[BioC] getBioC problem

[Gaj Stan (BIGCAT)]

Hi all,

Currently having the same issue, although I don't use any proxy. I can
see the file perfectly when I enter its http-adress in FireFox, so a
Firewall block ought to be out of the question. Even disabling the
firewall didn't solve it.

The error I get is:

--------------------------------------------------
>source("http://www.bioconductor.org/getBioC.R)
Error in file(file, "r", encoding = encoding) :
        Unable to open connection
In addition: Warning Message:
Cannot open: HTTP status was '0 (null)'
--------------------------------------------------

If I interpret this correctly, then it would appear that no connection
could be made to the url, although it is possible with FireFox. 

Strange thing is that I installed the same R version on my notebook, and
there it worked perfectly (same network, same firewall).

Could this question be solved here, or do I need to send it towards the
general R maling-list?

Kind regards,

  - Stan

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon
Sent: 03 February 2006 19:42
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] getBioC problem

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

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