[BioC] How to install Rgraphviz on Windows - REALLY!

[Jenny Drnevich]

Hi Ernest, Kasper and others from previous threads of installing Rgraphviz...

As noted many times in different threads on this list, there are 
always problems with Windows users being able to successfully install 
and use Rgraphviz because of an outside program, Graphviz. I just 
went through 2 recent threads (links below) after the R 2.9/BioC 2.4 
releases, and I still don't have Rgraphviz loading completely without 
errors (although I think it's functional). First of all, somewhere in 
one of the threads, Kasper (I think) said he needed to getting around 
to writing a vignette on how to install everything properly, which 
would be nice to have in the Documentation section of the Rgraphviz page:
http://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html

Instead, the text at the top says to see the README file, which is in 
the source distribution (probably difficult for the average Windows 
user to actually get this file!). The instructions in the README file 
for using the Windows binary of Rgraphviz say to download the 
Graphviz ***2.22.2*** binary file. However, this is not the correct 
version, as indicated in the links below. I just tried the  Graphviz 
2.22.2, and got all the same errors documented before. Then I 
followed Patrick's suggestion on 4/29/09 to use Graphviz 2.20 
available from here:

http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi

So here are the step I went through:
1. No other Graphviz version installed on my computer, no C:\Program 
Files\GraphvizX.XX\bin in my PATH, R not running.
2. Installed Graphviz 2.20 using the file from the link above.
3. Made sure C:\Program Files\Graphviz2.20\bin is in my PATH.
4. Started R, downloaded and installed Rgraphviz using:
 > source("http://bioconductor.org/biocLite.R")
 > biocLite("Rgraphviz")

Now, according to everything I can find in the archives, this 
*should* have worked. But when I try:
 > library(Rgraphviz)

I still am getting a Windows error box that pops up. The top says "R 
Console: Rgui.exe - Entry Point Not Found" and the text in the box 
says "The procedure entry point g_intern_static_string could not be 
located in the dynamic link library libglib-2.0-0.dll."  However, 
when I then click OK on this error box, Rgraphviz appears to finish 
loading fine:

 > library(Rgraphviz)
Loading required package: graph
Loading required package: grid
 > sessionInfo()
R version 2.9.0 (2009-04-17)
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_1.22.1 graph_1.22.2

loaded via a namespace (and not attached):
[1] tools_2.9.0


 > graphvizVersion()
$installed_version
[1] '2.20.3'

$build_version
[1] '2.20.3'


I don't really use Rgraphviz, so I don't have any code to see if 
works completely. I had gotten to this same point a couple of R 
versions ago, which is where Ernest found my e-mail. I still think I 
had the Windows error message, which I guess I just ignored as 
everything I needed to do back then seemed to work. So, should I and 
others continue to ignore it now if we get to this point? Anything else to try?

Writing the "how to install" vignette would really come in handy!!!

Thanks,
Jenny






Recent threads on installing Rgraphviz:
https://stat.ethz.ch/pipermail/bioconductor/2009-April/027374.html

https://stat.ethz.ch/pipermail/bioconductor/2009-May/027495.html



At 05:10 AM 6/23/2009, Ernest Hobson wrote:
>Hi There Jenny
>
>I've tried your steps a number of times, but keep getting the same 
>error below!
>
>Could you kindly help?
>
>Thnx Ernest
>
>Loading required package: graph
>Loading required package: grid
>Error in inDL(x, as.logical(local), as.logical(now), ...) :
>   unable to load shared library 
> 'C:/PROGRA~1/R/R-29~1.0/library/Rgraphviz/libs/Rgraphviz.dll':
>   LoadLibrary failure:  The specified module could not be found.
>
>         [[alternative HTML version deleted]]
>
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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 at illinois.edu