[BioC] RBGL installation issues

Robert Gentleman rgentlem at fhcrc.org
Tue Oct 7 15:11:54 CEST 2008 

Hi Iain,
   The next step is to do what Li Long suggested and take a look at the 
compiler being used.  For our build machines we provide some explicit 
details (version numbers),

http://www.bioconductor.org/checkResults/2.2/bioc-LATEST/lamb1-NodeInfo.html

  if yours are different that would be the next thing to try and fix

  best wishes
    Robert


Iain Gallagher wrote:
> 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 at fhcrc.org>/* wrote:
> 
>     From: Robert Gentleman <rgentlem at fhcrc.org>
>     Subject: Re: [BioC] RBGL installation issues
>     To: iaingallagher at btopenworld.com
>     Cc: bioconductor at 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: ‘::system’ 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] stats     graphics  grDevices utils     datasets 
>     methods   base     
>     > 
>     > 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 at fhcrc.org
> 

-- 
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 at fhcrc.org

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