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 > > > >> -----Urspr?ngliche 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 >>>> _______________________________________________ >>>> 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 >>> >