Thank you.
Renaud
My setting:
- I am using R 2.13.2 on Ubuntu 11.04.
- I am accessing internet through a proxy (set up with cntlm, not
sure if this is the issue but I don't know how to check without it).
This means that http_proxy='http://localhost:8080/'.
- We have local CRNA/BioConductor mirrors that can be accessed
without going through the proxy.
- My .Rprofile sources a file 'setrepos.R' on the local network, that
sets all relevant repos to our local mirrors.
From the shell:
- I can wget any URL (local or internet) from command line without a
problem.
- In particular I can wget the file 'setrepos.R' from command line.
Symptoms:
- with options(download.file.method='wget'), I can download any URL
(local or internet) with download.file
- I _cannot_ source any local or internet URL if http_proxy is set.
It simply freezes. Using internet.info=0 gives the following messages:
############
Warning messages:
1: In file(file, "r", encoding = encoding) :
using HTTP proxy 'http://localhost:8080/'
2: In file(file, "r", encoding = encoding) :
connected to 'localhost' on port 8080.
3: In file(file, "r", encoding = encoding) :
-> (Proxy) GET http://*OUR_HOST*/~renaud/R/setrepos.R HTTP/1.0
Host: *OUR_HOST*
Pragma: no-cache
User-Agent: R (2.13.2 x86_64-pc-linux-gnu x86_64 linux-gnu)
4: In file(file, "r", encoding = encoding) : <- HTTP/1.1 200 OK
5: In file(file, "r", encoding = encoding) : <- Via: 1.1 SRVWINTMG004
6: In file(file, "r", encoding = encoding) : <- Connection: Keep-Alive
7: In file(file, "r", encoding = encoding) : <- Proxy-Connection:
Keep-Alive
8: In file(file, "r", encoding = encoding) : <- Content-Length: 1597
9: In file(file, "r", encoding = encoding) :
<- Date: Wed, 05 Oct 2011 06:43:13 GMT
10: In file(file, "r", encoding = encoding) : <- Content-Type:
text/plain
11: In file(file, "r", encoding = encoding) :
<- ETag: "30b8018-63d-4a627b821c980"
12: In file(file, "r", encoding = encoding) :
<- Server: Apache/2.2.9 (Ubuntu) DAV/2 SVN/1.5.1 PHP/5.2.6-2ubuntu4.6
with Suhosin-Patch mod_python/3.3.1 Python/2.5.2 mod_ssl/2.2.9
OpenSSL/0.9.8g mod_perl/2.0.4 Perl/v5.10.0
13: In file(file, "r", encoding = encoding) : <- Accept-Ranges: bytes
14: In file(file, "r", encoding = encoding) :
<- Last-Modified: Mon, 20 Jun 2011 17:03:50 GMT
15: In file(file, "r", encoding = encoding) : Code 200, content-type
'text/plain'
############
- Setting options(download.file.method='wget') before sourcing does
not change the behaviour.
- However, I can source any local URL if http_proxy='', without
changing download.file.method. But then download.file does not work
for internet URL any more since the proxy settings are wrong. I could
set http_proxy='', then source, then restore the proxy settings and
set options(download.file.method='wget'). But this is just a work
around and I would like to understand what is going on.
Session Info:
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_ZA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_ZA.UTF-8 LC_COLLATE=en_ZA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_ZA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_ZA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_0.4
loaded via a namespace (and not attached):
[1] RCurl_1.6-10 tools_2.13.2
--
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
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