[BioC] FW: Graphviz in Vista64

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Mon Mar 2 18:02:18 CET 2009

Hi Kasper,

The graphviz installations that I have tried include the following
versions downloaded from http://www.graphviz.org/ :

2.20.3 - In R, loads Rgraphviz package fine but crashes when layout
performed. Also, GVedit.exe did not work correctly and the graphViz
developer, Arif, suggested I try the developer version.

Tried both:

Both versions worked via GVedit.exe. The package loads but now with a
warning. RGUI.EXE continues to crash on attempts to perform

The term 'crash' here means, a pop-up dialog from Vista informing me
that RGUI.EXE has stopped working and Windows will close the program.
There are no additional details.

I have installed and used Rgraphviz on a number of XP32 boxes and so am
familiar with the quirks required to get it working. This is an entirely
different problem.

I have switched to Vista64 to work with larger datasets requiring
additional memory.


-----Original Message-----
From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu] 
Sent: Monday, March 02, 2009 11:48 AM
To: Sim, Fraser
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Graphviz in Vista64

Most likely something is wrong with your graphviz installation, but  
since you don't provide any details about that, it is impossible to  
help. We would also like to see the actual crash output from R or a  
better description of what you mean by "crash"


On Mar 2, 2009, at 7:48 , Sim, Fraser wrote:

> Hi Bioconductors,
> Has anyone successfully used the Rgraphviz package to plot graphs in R
> under Vista64??
> I have found that RGUI.EXE crashes upon execution of the layoutGraph
> step.
> Running the following reliably crashes R.
> library("Rgraphviz")
> g = new("graphNEL", nodes = c("a","b","c"))
> debug(Rgraphviz:::graphLayout)
> sessionInfo()
> layoutGraph(g)
> Thanks,
> Fraser
> PS. The crash occurs in :
> Rgraphviz:::graphLayout
> .Call("Rgraphviz_doLayout",graph,as.integer(type),PACKAGE="Rgraphviz")
> PPS.
> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets   
> methods
> [8] base
> other attached packages:
> [1] Rgraphviz_1.20.3 graph_1.20.0     rcom_2.0-4       rscproxy_1.0-12
> loaded via a namespace (and not attached):
> [1] cluster_1.11.12 tools_2.8.1
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