[Rd] How to maintain memory in R extension

Henrik Bengtsson hb at biostat.ucsf.edu
Wed Nov 12 22:56:27 CET 2014

On Wed, Nov 12, 2014 at 10:20 AM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
> On 11/12/2014 05:36 AM, Zheng Da wrote:
>> Hello,
>> I wrote a system to perform data analysis in C++. Now I am integrating
>> it to R. I need to allocate memory for my own C++ data structures,
>> which can't be represented by any R data structures. I create a global
>> hashtable to keep a reference to the C++ data structures. Whenever I
>> allocate one, I register it in the hashtable and return its key to the
>> R code. So later on, the R code can access the C++ data structures
>> with their keys.
>> The problem is how to perform garbage collection on the C++ data
>> structures. Once an R object that contains the key is garbage
>> collected, the R code can no longer access the corresponding C++ data
>> structure, so I need to deallocate it. Is there any way that the C++
>> code can get notification when an R object gets garbage collected? If
>> not, what is the usual way to manage memory in R extensions?
> register a finalizer that runs when there are no longer references to the R
> object, see ?reg.finalizer or the interface to R and C finalizers in
> Rinternals.h. If you return more than one reference to a key, then of course
> you'll have to manage these in your own C++ code.

A small but important addition: Make sure your registered finalizer
also works, or at least don't core dump R, if your package (or one of
its dependencies) happens be unloaded by the time the garbage
collector runs.  This task seems easy but can be quite tricky, e.g.
should you reload you package temporarily and what are the side
effects from doing that?


> Martin Morgan
>> Thanks,
>> Da
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