Hello all, When trying to install GOstats (via biocLite), this fails because of the RBGL library: > biocLite("GOstats") Using R version 2.10.1, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "GOstats" Please wait... also installing the dependencies 'GSEABase', 'Category', 'RBGL' trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/ GSEABase_1.8.0.tar.gz' Content type 'application/x-gzip' length 172840 bytes (168 Kb) opened URL ================================================== downloaded 168 Kb trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/ Category_2.12.0.tar.gz' Content type 'application/x-gzip' length 472185 bytes (461 Kb) opened URL ================================================== downloaded 461 Kb trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/ RBGL_1.22.0.tar.gz' Content type 'application/x-gzip' length 1895494 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/ GOstats_2.12.0.tar.gz' Content type 'application/x-gzip' length 2510297 bytes (2.4 Mb) opened URL ================================================== downloaded 2.4 Mb * installing *source* package 'GSEABase' ... ** R ** inst ** preparing package for lazy loading Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: AnnotationDbi ** help *** installing help indices ** building package indices ... * DONE (GSEABase) * installing *source* package 'RBGL' ... untarring boost include tree... ** libs /usr/bin/g++ -I/geninf/prog64/R/R-2.10.1/lib64/R/include -I/geninf/prog64/R/curl-7.19.7/src -IboostIncl -fpic -g -O2 -c bbc.cpp -o bbc.o boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of ` enumeral_type' in template type unification boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of ` enumeral_type' in template type unification make: *** [bbc.o] Error 1 ERROR: compilation failed for package 'RBGL' * removing '/mnt/geninf12/prog64/R/R-2.10.1/lib64/R/library/RBGL' > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.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_2.10.1 gcc version: gcc (GCC) 3.3.3 (SuSE Linux) Copyright (C) 2003 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. It could be that the compiler is outdated, but I only have a problem with RBGL. For the moment, I fixed it by installing RBGL version 1.20 (from the previous Bioconductor release) and this compiles and installs fine. Loading GOstats works, but I am not sure whether I might run into problems later on. Just to let you know. Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot at wur.nl <mailto:philip.degroot at="" wur.nl=""> Internet: http://www.nutrigenomicsconsortium.nl <http: www.nutrigenomicsconsortium.nl=""/> http://humannutrition.wur.nl <http: humannutrition.wur.nl=""/> https://madmax.bioinformatics.nl <https: madmax.bioinformatics.nl=""/>

I just had an absolutely clean compile/install with g++ 4.1.2 on x86_64 with R 2.10.1 We can see from http://bioconductor.org/checkResults/2.5/bioc- LATEST/wilson2-NodeInfo.html and related pages that the build machines are using g++ 4.0.1 or greater. It is probably time to upgrade your compiler if you want to build from source. On Tue, Jan 5, 2010 at 4:24 AM, Groot, Philip de <philip.degroot at="" wur.nl=""> wrote: > Hello all, > > When trying to install GOstats (via biocLite), this fails because of the RBGL library: >> biocLite("GOstats") > Using R version 2.10.1, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "GOstats" > Please wait... > also installing the dependencies 'GSEABase', 'Category', 'RBGL' > trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contri b/GSEABase_1.8.0.tar.gz' > Content type 'application/x-gzip' length 172840 bytes (168 Kb) > opened URL > ================================================== > downloaded 168 Kb > trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contri b/Category_2.12.0.tar.gz' > Content type 'application/x-gzip' length 472185 bytes (461 Kb) > opened URL > ================================================== > downloaded 461 Kb > trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contri b/RBGL_1.22.0.tar.gz' > Content type 'application/x-gzip' length 1895494 bytes (1.8 Mb) > opened URL > ================================================== > downloaded 1.8 Mb > trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contri b/GOstats_2.12.0.tar.gz' > Content type 'application/x-gzip' length 2510297 bytes (2.4 Mb) > opened URL > ================================================== > downloaded 2.4 Mb > * installing *source* package 'GSEABase' ... > ** R > ** inst > ** preparing package for lazy loading > Welcome to Bioconductor > ?Vignettes contain introductory material. To view, type > ?'openVignette()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation(pkgname)'. > Loading required package: AnnotationDbi > ** help > *** installing help indices > ** building package indices ... > * DONE (GSEABase) > * installing *source* package 'RBGL' ... > untarring boost include tree... > ** libs > /usr/bin/g++ -I/geninf/prog64/R/R-2.10.1/lib64/R/include ?-I/geninf/prog64/R/curl-7.19.7/src ? -IboostIncl ?-fpic ?-g -O2 -c bbc.cpp -o bbc.o > boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of ` > ? enumeral_type' in template type unification > boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of ` > ? enumeral_type' in template type unification > make: *** [bbc.o] Error 1 > ERROR: compilation failed for package 'RBGL' > * removing '/mnt/geninf12/prog64/R/R-2.10.1/lib64/R/library/RBGL' > > > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-unknown-linux-gnu > > locale: > ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.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_2.10.1 > > > gcc version: > > gcc (GCC) 3.3.3 (SuSE Linux) > Copyright (C) 2003 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. ?There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > It could be that the compiler is outdated, but I only have a problem with RBGL. For the moment, I fixed it by installing RBGL version 1.20 (from the previous Bioconductor release) and this compiles and installs fine. Loading GOstats works, but I am not sure whether I might run into problems later on. > > Just to let you know. > > Regards, > > Dr. Philip de Groot Ph.D. > Bioinformatics Researcher > > Wageningen University / TIFN > Nutrigenomics Consortium > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > PO Box 8129, 6700 EV Wageningen > Visiting Address: Erfelijkheidsleer: De Valk, Building 304 > Dreijenweg 2, 6703 HA ?Wageningen > Room: 0052a > T: +31-317-485786 > F: +31-317-483342 > E-mail: ? Philip.deGroot at wur.nl <mailto:philip.degroot at="" wur.nl=""> > Internet: http://www.nutrigenomicsconsortium.nl <http: www.nutrigenomicsconsortium.nl=""/> > ? ? ? ? ? ? http://humannutrition.wur.nl <http: humannutrition.wur.nl=""/> > ? ? ? ? ? ? https://madmax.bioinformatics.nl <https: madmax.bioinformatics.nl=""/> > > > > > _______________________________________________ > 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 >

