[BioC] biomaRt proxy issues

[Steve Pederson]

Hi Ramona,

Unfortunately I couldn't find a way to work around it, so I've taken to 
doing those stages of analysis on an alternate machine with a more 
straight-forward internet connection (i.e. at home).

All the best,

Steve


Ramona.Schmid at boehringer-ingelheim.com wrote:
> Hi Steve,
> 
> did you solve the problem, I am running into exactly the same error
> messages/proxy problems.
> 
> Would be great if you could help!
> 
> Many thanks,
> Ramona
> 
> 
> 
>> -----Ursprüngliche Nachricht-----
>> Von: bioconductor-bounces at stat.math.ethz.ch 
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag 
>> von Steve Pederson
>> Gesendet: Mittwoch, 11. Februar 2009 02:03
>> An: steffen at stat.berkeley.edu
>> Cc: bioconductor at stat.math.ethz.ch
>> Betreff: Re: [BioC] biomaRt proxy issues
>>
>>
>> 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.1
>> 252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=En
>> glish_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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>>>
>