Patches to add code coverage support in the R interpreter.

This repository contains patches of the R interpreter source code to add code coverage support. It allows to know which exact lines of source code were exercized/hit/covered while running some piece of code (usually a test suite). The easiest way to test it is using our docker container: https://github.com/quartzbio/r-coverage-docker

As stated above, you can just use the docker container. To patch it manually:

1. choose the appropriate patch corresponding to the version of the R interpreter you are going to use.
2. get the source code of the R version (download and untar)
3. patch the source code (patch)
4. configure the source directory (./configure)
5. compile and install (make; make install)

The project is organized in sudirectories per supported R version, e.g. r302 for R version 3.0.2. The above steps are somewhat automated using a Makefile (you need probably GNU make). For example, to download, untar, patch, configure, make and install R-3.0.2:

git clone https://github.com/quartzbio/r-coverage-patch.git
cd r-coverage-patch/r302/
# download, untar and patch
make apply_production_patch 
# install in ./local/
make install 
# Or install in a custom place
make install PREFIX=/whatever/
# run it
./local/bin/R

I added a condition in the internal C function getSrcref(), that records the line numbers if the code coverage is started (via Rcov_start()). The overhead should be minimal since for a given file, subsequent covered lines will be stored in constant time. I use a hashed env to store the occurrences by file.

I added two entry points in the utils package (Rcov_start() and Rcov_stop())

For convenience (Caution: it can be outdated), I included the main patched file in the repo, you can view it here: https://github.com/quartzbio/r-coverage-patch/blob/master/r302/patched_files/eval.c

(see also https://github.com/quartzbio/r-coverage-docker#usage).

Start the patched R interpreter, then:

library(devtools)
pkg  <- download.packages('testthat', '.', repos = "https://stat.ethz.ch/CRAN")
untar(pkg[1, 2])
Rcov_start()
test('testthat')
res <- as.list(Rcov_stop())
print(res)