RcppAramadillo Cube::operator() : index out of bounds - rcpp

Question

I have been fiddling with the following C++ code for integration with R code that I have written (too much to include here), but keep getting an error that the Cube::operator() index is out of bounds and I am unsure as to why this is occurring. My suspicion is that the 3D array is not being filled correctly as described in
making 3d array with arma::cube in Rcpp shows cube error
but I am uncertain how to properly solve the issue.
Below is my full C++ code:
// [[Rcpp::depends(RcppArmadillo)]]
#define ARMA_DONT_PRINT_OPENMP_WARNING
#include <RcppArmadillo.h>
#include <RcppArmadilloExtensions/sample.h>
#include <set>
using namespace Rcpp;
int sample_one(int n) {
return n * unif_rand();
}
int sample_n_distinct(const IntegerVector& x,
int k,
const int * pop_ptr) {
IntegerVector ind_index = RcppArmadillo::sample(x, k, false);
std::set<int> distinct_container;
for (int i = 0; i < k; i++) {
distinct_container.insert(pop_ptr[ind_index[i]]);
}
return distinct_container.size();
}
// [[Rcpp::export]]
arma::Cube<int> fillCube(const arma::Cube<int>& pop,
const IntegerVector& specs,
int perms,
int K) {
int num_specs = specs.size();
arma::Cube<int> res(perms, num_specs, K);
IntegerVector specs_C = specs - 1;
const int * pop_ptr;
int i, j, k;
for (i = 0; i < K; i++) {
for (k = 0; k < num_specs; k++) {
for (j = 0; j < perms; j++) {
pop_ptr = &(pop(0, sample_one(perms), sample_one(K)));
res(j, k, i) = sample_n_distinct(specs_C, k + 1, pop_ptr);
}
}
}
return res;
}
Does someone have an idea as to what may be producing the said error?
Below is the R code with a call to the C++ function (including a commented-out triply-nested 'for' loop that the C++ code reproduces).
## Set up container(s) to hold the identity of each individual from each permutation ##
num.specs <- ceiling(N / K)
## Create an ID for each haplotype ##
haps <- 1:Hstar
## Assign individuals (N) to each subpopulation (K) ##
specs <- 1:num.specs
## Generate permutations, assume each permutation has N individuals, and sample those individuals' haplotypes from the probabilities ##
gen.perms <- function() {
sample(haps, size = num.specs, replace = TRUE, prob = probs)
}
pop <- array(dim = c(perms, num.specs, K))
for (i in 1:K) {
pop[,, i] <- replicate(perms, gen.perms())
}
## Make a matrix to hold individuals from each permutation ##
# HAC.mat <- array(dim = c(perms, num.specs, K))
## Perform haplotype accumulation ##
# for (k in specs) {
# for (j in 1:perms) {
# for (i in 1:K) {
# select.perm <- sample(1:nrow(pop), size = 1, replace = TRUE) # randomly sample a permutation
# ind.index <- sample(specs, size = k, replace = FALSE) # randomly sample individuals
# select.subpop <- sample(i, size = 1, replace = TRUE) # randomly sample a subpopulation
# hap.plot <- pop[select.perm, ind.index, select.subpop] # extract data
# HAC.mat[j, k, i] <- length(unique(hap.plot)) # how many haplotypes are recovered
# }
# }
# }
HAC.mat <- fillCube(pop, specs, perms, K)

Answer 1

This is an out-of-bounds error. The gist of problem is the call
pop_ptr = &(pop(0, sample_one(perms), sample_one(K)));
since
sample_one(perms)
is being placed as an access index where the max length is num_specs. This is seen by how res is defined:
arma::Cube<int> res(perms, num_specs, K);
Thus, moving out perms out of num_specs place should resolve the issue.
// [[Rcpp::export]]
arma::Cube<int> fillCube(const arma::Cube<int>& pop,
const IntegerVector& specs,
int perms,
int K) {
int num_specs = specs.size();
arma::Cube<int> res(perms, num_specs, K);
IntegerVector specs_C = specs - 1;
const int * pop_ptr;
int i, j, k;
for (i = 0; i < K; i++) {
for (k = 0; k < num_specs; k++) {
for (j = 0; j < perms; j++) {
// swapped location
pop_ptr = &(pop(sample_one(perms), 0, sample_one(K)));
// should the middle index be 0?
res(j, k, i) = sample_n_distinct(specs_C, k + 1, pop_ptr);
}
}
}
return res;
}