fix: add user interrupt checks and bounds validation for CRAN compliance

Co-authored-by: aider (anthropic/claude-sonnet-4-20250514) <aider@aider.chat>

Author: osorensen

src/all_topological_sorts.cpp

@@ -7,7 +7,7 @@
 #include <list>
 #include <string>
 #include <sstream>
-#include <filesystem>
+#include <R_ext/Utils.h>
 using namespace std;
 
 class Graph {
@@ -37,6 +37,11 @@ void Graph::alltopologicalSortUtil(
     std::vector<arma::ivec>& sorts, double save_frac) {
   bool flag = false;
 
+  // Check for user interrupts in long-running recursive function
+  if (sort_count % 1000 == 0) {
+    R_CheckUserInterrupt();
+  }
+
   for (size_t i{}; i < n_items; i++) {
     if (indegree[i] == 0 && !visited[i]) {
       list<int>::iterator j;
@@ -102,7 +107,7 @@ arma::imat Graph::alltopologicalSort(long long int& sort_count, double save_frac
 //' The function generates all possible topological sorts for the provided preference matrix
 //' and saves approximately `save_frac` of the sorts in a matrix which is returned.
 //'
-//' @return This function returns the number of topological sorts.
+//' @return A list containing the number of topological sorts and optionally a matrix of sorts.
 //'
 //' @export
 //' @examples

src/distances.cpp

@@ -36,6 +36,9 @@ unsigned int CayleyDistance::d(const uvec& r1, const uvec& r2) {
 }
 
 unsigned int FootruleDistance::d(const uvec& r1, const uvec& r2) {
+  if(r1.size() != r2.size()) {
+    Rcpp::stop("Rankings must have the same length");
+  }
   unsigned int value{};
   for(size_t i{}; i < r1.size(); i++) {
     value += r1[i] > r2[i] ? r1[i] - r2[i] : r2[i] - r1[i];
@@ -61,6 +64,9 @@ unsigned int KendallDistance::d(const uvec& r1, const uvec& r2) {
 }
 
 unsigned int SpearmanDistance::d(const uvec& r1, const uvec& r2) {
+  if(r1.size() != r2.size()) {
+    Rcpp::stop("Rankings must have the same length");
+  }
   unsigned int value{};
   for(size_t i{}; i < r1.size(); i++) {
     value += r1[i] > r2[i] ? pow(r1[i] - r2[i], 2) : pow(r2[i] - r1[i], 2);

src/run_smc.cpp

@@ -1,5 +1,6 @@
 // [[Rcpp::depends(RcppArmadillo)]]
 #include <RcppArmadillo.h>
+#include <R_ext/Utils.h>
 #include "prior.h"
 #include "data.h"
 #include "distances.h"
@@ -42,6 +43,7 @@ Rcpp::List run_smc(
   std::vector<double> iteration_times;
 
   for(size_t t{}; t < T; t++) {
+    R_CheckUserInterrupt();
     reporter.report_time(t);
 
     for(auto& p : particle_vector) {