Dear Jenny
using your instructions I can get Rgraphviz to load with no problems (2.16 or 2.18)! But like Sebastian when I try and plot ,R crashes with no error messages. Could this be something simple like missing/incorrect environmental variable??
John

________________________________

From: sgerega@gmail.com on behalf of Sebastien Gerega
Sent: Wed 11/06/2008 02:56
To: Jenny Drnevich
Cc: Li Long; Robert Gentleman; John Barrett [jzb]; Myroslav Sypa; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!


Hi,
I followed these instructions and am now able to load Rgraphviz without error. However, when I attempt to use it R crashes.
I am not directly using Rgraphviz but am using the topGO package which is calling it. I am basically just running through the example in the topGO vignette when R crashes.

Here is my sessionInfo():
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

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

other attached packages:
 [1] Rgraphviz_1.18.1    topGO_1.8.1         SparseM_0.77        GO.db_2.2.0         AnnotationDbi_1.2.0 RSQLite_0.6-8       DBI_0.2-4          
 [8] graph_1.18.0        arrayQuality_1.18.0 RColorBrewer_1.0-2  gridBase_0.4-3      hexbin_1.14.0       lattice_0.17-6      convert_1.16.0     
[15] Biobase_2.0.0       marray_1.18.0       limma_2.14.4        GDD_0.1-12         

loaded via a namespace (and not attached):
[1] cluster_1.11.10

thanks,
Sebastien




On Wed, Jun 11, 2008 at 3:03 AM, Jenny Drnevich <drnevich@illinois.edu> wrote:


	Hi everyone,
	
	I finally got Rgraphviz to work from the Windows binary. For some reason, Graphviz versions that didn't seem to work last week are working this week! I just tried the following on two "virgin" Windows machines, and it seems to work:
	
	1. Download and install Microsoft Visual C++ 2005 SP1 Redistributable Package: http://www.microsoft.com/downloads/details.aspx?familyid=200B2FD9-AE1A-4A14-984D-389C36F85647&displaylang=en
	
	2. Download and install the current stable release for Windows of Graphviz 2.18.1: http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz-2.18.1.exe (yes, I know before we were saying 2.16.1 was needed, but for some reason 2.18.1 is working this week!)
	
	
	3. From within R, download and install Rgraphviz using:
	> source("http://bioconductor.org/biocLite.R")
	> biocLite("Rgraphviz")
	
	4. If everything goes well, this should work:
	> library(Rgraphviz)
	
	I'm not having any troubles now, at least in loading the package!  Special thanks to Martin Morgan and Tony Chiang for helping me sort this out off-list.
	
	Cheers,
	Jenny
	
	BTW - there's a known bug in graphviz-2.18.exe that the uninstall.exe file doesn't work. Won't matter until you try to uninstall it! They said to install the development release to the same folder and start menu and then uninstall.
	
	
	At 03:51 AM 6/4/2008, Li Long wrote:
	

		>
		>    In the short - and likely even medium term that may be the only
		> solution.  There do not seem to be easy ways to build a DLL that is
		> compliant (which is why the very old one was retained for such a long
		> time) and it requires a substantial effort with every new version of
		> Graphviz that comes out - given competing needs for scarce resources, I
		> am afraid that this is likely to be a month or more.
		>
		>    best wishes
		>     Robert
		>
		
		Hi,
		
		Graphviz releases are also not as stable as one would hope:
		
		(1) graphviz 2.16 didn't contain some required .dlls as graphviz 2.15,
		which causes a lot of confusions, it seems like graphviz 2.18 contains all
		the .dlls needed and it works ok in linking;  the README was written when
		testing was done for graphviz 2.15, assuming graphviz releases are
		somewhat stable...
		
		(2) graphviz built on Windows uses Microsoft Visual Studio, not minGW or
		any thing Linux-like, and the developers strongly discourage
		build-your-own approach; when mixing the .obj from these different
		sources, things are pretty nasty, and we (me and graphviz developers)
		haven't found a way out; it seems that the suggestion from graphviz users
		and developers is to use .dlls;
		
		It's not without trying...
		
		Li
		
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	Jenny Drnevich, Ph.D.
	
	Functional Genomics Bioinformatics Specialist
	W.M. Keck Center for Comparative and Functional Genomics
	Roy J. Carver Biotechnology Center
	University of Illinois, Urbana-Champaign
	
	330 ERML
	1201 W. Gregory Dr.
	Urbana, IL 61801
	USA
	
	ph: 217-244-7355
	fax: 217-265-5066
	e-mail: drnevich@illinois.edu
	
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