I'm trying to write a wrapper for a C++ function I've written, making use of the Point Clouds Library (PCL). This is my first try interfacing R and C++, so I apologise if any solution is too trivial. My goal is to make a few functions available for myself and my colleagues directly in R, on mac and windows. My example function cloudSize is included at the bottom of the text. I will try to be as clear as possible.
I've installed PCL with the vcpkg package manager for winx64 at C:\src\vcpkg\vcpkg.
This is added to my Environmental Variable Path for my user.
I created an empty R-package with Rcpp.package.skeleton():
C:/User/csvi0001/Desktop/GitHub/RPCLpackage/PCLR
PCL is a massive library, but thankfully modular,and so I only #include the headers that are needed to compile the executable: pcl/io/pcd_io.h, pcl/point_types.h, pcl/registration/icp.h.
Now, since I'd like this to work on more than one OS - and therefore compile on install (?) - I should use a dynamic library? I'll presume that the person installing my package already has a compiled copy of pcl. However, I do not know how to find a flag showing that pcl is installed - how do I find these for inclusion in Makevars(?). CMake must find them when testing the C++ function in VSCode after adding an include path. In lieu of this:
I copy the pcl folder installed by vcpkg to ./src . When I tried copying all the .h files, they seemed to lose track of one another as they refer to eachother through which module they are placed in, e.g. <pcl/memory.h> cannot be found if memory.h is placed directly in ./src. However, flattening the structure of the modules means that every single dependency and #include must be manually changed, in some cases there are also files with the same name in different folders. e.g. pcl/kdtree.h and pcl/search/kdtree.h. After this, it must be done again when replacing < > with " " for each header.
Is there any way of telling Rcpp that the library included in /src is structured?
I'm working on Win 10 winx64.
Since I'm making use of the depends RcppEigen and BH; and I must have C++14 or higher (choice: C++17) I add to my DESCRIPTION file:
LinkingTo: Rcpp, RcppEigen, BH
SystemRequirements: C++17
My actual C++ function:
//PCL requires at least C++14
//[[Rcpp::plugins(cpp17)]]
//[[Rcpp::depends(RcppEigen)]]
//[[Rcpp::depends(BH)]]
#include <Rcpp.h>
#include <iostream>
#include "pcl/io/pcd_io.h"
#include "pcl/point_types.h"
#include "pcl/registration/icp.h"
//[[Rcpp::export]]
int cloudSize(Rcpp::DataFrame x)
{
pcl::PointCloud<pcl::PointXYZ> sourceCloud;
for(int i=0;i<x.nrows();i++)
{
sourceCloud.push_back(pcl::PointXYZ(x[0][i],x[1][i],x[2][i])); //This way of referring to elements in a Rcpp::DataFrame may be erroneous.
}
int cloudSize = sourceCloud->size();
return (cloudSize);
}
That is a non-trivial question. In the simplest case, use a 'hook' offered by configure and configure.win to pre-build a (static) library you ship in your sources and then link your package to that.
That said, the Writing R Extensions manual and/or the CRAN Repository Policy (both of which are the references here) expressed more of a preference for an external library -- which may not be an option here if PCL is too exotic.
As the topic comes up with Rcpp, I wrote a short paper about it (at arXiv here) which is also included as a vignette in the package. It requires a few pages to cover the common cases but even then it cannot cover all.
Your main source of reference may be CRAN. The are lots of packages in this space. A few of mine use external libraries, I contributed to package nloptr which uses a hybrid approach ("use system library if found, else build") and some like httpuv always build (a small-ish library).