[BioC] I have trouble running the AnnBuilder Vignette

[James W. MacDonald]

Richard Friedman wrote:
> Dear John (and Everyone),
> 
> 	Thank you very much for your quick reply. I tried what you said,
> but I got a warrning and an error message but I still can't reachthe
> object. The warning was that gzip was not found.
> The error was Error in parseKEGGGenome() : Faild to obtain KEGG organism
> code
You need to download the tool set found here 
(http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure that 
you add the directory where you place the tools to your PATH variable, 
preferably before your windows folder.

In other words, download the tools, unzip in e.g., C:\Rtools, and then 
add this to your PATH by right clicking My Computer --> 
Properties/Advanced/Environment Variables/System variables. Click on the 
path variable, then the edit button and add C:\Rtools. As an example, my 
PATH looks like this:

.;C:\Perl\bin\;C:\Rtools;C:\Program 
Files\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;c:\mingw\bin;C:\Program 
Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs 
1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program 
Files\Subversion\bin

Note that C:\Rtools comes *before* C:\WINDOWS

HTH,

Jim


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109