[BioC] Bioconductor installation

[Seth Falcon]

"ruma" <rumas at cdac.in> writes:

> Hi
>
> I have installed R-2.5.0 on Linux(Redhat Enterprise 64bit o.s.) and have
> been trying to install the
> BioConductor packages without success.
>
> when I try to access the packages i get the following error:
>
>> source("http://bioconductor.org/biocLite.R")
> Error in file(file, "r", encoding = encoding) :
> 	unable to open connection
> In addition: Warning message:
> unable to connect to 'bioconductor.org' on port 80.
>  I tried looking at the posts and tried using the To get R to connect to the
> proxy server, by giving the
> following(which has been suggested in the posts):
>
> Sys.putenv("http_proxy"="http://name_of_proxy_server")
>  but that too gave the same error.
>
> Is there an easy way to overcome this problem?
> I have looked at the posts and it seems to be a firewall issue. Can you
> please help me solve this issue?

Have a look at the man page for download.file:  help("download.file")
This looks like a proxy issue to me and if after reading the
download.file man page and following its suggestions you don't get
things working, you might post to R-help -- sorry, but what you are
describing is a general R problem and not Bioconductor specific.  You
might also try searching the R-help list for solutions.

Note in particulr this bit:

    These environment variables must be set before the download code
    is first used: they cannot be altered later by calling
    'Sys.setenv'.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org