RBGL installation issues
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@iain-gallagher-2532
Last seen 6.5 years ago
United Kingdom
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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTI FICATION=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]]
RBGL GOstats RBGL GOstats • 862 views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 6.7 years ago
United States
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_IDEN TIFICATION=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 at 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 at fhcrc.org
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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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTI FICATION=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: ‘::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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTI FICATION=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]]
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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.t ar.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_IDEN TIFICATION=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]] > > > > > > > > -------------------------------------------------------------- ---------- > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at 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 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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@lilongisb-sibch-1725
Last seen 7.4 years ago
RBGL uses C++ templates extensively, previously we encountered various issues using different C++ compilers, even different versions of g++ compilers. Somehow the error msg in the mail is scrambled, I cannot tell what it complains about, but it looks like something related to C++. Probably you could look further into that. Li > 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_IDEN TIFICATION=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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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