[BioC] KEGGSOAP

[Steven McKinney]

Hi Naomi,

Sounds like you've loaded a function that
has a browser() call in it, often used
in debugging functions.  Looks like
someone forgot to remove the browser call.

To get out of browser mode, type a capital Q

> myfun <- function(x) {y <- x^2; browser(); return(y)}
> myfun(2)
Called from: myfun(2)
Browse[1]> myfun(3)
Called from: myfun(3)
Browse[2]> Q
> 

That should get you back to the top-level prompt.

lower case c also continues function execution,
exiting one level of browser at a time.



Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Naomi Altman
Sent: Mon 11/27/2006 2:01 PM
To: Seth Falcon; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] KEGGSOAP
 
Thanks, Seth, but I am still having problems.

Firstly, I cannot seem to get out of the Browser.  Some R commands 
work, but not exit.

More importantly, I cannot install SSOAP, possibly because it is a 
tar.gz file, rather than a zip file.  (Yup, I am working on Windows.)

Regarding versions:

I installed R 2.4.0 yesterday, and then installed everything else 
using the GUI.  However, for KEGGSOAP and SSOAP, I downloaded from 
BiocLite (which was following a  suggestion from the email archive.

--Naomi

At 03:05 PM 11/27/2006, Seth Falcon wrote:
>Naomi Altman <naomi at stat.psu.edu> writes:
>
> > After reading all the email about KEGGSOAP I think I have the entire
> > thing installed.  However, it does not seem to work:
> >
> > list.organisms()
> > Called from: parseArrayType(type)
> >
> >
> > Also, it seems to have changed my prompt from ">" to
> > "Browse[n]"  where "n" is an integer which is increasing - but not
> > with every command.  This makes me nervous, because I do not know if
> > I have changed something in my R environment.
>
>I think you have a bad version of the SSOAP package [but you didn't
>give us many details on what software you have installed :-)].
>
>I would suggest getting the latest version of SSOAP here:
>http://www.omegahat.org/SSOAP/
>
>I think the BioC mirror is out of date and we will make sure it gets
>updated this week after we do some testing.
>
>+ seth
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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