[R] Problems with url/download and http_proxy

[Warnes, Gregory R]

I would like to use the getBioC.R script from
http://www.bioconductor.org/getBioC.R to install the biobase packages.
Unfortunately, url() and download.file() die when trying to talk to my
proxy:

	> getBioC("exprs")
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	[1] "Get Biobase failed"     "Get annotate failed"    "Get
genefilter failed" 
	[4] "Get geneplotter failed" "Get edd failed"         "Get ROC
failed"        
	[7] "Get tkWidgets failed"  

Which is caused by:

	> url(getUrl("unix","Biobase", F),'r')
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	Error in url(getUrl("unix", "Biobase", F), "r") : 
	 cannot open URL
`http://www.bioconductor.org/packages/release/distrib/Source/Biobase_1.0.tar
.gz'

and similarly:

	> download.file(getUrl("unix","Biobase", F),dest="test.tgz")
	trying URL
`http://www.bioconductor.org/packages/release/distrib/Source/Biobase_1.0.tar
.gz'
	connect: Cannot assign requested address
	unable to connect to 'gproxy1.pfizer.com'.
	Error in download.file(getUrl("unix", "Biobase", F), dest =
"test.tgz") : 
	 cannot open URL
`http://www.bioconductor.org/packages/release/distrib/Source/Biobase_1.0.tar
.gz'

So, it looks like R's internal http code can't handle my proxy settings:

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

However, this proxy value works just fine for wget/lynx etc:

	> download.file(getUrl("unix","Biobase", F),dest="test.gz",
method="wget")
	--11:12:07--
http://www.bioconductor.org:80/packages/release/distrib/Source/Biobase_1.0.t
ar.gz
	           => `affy.tar.gz'
	Connecting to gproxy1.pfizer.com:80... connected!
	Proxy request sent, awaiting response... 200 OK
	Length: 292,800 [application/x-tar]
	
	    0K -> .......... .......... .......... .......... .......... [
17%]
	   50K -> .......... .......... .......... .......... .......... [
34%]
	...


So, does R need the proxy settings to be in a different format? Other ideas
on what might be wrong?

Obligatory version info:

> version
         _                   
platform sparc-sun-solaris2.8
arch     sparc               
os       solaris2.8          
system   sparc, solaris2.8   
status   Patched             
major    1                   
minor    5.1                 
year     2002                
month    06                  
day      18                  
language R                   


-Greg


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