[Rd] SIGSEGV in R_RunWeakRefFinalizer, object allocated with Rcpp

Tomas Kalibera tom@@@k@liber@ @ending from gm@il@com
Thu Aug 9 20:37:50 CEST 2018

R's dyn.unload() will unconditionally unload the given shared object; it 
does not check whether there is any object (external pointer or weak 
reference) with a C finalizer pointing into the space of the shared 
object being unloaded. So it is expected that R will segfault later when 
such finalizer is run.

Currently there is no other way than to handle this on the side of the 
shared library/package, e.g. as Luke does in his simplemmap package. A 
library can declare R_unload_XXX function (see Writing R Extensions) 
that will be called before it is unloaded. So, one can keep say a list 
of objects with finalizers and clear/run the finalizers in R_unload_XXX.

I don't think we could do this automatically on the R's side with the 
current API. I don't think there is a portable way to check if a given C 
pointer is from a given loaded shared object (non-portable way on Linux 
might be scanning the maps in the /proc filesystem). Also, doing this 
for all objects with finalizers when unloading any library would 
probably be slow. Adding some API to aid libraries in doing the 
housekeeping is possible in principle.

So to answer your original question, this could probably be handled in 
Rcpp, but in either case I would not use dyn.unload() in the first 
place. This problem may be just one of many.


On 6.8.2018 17:35, Iñaki Úcar wrote:
> Hi all,
> I'm not sure if I'm not supposed to do the following (the dyn.unload
> part, I mean) or this could be a bug (in R or Rcpp):
> ```
> Rcpp::sourceCpp(code='
>    #include <Rcpp.h>
>    class Object {};
>    //[[Rcpp::export]]
>    SEXP new_object() {
>      return Rcpp::XPtr<Object>(new Object());
>    }'
> )
> new_object()
> dyn.unload(list.files(tempdir(), ".(so|dll)$", recursive=TRUE, full.names=TRUE))
> gc() # segfault in R_RunWeakRefFinalizer
> message("This is not printed")
> ```
> This is the backtrace I get with R 3.5.1:
> #0  0x61ec4fd0 in ?? ()
> #1  0x6ca1cafc in R_RunWeakRefFinalizer (w=0xc786a98) at memory.c:1393
> #2  0x6ca1cdba in RunFinalizers () at memory.c:1459
> #3  0x6ca1d024 in R_RunPendingFinalizers () at memory.c:1495
> #4  R_gc () at memory.c:2893
> #5  do_gc (call=0x1d45b88, op=0x15241d0, args=0x1d454b8,
> rho=0x1d45318) at memory.c:2013
> #6  0x6c9db60f in bcEval (body=body using entry=0x1d45a88,
> rho=rho using entry=0x1d45318, useCache=useCache using entry=TRUE)
>      at eval.c:6781
> #7  0x6c9ecfb2 in Rf_eval (e=0x1d45a88, rho=0x1d45318) at eval.c:624
> #8  0x6c9ee6f1 in R_execClosure (call=call using entry=0x0,
> newrho=<optimized out>, sysparent=<optimized out>,
>      rho=0x15a3370, arglist=0x18c2498, op=0x1d45968) at eval.c:1773
> #9  0x6c9ef605 in Rf_applyClosure (call=0x15a3370,
> call using entry=0x1d45828, op=0x18c2498, op using entry=0x1d45968,
>      arglist=0x1d45968, rho=rho using entry=0x15a3370,
> suppliedvars=0x18c2498) at eval.c:1701
> #10 0x6c9ecf78 in Rf_eval (e=e using entry=0x1d45828,
> rho=rho using entry=0x15a3370) at eval.c:747
> #11 0x6ca11170 in Rf_ReplIteration (rho=0x15a3370, savestack=0,
> browselevel=0, state=0x142edec) at main.c:258
> #12 0x6ca11567 in R_ReplConsole (rho=<optimized out>, savestack=0,
> browselevel=0) at main.c:308
> #13 0x6ca11604 in run_Rmainloop () at main.c:1082
> #14 0x6ca11700 in Rf_mainloop () at main.c:1089
> #15 0x00401836 in AppMain (argc=1, argv=0x15c16f8) at rterm.c:86
> #16 0x00401649 in WinMain using 16 (Instance=0x400000, PrevInstance=0x0,
> CmdLine=0x1904797 "", CmdShow=10)
>      at graphappmain.c:23
> #17 0x00402a8d in main ()
> Any ideas?
> Iñaki
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