On Wed, 5 Oct 2011, Renaud Gaujoux wrote:
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?
No. They use url() connections. See ?file.
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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--
Brian D. Ripley, [email protected]
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 272866 (PA)
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
