From duncan at wald.ucdavis.edu  Tue Dec 12 22:51:13 2006
From: duncan at wald.ucdavis.edu (Duncan Temple Lang)
Date: Tue, 12 Dec 2006 13:51:13 -0800
Subject: [Rd] include libraries for C code called from R
In-Reply-To: <20061212155050.umhvo2m41gggcgo4@webmail.mit.edu>
References: <20061212155050.umhvo2m41gggcgo4@webmail.mit.edu>
Message-ID: <457F2451.4090508@wald.ucdavis.edu>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Michael.

 [There's no need to send two pieces of mail that are essentially the
same issue.]

 The problem is that when you are creating the shared object
gslTestHG.so, you are not telling the linker to combine information
from the libgsl.so or libgsl.a file.  The linker needs that to resolve
the symbols that were referenced in your RgslTest.c code.
Without this, the linker then assumes that these missing symbols will be
found when the .so is loaded, i.e. in the host application, namely R.
Compiling, linking and loading are three different steps in this
process. It helps to diagnose problems if one has an understanding
of what each does (approximately). Otherwise, the error messages
can be cryptic.

 One way to fix the problem is to create a file names Makevars in the
same directory as  RgslTest.c and add to it

  PKG_CPPFLAGS=-I/usr/include
  PKG_LIBS=-L/usr/lib -lgsl

The second of these lines tells the linker to include the symbols in
libgsl.so or libgsl.a  and that it should look for this in /usr/lib/
(You may have to change this, but it looks like that is where you have
gsl installed juding from the #include).
The -I/usr/include and -L/usr/lib  are likely to be unnecessary
but illustrate the idea that one adds library-specific include
and library directories to allow the compiler and linker
respectively find files it needs for that library's code.

And change your RgslTest.c code to have
   #include <gsl/gsl_sf_hyperg.h>
not the full path name to the .h file.


D.


braunm at MIT.EDU wrote:
> I hope that someone on this list can help me with this issue.  I have searched
> through all of the documentation and mail archives for a solution, but have
> been unable to find an answer that addresses my particular problem directly.
> 
> Suppose I am writing some C code that I want to access from R through the .C
> function.  As part of the C function, I want to include an external C library,
> such as the GNU gsl library.  So, if I want to compute the value of a Gaussian
> hypergeometric function, my C code would be:
> 
> #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 then compile this file (successfully, on a Linux machine with gcc installed)
> using R CMD SHLIB gslTest.c.  The message from the complier is:
> 
> 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
> 
> 
> When I go into R and enter the command dyn.load("gslTestHG.so"), I get the
> following error:
> 
> 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
> 
> So, it looks like R is not recognizing the function call within my own C
> function, even though the library was included.
> 
> Note that this is a simpler example of my "real" problem, the details of which
> would bog down discussion.  I know that I could use the gsl package, or include
> the Rmath.h library, to perform this particular task.  My primary need is the
> ability to call C libraries from wtihin my own C code.
> 
> But I would greatly appreciate any advice or suggestions on how to solve this
> problem.  I am a novice C programmer and Linux user, but it seems like this
> should be a simple fix.
> 
> Many thanks in advance,
> 
> Michael Braun
> MIT Sloan School of Management
> braunm at mit.edu
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

- --
Duncan Temple Lang                    duncan at wald.ucdavis.edu
Department of Statistics              work:  (530) 752-4782
4210 Mathematical Sciences Building   fax:   (530) 752-7099
One Shields Ave.
University of California at Davis
Davis,
CA 95616,
USA
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.3 (Darwin)

iD8DBQFFfyRR9p/Jzwa2QP4RAvBBAJ9nNDK4kWNt2fpCv9pw/r3XPpq6VQCfU9CL
ziDU+0OcPTEJgVV1RR/OFvA=
=oMxN
-----END PGP SIGNATURE-----



[Rd] include libraries for C code called from R
Duncan Temple Lang