[BioC] I have trouble running the AnnBuilder Vignette

[James MacDonald]

I have the ActiveState perl port, which is what you need to build R
libraries from source. If that is what you have then you should be
alright. Note that your path should point to the bin directory of your
perl installation.

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
734-647-5623
>>> Richard Friedman <friedman at cancercenter.columbia.edu> 11/11/04 4:57
PM >>>
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

C:\Perl\bin\

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,
Rich


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
Lecturer
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
http://cancercenter.columbia.edu/~friedman/

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



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