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 wrote: From: Robert Gentleman 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: ‘::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]] > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 [[alternative HTML version deleted]]