[BioC] How to install BioConductor packages with a computer behind a proxy

[Aswin Seshasayee]

Martin Morgan <mtmorgan at ...> writes:

> 
> On 12/17/2010 10:08 PM, Barco You wrote:
> > Dear All,
> > 
> > Because my computer is behind a http proxy, every time I got nothing when
> > running source("http://bioconductor.org/biocLite.R"); biocLite(), and I
> > tried to set the proxy with Sys.setenv(http_proxy="http://.....:8080") but
> > it did't work either.
> > 
> > Could you please tell me how to set http proxy for R? Thanks!
> 
> Hi
> 
> Probably it would help to show
> 
>   sessionInfo()
> 
> Your issues might be addressed by an R FAQ
> 
>   http://cran.r-project.org/faqs.html
> 
> e.g., for Windows
> 
>   http://cran.r-project.org/bin/windows/base/rw-FAQ.html
> 
> FAQ 2.19.
> 
> Martin
> 

I tried setting http_proxy in the ~/.Renviron file (I use a Mac Pro), but still
it did not work.

The following two lines of code seems to be doing the job of installing all of
bioconductor (in fact it is running on my computer as I type this).

softwarelist<-available.packages(contriburl="http://bioconductor.org/packages/2.6/bioc/bin/macosx/leopard/contrib/2.11",method="wget",filters="duplicates")

for(i in
1:length(rownames(softwarelist))){install.packages(rownames(softwarelist)[i],contriburl=c("http://bioconductor.org/packages/2.6/bioc/bin/macosx/leopard/contrib/2.11","http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.12/"),method="wget")}

Aswin