Dyn.load of sharing object with GSL library

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