[BioC] I have trouble running the AnnBuilder Vignette
jmacdon at med.umich.edu
Tue Nov 16 04:26:40 CET 2004
If I type
at a command prompt, I get the following
This is perl, v5.8.2 built for MSWin32-x86-multi-thread
(with 25 registered patches, see perl -V for more detail)
Copyright 1987-2003, Larry Wall
Binary build 808 provided by ActiveState Corp.
ActiveState is a division of Sophos.
Built Dec 9 2003 10:19:40
Perl may be copied only under the terms of either the Artistic License
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using `man perl' or `perldoc perl'. If you have access to
Internet, point your browser at http://www.perl.com/, the Perl Home
As noted in the version information, you can get this port of perl at
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
>>> Richard Friedman <friedman at cancercenter.columbia.edu> 11/15/04 4:48
How do I know if I have that. Otherwise where do I get it?
Thanks and best wishes,
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.
> 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 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
> 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
> 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
>> You need to download the tool set found here
>> (http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure
>> you add the directory where you place the tools to your PATH
>> preferably before your windows folder.
>> In other words, download the tools, unzip in e.g., C:\Rtools, and
>> add this to your PATH by right clicking My Computer -->
>> Properties/Advanced/Environment Variables/System variables. Click on
>> path variable, then the edit button and add C:\Rtools. As an example,
>> PATH looks like this:
>> Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs
>> 1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program
>> Note that C:\Rtools comes *before* C:\WINDOWS
>> 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
> 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
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?"
-RoseFriedman, age 8
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