[BioC] RE: [R] Problems with url/download and http_proxy

[Warnes, Gregory R]

Just adding the trailing slash doesn't seem to help:

	> Sys.getenv('http_proxy')
	                  http_proxy 
	"http://gproxy1.pfizer.com/" 

	> url("http://cran.r-project.org/src/contrib/PACKAGES",'r')
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	Error in url("http://cran.r-project.org/src/contrib/PACKAGES", "r")
: 
	        cannot open URL
`http://cran.r-project.org/src/contrib/PACKAGES'

But adding the port explicitly does:

	> Sys.getenv("http_proxy")
	                     http_proxy 
	"http://gproxy1.pfizer.com:80/" 
	>  url("http://cran.r-project.org/src/contrib/PACKAGES",'r')
	                                     description 
	"http://cran.r-project.org/src/contrib/PACKAGES" 
	                                           class 
	                                           "url" 
	                                            mode 
	                                             "r" 
	                                            text 
	                                          "text" 
	                                          opened 
	                                        "opened" 
	                                        can read 
	                                           "yes" 
	                                       can write 
	                                            "no" 



even if the trailing slash is not present:

> Sys.getenv("http_proxy")
                    http_proxy 
"http://gproxy1.pfizer.com:80" 

> url("http://cran.r-project.org/src/contrib/PACKAGES",'r')
                                     description 
"http://cran.r-project.org/src/contrib/PACKAGES" 
                                           class 
                                           "url" 
                                            mode 
                                             "r" 
                                            text 
                                          "text" 
                                          opened 
                                        "opened" 
                                        can read 
                                           "yes" 
                                       can write 
                                            "no" 


Perhaps the documentation for download.file should be changed to note the
requirement of the port.  The paragraph on proxies could be changed from


     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"'.


to something like:

     Proxies can be specified via the environment variables `"http_proxy"'
     or `"HTTP_PROXY"' and `"ftp_proxy'" or `"FTP_PROXY"'.  These variables 
     must be of the form `protocol://machine.domain.tld:port'.  For FTP 
     transfers, the username and password on the proxy can be specified by
    `"ftp_proxy_user"' and `"ftp_proxy_password"'.  Setting `"no_proxy"' 
     prevents the use of any proxy.  


-Greg

> -----Original Message-----
> From: ripley@stats.ox.ac.uk [mailto:ripley@stats.ox.ac.uk]
> Sent: Tuesday, June 18, 2002 11:43 AM
> To: Warnes, Gregory R
> Cc: 'r-help@stat.math.ethz.ch'; 'bioconductor@stat.math.ethz.ch'
> Subject: Re: [R] Problems with url/download and http_proxy
> 
> 
> The code (which you do have available to you) says http_proxy
> 
>  * Should be like http://myproxy/ or http://myproxy:3128/
> 
> which yours is not, so please try that format.  The code suggests
> that the traling / can be omitted, but the words do not.
> 
> -- 
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272860 (secr)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
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