Ever used an R function that produced a not-very-helpful error message, just to discover after minutes of debugging that you simply passed a wrong argument?

Blaming the laziness of the package author for not doing such standard checks (in a dynamically typed language such as R) is at least partially unfair, as R makes theses types of checks cumbersome and annoying. Well, that’s how it was in the past.

Enter checkmate.

Virtually every standard type of user error when passing arguments into function can be caught with a simple, readable line which produces an informative error message in case. A substantial part of the package was written in C to minimize any worries about execution time overhead.

## Intro

As a motivational example, consider you have a function to calculate the faculty of a natural number and the user may choose between using either the stirling approximation or R’s factorial function (which internally uses the gamma function). Thus, you have two arguments, n and method. Argument n must obviously be a positive natural number and method must be either "stirling" or "factorial". Here is a version of all the hoops you need to jump through to ensure that these simple requirements are met:

fact <- function(n, method = "stirling") {
if (length(n) != 1)
stop("Argument 'n' must have length 1")
if (!is.numeric(n))
stop("Argument 'n' must be numeric")
if (is.na(n))
stop("Argument 'n' may not be NA")
if (is.double(n)) {
if (is.nan(n))
stop("Argument 'n' may not be NaN")
if (is.infinite(n))
stop("Argument 'n' must be finite")
if (abs(n - round(n, 0)) > sqrt(.Machine$double.eps)) stop("Argument 'n' must be an integerish value") n <- as.integer(n) } if (n < 0) stop("Argument 'n' must be >= 0") if (length(method) != 1) stop("Argument 'method' must have length 1") if (!is.character(method) || !method %in% c("stirling", "factorial")) stop("Argument 'method' must be either 'stirling' or 'factorial'") if (method == "factorial") factorial(n) else sqrt(2 * pi * n) * (n / exp(1))^n } And for comparison, here is the same function using checkmate: fact <- function(n, method = "stirling") { assertCount(n) assertChoice(method, c("stirling", "factorial")) if (method == "factorial") factorial(n) else sqrt(2 * pi * n) * (n / exp(1))^n } ## Function overview The functions can be split into four functional groups, indicated by their prefix. If prefixed with assert, an error is thrown if the corresponding check fails. Otherwise, the checked object is returned invisibly. There are many different coding styles out there in the wild, but most R programmers stick to either camelBack or underscore_case. Therefore, checkmate offers all functions in both flavors: assert_count is just an alias for assertCount but allows you to retain your favorite style. The family of functions prefixed with test always return the check result as logical value. Again, you can use test_count and testCount interchangeably. Functions starting with check return the error message as a string (or TRUE otherwise) and can be used if you need more control and, e.g., want to grep on the returned error message. expect is the last family of functions and is intended to be used with the testthat package. All performed checks are logged into the testthat reporter. Because testthat uses the underscore_case, the extension functions only come in the underscore style. All functions are categorized into objects to check on the package help page. ## In case you miss flexibility You can use assert to perform multiple checks at once and throw an assertion if all checks fail. Here is an example where we check that x is either of class foo or class bar: f <- function(x) { assert( checkClass(x, "foo"), checkClass(x, "bar") ) } Note that assert(, combine = "or") and assert(, combine = "and") allow to control the logical combination of the specified checks, and that the former is the default. ## Argument Checks for the Lazy The following functions allow a special syntax to define argument checks using a special format specification. E.g., qassert(x, "I+") asserts that x is an integer vector with at least one element and no missing values. This very simple domain specific language covers a large variety of frequent argument checks with only a few keystrokes. You choose what you like best. ## checkmate as testthat extension To extend testthat, you need to IMPORT, DEPEND or SUGGEST on the checkmate package. Here is a minimal example: # file: tests/test-all.R library(testthat) library(checkmate) # for testthat extensions test_check("mypkg") Now you are all set and can use more than 30 new expectations in your tests. test_that("checkmate is a sweet extension for testthat", { x = runif(100) expect_numeric(x, len = 100, any.missing = FALSE, lower = 0, upper = 1) # or, equivalent, using the lazy style: qexpect(x, "N100[0,1]") }) ## Speed considerations In comparison with tediously writing the checks yourself in R (c.f. factorial example at the beginning of the vignette), R is sometimes a tad faster while performing checks on scalars. This seems odd at first, because checkmate is mostly written in C and should be comparably fast. Yet many of the functions in the base package are not regular functions, but primitives. While