Hi there, On 1/5/10 1:24 AM, Groot, Philip de wrote: > gcc version: > > gcc (GCC) 3.3.3 (SuSE Linux) As Vince and Li have suggested, upgrading to a more recent gcc is the thing to do. > It could be that the compiler is outdated, but I only have a problem > with RBGL. For the moment, I fixed it by installing RBGL version 1.20 > (from the previous Bioconductor release) and this compiles and > installs fine. Loading GOstats works, but I am not sure whether I > might run into problems later on. In general, mixing versions is not a good idea and is not supported. However, you might be ok for GOstats use since GOstats and Category use only a couple of RBGL functions that have been fairly stable for some time. + seth -- Seth Falcon Program in Computational Biology | Fred Hutchinson Cancer Research Center

the issue is mostly related to gcc. Like you said, your gcc is 3.3, pretty old. There were fixes put in to address gcc-related issues. The reason that the problem (only) shows up in RBGL is because RBGL uses boost-library, which depends on templates in C++ heavily. Li > Hello all, > > When trying to install GOstats (via biocLite), this fails because of the > RBGL library: >> biocLite("GOstats") > Using R version 2.10.1, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "GOstats" > Please wait... > also installing the dependencies 'GSEABase', 'Category', 'RBGL' > trying URL > 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GSEABase_ 1.8.0.tar.gz' > Content type 'application/x-gzip' length 172840 bytes (168 Kb) > opened URL > ================================================== > downloaded 168 Kb > trying URL > 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/Category_ 2.12.0.tar.gz' > Content type 'application/x-gzip' length 472185 bytes (461 Kb) > opened URL > ================================================== > downloaded 461 Kb > trying URL > 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/RBGL_1.22 .0.tar.gz' > Content type 'application/x-gzip' length 1895494 bytes (1.8 Mb) > opened URL > ================================================== > downloaded 1.8 Mb > trying URL > 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GOstats_2 .12.0.tar.gz' > Content type 'application/x-gzip' length 2510297 bytes (2.4 Mb) > opened URL > ================================================== > downloaded 2.4 Mb > * installing *source* package 'GSEABase' ... > ** R > ** inst > ** preparing package for lazy loading > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > Loading required package: AnnotationDbi > ** help > *** installing help indices > ** building package indices ... > * DONE (GSEABase) > * installing *source* package 'RBGL' ... > untarring boost include tree... > ** libs > /usr/bin/g++ -I/geninf/prog64/R/R-2.10.1/lib64/R/include > -I/geninf/prog64/R/curl-7.19.7/src -IboostIncl -fpic -g -O2 -c bbc.cpp > -o bbc.o > boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of ` > enumeral_type' in template type unification > boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of ` > enumeral_type' in template type unification > make: *** [bbc.o] Error 1 > ERROR: compilation failed for package 'RBGL' > * removing '/mnt/geninf12/prog64/R/R-2.10.1/lib64/R/library/RBGL' > > > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.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_2.10.1 > > > gcc version: > > gcc (GCC) 3.3.3 (SuSE Linux) > Copyright (C) 2003 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR > PURPOSE. > > It could be that the compiler is outdated, but I only have a problem with > RBGL. For the moment, I fixed it by installing RBGL version 1.20 (from the > previous Bioconductor release) and this compiles and installs fine. > Loading GOstats works, but I am not sure whether I might run into problems > later on. > > Just to let you know. > > Regards, > > Dr. Philip de Groot Ph.D. > Bioinformatics Researcher > > Wageningen University / TIFN > Nutrigenomics Consortium > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > PO Box 8129, 6700 EV Wageningen > Visiting Address: Erfelijkheidsleer: De Valk, Building 304 > Dreijenweg 2, 6703 HA Wageningen > Room: 0052a > T: +31-317-485786 > F: +31-317-483342 > E-mail: Philip.deGroot at wur.nl <mailto:philip.degroot at="" wur.nl=""> > Internet: http://www.nutrigenomicsconsortium.nl > <http: www.nutrigenomicsconsortium.nl=""/> > http://humannutrition.wur.nl <http: humannutrition.wur.nl=""/> > https://madmax.bioinformatics.nl > <https: madmax.bioinformatics.nl=""/> > > > > >