[BioC] difficulty loading rsbml

[Paul Shannon]

Thanks for your replies, Dan and Martin.

My original post mostly concealed that I do have libsbml installed.  A quick test from python shows that it works: python can read the latest, full yeastNet sbml file.  So the problem appears to be that something I have done, or not done, leads to rsbml not being able to find libsbml.

I thought that perhaps the macos version of LD_LIBRARY_PATH (which is 'DYLD_LIBRARY_PATH') might not be properly set.  
Here's what I tried.  Maybe wiser heads than my own can see what I am doing wrong.

  bash> export DYLD_LIBRARY_PATH=/usr/local/lib
  bash> R
  > env = Sys.getenv ()
  > env [grep ('DYLD', names (env))]  # find out the value of this path to the running R process
                                                       DYLD_LIBRARY_PATH
    "/Library/Frameworks/R.framework/Resources/lib/x86_64:/usr/local/lib"

  > grep ('libsbml', list.files ('/usr/local/lib'), value=TRUE)   # is libsbml findable down that path?
     [1] "libsbml.4.2.0.dylib" "libsbml.4.dylib"     "libsbml.a"           "libsbml.dylib"       "libsbml.la"          "libsbmlj.jnilib"

  > library (rsbml)   # try to load.  as rsbml.so loads, it looks for, but cannot find, libsbml (apparently)
    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'

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






On Feb 6, 2011, at 12:12 AM, Dan Tenenbaum wrote:

> 
> 
> On Sat, Feb 5, 2011 at 8:23 PM, Paul Shannon <pshannon at systemsbiology.org> wrote:
> 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
> 
> 
> 
> Hi Paul,
> 
> rsbml requires that you install libsbml. rsbml does not do this for you.
> 
> You can get libsbml from http://www.sbml.org.
> 
> Dan
>  
> 
> > 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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