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

Li.Long at isb-sib.ch Li.Long at isb-sib.ch
Wed Jun 14 11:56:36 CEST 2006

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/usr/local/include  -IboostIncl  -fpic  -g -O2 -M interfaces.cpp  >

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.



> 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)
>> /usr/local/lsf/6.1/linux2.4-glibc2.3-ia64/lib:/usr/X11R6/lib:/usr/
>> X11R6/lib/modules
>> INCLUDE_PATH not set.

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