Yurii,
On Sep 4, 2009, at 16:54 , Yurii Aulchenko wrote:
Dear All,
I would like to have an advice for designing an R library, and
thought that R-devel may be the best place to ask given so many
people who are highly expert in R are around.
We are at an early stage of designing an R library, which is
effectively an interface to a C++ library providing fast access to
large matrices stored on HDD as binary files.
[FWIW there are already several packages that do waht you describe -
see e.g. ff, bigMemory, nws, ...]
The core of the C++ library is relatively sophisticated class, which
we try to "mirror" using an S4 class in R. Basically when a new
object of that class is initiated, the C++ constructor is called and
essential elements of the new object are reflected as slots of the R
object.
Now as you can imagine the problem is that if the R object is
removed using say "rm" command, and not our specifically designed
one, the C++ object still hangs around in RAM until R session is
terminated.
You must have some link between the S4 object and your C++ object -
ideally an external pointer - so all you have to do is to attach a
finalizer to it via R_RegisterCFinalizer or R_RegisterCFinalizerEx. In
that finalizer you simply free the C++ object and all is well.
Note that R uses a garbage collector so the object won't go away
immediately after it went out of scope - only after R thinks it needs
to reclaim memory. You can use gc() to force garbage collection to
test it.
This is not nice, and also may be a problem, as the C++ object may
allocate large part of RAM. We can of cause replace generic "rm" and
"delete" functions, but this is definitely not a nice solution.
... and it doesn't tackle the issue - objects can go out of scope by
other means than just rm(), e.g.:
f <- function() { ...; myGreatObject }
f()
# the great object is gone now since it was not assigned anywhere
Sounds like rather common problem people may face, but unfortunately
I was not able to find a solution.
Cheers,
Simon
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