[BioC] biomaRt proxy issues

[Steve Pederson]

Hi Steffen,

Thanks for the quick response. Unfortunately it doesn't work either, 
although I used Sys.setenv as Sys.putenv seems to be deprecated.

Cheers,

Steve

steffen at stat.Berkeley.EDU wrote:
> Hi Steve,
> 
> I'm not sure if this works different than setting Renviron.site but we
> used to be able to go around this by doing:
> 
> Sys.putenv("http_proxy" = "http://my.proxy.org:9999")
> 
> within the R session before calling any biomaRt functions.
> 
> Cheers,
> Steffen
> 
>> Hi,
>>
>> I'm having trouble getting biomaRt to connect to anything, and am pretty
>> sure it's something to do with my proxy, which I have set via
>> Renviron.site using:
>>
>> http_proxy=http://my.proxy.org:9999/ http_proxy_user=ask
>>
>> This seems to work fine for other things such as downloading packages
>> from BioConductor. However, I noticed that I wasn't asked for my
>> username & password like most other things do either.
>>
>> Not using a proxy didn't work either, but when I connect at home using
>> my home ISP, everything is fine & works like a charm. Being able to
>> connect at my University is obviously rather important though as that's
>> where all my data is.
>>
>> Thanks in advance,
>>
>> Steve
>>
>>
>> The code & error I'm getting is as follows:
>>
>>  > library(biomaRt)
>>  > listMarts()
>> Opening and ending tag mismatch: meta line 4 and HEAD
>> Opening and ending tag mismatch: head line 2 and HTML
>> Specification mandate value for attribute noshade
>> attributes construct error
>> Couldn't find end of Start Tag HR line 10
>> Opening and ending tag mismatch: BR line 9 and BODY
>> Opening and ending tag mismatch: html line 1 and HTML
>> Error: 1: Opening and ending tag mismatch: meta line 4 and HEAD
>> 2: Opening and ending tag mismatch: head line 2 and HTML
>> 3: Specification mandate value for attribute noshade
>> 4: attributes construct error
>> 5: Couldn't find end of Start Tag HR line 10
>> 6: Opening and ending tag mismatch: BR line 9 and BODY
>> 7: Opening and ending tag mismatch: html line 1 and HTML
>>  > sessionInfo()
>> R version 2.8.0 (2008-10-20)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] biomaRt_1.16.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.92-0 XML_1.99-0
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> 
>