S4 object with a pointer to a C struct - c

Question

I have a third-party C library I am using to write an R extension. I am required to create a few structs defined in the library (and initialize them) I need to maintain them as part of an S4 object (think of these structs as defining to state of a computation, to destroy them would be to destroy all remaining computation and the results of all that has been already computed).
I am thinking of creating a S4 object to hold pointers these structs as void* pointers but it is not at all clear how to do so, what would be the type of the slot?

Answer 1

As pointed out by #hrbrmstr, you can use the externalptr type to keep such objects "alive", which is touched on in this section of Writing R Extensions, although I don't see any reason why you will need to store anything as void*. If you don't have any issue with using a little C++, the Rcpp class XPtr can eliminate a fair amount of the boilerplate involved with managing EXTPTRSXPs. As an example, assume the following simplified example represents your third party library's API:
#include <Rcpp.h>
#include <stdlib.h>
typedef struct {
unsigned int count;
double total;
} CStruct;
CStruct* init_CStruct() {
return (CStruct*)::malloc(sizeof(CStruct));
}
void free_CStruct(CStruct* ptr) {
::free(ptr);
::printf("free_CStruct called.\n");
}
typedef Rcpp::XPtr<CStruct, Rcpp::PreserveStorage, free_CStruct> xptr_t;
When working with pointers created via new it is generally sufficient to use Rcpp::XPtr<SomeClass>, because the default finalizer simply calls delete on the held object. However, since you are dealing with a C API, we have to supply the (default) template parameter Rcpp::PreserveStorage, and more importantly, the appropriate finalizer (free_CStruct in this example) so that the XPtr does not call delete on memory allocated via malloc, etc., when the corresponding R object is garbage collected.
Continuing with the example, assume you write the following functions to interact with your CStruct:
// [[Rcpp::export]]
xptr_t MakeCStruct() {
CStruct* ptr = init_CStruct();
ptr->count = 0;
ptr->total = 0;
return xptr_t(ptr, true);
}
// [[Rcpp::export]]
void UpdateCStruct(xptr_t ptr, SEXP x) {
if (TYPEOF(x) == REALSXP) {
R_xlen_t i = 0, sz = XLENGTH(x);
for ( ; i < sz; i++) {
if (!ISNA(REAL(x)[i])) {
ptr->count++;
ptr->total += REAL(x)[i];
}
}
return;
}
if (TYPEOF(x) == INTSXP) {
R_xlen_t i = 0, sz = XLENGTH(x);
for ( ; i < sz; i++) {
if (!ISNA(INTEGER(x)[i])) {
ptr->count++;
ptr->total += INTEGER(x)[i];
}
}
return;
}
Rf_warning("Invalid SEXPTYPE.\n");
}
// [[Rcpp::export]]
void SummarizeCStruct(xptr_t ptr) {
::printf(
"count: %d\ntotal: %f\naverage: %f\n",
ptr->count, ptr->total,
ptr->count > 0 ? ptr->total / ptr->count : 0
);
}
// [[Rcpp::export]]
int GetCStructCount(xptr_t ptr) {
return ptr->count;
}
// [[Rcpp::export]]
double GetCStructTotal(xptr_t ptr) {
return ptr->total;
}
// [[Rcpp::export]]
void ResetCStruct(xptr_t ptr) {
ptr->count = 0;
ptr->total = 0.0;
}
At this point, you have done enough to start handling CStructs from R:
ptr <- MakeCStruct() will initialize a CStruct and store it as an externalptr in R
UpdateCStruct(ptr, x) will modify the data stored in the CStruct, SummarizeCStruct(ptr) will print a summary, etc.
rm(ptr); gc() will remove the ptr object and force the garbage collector to run, thus calling free_CStruct(ptr) and destroying the object on the C side of things as well
You mentioned the use of S4 classes, which is one option for containing all of these functions in a single place. Here's one possibility:
setClass(
"CStruct",
slots = c(
ptr = "externalptr",
update = "function",
summarize = "function",
get_count = "function",
get_total = "function",
reset = "function"
)
)
setMethod(
"initialize",
"CStruct",
function(.Object) {
.Object#ptr <- MakeCStruct()
.Object#update <- function(x) {
UpdateCStruct(.Object#ptr, x)
}
.Object#summarize <- function() {
SummarizeCStruct(.Object#ptr)
}
.Object#get_count <- function() {
GetCStructCount(.Object#ptr)
}
.Object#get_total <- function() {
GetCStructTotal(.Object#ptr)
}
.Object#reset <- function() {
ResetCStruct(.Object#ptr)
}
.Object
}
)
Then, we can work with the CStructs like this:
ptr <- new("CStruct")
ptr#summarize()
# count: 0
# total: 0.000000
# average: 0.000000
set.seed(123)
ptr#update(rnorm(100))
ptr#summarize()
# count: 100
# total: 9.040591
# average: 0.090406
ptr#update(rnorm(100))
ptr#summarize()
# count: 200
# total: -1.714089
# average: -0.008570
ptr#reset()
ptr#summarize()
# count: 0
# total: 0.000000
# average: 0.000000
rm(ptr); gc()
# free_CStruct called.
# used (Mb) gc trigger (Mb) max used (Mb)
# Ncells 484713 25.9 940480 50.3 601634 32.2
# Vcells 934299 7.2 1650153 12.6 1308457 10.0
Of course, another option is to use Rcpp Modules, which more or less take care of the class definition boilerplate on the R side (using reference classes rather than S4 classes, however).