[BioC] RBGL 1.8.1 installation error on linux

[Li.Long at isb-sib.ch]

Pretty much all the msgs are about templates, so I would look more into
what your g++/STL and the likes on your machine.

Li

> hi Li
>
> thanks for your quick reply,
> concerning the extra parameters, i have not defined anything, i just
> downloaded the RBGL_1.8.1.tar.gz and run R CMD INSTALL on it, i did not
> specify any extra parameter... don't know from where they are coming.
> actually the R i installed is a precompiled one, i got it from one of the
> fedora repositories, before i installed this one i compiled it myself, but
> was also not able to install RBGL.
>
> R CMD INSTALL --configure-args='-g -O2' RBGL_1.8.1.tar.gz
>
> also resulted in an error (see the attachment).
> the version of g++ (i suppose it is an x86_64 version, at least it
> supports
> m32 and m64...):
>
> [jo at bugblatterbeast ~]$ g++ --version
> g++ (GCC) 4.1.0 20060304 (Red Hat 4.1.0-3)
> Copyright (C) 2006 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.
>
> i will now try to install it on an other machine running FC5, perhaps
> there
> is something wrong with my system...
>
> thanks
> jo
>
>
> On 5/11/06, Li.Long at isb-sib.ch <Li.Long at isb-sib.ch> wrote:
>>
>>
>> Hi,
>>
>> I'll be really interested in finding out what's happening in your
>> settings.
>> Could you provide additional info
>> o. why/how did you decide to use the extra parameters when compiling?
>> (such as protect-stack, and the like)  If you just use "-g -O2", what do
>> you get?
>> o. what version of g++ do you have?  is it for 64bit?
>>
>> It's my package, I'll try to help you figure it out.
>>
>> Thanks
>>
>> Li
>>
>> > hi,
>> > i'm just moving from R 2.2 and BioC 1.7 to R 2.3 and BioC 1.8, but got
>> a
>> > problem when i tried to install the RBGL package. i included the whole
>> > output of the R CMD INSTALL call in the attachment, below is just the
>> > error
>> > message that causes the installation failure:
>> >
>> >
>> > boostIncl/boost/graph/depth_first_search.hpp:324: error: no matching
>> > function for call to 'vertices(const std::vector<std::vector<long
>> unsigned
>> > int, std::allocator<long unsigned int> >,
>> std::allocator<std::vector<long
>> > unsigned int, std::allocator<long unsigned int> > > >&)'
>> > make: *** [interfaces.o] Error 1
>> > chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file
>> or
>> > directory
>> > ERROR: compilation failed for package 'RBGL'
>> > ** Removing '/usr/lib64/R/library/RBGL'
>> >
>> > i don't know if that is a problem of my system (running fedora core 5
>> on
>> a
>> > amd64) or not. has anyone experienced the same problems, or has anyone
>> a
>> > solution to this problem?
>> >
>> > thanks in advance,
>> > jo
>> > --
>> > Johannes Rainer, Msc
>> > Tyrolean Cancer Research Institute
>> > Innrain 66, 6020 Innsbruck, Austria
>> > Tel.: +43 512 570485 15
>> > Email: johannes.rainer at tcri.at
>> >           johannes.rainer at tugraz.at
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>>
>
>
> --
> Johannes Rainer, Msc
> Tyrolean Cancer Research Institute
> Innrain 66, 6020 Innsbruck, Austria
> Tel.: +43 512 570485 15
> Email: johannes.rainer at tcri.at
>           johannes.rainer at tugraz.at
> _______________________________________________
> 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