[BioC] FW: Graphviz in Vista64

[Kasper Daniel Hansen]

On Mar 2, 2009, at 9:46 , Sim, Fraser wrote:

> 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.

sessionInfo() is not a reliable way to tell whether you are running 64  
bit or not. I am doing 64 bit on my Mac, and sessionInfo reports

R> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-25 r48005)
i386-apple-darwin9.6.0

My pointer size is 8 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
> details).
>
> I haven't touched using 64-bit source as it's not supported or
> documented at the moment.
>
> Hope that clears up the confusion,

Yes, thanks.

And I assume that you are using a binary version of Rgraphviz?

It is pretty standard that any graphviz problems don't occur until you  
actually do something like
R> example(layoutGraph)

What you see is somewhat typical of some problems with the R-Graphviz  
interaction. Unfortunately I am not that familiar with 64bit Vista  
(and frankly I have no interest in becoming familiar :)

Given that it does not work now, and that Graphviz seems to work  
separately, I would try to compile Rgraphviz from source. The hope is  
that doing this, might actually make everything work, or it might  
provide some clues as to what needs to be done. It may also be wasted  
work. But if you really want to get it to work, I would suggest  
spending 30 minutes compiling from source. I would be using the mingw  
version that the graphviz developer suggests, because it seems that  
the recommended version 2.20.3 does not work on Vista 64bit.  
Unfortunately, the graphviz developers tends to change the internals  
frequently, so it is not without reason that RGraphviz recommends a  
specific Graphviz version. In fact, what happens might be
   Graphviz 2.20.3 does not work on Vista 64 bit
   Rgraphviz does not work with the newer version
But this is all speculation.

Unless of course someone is actually experienced with the situation  
and can provide actual help instead of guesswork :)

Kasper

> Fraser
>
> -----Original Message-----
> 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
> R> .Machine$sizeof.pointer
> (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
> compilation output.
>
> 3) Are you sure the version of Graphviz you are running, is 64 bit?
>
> Kasper
>
> 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:
>> graphviz-2.21.20090202.1215.msi
>> graphviz-mingw-2.21.20090202.1215.msi
>>
>> Both versions worked via GVedit.exe. The package loads but now with a
>> warning. RGUI.EXE continues to crash on attempts to perform
>> layoutGraph().
>>
>> 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.
>>
>> Thanks,
>> Fraser
>>
>> -----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"
>>
>> Kasper
>>
>> 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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