RcppChoose

RcppChoose is an example of project that combines two parts, C++ code (libChoose/) and R package (rpackage/).

Install

# 1. compile the c++ library 
# - output: libChoose/libChoose.a
pushd libChoose/
make
popd

# 2. prepare Makefile for R package
# - output: rpkg/RcppChoose/src/Makevars
pushd rpkg
autoconf
./configure
popd

# 3. check R package is ready to use 
Rscript --slave -e "devtools::load_all('rpkg/RcppChoose')"

Usage

devtools::load_all("rpkg/RcppChoose")
#> Loading RcppChoose

Example

This is a basic example which shows you how to choose k out of n numbers.

library(RcppChoose)

# 1. choose: base R vs. RcppChoose implementation
# 1a. choose(10, 5)
choose(10, 5)
#> [1] 252
rcpp_choose(10, 5)
#> [1] 252
# 1b. choose(40, 20)
choose(40, 20)
#> [1] 137846528820
rcpp_choose(40, 20)
#> [1] 106285226

# 100 samples of sets of size k = 500 out of n = 1000
rcpp_nchoosek_sample(1000, 500, 100)
#> [1] 100

Notes

Main references that explain how to link external C++ libraries to the R/Rcpp package.

Blog post An Autoconf Primer for R Package Authors.
Minimal Makevars.in example in SO.
Example rbgen R package; see blog posts.
The R official manual.

Other notes

configure.ac is included in the list of known files relevant for the R package development. So adding configure.ac to .Rbuildignore will have no effect, and the R building/loading commands will execute configure.ac.

Here, this configuration file is separated from the source of R package in the directory rpkg/: rpkg/configure.ac and the R package directory rpkg/RcppChoose/.

The compilation flag -fPIC is necessary for building shared libraries. Ommiting this flag will lead to the following error.

/usr/bin/ld: RcppChoose/rpkg/../libChoose//libChoose.a(choose.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
RcppChoose/rpkg/../libChoose//libChoose.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'RcppChoose.so' failed

SO on compilation of the shared library.
Notes on using C++11 with Rcpp.

As even the current g++ version does of course support C++11 by default, one still needs to explicitly enable C++11 support which we can do here from R prior to compiling.