Help, What am I doing wrong. http access behind a proxy. I have proxy behaviour set up with wget. Here is the success with download.file ... > download.file("http://lwn.net","check",method="wget") --20:33:11-- http://lwn.net/ => `check' Resolving proxy.newcastle.edu.au... 134.148.172.1 Connecting to proxy.newcastle.edu.au[134.148.172.1]:8080... connected. Proxy request sent, awaiting response... 200 OK Length: 17,265 [text/html] 100%[====================================>] 17,265 26.47K/s 20:33:12 (26.39 KB/s) - `check' saved [17265/17265] Here is the failure with getBioC() - I have the function from download.file() and then source() > getBioC(method="wget") Running getBioC version 1.2.69.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Warning message: cannot open: HTTP status was `407 Proxy Authentication Required' Error in getBioC(method = "wget") : Your R can not connect to the Bioconductor website, which is required for getBioC to work properly. The most likely cause of this is the internet configuration of R ---- Robert King, Statistics, School of Mathematical & Physical Sciences, University of Newcastle, Australia Room V133 ph +61 2 4921 5548 Robert.King@newcastle.edu.au http://maths.newcastle.edu.au/~rking/ "The worst moment for me was when [John Howard] said that ``the things that unite us are more important than the things which divide us''. Not to me, John. The things that divide us are now more important." -- Margo Kingston, reacting to the Australian Prime minister, re-elected by people who think pushing desperate refugees back to sea is what Australia is about http://www.smh.com.au/news/webdiary/2001/11/12/FFX9WJ94XTC.html

Hi Robert, Robert King <robert.king@newcastle.edu.au> writes: > http access behind a proxy. I have proxy behaviour set up with wget. > > Here is the success with download.file ... > [snip] > > Here is the failure with getBioC() - I have the function from download.file() > and then source() I think you've identified a bug in the getBioC script. Although the method argument is honored for the package downloads, it is not honored for testing connectivity. We will fix this. In the meantime, I can offer a couple of suggestions to get you going: 1. You can tell R about your proxy setup and this should allow getBioC to function. Read the help for download.file. I believe there are a handful of environment variables that must be set. OR 2. Download the reposTools package from the Bioconductor website, install it manually, and then use the install.packages2 function to install desired Bioc packages. + seth