Hi again,

I have installed everything as binary (R, graphviz (now 2.8 with same  
error after logout/login) and Rgraphviz ).

The file Rgraphviz.so is located in the i386 directory:
 > system.file("libs", package="Rgraphviz")
[1] "/Users/danielk/Library/R/library/Rgraphviz/libs"
 > dir(system.file("libs", package="Rgraphviz"))
[1] "i386" "ppc"
 > system("otool -L ~/Library/R/library/Rgraphviz/libs/i386/ 
Rgraphviz.so")
/Users/danielk/Library/R/library/Rgraphviz/libs/i386/Rgraphviz.so:
	Rgraphviz.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/2.4/Resources/lib/ 
libR.dylib (compatibility version 2.4.0, current version 2.4.1)
	/Library/Frameworks/R.framework/Versions/2.4/Resources/lib/libgcc_s. 
1.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version  
1.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current  
version 88.3.4)
 >

After I installed graphviz 2.8 I can't run the command line tools of  
graphviz:
danielk:~ danielk$ dot
dyld: Library not loaded: /usr/local/lib/graphviz/libgcc_s.1.0.dylib
   Referenced from: /usr/local/lib/graphviz/libgvc.2.dylib
   Reason: image not found
Trace/BPT trap

which I could do in graphviz 2.12.


/daniel
--

Contact information:

Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden

Visiting address: Roslagstullsbacken 21, B3
Delivery address: Roslagsvägen 30B, 104 06, Stockholm
E-mail: daniel@biotech.kth.se
E-mail: daniel@arrayadvice.se
Phone: +46 8 5537 8337 (Office)
Phone: +46 704 71 65 91 (Mobile)
Web: http://www.ktharray.se/
Web: http://www.arrayadvice.se/
Fax: +46 8 5537 8481
MSN messenger: klevebring@msn.com


On 14 Apr 2007, at 17:07, Seth Falcon wrote:

> 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@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:
>
>   http://r.research.att.com/
>
> 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
> R...
>
> + seth
>
> -- 
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer  
> Research Center
> http://bioconductor.org


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