[BioC] I have trouble running the AnnBuilder Vignette

Richard Friedman friedman at cancercenter.columbia.edu
Thu Nov 11 22:57:28 CET 2004

Dear Jim (and John and Everybody):

	What you wrote helps considerably. I have another question before
I proceed. In your note below, the second  entry in the path file is


The AnnBuilder documentation states thatit requires Perl to run.
The only Perl I have on my PC is
C:\Documents and Settings\Richard\Local Settings\Temp\R-2.0.0\share\perl

Is this sufficient, or do I have to download Perl and place it in a
directory for AnnBuilder to run?

Thanks and best wishes,

On Thu, 11 Nov 2004, James W. MacDonald wrote:

> 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

Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu

"That was written by Felix Mendelsohn?
Did he start Mendelsohn's Pizza?"
-Rose Friedman, age 8

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