[BioC] FW: Graphviz in Vista64
Fraser_Sim at URMC.Rochester.edu
Mon Mar 2 18:46:03 CET 2009
R and graphviz were installed from 32-bit binaries and are running as
such (as shown in TaskManager). You can see from my sessionInfo() that R
is a 32bit install, and the pointer value was 4 as expected.
64-bit Vista allows access to 4Gb of user memory rather than the less
than 3Gb on offer from a typical 32-bit Windows box (see the R-faq for
I haven't touched using 64-bit source as it's not supported or
documented at the moment.
Hope that clears up the confusion,
From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu]
Sent: Monday, March 02, 2009 12:30 PM
To: Sim, Fraser
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] FW: Graphviz in Vista64
My guess is that there is some problems between the fact that you are
(supposedly) running 64bit R and Graphviz may or may not be compiled
as a 64 bit binary. There could also be problems with Rgraphviz. So,
please tell me the following
1) You you running 64 bit R? You can check this by doing
(should be 8 if you are runngin 64 bit R).
2) How exactly did you install Rgraphviz. Especially, did you compile
it from Source (This may be necessary, I am not too familiar with
64Bit windows and Bioconductor binaries). Please provide the
3) Are you sure the version of Graphviz you are running, is 64 bit?
On Mar 2, 2009, at 9:02 , Sim, Fraser wrote:
> 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
> familiar with the quirks required to get it working. This is an
> 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
>> Running the following reliably crashes R.
>> g = new("graphNEL", nodes = c("a","b","c"))
>> PS. The crash occurs in :
>> R version 2.8.1 (2008-12-22)
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>> attached base packages:
>>  grid stats graphics grDevices utils datasets
>>  base
>> other attached packages:
>>  Rgraphviz_1.20.3 graph_1.20.0 rcom_2.0-4
>> loaded via a namespace (and not attached):
>>  cluster_1.11.12 tools_2.8.1
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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