[Rd] Problem with dyn.load'ed code

[Simon Urbanek]

Matt,

On Dec 30, 2007, at 5:25 PM, Matt Calder wrote:

> 	I am still having trouble dyn.load'ing some code into R. I have  
> isolated the problem, I wonder if someone could explain what I am  
> seeing.
> 	I think the problem is that a symbol defined in my compiled code  
> clashes with one already defined in R.

The result of redefining a symbol is very much system-dependent. For  
example on Mac OS X it has no adverse effects (i.e your symbols are  
always private unless linked against), because it uses a two-level  
namespace, but on Linux (and most other unices) it does as the  
namespace of an executable is shared among all modules (dynamic and  
static).


> The result is that the function in my code is not called. Here is an  
> example
>
> // lnktst.cc
> extern "C"
> {
>  void func(double *out1, double *out2);
>  void dnrm2_(double *out);
>  void dnrm3_(double *out);
> }
>
> void func(double *out1, double *out2)
> {
>  dnrm2_(out1);
>  dnrm3_(out2);
> }
>
> void dnrm2_(double *out)
> {
>  *out = 1234.5;
> }
>
> void dnrm3_(double *out)
> {
>  *out = 6789.0;
> }
> // End of lnktst.cc
>
> When I compile:
>
> g++ -shared -static -o lnktst.so lnktst.cc
>
> and then in R I call "func"
>
>> dyn.load("lnktst.so")
>> .C('func', double(1), double(1))
> [[1]]
> [1] 0
>
> [[2]]
> [1] 6789
>
> So, as you can see, the function "dnrm2_" is not called whereas  
> "dnrm3_" is, even though both functions are identical in form. Now,  
> I believe dnrm2_ is a BLAS function, and so it is likely R already  
> has a copy floating around.

Yes, indeed (it's a BLAS level 1 Fortran function, and usually to be  
found in libRblas.so or the external BLAS implementation).


> However, it surprises me that the "-static" option does
> not force the call in my code to "dnrm2_" to be linked to the function
> defined in my code.

You are confusing the purpose of -static: it only ensures that static  
libraries are used at link time where possible, it doesn't affect your  
code in any way. What you really want is to use
static void dnrm2_(double *out);
in your code instead.

In general, it is a bad idea to use external symbols that clash with  
other libraries (in particular widespread ones such as BLAS),  
especially if your function doesn't perform the same operation. It is  
a good idea to declare all functions that you use internally (i.e.  
that should not be visible to R) as static. However, all this is true  
for C programming in general, not just in conjunction with R.

Cheers,
Simon


> 	I have been writing C code for Splus for quite a while and don't  
> recall
> ever running across this issue. However, I am new to R, so I wonder,  
> am
> I missing something obvious?
> 	I am running this on Ubuntu Linux, the output of uname -a is:
>
> Linux calder-linux 2.6.22-14-generic #1 SMP Sun Oct 14 23:05:12 GMT  
> 2007 i686 GNU/Linux
>
> Thanks for any help,
>
> 	Matt
>
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