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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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 at 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 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
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 at stats.ox.ac.uk [mailto:ripley at stats.ox.ac.uk]
> Sent: Tuesday, June 18, 2002 11:43 AM
> To: Warnes, Gregory R
> Cc: 'r-help at stat.math.ethz.ch'; 'bioconductor at
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 at 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
>
> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
> -.-.-.-.-.-.-.-.-
> r-help mailing list -- Read
> http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !) To:
> r-help-request at stat.math.ethz.ch
> _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._.
> _._._._._._._._._
>
LEGAL NOTICE
Unless expressly stated otherwise, this message is confidential and may be
privileged. It is intended for the addressee(s) only. Access to this E-mail by
anyone else is unauthorized. If you are not an addressee, any disclosure or
copying of the contents of this E-mail or any action taken (or not taken) in
reliance on it is unauthorized and may be unlawful. If you are not an addressee,
please inform the sender immediately.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-help-request at
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