Segfault: .Call and classes with logical slots

torsten@hothorn.de writes:
On Mon, 26 Apr 2004, John Chambers wrote:

I think you need to PROTECT the vector you're putting in the slot as
well as the overall object.  At any rate, the problem goes away for me
with the revised version of dummy.c below.
yes, and it seems that PROTECT'ing the logical variable is sufficient
while PROTECT'ing the class but not the logical variable causes a
segfault again. I tried with numeric slots too: No problems.

(Empirically, PROTECT'ing
the class definition didn't seem to be needed, but experience suggests
that too much protection  is better than too little.)
I tried to save (UN)PROTECT calls because of efficiency reasons. Anyway,
this helps me a lot, thanks!
Perhaps this example is an indication that gctorture is too
aggressive.  I use constructions like

   PROTECT(ans = ...);

   SET_SLOT(ans, install("lgl"), allocVector(LGLSXP,1));
   LOGICAL(GET_SLOT(ans, install("lgl")))[0] = TRUE;

in many places in my code, having been assured by a usually reliable
source (Luke) that SET_SLOT applied to a freshly allocated vector
would be atomic with respect to garbage collection.  That is, under
the usual conditions there would be no chance of a garbage
collection being triggered between the allocVector and SET_SLOT
operations.  It may be that gctorture is causing a garbage collection
at a place where it otherwise could not occur and the additional
(UN)PROTECT are redundant except when gctorture is active.

In trying to avoid (UN)PROTECT calls I'm not as concerned about
efficiency as I am about clarity of the code.  I would prefer not to
clutter the code with (UN)PROTECT calls if they are known to be
redundant.

At the time we discussed this Luke suggested that we document a set of
C calls that are atomic with respect to garbage collection.  I think
this would be a good idea but I suspect that no one has the time to do
it right now.
Torsten

#include <Rdefines.h>

SEXP foo() {

    SEXP ans, cl, el;

    PROTECT(cl = MAKE_CLASS("test"));
    PROTECT(ans = NEW_OBJECT(cl));
    PROTECT(el = allocVector(LGLSXP, 1));
    SET_SLOT(ans, install("lgl"), el);
    LOGICAL(GET_SLOT(ans, install("lgl")))[0] = TRUE;
    UNPROTECT(3);
    return(ans);
}

Torsten Hothorn wrote:
Hi,

the following example aiming at a class containing a logical slot
segfaults under R-1.9.0 when `gctorture(on = TRUE)' is used:

Code code (dummy.c):

#include <Rdefines.h>

SEXP foo() {

    SEXP ans;

    PROTECT(ans = NEW_OBJECT(MAKE_CLASS("test")));
    SET_SLOT(ans, install("lgl"), allocVector(LGLSXP, 1));
    LOGICAL(GET_SLOT(ans, install("lgl")))[0] = TRUE;
    UNPROTECT(1);
    return(ans);
}

R code (dummy.R):

dyn.load("dummy.so")

setClass("test", representation = representation(lgl = "logical"))

a = .Call("foo")
a # OK

gctorture(on = TRUE)
a = .Call("foo")
gctorture(on = FALSE)
a # segfault

which gives

R>
R>
R> dyn.load("dummy.so")
R>
R> setClass("test", representation = representation(lgl = "logical"))
[1] "test"
R>
R> a = .Call("foo")
R> a
An object of class "test"
Slot "lgl":
[1] TRUE

R>
R> gctorture(on = TRUE)
R> a = .Call("foo")
R> gctorture(on = FALSE)
Segmentation fault

Best,

Torsten

R> version
         _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    1
minor    9.0
year     2004
month    04
day      12
language R
R>

 _______________________________________________________________________
|                                                                       |
|       Dr. rer. nat. Torsten Hothorn                                   |
|       Institut fuer Medizininformatik, Biometrie und Epidemiologie    |
|       Waldstrasse 6, D-91054 Erlangen, Deutschland                    |
|       Tel: ++49-9131-85-22707 (dienstl.)                              |
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|       Email:  Torsten.Hothorn@rzmail.uni-erlangen.de                  |
|               PLEASE send emails cc to torsten@hothorn.de             |
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|_______________________________________________________________________|

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John M. Chambers                  jmc@bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-2681
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Douglas Bates                            bates@stat.wisc.edu
Statistics Department                    608/262-2598
University of Wisconsin - Madison        http://www.stat.wisc.edu/~bates/

Segfault: .Call and classes with logical slots

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