[BioC] biomaRt proxy issues

[Steve Pederson]

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