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

Liaw, Andy andy_liaw at merck.com
Fri Sep 10 00:19:16 CEST 2004 

As Prof. Ripley said, twice already: seek local expert help.  If you don't
know who that is, start with the person that setup your user account on that
machine.  Such system-specific problem is much easier to resolve that way,
instead of having others on the list guessing.

Andy

> From: Vicky Landsman
> 
> Dear Prof. Ripley,
> The GSL reference book explains that lm should be added as 
> well (as far as I
> understand, and this is what I saw when I run the file in C 
> in a standard
> way). No matter, with lm and without, I get the same picture.
> Here is what I get after R CMD SHLIB Example3.c
> 
> make: Warning: File `Makevars' has modification time 3.4e+03 
> s in the future
> gcc -I/usr/local/sbin/R-1.9/R-1.9.1/include  
> -I/usr/local/include   -fPIC  -
> g -O2 -c Example3.c -o Example3.o
> gcc -G -L/usr/local/lib -o Example3.so Example3.o
> -L/usr/local/lib/ -lgsl  -L/usr/local/lib/ -lgslcblas"
> make: warning:  Clock skew detected.  Your build may be incomplete.
> 
> Running ldd line as you stated, I get the following:
>         libc.so.1 =>     /usr/lib/libc.so.1
>         libdl.so.1 =>    /usr/lib/libdl.so.1
>         /usr/platform/SUNW,Sun-Fire-280R/lib/libc_psr.so.1
> 
> Sorry for my ignorance in UNIX, where should I run the line
> export LD_LIBRARY_PATH=:${LD_LIBRARY_PATH}:/usr/local/lib ?
> 
> Vicky.
> 
> 
> > On Thu, 9 Sep 2004, Vicky Landsman wrote:
> >
> > > Following the recommendation of Prof. Ripley, I have created the
> Makevars
> > > file with the line:
> > >
> PKG_LIBS="-L/usr/lib/libm -lm -L/usr/local/lib/libgsl -lgsl 
> -L/usr/local/lib
> > > /libgslcblas -lgslcblas"
> > > in the working directory.
> >
> > No, that's not what I recommended. -L/path/to/libgsl would 
> probably be
> > -L/usr/local/lib if libgsl is in /usr/local/lib.  And why 
> do you want -lm?
> >
> > Please consult your unstated OS's documentation for ld.
> >
> > > Now I have the code file Example3.c which computes the 
> Bessel function
> value
> > > (the example is taken from the GSL reference book).
> > > I am running:
> > > R CMD SHLIB Example3.c
> >
> 
> 
> > > and all looks good.
> > > The dyn.load("Example3.so") fails with the following 
> error message:
> > >
> > > Error in dyn.load(x, as.logical(local), as.logical(now)) :
> > >         unable to load shared library
> > > "/fs/users1/guest/msvika/PhD/R_04/Example3.so":
> > >   ld.so.1: /usr/local/sbin/R-1.9/R-1.9.1/bin/R.bin: 
> fatal: relocation
> error:
> > > file /fs/users1/guest/msvika/PhD/R_04/Example3.so: symbol
> gsl_sf_bessel_J0:
> > > referenced symbol not found
> >
> > Try ldd /fs/users1/guest/msvika/PhD/R_04/Example3.so and get a local
> > expert to interpret it for you.
> >
> > You will need anything you had in -L in PKG_LIBS in your 
> library run path
> > as well.  You may need e.g.
> >
> > export LD_LIBRARY_PATH=:${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
> > > >
> > >
> > > ______________________________________________
> > > 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
> > >
> > >
> >
> > -- 
> > 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
> >
> >
> 
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