[Rd] Problem with dyn.load'ed code
simon.urbanek at r-project.org
Mon Dec 31 02:21:41 CET 2007
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
> 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
> The result is that the function in my code is not called. Here is an
> // lnktst.cc
> extern "C"
> void func(double *out1, double *out2);
> void dnrm2_(double *out);
> void dnrm3_(double *out);
> void func(double *out1, double *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"
>> .C('func', double(1), double(1))
>  0
>  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.
> I have been writing C code for Splus for quite a while and don't
> ever running across this issue. However, I am new to R, so I wonder,
> 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,
> R-devel at r-project.org mailing list
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