[R] Behaviour of 'source' with URLs and proxy

[Renaud Gaujoux]

Hi,

I am having troubles sourcing a file from our local network from R.
It looks like this file are not properly accessed by 'source', even they 
can be downloaded with download.file. (See below my settings and some 
tests I did). I ended up with a work around, but I would like to 
understand what is going on.

Doesn't source/readLines uses the same mechanism as download.file to 
access URLs?

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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UNIVERSITY OF CAPE TOWN 

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