covr
Test Coverage for Packages
Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' < https://codecov.io> or 'Coveralls' < https://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.
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 versiondevtools::install_github("r-lib/covr")The easiest way to setup covr on Travis-CI is with usethis.
usethis::use_coverage()Usage
A coverage report can be used to inspect coverage for each line in your
package. Using report() requires shiny.
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 `getwd()` is the package's directory.package_coverage() # or a package in another directorycov <- package_coverage("/dir/lintr") # view results as a data.frameas.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)Manual Installation
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.
r_github_packages: - r-lib/covr after_success: - Rscript -e 'covr::codecov()'If you are using Appveyor CI, and are not using
Travis-CI at the same time, then you can add the
lines below to your project's appveyor.yml:
on_success: - Rscript -e "covr::codecov()"Don't forget to add covr to the Suggests: field of your package's
DESCRIPTION file; possibly also to Remotes: for r-lib/covr.
For further details regarding Appveyor CI integration, also have a look at r-appveyor.
To use a different CI service or call codecov() locally you can set the
environment variable CODECOV_TOKEN to the token generated on codecov.io.
Codecov currently has support for the following CI systems (* denotes support
without needing CODECOV_TOKEN).
You will also need to enable the repository on Codecov.
Coveralls
Alternatively you can upload your results to Coveralls
using coveralls().
r_github_packages: - r-lib/covr 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 functionspackage_coverage(function_exclusions = "print\\.") # exclude `.onLoad` functionpackage_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.Rpackage_coverage(line_exclusions = "R/test.R") # exclude lines 1 to 10 and 15 from R/test.Rpackage_coverage(line_exclusions = list("R/test.R" = c(1:10, 15))) # exclude lines 1 to 10 from R/test.R, all of R/test2.Rpackage_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 endThe patterns used can be specified by setting the global options
covr.exclude_pattern, covr.exclude_start, covr.exclude_end.
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
News
3.2.1
- Fix for regression when testing coverage of packages using mclapply (#335).
3.2.0
Breaking changes
- Previously deprecated
shine()has been removed. Instead usereport().
New Features
-
file_report()added when viewing coverage for a single file (#308). -
display_name()is now exported, which can be useful to filter the coverage object by filename. -
environment_coverage()added, mainly so it can be used fordevtools::test_coverage_file(). -
gitlab()function added to create a coverage report for GitLab using GitLab's internal pages (@surmann, #327, #331). -
The (optional) dependency on shiny has been removed.
report()can now be built with only DT and htmltools installed.
Bugfixes and minor improvements
-
Fix for gcc-8 gcov output producing lines with no coverage counts in them (#328)
-
impute_srcref()now handles...and drop through arguments in switch statements (#325). -
tally_coverage()now avoids an error when there are NA values in the source references (#322). -
covr(clean = TRUE)now cleans the temporary library as well (#144) -
package_coverage()now returns the end of the file if there is a test error (#319) -
report()now handles reports in relative paths with subdirectories correctly (#329) -
report()reworked to look more like codecov.io and to display the overall coverage (#302, #307). -
DT explicitly loaded early in
report()so that failures will occur fast if it is not installed. (#321, @renkun-ken).
3.1.0
Breaking changes
shine()has been deprecated in favor ofreport().
New Features
-
Add support for
.covrignorefiles (#238), to exclude files from the coverage. -
Support future versions of R which do not use parse data by default (#309).
-
Allow using
trace_calls()for manually adding functions to package trace that are not found automatically (#295, @mb706).
Bugfixes
-
Fix errors when R is not in the
PATH(#291) -
Fix line computations when relative paths are being used (#242).
-
Fix for Coveralls
Build processing error.(#285) on pro accounts from Travis CI (#306, @kiwiroy). -
Keep attributes of function bodies (#311, @gaborcsardi)
3.0.1
-
Add an RStudio Addin for running a coverage report.
-
Never use mcexit fix on windows (#223).
-
Fix for a performance regression in parsing and reading parse data (#274).
-
Fix
switchsupport for packages, which was broken due to a bug in how parse data is stored in packages. -
Improve behavior of
switchcoverage, it now supports default values and fall through properly. -
Add
-pflag to gcov command to preserve file paths. Fixes a bug where gcov output didn't get reported when multiple compiled source files had the same name (#271, @patperry)
3.0.0
- The covr license has been changed to GPL-3.
- Set environment variable
R_COVR=truewhen covr is running (#236, #268). - Made the gather-and-merge-results step at the end of package_coverage() more memory efficient (#226, @HenrikBengtsson).
- Support code coverage with icc (#247, @QinWang).
2.2.2
filter_not_package_files()now works if a source reference does not have a filename (#254, @hughjonesd).- Fix test broken with xml2 v1.1.0
- Filter out non-local filenames from results (#237).
- Vignette rewrite / improvements (#229, @CSJCampbell).
- Fix code that returns
structure(NULL, *)which is deprecated in R 3.4.0 (#260, #261, @renkun-ken).
2.2.1
- Fix test broken with DT 0.2
2.2.0
- Fix tests broken with updated htmlwidgets
- Change report tab title based on filename (Chen Liang).
- Add support for cobertura XML output (@wligtenberg).
- Add mcparallel support by patching
mcparallel:::mcexit()automatically for packages using parallel (#195, @kforner).
2.1.0
- Add support for GitLab CI (#190, @enbrown).
- Update exclusion documentation to include line_exclusions and function exclusions (#191).
- Support coverage of R6 methods (#174).
- Explicitly set default packages (including methods) (#183, #180)
- Set R_LIBS and R_LIBS_SITE as well as R_LIBS_USER (#188).
- Automatically exclude RcppExport files (#170).
- Memoised and Vectorized functions now able to be tracked.
2.0.1
- Support for filtering by function as well as line.
- Now tracks coverage for RC methods
- Rewrote loading and saving to support parallel code and tests including
quit()calls. - Made passing code to
function_coverage()andpackage_coverage()not use non-standard evaluation. NULLstatements are analyzed for coverage (#156, @krlmlr).- Finer coverage analysis for brace-less
if,whileandforstatements (#154, @krlmlr). - Run any combination of coverage types (#104, #133)
- Remove inconsistencies in line counts between shiny app and services (#129)
- Include header files in gcov output (#112)
- Add support for C++11 (#131)
- Always clean gcov files even on failure (#108)
- zero_coverage works with RStudio markers (#119)
- Remove the devtools dependency
1.3.0
- Set
.libPaths()in subprocess to match those in calling process (#140, #147). - Move devtools dependency to suggests, only needed on windows
- move htmltools to suggests