[BioC] help with internet connection

[Robert Gentleman]

Hi,


joanne.m.cox at gsk.com wrote:
> Hi,
> 
> I thought I would try to run a normalisation in R via unix although I get 
> an error. I understand from the help that I need to use '--internet2' when 
> invoking R but it is not recognised. Can you please help? - see code 

   could you tell us which man page pointed you to --internet2 (it is a 
windows only option, AFAIK, and while you did not say your script looks 
like it is on Unix, whence the failure).

   You most likely need to talk with someone local on setting up a proxy;

?download.file

gives some details


   best wishes
     Robert

> below:
> 
> 
> 
> Computing affinitiesError in getCDF(cdfpackagename) :
>   The current operation could not access the Bioconductor repository. 
> Please check your internet connection, and report further problems to 
> bioconductor at stat.math.ethz.ch
> 
> 'server name': /bioinfo/tools/bin/R64-2.7.0 --internet2
> WARNING: unknown option '--internet2'
> 
> 
> 
> 
> Jo
> 
> 
> -----------------------------------------------------------
> This e-mail was sent by GlaxoSmithKline Services Unlimited 
> (registered in England and Wales No. 1047315), which is a 
> member of the GlaxoSmithKline group of companies. The 
> registered address of GlaxoSmithKline Services Unlimited 
> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
> -----------------------------------------------------------
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org