Debugging an R package with Compiled Code

Author :

License: MIT

Purpose:

This package is my attempt to understand debugging compiled code. I'm having difficulty debugging segmentation faults in R-TDA. Some outstanding questions :

1. How is the compiled code in R-TDA actually compiled. There isn't a Makefile or configure file?
2. Why can't I get useful debugging information in _TDA_Kde()?
3. How does R mangle (see Rcppexports.cpp) the functions in the src code?
4. How does ~/.R/Makevars control compilation flags.

Installation :

Steps :

1. install.packages("devtools")
2. devtools::install_github("klutometis/roxygen")

Running :

Notes :

If you've cloned this repo:

1. library(devtools); library(roxygen2)
2. document()

To create a raw package (NOT what you'll do if you've cloned this repo):

1. load devtools and roxygen2
2. create("debug.Compiled.R.Packages") # Create director
3. document() # Generates man and NAMESPACE
4. setwd(".."); install("debug.Compiled.R.Packages") a) Evidently, MUST have all code wrapped within functions. The files get sourced.
5. usethis::use_rcpp() a) Creates src b) Adds Rcpp to LinkingTo and Imports in DESCRIPTION c) Creates src/.gitignore so that compiled code doesn't accidently get committed to git repo
6. devtools::load_all() per ref 4 this is dangerous

On Compiling :

1. Note that package/src/Makevars takes precedence over ~/.R/Makevars. This is largely why I'm having difficulty debugging R-TDA
2. R magically compiles code into shared library

On Namespace :

1. Can selectively export functions to users, hold back other functions for internal use.
2. search() provides a list of search paths.
3. library() loads the package into memory and then adds it to search path. a) Never use in a package, only in external scripts calling the package

References :

1. Not So Standard Deviations by Hillary Parker
2. Fong Chun Chan's Blog
3. Compiled Code - R-pkgs.org
4. Understanding Makevars - Stackoverflow
5. Rcpp Vignettes
6. Writing R Extensions