biomaRt proxy issues
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@steve-pederson-2103
Last seen 7.1 years ago
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_M ONETARY=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
biomaRt charm biomaRt charm • 4.9k views
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@steffenstatberkeleyedu-2907
Last seen 7.1 years ago
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_Australi a.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
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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 > >
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