[R] Dyn.load of sharing object with GSL library

[Prof Brian Ripley]

On Thu, 9 Sep 2004, Vicky Landsman wrote:

> Following the recommendation of Prof. Ripley, I have created the Makevars
> file with the line:
> PKG_LIBS="-L/usr/lib/libm -lm -L/usr/local/lib/libgsl -lgsl -L/usr/local/lib
> /libgslcblas -lgslcblas"
> in the working directory.

No, that's not what I recommended. -L/path/to/libgsl would probably be
-L/usr/local/lib if libgsl is in /usr/local/lib.  And why do you want -lm?

Please consult your unstated OS's documentation for ld.

> Now I have the code file Example3.c which computes the Bessel function value
> (the example is taken from the GSL reference book).
> I am running:
> R CMD SHLIB Example3.c

Pleae show us exactly what you get here.

> and all looks good.
> The dyn.load("Example3.so") fails with the following error message:
> 
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>         unable to load shared library
> "/fs/users1/guest/msvika/PhD/R_04/Example3.so":
>   ld.so.1: /usr/local/sbin/R-1.9/R-1.9.1/bin/R.bin: fatal: relocation error:
> file /fs/users1/guest/msvika/PhD/R_04/Example3.so: symbol gsl_sf_bessel_J0:
> referenced symbol not found

Try ldd /fs/users1/guest/msvika/PhD/R_04/Example3.so and get a local
expert to interpret it for you.

You will need anything you had in -L in PKG_LIBS in your library run path
as well.  You may need e.g.

export LD_LIBRARY_PATH=:${LD_LIBRARY_PATH}:/usr/local/lib

and please check with a local expert about this.

> What is wrong?
> Much thanks, Vicky.
> 
> ----- Original Message ----- 
> From: "Vicky Landsman" <msvika at mscc.huji.ac.il>
> To: "r-help" <r-help at stat.math.ethz.ch>
> Sent: Thursday, September 09, 2004 6:18 PM
> Subject: Re: [R] Adding GSL library path to SHLIB
> 
> 
> > Dear Prof. Ripley,
> > We read the archive thread
> > http://maths.newcastle.edu.au/~rking/R/help/02b/0547.html
> > Thank you for your help, we will try to create the Makevars file.
> > Vicky.
> >
> >
> >
> > ----- Original Message ----- 
> > From: "Prof Brian Ripley" <ripley at stats.ox.ac.uk>
> > To: "Vicky Landsman" <msvika at mscc.huji.ac.il>
> > Cc: "r-help" <r-help at stat.math.ethz.ch>; <leonid at cc.huji.ac.il>
> > Sent: Thursday, September 09, 2004 3:17 PM
> > Subject: Re: [R] Adding GSL library path to SHLIB
> >
> >
> > > On Thu, 9 Sep 2004, Vicky Landsman wrote:
> > >
> > > > Dear R-list people,
> > >
> > > > I asked a similar question a few hours before. I will try to be more
> > > > specific.  We like to add the GSL library to the file SHLIB in order
> to
> > > > make it possible to run the C code using GSL functions from R.  We
> read
> > >
> > > Read where?  It's incorrect information and only used for Fortran
> linking.
> > >
> > > > that the path to the libgsl.a should be added to the line
> shlib_libadd='
> > > > ' in the file SHLIB but it does not work on our system. Dyn.load fails
> > > > with error "referenced symbol <symbolname> not found". What is wrong?
> > > > We will much appreciate any help on this.
> > > >
> > > > We are using R-1.9.1 on Unix.
> > >
> > > You should have a file called Makevars in the directory from which
> > > you are doing the building, defining PKG_LIBS, maybe
> > >
> > > PKG_LIBS="-L/path/to/libgsl -lgsl"
> > >
> > > in the same way as you would for a package: see `Writing R Extensions'.
> > > I don't think that is documented anywere, though.
> > >
> > > -- 
> > > Brian D. Ripley,                  ripley at stats.ox.ac.uk
> > > Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> > > University of Oxford,             Tel:  +44 1865 272861 (self)
> > > 1 South Parks Road,                     +44 1865 272866 (PA)
> > > Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> > >
> > >
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
> >
> 
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> 

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595