R devel - Dec 2006 - Undefined symbol when trying to dyn.load a shared object

I hope that someone reading this list can offer some suggestions on how I can
incorporate external C libraries in C functions that I want to call from R.  I
have gone through all of the documentation, help files and mailing list archives
and have not been able to find a satisfactory solution.

I have constructed a simple example of the problem, since my "real"
program is much more complex and would bog down discussion.  Suppose I want to
compute the value of a Gaussian hypergeometric function using the function in
the GSL library.  My C code is:

	#include </usr/include/gsl/gsl_sf_hyperg.h>

	void gslTestHG (double *a, double *b, double *c, double *x, double *val ) {
		*val = gsl_sf_hyperg_2F1(*a,*b,*c,*x); 
	}

I compile this code (successfully) using R CMD SHLIB gslTest.c and get the
following result

	-bash-3.00$ R CMD SHLIB RgslTest.c
	gcc -I/usr/lib64/R/include -I/usr/lib64/R/include  -I/usr/local/include   -fpic
-O2 -g -c RgslTest.c -o RgslTest.o
	gcc -shared -L/usr/local/lib64 -o RgslTest.so RgslTest.o   -L/usr/lib64/R/lib
-lR

Next, I try to load the shared object into R using
dyn.load("RgslTest.so") and get the following error in R:

	> dyn.load("RgslTest.so")
	Error in dyn.load(x, as.logical(local), as.logical(now)) : 
        unable to load shared library
'/mnt/san2/braunm/winshare/braunm/Cpractice/RgslTest.so':
 	 /mnt/san2/braunm/winshare/braunm/Cpractice/RgslTest.so: undefined symbol:
gsl_sf_hyperg_2F1

I am certain that the file path in the #include statement is correct.  It looks
like R can't find the gsl function in the C program, even though the
compiler did.

I would greatly appreciate any help you can provide.  Many thanks in advance.

Best wishes,

Michael

------------------------------------------
Michael Braun
Assistant Professor of Marketing
MIT Sloan School of Management
38 Memorial Drive, E56-329
Cambridge, MA 02139
braunm at mit.edu
(617) 253-3436

On 12/12/2006 4:03 PM, Michael Braun wrote:
> I hope that someone reading this list can offer some suggestions on how I
can incorporate external C libraries in C functions that I want to call from R. 
I have gone through all of the documentation, help files and mailing list
archives and have not been able to find a satisfactory solution.
> 
> I have constructed a simple example of the problem, since my
"real" program is much more complex and would bog down discussion. 
Suppose I want to compute the value of a Gaussian hypergeometric function using
the function in the GSL library.  My C code is:
> 
> 	#include </usr/include/gsl/gsl_sf_hyperg.h>
> 
> 	void gslTestHG (double *a, double *b, double *c, double *x, double *val )
{
> 		*val = gsl_sf_hyperg_2F1(*a,*b,*c,*x); 
> 	}
> 
> I compile this code (successfully) using R CMD SHLIB gslTest.c and get the
following result
> 
> 	-bash-3.00$ R CMD SHLIB RgslTest.c
> 	gcc -I/usr/lib64/R/include -I/usr/lib64/R/include  -I/usr/local/include  
-fpic  -O2 -g -c RgslTest.c -o RgslTest.o
> 	gcc -shared -L/usr/local/lib64 -o RgslTest.so RgslTest.o  
-L/usr/lib64/R/lib -lR
> 
> Next, I try to load the shared object into R using
dyn.load("RgslTest.so") and get the following error in R:
> 
> 	> dyn.load("RgslTest.so")
> 	Error in dyn.load(x, as.logical(local), as.logical(now)) : 
>         unable to load shared library
'/mnt/san2/braunm/winshare/braunm/Cpractice/RgslTest.so':
>  	 /mnt/san2/braunm/winshare/braunm/Cpractice/RgslTest.so: undefined
symbol: gsl_sf_hyperg_2F1
> 
> I am certain that the file path in the #include statement is correct.  It
looks like R can't find the gsl function in the C program, even though the
compiler did.
The #include statement just includes the headers, so that calls to the 
functions are constructed properly by the compiler.  It doesn't pull in 
the library.  That's done at link time.

You need at least a Makevars file which defines PKG_LIBS to tell the 
linker where to find the external library.  That macro should contain 
linker options -l and -L that point out the need for gsl, and where to 
find it. If you want to distribute this package to others, you'll 
probably need a configure script too, in order to construct those values.

Duncan Murdoch
> I would greatly appreciate any help you can provide.  Many thanks in
advance.
> 
> Best wishes,
> 
> Michael
> 
> ------------------------------------------
> Michael Braun
> Assistant Professor of Marketing
> MIT Sloan School of Management
> 38 Memorial Drive, E56-329
> Cambridge, MA 02139
> braunm at mit.edu
> (617) 253-3436
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel