[BioC] Rgraphviz load problem

Seth Falcon sfalcon at fhcrc.org
Sat Apr 14 17:07:35 CEST 2007

Hi Daniel,

Can you tell us how you installed R, graphviz, and Rgraphviz?  And
what compilers you have installed?

If you install the binary version of R, then I suspect you will have
the best luck with the binary graphviz install and binary Rgraphviz
package.  OTOH, if you want to compile packages from source, it is
safest to also compile R from source.  The reason is that you can then
be sure that the compiles all match up.

Daniel Klevebring <daniel at biotech.kth.se> writes:
> 1. Rechecked Rgraphviz version, 1.12.3

I think you should try installing the binary version of graphviz
available from the att website:


And then install Rgraphviz via biocLite to obtain the binary version.

> 2. My DYLD_LIBRARY_PATH does not seem to be visible to R, see the  
> export R_GUI_APP_REVISION="4038"
> export R_GUI_APP_VERSION="1.18"
> export
> R_HOME="/Library/Frameworks/R.framework/Versions/2.4/Resources"

This looks to me like you have installed a binary version of R and not
built from source.

> where DYLD_LIBRARY_PATH is present, but R doesn't seem to get the  
> message.

I think the binary version of R quite purposely ignores it, but you
would have to ask for details on the r-sig-mac list.

> 3. No .so files are available in the given path, but lots of  
> lib*.dylib files. Where would the .so files be loacted?

No, that looks about right for OSX.

> 4. Running  nm lib*.dylib | grep agfstnode indeed gives
>     U _agfstnode
>           U _agfstnode
>           U _agfstnode
>           U _agfstnode

And that looks fine too.  But unless you install Rgrphviz from source
you can't link it to your newer graphviz libs and I'm not certain this
will work for you since you may have compiler mismatch issues with

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

More information about the Bioconductor mailing list