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;L C_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Austral ia.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 >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >