml.so

Any suggestions?  Thanks.

 - Paul


> sessionInfo ()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] graph_1.29.2 tools_2.12.1


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