primitives jump directly into the C code, checkmate has to use the considerably slower .Call interface. As a result, it is possible to write (very simple) checks using only the base functions which, under some circumstances, slightly outperform checkmate. However, if you go one step further and wrap the custom check into a function to convenient re-use it, the performance gain is often lost (see benchmark 1). For larger objects the tide has turned because checkmate avoids many unnecessary intermediate variables. Also note that the quick/lazy implementation in qassert/qtest/qexpect is often a tad faster because only two arguments have to be evaluated (the object and the rule) to determine the set of checks to perform. Below you find some (probably unrepresentative) benchmark. But also note that this one here has been executed from inside knitr which is often the cause for outliers in the measured execution time. Better run the benchmark yourself to get unbiased results. ### Benchmark 1: Assert that x is a flag library(checkmate) library(ggplot2) library(microbenchmark) x = TRUE r = function(x, na.ok = FALSE) { stopifnot(is.logical(x), length(x) == 1, na.ok || !is.na(x)) } cm = function(x) assertFlag(x) cmq = function(x) qassert(x, "B1") mb = microbenchmark(r(x), cm(x), cmq(x)) print(mb) ## Unit: microseconds ## expr min lq mean median uq max neval ## r(x) 5.251 5.6160 175.31084 5.7850 5.965 16931.787 100 ## cm(x) 3.498 3.7205 16.89482 4.0100 4.179 1123.842 100 ## cmq(x) 2.535 2.6820 49.81749 2.9155 3.126 4627.816 100 autoplot(mb) ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. ### Benchmark 2: Assert that x is a numeric of length 1000 with no missing nor NaN values x = runif(1000) r = function(x) stopifnot(is.numeric(x), length(x) == 1000, all(!is.na(x) & x >= 0 & x <= 1)) cm = function(x) assertNumeric(x, len = 1000, any.missing = FALSE, lower = 0, upper = 1) cmq = function(x) qassert(x, "N1000[0,1]") mb = microbenchmark(r(x), cm(x), cmq(x)) print(mb) ## Unit: microseconds ## expr min lq mean median uq max neval ## r(x) 18.592 20.6575 92.16226 26.6315 33.1000 6227.570 100 ## cm(x) 8.029 8.6795 30.18130 9.8305 11.2345 1739.368 100 ## cmq(x) 7.726 8.1335 22.70707 9.1835 10.1870 1241.411 100 autoplot(mb) ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. ### Benchmark 3: Assert that x is a character vector with no missing values nor empty strings x = sample(letters, 10000, replace = TRUE) r = function(x) stopifnot(is.character(x), !any(is.na(x)), all(nchar(x) > 0)) cm = function(x) assertCharacter(x, any.missing = FALSE, min.chars = 1) cmq = function(x) qassert(x, "S+[1,]") mb = microbenchmark(r(x), cm(x), cmq(x)) print(mb) ## Unit: microseconds ## expr min lq mean median uq max neval ## r(x) 1343.663 1421.1435 1656.7193 1443.869 1532.3315 10128.188 100 ## cm(x) 101.990 105.6155 131.1643 109.284 119.2535 1461.645 100 ## cmq(x) 114.415 117.5250 144.1785 118.736 127.0350 1684.160 100 autoplot(mb) ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. ### Benchmark 4: Test that x is a data frame with no missing values N = 10000 x = data.frame(a = runif(N), b = sample(letters[1:5], N, replace = TRUE), c = sample(c(FALSE, TRUE), N, replace = TRUE)) r = function(x) is.data.frame(x) && !any(sapply(x, function(x) any(is.na(x)))) cm = function(x) testDataFrame(x, any.missing = FALSE) cmq = function(x) qtest(x, "D") mb = microbenchmark(r(x), cm(x), cmq(x)) print(mb) ## Unit: microseconds ## expr min lq mean median uq max neval ## r(x) 137.140 172.0190 218.23345 174.0405 177.6215 4275.365 100 ## cm(x) 49.142 51.4285 70.60613 53.0165 54.5490 1530.961 100 ## cmq(x) 37.447 38.6460 51.36826 39.4460 39.8985 1132.218 100 autoplot(mb) ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. # checkmate tries to stop as early as possible x$a = NA
mb = microbenchmark(r(x), cm(x), cmq(x))
print(mb)
## Unit: microseconds
##    expr    min       lq      mean   median       uq     max neval
##    r(x) 94.467 151.4685 155.32901 154.0175 156.5345 209.756   100
##   cm(x)  7.626   8.4795  10.61491  11.0470  12.4250  28.137   100
##  cmq(x)  1.467   1.8405   2.75603   2.5805   3.6205  14.948   100
autoplot(mb)
## Coordinate system already present. Adding new coordinate system, which will replace the existing one. ### Benchmark 5: Assert that x is an increasing sequence of integers with no missing values

N = 10000
x.altrep = seq_len(N) # this is an ALTREP in R version >= 3.5.0
x.sexp = c(x.altrep)  # this is a regular SEXP OTOH
r = function(x) stopifnot(is.integer(x), !any(is.na(x)), !is.unsorted(x))
cm = function(x) assertInteger(x, any.missing = FALSE, sorted = TRUE)
mb = microbenchmark(r(x.sexp), cm(x.sexp), r(x.altrep), cm(x.altrep))
print(mb)
## Unit: microseconds
##          expr    min      lq      mean  median      uq      max neval
##     r(x.sexp) 47.345 65.7290 102.99725 66.6845 68.1475 3541.364   100
##    cm(x.sexp) 19.031 19.7945  21.16492 21.2755 22.1755   35.944   100
##   r(x.altrep) 56.966 76.2870  79.29206 77.1715 78.7520  138.955   100
##  cm(x.altrep)  5.102  5.9010  19.81671  7.7730  8.3825 1175.151   100
autoplot(mb)
## Coordinate system already present. Adding new coordinate system, which will replace the existing one. ## Extending checkmate

