[BioC] [Fwd: Re: RBGL1.8 on 64bit Linux?]

[Celine Carret]

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/