Question

Say I have two independent cpp codes in two different R packages:
(please do not take these examples literally, these are meant to be
a minimal version of my question).

#include <algorithm>
#include <Eigen/Dense>

using namespace std;
using namespace Eigen;
using Eigen::VectorXf;
using Eigen::VectorXi;
using Eigen::RowVectorXf;

float Fmedian(VectorXf& x){
    const int n=x.rows();
    const int half=(n+1)/2-1;               
    float med;
    std::nth_element(x.data(),x.data()+half,x.data()+x.size()); 
    if((n%2)==1){
        med=x(half);
    } else {
        float tmp0=x(half);
        float tmp1=x.segment(half+1,half-1).minCoeff(); 
        med=0.5*(tmp0+tmp1);
    }
    return med;
}
extern "C"{
    void R_Fastmedian(int* n,float* X,int* fMet){
        MatrixXf xi=Map<VectorXf>(X,*n);        
        float Um=Fmedian(xi);
        *fMet=Um;
    }
}

then, in another file, i have:

#include <algorithm>
#include <Eigen/Dense>

using namespace std;
using namespace Eigen;
using Eigen::VectorXf;
using Eigen::VectorXi;
using Eigen::RowVectorXf;

float Fmedian(VectorXf& x){
    const int n=x.rows();
    const int half=(n+1)/2-1;               
    float med;
    std::nth_element(x.data(),x.data()+half,x.data()+x.size()); 
    if((n%2)==1){
        med=x(half);
    } else {
        float tmp0=x(half);
        float tmp1=x.segment(half+1,half-1).minCoeff(); 
        med=0.5*(tmp0+tmp1);
    }
    return med;
}
float Fmad(VectorXf& x,float& med){
    const int n=x.rows();
    const int half=(n+1)/2-1;
    float mad;              
    x-=med;
    x=x.cwiseAbs();
    std::nth_element(x.data(),x.data()+half,x.data()+x.size()); 
    if((n%2)==1){
        mad=x(half);
    } else {
        float tmp0=x(half);
        float tmp1=x.segment(half+1,half-1).minCoeff(); 
        mad=0.5*(tmp0+tmp1);
    }
    return(mad*1.4826);
}
extern "C"{
    void R_Fastmad(int* n,float* X,int* fMet){
        MatrixXf xi=Map<VectorXf>(X,*n);        
        float U1=Fmedian(xi);
            float U2=Fmad(xi,U1);
        *fMet=U2;
    }
}

Now, i want to combine these two functions in a package. When i will compile
the second code using R CMD, i will get an error for Fmedian to the effect
that this function is already defined in the first file. What is the most
straightforward way to link these two files together?

Answer 1

If I’m reading correctly, your Fmedian implementations are exactly the same in both files. But the compiler doesn’t actually know that, for it they may be different and cause ambiguity, hence the error. To fix it, you should unify both implementations into one.

One way to do that would be this:

// the first file
#include <algorithm>
#include <Eigen/Dense>

using namespace std;
using namespace Eigen;
using Eigen::VectorXf;
using Eigen::VectorXi;
using Eigen::RowVectorXf;

// Forward-declare Fmedian as an external function.
// This means that its definition will be found
// in some other file (C++ translation unit) during compilation.
extern float Fmedian(VectorXf& x);

extern "C" {
    void R_Fastmedian(int* n,float* X,int* fMet){
        MatrixXf xi=Map<VectorXf>(X,*n);        
        float Um=Fmedian(xi);
        *fMet=Um;
    }
}

And your second file remains the same.

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See also Externing functions in C++, How does the linker know where is the definition of an extern function?