Hi Robert & list

Sorry for the brevity of my previous message. I am indeed using biocLite. Below is the output from my attempted installation.

> source('http://bioconductor.org/biocLite.R')
> biocLite('RBGL')
Running biocinstall version 2.2.11 with R version 2.7.2 
Your version of R requires version 2.2 of BioConductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  argument 'lib' is missing: using '/home/iain/R/i486-pc-linux-gnu-library/2.7'
trying URL 'http://bioconductor.org/packages/2.2/bioc/src/contrib/RBGL_1.16.0.tar.gz'
Content type 'application/x-gzip' length 1327240 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/usr/share/R/include     -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
/usr/lib/gcc/i486-linux-gnu/4.1.2/../../../../include/c++/4.1.2/cstdlib:135: error: ‘::system’ has not been declared
make: *** [bbc.o] Error 1
chmod: cannot access `/home/iain/R/i486-pc-linux-gnu-library/2.7/RBGL/libs/*': No such file or directory
ERROR: compilation failed for package 'RBGL'
** Removing '/home/iain/R/i486-pc-linux-gnu-library/2.7/RBGL'

The downloaded packages are in
        /tmp/RtmpU6Vywx/downloaded_packages
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  installation of package 'RBGL' had non-zero exit status

> sessionInfo()
R version 2.7.2 (2008-08-25) 
i486-pc-linux-gnu 

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.7.2
> 

I'd be grateful for any advice.

Thanks

Iain


--- On Tue, 7/10/08, Robert Gentleman <rgentlem@fhcrc.org> wrote:
From: Robert Gentleman <rgentlem@fhcrc.org>
Subject: Re: [BioC] RBGL installation issues
To: iaingallagher@btopenworld.com
Cc: bioconductor@stat.math.ethz.ch
Date: Tuesday, 7 October, 2008, 1:49 AM

Hi Iain,
  Probably the reason for no response is that you have not given 
sufficient details for anyone to help.

   Did you use biocLite, and if so, could you show us a bit more than 
you are? And if you did not - would you please try that, as it is the 
recommended route.

  best wishes
    Robert


Iain Gallagher wrote:
> Hi 
> 
> I posted this a few hours ago on the R-help list but have had no replies.
I thought it might be better here. Apologies for cross posting.
> 
> I'm trying to install the RBGL package in order to install GOstats.
However I am getting
> the following error; can anybody shed some light on what I'm missing?
> 
>
/usr/lib/gcc/i486-linux-gnu/4.1.2/../../../../include/c++/4.1.2/cstdlib:135:
error: â€˜::systemâ€™ has not been declared
> 
> Thanks.
> 
> Iain
> 
>> sessionInfo()
> R version 2.7.2 (2008-08-25) 
> i486-pc-linux-gnu 
> 
> locale:
>
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] statsÂ Â Â Â  graphicsÂ  grDevices utilsÂ Â Â Â  datasetsÂ 
methodsÂ Â  baseÂ Â Â Â  
> 
> loaded via a namespace (and not attached):
> [1] tcltk_2.7.2 tools_2.7.2
> 	[[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem@fhcrc.org


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