ok now i tested some other things. on a system (FC4) with the gcc 4.0 there
is no problem installing the package. could it be that it does not work with
gcc4.1? (although it compiles the source files neatly, but after the
compilation it gets that error).
i edited also the Makeconf file located in /usr/lib64/R/etc and set the the
CXXFLAGS to CXXFLAGS = -O2 -g -m64. nothing worked (i only got less warnings
during the compilation).
actually i run out of ideas what i could try next...

jo


On 5/11/06, Li.Long@isb-sib.ch <Li.Long@isb-sib.ch> wrote:
>
>
> That's right version.  boost lib is packaged in RBGL.  That's not what I
> would worry about.
>
> Li
>
> > which version of the boost library do i need? i have boost 1.33.1
> >
> > jo
> >
> > On 5/11/06, Li.Long@isb-sib.ch <Li.Long@isb-sib.ch> wrote:
> >>
> >>
> >> 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@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@isb-sib.ch <Li.Long@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@tcri.at
> >> >> >           johannes.rainer@tugraz.at
> >> >> > _______________________________________________
> >> >> > Bioconductor mailing list
> >> >> > Bioconductor@stat.math.ethz.ch
> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >> > Search the archives:
> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >>
> >> >>
> >> >
> >> >
> >> > --
> >> > Johannes Rainer, Msc
> >> > Tyrolean Cancer Research Institute
> >> > Innrain 66, 6020 Innsbruck, Austria
> >> > Tel.: +43 512 570485 15
> >> > Email: johannes.rainer@tcri.at
> >> >           johannes.rainer@tugraz.at
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@stat.math.ethz.ch
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >
> >
> > --
> > Johannes Rainer, Msc
> > Tyrolean Cancer Research Institute
> > Innrain 66, 6020 Innsbruck, Austria
> > Tel.: +43 512 570485 15
> > Email: johannes.rainer@tcri.at
> >           johannes.rainer@tugraz.at
> >
>
>


-- 
Johannes Rainer, Msc
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 15
Email: johannes.rainer@tcri.at
          johannes.rainer@tugraz.at

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