Hey, I have good experience with Rcpp, I manage to create IRanges objects etc, and pass them back to R, but GRanges is a bit trickier, since it uses factor for some columns like strand etc.

IRanges is easy, something like this:

S4 getIRangesFromC(int start, int end){
    S4 iranges("IRanges");
    iranges.slot("start") = start;
    iranges.slot("width) = end-start+1;
    return iranges;
}

This is my code so far, it can return GRanges but is not valid for conversion to GRangesList, because columns are wrong types.

#IN R ->:

library(Rcpp)
require("IRanges")
require("GenomicRanges")
Sys.setenv("PKG_CXXFLAGS"="-std=c++11")
sourceCpp("foo.cpp")

a = GRangesC()    #<----GRanges object returned from rcpp here

//IN foo.cpp ->

#include <Rcpp.h>
using namespace Rcpp;

using ui = unsigned int;

// [[Rcpp::export]]
S4 GRangesC(){
  S4 G("GRanges"); //Construct empty GRanges

  ui seqnames = 1; //Chromosone number
 
  S4 ranges ("IRanges");  //Ranges used
  ranges.slot("start") = 0;
  ranges.slot("width") = 2;
 
  char strand = '+';    //Strand
  string names = "abc";   //Names of GRanges

  G.slot("seqnames")= seqnames;
  G.slot("ranges")= ranges;
  G.slot("strand")=  strand;

  return G;
}

Error is this:

> GRangesList(a)
Error in validObject(.Object) :
  invalid class “GRanges” object: 1: invalid object for slot "seqnames" in class "GRanges": got class "numeric", should be or extend class "Rle"
invalid class “GRanges” object: 2: invalid object for slot "strand" in class "GRanges": got class "character", should be or extend class "Rle"
invalid class “GRanges” object: 3: 'mcols(x)' is not parallel to 'x'

Is there a better and more safe way to make GRanges from Cpp that uses a safe constructor for GRanges, and not the .slot method ?

BTW: reason I do this is because GRanges is too slow in R for millions of rows, it takes days to combine with lapply etc.

I created a file "CPPRanges.cpp"

#include <Rcpp.h>
using namespace Rcpp;

// [[Rcpp::export]]
S4 CPPRanges(Function GRanges, Function IRanges) {
    IntegerVector start = IntegerVector::create( 10, 20, 30 );
    IntegerVector end = IntegerVector::create( 40 );
    CharacterVector seqname = CharacterVector::create( "chr1" );
    return GRanges(seqname, IRanges(start, end));
}

and in R did

library(GenomicRanges)
library(Rcpp)
sourceCpp("CPPRanges.cpp")

and then

> CPPRanges(GRanges, IRanges)
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  [10, 40]      *
  [2]     chr1  [20, 40]      *
  [3]     chr1  [30, 40]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

As an extension to the previous answer, you can do the same without the need to provide constructors as arguments:

#include <Rcpp.h>
using namespace Rcpp;

// [[Rcpp::export]]
S4 CPPRanges() {
    Environment envGenomicRanges("package:GenomicRanges");
    Environment envIRanges("package:IRanges");
    Function GRanges = envGenomicRanges["GRanges"];
    Function IRanges = envIRanges["IRanges"];
    IntegerVector start = {10, 20, 20};
    IntegerVector end = {40};
    CharacterVector seqname = "chr1";
    return GRanges(seqname, IRanges(start, end));
}