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 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@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]]

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