On Sun, Feb 6, 2011 at 8:19 AM, Paul Shannon <pshannon@systemsbiology.org>wrote:

> 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?
>


You might try building rsbml from source--it will prompt you to configure
some variables (such as the location of libsbml) if they are needed.

source("http://bioconductor.org/biocLite.R")
biocLite("rsbml", type="source")

Dan



> 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@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
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>

	[[alternative HTML version deleted]]

