Undefined reference to a custom function in a worker (C++ and RcppParallel)

Question

I'm new to C++ programming, trying to experiment with Rcpp through R. I created a function to produce all possible k-mers from a string. It works well in the serial form of it:

#include <Rcpp.h>
#include <string>
#include <iostream>
#include <ctime>
// using namespace Rcpp;

// [[Rcpp::export]]
std::vector< std::string > cpp_kmer( std::string s, int k ){
  std::vector< std::string > kmers;
  int seq_loop_size = s.length() - k+1;
  for ( int z=0; z < seq_loop_size; z++ ) {
    std::string  kmer;
    kmer = s.substr( z, k );
    kmers.push_back( kmer ) ;
  }
  return kmers;
}

However, when I try to use this function in a parallel implementation (using RcppParallel), with the code below:

#include <Rcpp.h>
#include <string>
#include <iostream>
#include <ctime>
using namespace Rcpp;

// [[Rcpp::depends(RcppParallel)]]
#include <RcppParallel.h>
using namespace RcppParallel;

struct p_cpp_kmer : public Worker {
  // input string
  std::vector< std::string > seqs;
  int k;
  std::vector< std::string > cpp_kmer( std::string s, int k );
  // destination list
  List output;
  std::string
    sub_s;
  // initialize with source and destination
  p_cpp_kmer(std::vector< std::string > seqs, int k, List output) 
    : seqs(seqs), k(k), output(output) {}

  // calculate k-mers for the range of sequences requested
  void operator()(std::size_t begin, std::size_t end) {
    for (std::size_t i = begin; i < end; i++)
      sub_s = seqs[i];
      cpp_kmer(sub_s, k);
  }
};

// [[Rcpp::export]]
List par_cpp_kmer(std::vector< std::string > seqs, int k, bool v){
  // allocate output list 
  List outpar(num_seqs);
  int num_seqs = seqs.size();
  // p_cpp_kmer functor (pass input and output matrixes)
  p_cpp_kmer par_kmer(seqs, k, outpar);
  parallelFor(0, num_seqs, par_kmer);
  return wrap(outpar);
}

std::vector< std::string > cpp_kmer( std::string s, int k ){
  std::vector< std::string > kmers;
  int seq_loop_size = s.length() - k+1;
  for ( int z=0; z < seq_loop_size; z++ ) {
    std::string  kmer;
    kmer = s.substr( z, k );
    kmers.push_back( kmer ) ;
  }
  return kmers;
}

It fails to compile, giving an: undefined reference to p_cpp_kmer::cpp_kmer(std::string, int)' error.

I know it has to do with declaring/referencing the cpp_kmer, but I just can't figure out where/how to do so appropriately (due to my lack of knowledge in C++).

Thank you very much in advance.

Answer 1

What happens is that your p_cpp_kmer struct declares a cpp_kmer method but it is never defined. Instead what is defined later is the free function cpp_kmer .

You declare this method

std::vector< std::string > cpp_kmer( std::string s, int k );

You seem to want to use it:

void operator()(std::size_t begin, std::size_t end) {
  for (std::size_t i = begin; i < end; i++)
    sub_s = seqs[i];
    cpp_kmer(sub_s, k);
}

But instead you define the free function cpp_kmer here:

std::vector< std::string > cpp_kmer( std::string s, int k ){
  std::vector< std::string > kmers;
  int seq_loop_size = s.length() - k+1;
  for ( int z=0; z < seq_loop_size; z++ ) {
    std::string  kmer;
    kmer = s.substr( z, k );
    kmers.push_back( kmer ) ;
  }
  return kmers;
}

You could either remove the definition of the cpp_kmer method in the struct so that the free function is used, or actually define it.

There are additional problems with the code:

• In your operator() you discard the result. I guess you mean to have this instead output[i] = cpp_kmer(sub_s, k);

• even if you do something like the above the code is unsafe, because output[i] = cpp_kmer(sub_s, k); allocates R objects (each individual R string and the string vector) , that cannot happen in a separate thread.

If you really want to do this in parallel, you need to make sure that you don't allocate any R object in the workers.

Furthermore, writing parallel code is much easier when you consider using C++11 and the tbb library that is underlying RcppParallel . For example:

#include <Rcpp.h>
#include <RcppParallel.h>

using namespace Rcpp;
using namespace RcppParallel;

// [[Rcpp::depends(RcppParallel)]]
// [[Rcpp::plugins(cpp11)]]

using string_vector = std::vector< std::string > ; 
using list_string_vector = std::vector<string_vector> ;

// [[Rcpp::export]]
list_string_vector par_cpp_kmer( string_vector  seqs, int k, bool v){
  int num_seqs = seqs.size() ;

  list_string_vector out(num_seqs) ;

  tbb::parallel_for( 0, num_seqs, 1, [&seqs,k,&out](int i){
    std::string& s = seqs[i] ;
    int seq_loop_size = s.length() - k+1;

    std::vector<std::string> vec(seq_loop_size) ;
    for ( int z=0; z < seq_loop_size; z++ ) {
      vec[z] = s.substr( z, k );
    }
    out[i] = vec ;

  }) ;
  return out ;
}

This is assuming that std::string can be allocated in separate threads:

> par_cpp_kmer( c("foobar", "blabla"), 3 )
[[1]]
[1] "foo" "oob" "oba" "bar"

[[2]]
[1] "bla" "lab" "abl" "bla"

Answer 2

You probably have an implementation for cpp_kmer for a different struct (or in the public namespace), but you lack an implementation of member function cpp_kmer at your struct p_cpp_kmer . You will have to add an implementation like:

std::vector< std::string > p_cpp_kmer::cpp_kmer( std::string s, int k ) {
  // your implementation goes here
}