Entering edit mode
Warnes, Gregory R
▴
460
@warnes-gregory-r-43
Last seen 10.3 years ago
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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