covr

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Track test coverage for your R package and view reports locally or (optionally) upload the results to codecov or coveralls.

Installation

install.packages("covr")

# For devel version
devtools::install_github("r-lib/covr")

The easiest way to setup covr on Travis-CI is with usethis.

usethis::use_coverage()

Usage

For local development a coverage report can be used to inspect coverage for each line in your package. Note requires the DT package to be installed.

library(covr)

# If run with no arguments implicitly calls `package_coverage()`
report()

covr also defines an RStudio Addin, which runs report() on the active project. This can be used via the Addin menu or by binding the action to a shortcut, e.g. Ctrl-Shift-C.

Interactively

# If run with the working directory within the package source.
package_coverage()

# or a package in another directory
cov <- package_coverage("/dir/lintr")

# view results as a data.frame
as.data.frame(cov)

# zero_coverage() shows only uncovered lines.
# If run within RStudio, `zero_coverage()` will open a marker pane with the
# uncovered lines.
zero_coverage(cov)

Automated reports

Codecov

If you are already using Travis-CI add the following to your project’s .travis.yml to track your coverage results over time with Codecov.

after_success:
  - Rscript -e 'covr::codecov()'

If you are using Appveyor CI then you can add the lines below to your project’s appveyor.yml:

on_success:
  - Rscript -e "covr::codecov()"

You also need to install covr, either by adding it to the Suggests: field of your package’s DESCRIPTION file or also to Remotes: r-lib/covr if you want to install the development version.

To use other CI services or if you want to upload a coverage report locally you can set environment variable CODECOV_TOKEN to the token generated on the settings page of https://codecov.io.

Coveralls

Alternatively you can upload your results to Coveralls using covr::coveralls().

after_success:
  - Rscript -e 'covr::coveralls()'

For CI systems not supported by coveralls you need to set the COVERALLS_TOKEN environment variable. It is wise to use a Secure Variable so that it is not revealed publicly.

Also you will need to turn on coveralls for your project at https://coveralls.io/repos.

Exclusions

covr supports a few of different ways of excluding some or all of a file.

.covrignore file

A .covrignore file located in your package’s root directory can be used to exclude files or directories.

The lines in the .covrignore file are interpreted as a list of file globs to ignore. It uses the globbing rules in Sys.glob(). Any directories listed will ignore all the files in the directory.

Alternative locations for the file can be set by the environment variable COVR_COVRIGNORE or the R option covr.covrignore.

The .covrignore file should be added to your .RBuildignore file unless you want to distribute it with your package. If so it can be added to inst/.covrignore instead.

Function Exclusions

The function_exclusions argument to package_coverage() can be used to exclude functions by name. This argument takes a vector of regular expressions matching functions to exclude.

# exclude print functions
package_coverage(function_exclusions = "print\\.")

# exclude `.onLoad` function
package_coverage(function_exclusions = "\\.onLoad")

Line Exclusions

The line_exclusions argument to package_coverage() can be used to exclude some or all of a file. This argument takes a list of filenames or named ranges to exclude.

# exclude whole file of R/test.R
package_coverage(line_exclusions = "R/test.R")

# exclude lines 1 to 10 and 15 from R/test.R
package_coverage(line_exclusions = list("R/test.R" = c(1:10, 15)))

# exclude lines 1 to 10 from R/test.R, all of R/test2.R
package_coverage(line_exclusions = list("R/test.R" = c(1, 10), "R/test2.R"))

Exclusion Comments

In addition you can exclude lines from the coverage by putting special comments in your source code.

This can be done per line.

f1 <- function(x) {
  x + 1 # nocov
}

Or by specifying a range with a start and end.

f2 <- function(x) { # nocov start
  x + 2
} # nocov end

The patterns used can be specified by setting the global options covr.exclude_pattern, covr.exclude_start, covr.exclude_end.

NB: The same pattern applies to exclusions in the src folder, so skipped lines in, e.g., C code (where comments can start with //) should look like // # nocov.

FAQ

Will covr work with testthat, RUnit, etc…

Covr should be compatible with any testing package, it uses tools::testInstalledPackage() to run your packages tests.

Will covr work with alternative compilers such as ICC

Covr now supports Intel’s icc compiler, thanks to work contributed by Qin Wang at Oracle.

Covr is known to work with clang versions 3.5+ and gcc version 4.2+.

If the appropriate gcov version is not on your path you can set the appropriate location with the covr.gcov options. If you set this path to "" it will turn off coverage of compiled code.

options(covr.gcov = "path/to/gcov")

How does covr work?

covr tracks test coverage by modifying a package’s code to add tracking calls to each call.

The vignette vignettes/how_it_works.Rmd contains a detailed explanation of the technique and the rationale behind it.

You can view the vignette from within R using

vignette("how_it_works", package = "covr")

Why can’t covr run during R CMD check

Because covr modifies the package code it is possible there are unknown edge cases where that modification affects the output. In addition when tracking coverage for compiled code covr compiles the package without optimization, which can modify behavior (usually due to package bugs which are masked with higher optimization levels).

Alternative Coverage Tools