To extend checkmate a custom check* function has to be written. For example, to check for a square matrix one can re-use parts of checkmate and extend the check with additional functionality:

checkSquareMatrix = function(x, mode = NULL) {
# check functions must return TRUE on success
# and a custom error message otherwise
res = checkMatrix(x, mode = mode)
if (!isTRUE(res))
return(res)
if (nrow(x) != ncol(x))
return("Must be square")
return(TRUE)
}

# a quick test:
X = matrix(1:9, nrow = 3)
checkSquareMatrix(X)
##  TRUE
checkSquareMatrix(X, mode = "character")
##  "Must store characters"
checkSquareMatrix(X[1:2, ])
##  "Must be square"

The respective counterparts to the check-function can be created using the constructors makeAssertionFunction, makeTestFunction and makeExpectationFunction:

# For assertions:
assert_square_matrix = assertSquareMatrix = makeAssertionFunction(checkSquareMatrix)
print(assertSquareMatrix)
## function (x, mode = NULL, .var.name = checkmate::vname(x), add = NULL)
## {
##     if (missing(x))
##         stop(sprintf("argument \"%s\" is missing, with no default",
##             .var.name))
##     res = checkSquareMatrix(x, mode)
## }
# For tests:
test_square_matrix = testSquareMatrix = makeTestFunction(checkSquareMatrix)
print(testSquareMatrix)
## function (x, mode = NULL)
## {
##     isTRUE(checkSquareMatrix(x, mode))
## }
# For expectations:
expect_square_matrix = makeExpectationFunction(checkSquareMatrix)
print(expect_square_matrix)
## function (x, mode = NULL, info = NULL, label = vname(x))
## {
##     if (missing(x))
##         stop(sprintf("Argument '%s' is missing", label))
##     res = checkSquareMatrix(x, mode)
##     makeExpectation(x, res, info, label)
## }

Note that all the additional arguments .var.name, add, info and label are automatically joined with the function arguments of your custom check function. Also note that if you define these functions inside an R package, the constructors are called at build-time (thus, there is no negative impact on the runtime).

## Calling checkmate from C/C++

The package registers two functions which can be used in other packages’ C/C++ code for argument checks.

SEXP qassert(SEXP x, const char *rule, const char *name);
Rboolean qtest(SEXP x, const char *rule);

These are the counterparts to qassert and qtest. Due to their simplistic interface, they perfectly suit the requirements of most type checks in C/C++.

For detailed background information on the register mechanism, see the Exporting C Code section in Hadley’s Book “R Packages” or WRE. Here is a step-by-step guide to get you started:

1. Add checkmate to your “Imports” and “LinkingTo” sections in your DESCRIPTION file.
2. Create a stub C source file "checkmate_stub.c", see below.
3. Include the provided header file <checkmate.h> in each compilation unit where you want to use checkmate.

File contents for (2):

#include <checkmate.h>
#include <checkmate_stub.c>

## Session Info

For the sake of completeness, here the sessionInfo() for the benchmark (but remember the note before on knitr possibly biasing the results).

sessionInfo()
## R version 4.0.0 (2020-04-24)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.4
##
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
##  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
##  stats     graphics  grDevices utils     datasets  methods   base
##
## other attached packages:
##  microbenchmark_1.4-7 ggplot2_3.3.1        checkmate_2.0.0-9000
##
## loaded via a namespace (and not attached):
##   Rcpp_1.0.4.6       knitr_1.28         magrittr_1.5       MASS_7.3-51.5
##   munsell_0.5.0      colorspace_1.4-1   R6_2.4.1           rlang_0.4.6
##   stringr_1.4.0      tools_4.0.0        grid_4.0.0         gtable_0.3.0
##  xfun_0.14          withr_2.2.0        ellipsis_0.3.1     htmltools_0.4.0
##  yaml_2.2.1         assertthat_0.2.1   digest_0.6.25      rprojroot_1.3-2
##  tibble_3.0.1       lifecycle_0.2.0    pkgdown_1.4.1.9000 crayon_1.3.4
##  farver_2.0.3       vctrs_0.3.0        fs_1.4.1           glue_1.4.1
##  memoise_1.1.0      evaluate_0.14      rmarkdown_2.2      stringi_1.4.6
##  pillar_1.4.4       compiler_4.0.0     scales_1.1.1       desc_1.2.0
##  backports_1.1.7    pkgconfig_2.0.3