2008/7/20 Duncan Murdoch <murdoch at stats.uwo.ca>:
On 20/07/2008 10:02 AM, Laurent Gautier wrote:
I tripped on that while crafting the example.
The problem still exists when moving the "releases" in the middle,
and removing the last "release".
I also see that the C code contains old/irrelevant comments at the top
of the function
lostobject. Sorry about that, the bug I am chasing is elusive...
I can't spot any problems in the new version of your code, but I can't
reproduce the problem, either. So it appears to be system specific -- I was
using the identical revision as you, but on Windows, not
"x86_64-unknown-linux-gnu". What exact Linux is that?
Ubuntu (hardy heron).
gcc is 4.2.3
The R source was built with "make clean; ./configure --enable-R-shlib"
before running "make; make install"
Can others using that system (or similar ones) reproduce it?
Duncan Murdoch
#include <R.h>
#include <Rdefines.h>
SEXP createObject(void)
{
SEXP x_R;
int len_x = 1000000;
PROTECT(x_R = allocVector(REALSXP, len_x));
Rprintf("Created 'x' at %p\n", x_R);
Rprintf(" (mode is %i, length is %i)\n", TYPEOF(x_R), LENGTH(x_R));
Rprintf(" (first element is %d)\n", REAL(x_R)[0]);
R_PreserveObject(x_R);
UNPROTECT(1);
return x_R;
}
void printObject(SEXP sexp)
{
Rprintf("object at %p\n", sexp);
Rprintf(" (mode is %i, length is %i, named is %i)\n",
TYPEOF(sexp), LENGTH(sexp), NAMED(sexp));
}
SEXP lostobject(SEXP n_R)
{
/*
* This function will:
* 1- create a numerical vector "x" and "preserve it"
* 2- make call "list(x)"
* 3- return "x" to R
*/
SEXP x_R;
int i;
int n = INTEGER(n_R)[0];
/* Create a numerical vector "x_R" */
for (i=0; i<n; i++) {
x_R = createObject();
printObject(x_R);
R_ReleaseObject(x_R);
R_gc();
}
x_R = createObject();
printObject(x_R);
R_gc();
Rprintf("Returning 'x' at %p\n", x_R);
Rprintf(" (first element is %d)\n", REAL(x_R)[0]);
return x_R;
}
2008/7/20 Duncan Murdoch <murdoch at stats.uwo.ca>:
On 20/07/2008 9:01 AM, Laurent Gautier wrote:
Dear list,
While trying to identify the root of a problem I am having with
garbage collected variables,
I have come across the following oddity: depending on whether --verbose
is
set
or not, I obtain different results.
You are working with variables without protecting them, so you just get
lucky whenever the code works.
More below...
I have made a small standalone example to demonstrate it.
The example is very artificial, but I had a hard time reproducing
reliably the problem.
So when I do: (the content of test.R is at the end of this email)
R --no-save < test.R
[The two last lines of the output are:]
[1] 0 0 0
while with
R --verbose --no-save < test.R
[The two last lines of the output are:]
[1] 3.733188e-317 3.137345e-317 3.137345e-317
The C code is compiled with:
R CMD SHLIB test_lostobject.c
R version 2.7.1 Patched (2008-07-19 r46081)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
### -- file test.R
dyn.load("test_lostobject.so")
x = .Call("lostobject", as.integer(5))
x[1:3]
### ---
###--- file lostobject.c
#include <R.h>
#include <Rdefines.h>
SEXP createObject(void)
{
SEXP x_R;
int len_x = 1000000;
PROTECT(x_R = allocVector(REALSXP, len_x));
Rprintf("Created 'x' at %p\n", x_R);
Rprintf(" (mode is %i, length is %i)\n", TYPEOF(x_R), LENGTH(x_R));
Rprintf(" (first element is %d)\n", REAL(x_R)[0]);
R_PreserveObject(x_R);
UNPROTECT(1);
return x_R;
}
void printObject(SEXP sexp)
{
Rprintf("object at %p\n", sexp);
Rprintf(" (mode is %i, length is %i, named is %i)\n",
TYPEOF(sexp), LENGTH(sexp), NAMED(sexp));
}
SEXP lostobject(SEXP n_R)
{
/*
* This function will:
* 1- create a numerical vector "x" and "preserve it"
* 2- make call "list(x)"
* 3- return "x" to R
*/
SEXP x_R;
int i;
int n = INTEGER(n_R)[0];
/* Create a numerical vector "x_R" */
for (i=0; i<n; i++) {
x_R = createObject();
R_ReleaseObject(x_R);
At this point, the variable is unprotected, i.e. you have declared that
its
memory is free for the taking. You should not try to do anything with
it.
printObject calls several functions, and one of those may have
overwritten
the memory. It's not surprising that different flags (--verbose or not)
result in different behaviour.
printObject(x_R);
R_gc();
}
x_R = createObject();
printObject(x_R);
R_gc();
R_ReleaseObject(x_R);
Same thing here. x_R is unprotected now, so you shouldn't use it.
Duncan Murdoch
Rprintf("Returning 'x' at %p\n", x_R);
Rprintf(" (first element is %d)\n", REAL(x_R)[0]);
return x_R;
}