Hi, here are the info: >> (1) what's g++ version? (you could find out by: g++ --version ) > > > g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-42) > >> (2) it seems you installed through some job queue, what do you get when >> you do it manually: .../R CMD INSTALL RBGL-1.8.1.tar.gz >> ? > > > The same thing happens if you try it that way. > >> (3) what are the include path and library path? >> (env variables like INCLUDE_PATH, LD_LIBRARY_PATH) > > > echo $LD_LIBRARY_PATH > /usr/local/lsf/6.1/linux2.4-glibc2.3-ia64/lib:/usr/X11R6/lib:/usr/ > X11R6/lib/modules > > INCLUDE_PATH not set. Thank you for helping, best wishes celine -- ---------------------------------------------------- Celine Carret PhD Pathogen Microarrays group The Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK. tel. +44 (0)1223 494 940 fax. +44 (0)1223 494 919 email: ckc at sanger.ac.uk http://www.sanger.ac.uk/PostGenomics/PathogenArrays/

Here's what I have on my machine: $ uname -a Linux devfrt01.vital-it.ch 2.6.9-22.0.1.EL_SFS2.1_0 #1 SMP Thu Feb 9 17:18:32 CET 2006 ia64 ia64 ia64 GNU/Linux $ g++ --version g++ (GCC) 3.4.3 20050227 (Red Hat 3.4.3-22.1) >From the error msgs you got, it seems like g++ has trouble handling the C++ templates, especially some involved stl. I would look first to make sure the default search paths for .h files are correct (for instance, they are 64-bit installations, compatible w/ g++, etc.) You can use '-M' option to find out exactly where g++ gets .h (command line is something like: > g++ -I/home/vital-it/lilong/R-install/R-2.3.0-gcc//lib/R/include -I/home/vital-it/lilong/R-install/R-2.3.0-gcc//lib/R/include -I/usr/local/include -IboostIncl -fpic -g -O2 -M interfaces.cpp > interfaces.dep ) I attach my output for your reference. It's possible that the Boost templates (which is used by RBGL) cause some hiccups for the older version of g++, but I would make sure the include paths are correct first. Best, Li > Hi, here are the info: > > >>> (1) what's g++ version? (you could find out by: g++ --version ) >> >> >> g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-42) >> >>> (2) it seems you installed through some job queue, what do you get >>> when >>> you do it manually: .../R CMD INSTALL RBGL-1.8.1.tar.gz >>> ? >> >> >> The same thing happens if you try it that way. >> >>> (3) what are the include path and library path? >>> (env variables like INCLUDE_PATH, LD_LIBRARY_PATH) >> >> >> echo $LD_LIBRARY_PATH >> /usr/local/lsf/6.1/linux2.4-glibc2.3-ia64/lib:/usr/X11R6/lib:/usr/ >> X11R6/lib/modules >> >> INCLUDE_PATH not set. >

Hi, problem solved using a newer version of g++ Thanks so much for your help and advices Celine Li.Long at isb-sib.ch wrote: >Here's what I have on my machine: >$ uname -a >Linux devfrt01.vital-it.ch 2.6.9-22.0.1.EL_SFS2.1_0 #1 SMP Thu Feb 9 >17:18:32 CET 2006 ia64 ia64 ia64 GNU/Linux >$ g++ --version >g++ (GCC) 3.4.3 20050227 (Red Hat 3.4.3-22.1) > >>From the error msgs you got, it seems like g++ has trouble >handling the C++ templates, especially some involved stl. I would look >first to make sure the default search paths for .h files are correct (for >instance, they are 64-bit installations, compatible w/ g++, etc.) > >You can use '-M' option to find out exactly where g++ gets .h > >(command line is something like: > > > >>g++ -I/home/vital-it/lilong/R-install/R-2.3.0-gcc//lib/R/include >> >> >-I/home/vital-it/lilong/R-install/R-2.3.0-gcc//lib/R/include >-I/usr/local/include -IboostIncl -fpic -g -O2 -M interfaces.cpp > >interfaces.dep >) > >I attach my output for your reference. > >It's possible that the Boost templates (which is used by RBGL) cause some >hiccups for the older version of g++, but I would make sure the include >paths are correct first. > >Best, > >Li > > > > >>Hi, here are the info: >> >> >> >> >>>>(1) what's g++ version? (you could find out by: g++ --version ) >>>> >>>> >>>g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-42) >>> >>> >>> >>>>(2) it seems you installed through some job queue, what do you get >>>>when >>>> you do it manually: .../R CMD INSTALL RBGL-1.8.1.tar.gz >>>> ? >>>> >>>> >>>The same thing happens if you try it that way. >>> >>> >>> >>>>(3) what are the include path and library path? >>>> (env variables like INCLUDE_PATH, LD_LIBRARY_PATH) >>>> >>>> >>>echo $LD_LIBRARY_PATH >>>/usr/local/lsf/6.1/linux2.4-glibc2.3-ia64/lib:/usr/X11R6/lib:/usr/ >>>X11R6/lib/modules >>> >>>INCLUDE_PATH not set. >>> >>> -- ---------------------------------------------------- Celine Carret PhD Pathogen Microarrays group The Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK. tel. +44 (0)1223 494 940 fax. +44 (0)1223 494 919 email: ckc at sanger.ac.uk http://www.sanger.ac.uk/PostGenomics/PathogenArrays/