[Rcpp-devel] Possible unprotected memory problems

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri Jul 22 18:24:21 CEST 2011

Hi D(oug|irk),

Thanks for taking the time to respond. Both of your emails have been
quite helpful in shedding some light on how the guts of these things
are working.

Still, I think I didn't describe the scenario I *think* I want well
(it might be that I might not actually want to do this when I realize
how dumb it might be :-) It could also be that I'm misunderstanding
what you folks are telling me, but the nut of where I think our wires
are crossed is here:

> | The "hand off" of the data/pointer to a C library would be like
> | calling PROTECT. After your C function returns control back to R, it
> | would still claim ownership/usage of the data. Things would hum along
> I think you have it inverse.  If you create an object in C++ and hand it to
> R, you typically do not expect to see that object ever again in C++ -- and
> hence you let R go about its business and even gc it.

I actually think I want the inverse :-)

The situation I am thinking of is constructing a large object (matrix
of whatever type) in R, then passing that down to my C++ layer. I want
the C++ layer to lay claim to that data, maybe as if there was another
('ghost') object on the R said that had an additional reference to it.

I see this will require some digging into R internals. I'm sorry I cut
out most of Dirk's message by this point. I think the point you make
below about setting some "bit" is what I think I want to chase down:

> We don't do PROTECT / UNPROTECT but a bit gets set that corresponds to the
> same. I would have to look up the details as it has been a while....

I'll try to pain the scenario I think I want using the *assumption*
that R does some simple reference counting to do its GC. In this
imaginary situation, this is what I want:

+ I want R to create the object (so there is 1 ref to it now).

+ Shoot this object down to C++, at which point I want my C++ library
to get no-copy access to the data (so, hold on to its pointer), and
add a +1 to R's refcount for this object, so that R won't free the
memory "under my feet"

+ My C++ function will do whatever it is does and return to R (but it
won't decrement this ref count) .. it is still holding on to the data
when it returns to R.

+ R will then go about its business as usual. On the R side, the
object I originally passed down to C may (or may not) fall out of
scope and the refcount will go -1, but it won't hit 0 since there is
still 1 refcount to it from the C++ side of things.

+ Eventually, the C++ object will be destroyed (a situation I will be
notified about), at which point I will decrement the refcount to my
object, which will set it to 0. Here two things can then happen:

(1) I can just free this memory myself in my C++ code (actually, I
guess this is dangerous if R will try to clean it again later); or
(2) Since the refcount is now 0 for this object, I can wait for R's GC
to free the memory whenever it decides to kick in.

As I said, this is kind of what I want to do. It is described in the
hypothetical situation where R does refcount-ing for its GC stuff.

All that having been said, I see that I need to really read some
R-internals stuff if I'm going to get serious about trying this out.

I guess this the document I need to read to start groking these types
of things a bit more:

Is there other material I can/should be looking at as well?

Thanks again for sharing your expertise,


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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