[BioC] I have trouble running the AnnBuilder Vignette

[Richard Friedman]

Jim,

How do I know if I have that. Otherwise where do I get it?

Thanks and best wishes,
Rich

On Nov 11, 2004, at 7:08 PM, James MacDonald wrote:

> 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
>
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should  
> not be used for urgent or sensitive issues.
>
>
------------------------------------------------------------
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?"
-RoseFriedman, age 8