Essentially it comes down to setting the environment variable http_proxy to your proxy server (note that it must be set before starting R). If your proxy server requires a user name and password you may also have to set http_proxy_user. Documentation on proxies is contained within the documentation on download.file (eg type ?download.file). I've appended the relevant sections below. Proxies can be specified via environment variables. Setting "no_proxy" stops any proxy being tried. Otherwise the setting of "http_proxy" or "ftp_proxy" (or failing that, the all upper-case version) is consulted and if non- empty used as a proxy site. For FTP transfers, the username and password on the proxy can be specified by "ftp_proxy_user" and "ftp_proxy_password". The form of "http_proxy" should be "http://proxy.dom.com/" or "http://proxy.dom.com:8080/" where the port defaults to 80 and the trailing slash may be omitted. For "ftp_proxy" use the form "ftp://proxy.dom.com:3128/" where the default port is 21. These environment variables must be set before the download code is first used: they cannot be altered later by calling Sys.putenv. Usernames and passwords can be set for HTTP proxy transfers via environment variable http_proxy_user in the form user:passwd. Alternatively, "http_proxy" can be of the form "http://user:pass@proxy.dom.com:8080/" for compatibility with wget. Only the HTTP/1.0 basic authentication scheme is supported. Under Windows, if "http_proxy_user" is set to "ask" then a dialog box will come up for the user to enter the username and password. NB: you will be given only one opportunity to enter this, but if proxy authentication is required and fails there will be one further prompt per download. Cheers Chris Dr Chris Wilkinson Research Officer (Bioinformatics) | ARC Research Associate Child Health Research Institute (CHRI) | Microarray Analysis Group 7th floor, Clarence Rieger Building | Room 121 Women's and Children's Hospital | School of Applied Mathematics 72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005 Math's Office (Room 121) Ph: 8303 3714 CHRI Office (CR2 52A) Ph: 8161 6363 Christopher.Wilkinson@adelaide.edu.au http://mag.maths.adelaide.edu.au/crwilkinson.html > -----Original Message----- > From: Isaac Neuhaus <isaac.neuhaus@bms.com> > Subject: [BioC] proxy configuration > To: bioconductor <bioconductor@stat.math.ethz.ch> > Message-ID: <40C6220B.7040903@bms.com> > Content-Type: text/plain; format=flowed; charset=us-ascii > > Does anybody know how to set up the proxy in R to be able to use the > getBioC() function and install the Bioconductor packages? Thanks. Isaac >

> From: Chris Wilkinson > > Essentially it comes down to setting the environment variable > http_proxy to > your proxy server (note that it must be set before starting > R). Not exactly. See ?Sys.setenv. Best, Andy

Hi Isaac Just for completeness, you didn't mention if you are using R on windows or on Linux. On windows, if you set your Desktop shortcut to point to: "C:\Program Files\R\rw1090\bin\Rgui.exe" --internet2 Then R will use the proxy configuration from Internet Explorer - which means that if IE works, then R will too. On Linux, you need to set your environment variable http_proxy to your proxy server address, and make sure there is NO environment variable called no_proxy. There are a variety of ways of doing this, but on Suse and many others, one can edit /my/home/directory/.bashrc to have the following line: export http_proxy=http://my.proxy.server.com:port Thanks Mick -----Original Message----- From: Isaac Neuhaus [mailto:isaac.neuhaus@bms.com] Sent: 08 June 2004 21:31 To: bioconductor Subject: [BioC] proxy configuration Does anybody know how to set up the proxy in R to be able to use the getBioC() function and install the Bioconductor packages? Thanks. Isaac _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor