protect

On Tue, 23 May 2006, Kasper Daniel Hansen wrote:

Thank you very much. I think I do have a clearer understanding,  
but I have a few questions

On May 23, 2006, at 12:55 AM, Prof Brian Ripley wrote:

On Tue, 23 May 2006, Prof Brian Ripley wrote:

On Mon, 22 May 2006, Kasper Daniel Hansen wrote:

I have a few simple questions about the usage of PROTECT, more
specifically how careful one needs to be. Simple yes/no answers  
are
fine.

(Except that in the last case they would be misleading.)

Most of the uses I have seen do protection when memory is  
allocated.
But what if one just want to assign a value of another function  
to a
variable. Say eg. that foo is a function that returns a SEXP.  
Would
the following code be fine?
SEXP bar;
PROTECT(bar = foo());

It would be fine but may be unnecessary.  It is objects and not  
pointers
which are protected, and a SEXP is a pointer.  So protection is  
needed
only if foo() might return a pointer to an unprotected object.

Ok. I have been coding foo in such a way that I unprotect  
everything in foo just before returning its value. I thought that  
was the "standard" way to do - is that true? Or should I leave the  
return value protected and then unprotect in the function calling  
foo?

That is indeed standard.  The issue is rather that if say foo()  
extracts an element of a list which has an R-level name, you know  
that it is already protected.

Also, basically in one use case I would want to return the  
value of
foo immediately, but I need to do some cleaning up first, which  
has
nothing to do with R (more specifically, I need to close various
files). Would I then need to protect foo, as in
SEXP bar;
bar = foo();
"close the file in C++"
return bar;

Fine, as PROTECT protects against R garbage collection, and that  
can only
happen if R's functions are called.

Finally, I am also assigning values to the components of a list.
Would the following be ok
SEXP bar;
PROTECT(bar = NEW_LIST(2));
SET_VECTOR_ELT(bar, 0, ScalarInteger(test());
(where test is a function returning int, which again has  
nothing to
do with R - it interfaces to an extern library), or do I need to
hedge myself against garbage collection in the SET_VECTOR_ELT  
macro?

You do need to protect but elsewhere in this call, as  
ScalarInteger does
memory allocation:
INLINE_FUN SEXP ScalarInteger(int x)
{
   SEXP ans = allocVector(INTSXP, 1);
   INTEGER(ans)[0] = x;
   return ans;
}
but SET_VECTOR_ELT does not.  So you need
SEXP bar, tmp;
PROTECT(bar = NEW_LIST(2));
PROTECT(tmp = test());
SET_VECTOR_ELT(bar, 0, ScalarInteger(tmp));
UNPROTECT(1);

Or a design that uses fewer PROTECTs
SEXP bar, tmp;
PROTECT(bar = allocVector(VECSXP, 2));
tmp = allocVector(INTSXP, 1);
SET_VECTOR_ELT(bar, 0, tmp);
INTEGER(tmp)[0] = test();

I thought I got this. Then I grepped the sources and found this in  
main/platform.c:

  PROTECT(ans = allocVector(VECSXP, 18));
  PROTECT(nms = allocVector(STRSXP, 18));
  SET_STRING_ELT(nms, 0, mkChar("double.eps"));
  SET_VECTOR_ELT(ans, 0, ScalarReal(R_AccuracyInfo.eps));

This looks very similar to what I did above. In my case "test" was  
a C++ function coming from outside of R returning an int. That was  
perhaps not clear from my original mail, since the first suggested  
correction had
PROTECT(tmp = test());
indicating that the return value for test is a SEXP. Or am I  
completely of?

If test() iself does not use anthing from R (that it is C++ is  
enough of the story), then you do not need to protect it.  Or as in  
the platform.c example, if it is a constant.  Sorry, the caveats  
were not clear to me, and I tend not to rely on them as people do  
sometimes change functions.

I have tried running my original suggestion with gctorture(TRUE)  
and it did not give any errors. But neither did the second  
suggested correction.

-- 
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