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

[Jenny Drnevich]

Hi everyone,

If you've been following the other thread on "Rgraphviz, R 2.7.0 and 
Windows XP", there's been quite a few trials on how to get the 
Windows binary of Rgraphviz corrected installed and working properly 
on R 2.7.0. I thought I had it all figured out with my  - SOLVED! 
post, but then Sebastien Gerega found that using some function from 
topGO caused R to crash because of the problems with Rgraphviz. 
Thanks to the help of quite a few people, the following steps SHOULD 
get Rgraphviz installed and working on Windows (except for one minor 
hiccup, noted at the end):

1. Close down any R sessions you have open.

2. 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 Graphviz 2.16.1 from the archives: 
http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz-2.16.1.exe . 
This link should automatically download the correct file, but if 
you're doing it manually, you have to get it from the ARCHIVE, not 
the Windows download page, which only has 2.18 and 2.16.1.static.

3. Check your PATH to see how Graphviz was added: Start Menu -> 
Control Panel -> System -> Advanced -> Environment Variables. In the 
box labeled "System variables" scroll down to "Path" and then click 
on Edit. Something like "C:\Program Files\Graphviz2.16\Bin"; should 
be at the very end. IF IT HAS QUOTES AROUND IT, DELETE THE QUOTES 
(leave the semicolon). Then click OK several times to get out of the 
System menu.

4. Now open R and download and install Rgraphviz using:
 > source("http://bioconductor.org/biocLite.R")
 > biocLite("Rgraphviz")
(if you've already downloaded Rgraphviz with these commands before 
doing steps 1-3 above, you do not have to do it again)

5. Try loading Rgraphviz:
 > library(Rgraphviz)

Hiccup: on my machine when I load Rgraphviz, I get a Windows error 
box that pops up saying: Point Not Found. "The procedure entry point 
g_intern_static_string could not be located in the dynamic link 
library libglib-2.0-0.dll". However, if I click OK, Rgraphviz 
continues to load fine and appears to work fine. I'm not sure what to 
do about this last little problem, other than it seems to be ignorable.

I hope this works for everyone!!
Jenny



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