From tom@@@k@liber@ @ending from gm@il@com  Fri Aug 10 14:17:29 2018
From: tom@@@k@liber@ @ending from gm@il@com (Tomas Kalibera)
Date: Fri, 10 Aug 2018 14:17:29 +0200
Subject: [Rd] 
 SIGSEGV in R_RunWeakRefFinalizer, object allocated with Rcpp
In-Reply-To: <CALEXWq0H8Qdtc18Enr+TTm5DbDSJx3YtaLHaGZxr7V9Okz8q+Q@mail.gmail.com>
References: <CALEXWq2E+-k=Oka1YZAzGzYU1bLmcC3ptUUrv8RUMUrpcviK-g@mail.gmail.com>
 <a03f65c7-3e0e-7857-0e1e-a809e1051b56@gmail.com>
 <23404.36580.740017.811392@rob.eddelbuettel.com>
 <alpine.DEB.2.20.1808091406240.3237@luke-Latitude-7480>
 <CALEXWq0H8Qdtc18Enr+TTm5DbDSJx3YtaLHaGZxr7V9Okz8q+Q@mail.gmail.com>
Message-ID: <e190406d-80f6-954d-572c-1141b837be0c@gmail.com>

Hi I?aki,

I think that "still reachable" memory is potentially a problem only if 
you cared about (frequent) package unloading, and if package unloading 
did not have correctness problems in the first place. I would only worry 
about "memory leaks" reported by valgrind.

That your example (unloading a library while there is still an object 
with a finalizer implemented in that library) segfaults on one system 
but not another is not too surprising. Depending on the OS, the dynamic 
linker, the current state of the system, etc - when the GC tries to run 
the finalizer, it may point to inaccessible memory (segfault), but also 
still to the code of the unloaded finalizer (possibly no segfault) or 
something else. There is no way to distinguish between all these cases 
before running the finalizer - neither the OS nor R can do it - we could 
only in principle, with a lot of other problems and platform-dependent 
hacks, detect when the memory is inaccessible, but that may not be worth it.

Best
Tomas


On 08/10/2018 12:46 AM, I?aki ?car wrote:
> Thanks, Tomas, Luke, for the clarifications. Then, I have another question.
>
> But first, let me introduce how I ended up here, because obviously I
> just don't go around dyn.unloading things that I've just compiled. I
> was testing a package with valgrind. Everything ok, no leaks. Great.
> But I'm always suspicious (probably unjustifiably) of all the memory
> that is reported as "still reachable", so I wanted to check whether
> there was any difference if I detach(unload=TRUE) the package after
> all the tests.
>
> In a nutshell, I ended up discovering that the following code:
>
> ```
> library(simmer)
> simmer() # allocates a C++ object, as in my initial example
> detach("package:simmer", unload=TRUE)
> ```
>
> segfaults on Windows, but not on Linux (then I built the example in my
> initial email to confirm it wasn't simmer's fault). So given that,
> from your explanation, I should expect a segfault here, the question
> is: what on Earth does (or does not) R on Linux do to avoid
> segfaulting compared to Windows? :) And a corolary would be, can't R
> on Windows do the same?
>
> Regards,
> I?aki
>
> El jue., 9 ago. 2018 a las 21:13, <luke-tierney at uiowa.edu> escribi?:
>> On Thu, 9 Aug 2018, Dirk Eddelbuettel wrote:
>>
>>> On 9 August 2018 at 20:37, Tomas Kalibera wrote:
>>> | So to answer your original question, this could probably be handled in
>>> | Rcpp,
>>>
>>> Hm. Why do you say that / what did you have in mind?
>> We say it because it is true. Rcpp registers C finalizers and running
>> them after unloading will segfault. For now it would be better for Rcpp
>> (and everyone else) to explicitly discourage unloading as it is
>> unreliable on many levels.
>>
>> What Rcpp could do to avoid segfaulting is to keep a weak list of all
>> objects to which it attaches C finalizers and arrange for those to be
>> cleaned up in an R_unload_<dllname> routine. Not clear it is worth the
>> trouble. At the R level we could provide more support for this since
>> we already have a weak list of objects with finalizers, but again not
>> clear it is worth the trouble.
>>
>> Best,
>>
>> luke
>>
>>> Recall that we do not alter SEXPs or introduce additional additional
>>> reference counters -- because we do not think that altering the basic R API
>>> for such calls would be a wise strategy.  So we do more or less what is done
>>> in C for R, with some additional hand-holding which circumvents a number of
>>> common errors.
>>>
>>> | but in either case I would not use dyn.unload() in the first
>>> | place. This problem may be just one of many.
>>>
>>> I think I'd second that. I never had much unloading packages or dynamic
>>> libraries and tend to "just say no". Both short-lived processes (ie via 'r')
>>> as well as long sessions (ie R via ESS, running for weeks) work for my
>>> workflows.
>>>
>>> Dirk
>>>
>>>
>> --
>> Luke Tierney
>> Ralph E. Wareham Professor of Mathematical Sciences
>> University of Iowa                  Phone:             319-335-3386
>> Department of Statistics and        Fax:               319-335-3017
>>      Actuarial Science
>> 241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
>> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
>
>
> --
> I?aki ?car
> http://www.enchufa2.es
> @Enchufa2



[Rd] SIGSEGV in R_RunWeakRefFinalizer, object allocated with Rcpp
Tomas Kalibera