Question: RBGL installation issues
0
gravatar for Iain Gallagher
10.6 years ago by
United Kingdom
Iain Gallagher930 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]]
rbgl gostats • 549 views
ADD COMMENTlink modified 10.6 years ago by Li.Long@isb-sib.ch510 • written 10.6 years ago by Iain Gallagher930
Answer: RBGL installation issues
0
gravatar for rgentleman
10.6 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
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
ADD COMMENTlink written 10.6 years ago by rgentleman5.5k
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]]
ADD REPLYlink written 10.6 years ago by Iain Gallagher930
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
ADD REPLYlink written 10.6 years ago by rgentleman5.5k
Answer: RBGL installation issues
0
gravatar for Li.Long@isb-sib.ch
10.6 years ago by
Li.Long@isb-sib.ch510 wrote:
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
ADD COMMENTlink written 10.6 years ago by Li.Long@isb-sib.ch510
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