Hello all, I am having great difficulties getting Bioconductor installed. I have followed the instructions and tried recommendations in the mailing list and FAQs as detailed below. Could someone please point out where I am going wrong? * Following the getBioC instructions, when typing /source("http://www.bioconductor.org/getBioC.R")/ I get the error message: Error in file(file, "r") : unable to open connection In addition: Warning message: unable to connect to 'www.bioconductor.org' on port 80. * Using the "Install packages from Bioconductor" item under the "Packages" menu item gives the error message Error in download.file(url = paste(contriburl, "PACKAGES", sep = "/"), : cannot open URL `http://www.bioconductor.org/bin/windows/contrib/2.0/PACKAGES' In addition: Warning message: unable to connect to 'www.bioconductor.org' on port 80. * From the mailing list I tried: Sys.putenv("http_proxy"="http://[your proxy server address]:[Port number]") using the automatic proxy configuration URL, I use for my browser but get the same error as above. * From the R FAQ I tried using the --internet2 option by running the command "C:\Program Files\R\rw2001\bin\Rgui.exe --internet2" from the Run prompt, but Windows does not recognise this (I have possibly got the Windows syntax wrong here??) Any ideas? Thanks, Jonathan

Hi Jonathan, Jonathan Arthur <jarthur@med.usyd.edu.au> writes: > I am having great difficulties getting Bioconductor installed. Sorry the hear that. From the error messages you report, a better characterization might be that you are having trouble getting R to talk to the internet given your proxy setup. > using the automatic proxy configuration URL, I use for my browser but > get the same error as above. Have you looked over the help for download.file? That is where the documentation about proxy setup lives. You might also want to direct a question over at R help where there are likely to be more users with experience setting up HTTP proxies with R. + seth

Hi Jonathan, You did a great job of trying to sort this out. In addition to Seth's suggestion, let me add the suggestion of tracking down a local IT person. They should be able to tell you how to negotiate your way through the local firewall (and in some cases they are the only ones that can), equipped with the R documentation you have tracked down, they should be able to sort this out quite quickly. Robert On Apr 13, 2005, at 10:36 PM, Jonathan Arthur wrote: > Hello all, > > I am having great difficulties getting Bioconductor installed. I have > followed the instructions and tried recommendations in the mailing > list and FAQs as detailed below. Could someone please point out where > I am going wrong? > > * Following the getBioC instructions, when typing > /source("http://www.bioconductor.org/getBioC.R")/ I get the error > message: > > Error in file(file, "r") : unable to open connection > In addition: Warning message: > unable to connect to 'www.bioconductor.org' on port 80. > > * Using the "Install packages from Bioconductor" item under the > "Packages" menu item gives the error message > > Error in download.file(url = paste(contriburl, "PACKAGES", sep = "/"), > : > cannot open URL > `http://www.bioconductor.org/bin/windows/contrib/2.0/PACKAGES' > In addition: Warning message: > unable to connect to 'www.bioconductor.org' on port 80. > > * From the mailing list I tried: > > Sys.putenv("http_proxy"="http://[your proxy server address]:[Port > number]") > > using the automatic proxy configuration URL, I use for my browser but > get the same error as above. > > * From the R FAQ I tried using the --internet2 option by running the > command "C:\Program Files\R\rw2001\bin\Rgui.exe --internet2" from the > Run prompt, but Windows does not recognise this (I have possibly got > the Windows syntax wrong here??) > > Any ideas? > > Thanks, > > Jonathan > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+