[BioC] biomaRt proxy issues

[steffen at stat.Berkeley.EDU]

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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