[BioC] getBioC problem

[Seth Falcon]

On  3 Feb 2006, tliu at fhcrc.org wrote:

>
> Hi Amy,
>
>>> source("http://www.bioconductor.org/getBioC.R")
>> Error in file(file, "r", encoding = encoding) :
>> unable to open connection
>> In addition: Warning message:
>> unable to connect to 'www.bioconductor.org' on port 80.
>
> It seems that your LAN has some special settings (such as firewall?)
> so that you are unable to find the file getBioC.R.  Could you try to
> put the address "http://www.bioconductor.org/getBioC.R" in your
> browser to see if you can browse this script in your browsers?  I
> will guess that you are unable to see it in the browsers.

A proxy that requires authentication is more likely the issue here and
so it is entirely possible that the web browser is properly configured
but that R is not.  

>> (a) if I add --internet2 to the target of the shortcut:
>>
>> [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2'
>> specified in the Target box is not valid.  Make sure the path and
>> file name are correct.]

Did you add a space betfore --internet2 ?

>> (b) I am connected to the internet via a LAN, which has a proxy so:
>>
>>> "path_to_R-2.2.1\bin\RGui.exe"
>> http_proxy=http://www.abdn.ac.uk/local/autoproxy.pac
>> Error: syntax error in ""path_to_R-2.2.1\bin\RGui.exe" http_proxy"
>>
>> that doesn't work either...
>>
>> What am I doing wrong, any ideas?

The help page for download.file() has details about proxy
configuration.  Without knowing more about your proxy setup it may be
hard for us to help further.  Also, there may be more expertise with
using R with web proxies on the R-help mail list.

Hope that helps some.

Best,

+ seth