[BioC] proxy configuration

[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). 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 at adelaide.edu.au

http://mag.maths.adelaide.edu.au/crwilkinson.html


> -----Original Message-----
> From: Isaac Neuhaus <isaac.neuhaus at bms.com>
> Subject: [BioC] proxy configuration
> To: bioconductor <bioconductor at stat.math.ethz.ch>
> Message-ID: <40C6220B.7040903 at 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
>