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
>
>
>
>
> ###
>
> UNIVERSITY OF CAPE TOWN
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--
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 272866 (PA)
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