[BioC] Ubuntu - Rgraphviz

[Gilbert Feng]

Hi, Sim

I think the Rgraphviz error is Graphviz installation failure. Some files
relative to Graphviz are not there. You might be able to get helps at
Graphviz or Ubuntu mailing list about this issue. But I think one option is
switching your ubuntu 8.04 to 9.04 or 9.10. Graphviz and Rgraphviz work very
well on both platform, even the Remix version.

Best

Gilbert

On 11/5/09 8:07 AM, "Fraser Sim" <fjsim at buffalo.edu> wrote:

> 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
> analyses/customPackages/Rgraphviz_1.24.0.tar.gz"
> 
> However when I run R and try to load the library I get the following error
> message:
> 
>> library(Rgraphviz)
> Loading required package: graph
> Loading required package: grid
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/home/fjsim/R/x86_64-pc-linux-gnu-library/2.10/Rgraphviz/libs/Rgraphviz.so'
> :
>   /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. 
> 
> Thanks,
> Fraser
> 
> Here's my R sessionInfo()
> 
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-pc-linux-gnu
> 
> locale:
>  [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
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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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-----------------------------------------------
Gang (Gilbert) Feng, PhD
Biomedical Informatics Center
Robert H. Lurie Comprehensive Cancer Center
Northwestern University
750 N. Lake Shore Drive, 11th Floor(11-175e)
Chicago, IL  60611
Phone:312-503-2358
Email g-feng (at) northwestern.edu