[BioC] Ubuntu - Rgraphviz

Fraser Sim fjsim at buffalo.edu
Thu Nov 5 15:07:27 CET 2009

I know I know another Rgraphviz loading problem.

But in case someone has already seen this and has a quick answer.

I am running a fully patched version of Ubuntu 8.04 with R.10.0.

I am having difficulty getting Rgraphviz to work. I compiled graphviz from
source using versions 2.2, 2.22.2, and 2.24.0. All versions compiled fine.
Once installed Graphviz-2.2 did not work correctly, dot loads but running
any commands in dot causes a segmentation fault. Both 2.22.2 and 2.24.0 work
in dot as expected returning results from the example code. 

I have used the Rgraphviz source code for BioC 2.5 version 1.24.0. Rgraphviz
compiled correctly using each version of graphviz with the following line 

R CMD INSTALL --configure-args='--with-graphviz=/usr/local'
"/mnt/hgfs/db/R-based manual

However when I run R and try to load the library I get the following error

> library(Rgraphviz)
Loading required package: graph
Loading required package: grid
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library
  /usr/local/lib/libgvc.so.5: undefined symbol: agputs
Error: package/namespace load failed for 'Rgraphviz'

I get the same error using either graphviz 2.22.2 or 2.24.0. Strangely
enough when 2.2 is installed, and Rgraphviz compiled it is able to load the
Rgraphviz library but R crashes when a call is made to layoutGraph just as
when I try to run commands via dot directly. My conclusion is that 2.2 is
not compatible with my version of Ubuntu as it's too old and Rgraphviz does
not like the new versions of graphviz (just as in windows). Any help?

I also tried a Google search for "undefined symbol agputs" and didn't get
any results. 


Here's my R sessionInfo()

> sessionInfo()
R version 2.10.0 (2009-10-26) 

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] graph_1.24.0

loaded via a namespace (and not attached):
[1] tools_2.10.0

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