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Each section provides a function that supposedly works as expected, but quickly proves to misbehave. The exercise aims at first writing some dedicated testing functions that will identify the problems and then update the function so that it passes the specific tests. This practice is called unit testing and we use the RUnit package for this. For details on unit testing using RUnit see http://bioconductor.org/developers/how-to/unitTesting-guidelines/.

Subsetting

The buggy function

## Example
isIn <- function(x, y) {
    sel <- match(x, y)
    y[sel]
}

## Expected
x <- sample(LETTERS, 5)
isIn(x, LETTERS)

## Bug!
isIn(c(x, "a"), LETTERS)

A unit test and a solution

## Unit test:
library("RUnit")
test_isIn <- function() {
    x <- c("A", "B", "Z")
    checkIdentical(x, isIn(x, LETTERS))
    checkIdentical(x, isIn(c(x, "a"), LETTERS))

}

test_isIn()

## updated function
isIn <- function(x, y) {
    sel <- x %in% y
    x[sel]
}

test_isIn()

Character matching

The buggy function

## Example
isExactIn <- function(x, y)
    y[grep(x, y)]

## Expected
isExactIn("a", letters)

## Bugs
isExactIn("a", c("abc", letters))
isExactIn(c("a", "z"), c("abc", letters))

A unit test and a solution

## Unit test:
library("RUnit")
test_isExactIn <- function() {
    checkIdentical("a", isExactIn("a", letters))
    checkIdentical("a", isExactIn("a", c("abc", letters)))
    checkIdentical(c("a", "z"), isExactIn(c("a", "z"), c("abc", letters)))
}

test_isExactIn()

## updated function:
isExactIn <- function(x, y)
    x[x %in% y]

test_isExactIn()

If conditions with length > 1

The buggy function

## Example
ifcond <- function(x, y) {
    if (x > y) {
        ans <- x*x - y*y
    } else {
        ans <- x*x + y*y
    } 
    ans
}

## Expected
do(3, 2)
do(2, 2)
do(1, 2)

## Bug!
do(3:1, c(2, 2, 2))

A unit test and a solution

## Unit test:
library("RUnit")
test_ifcond <- function() {
    checkIdentical(5, ifcond(3, 2))
    checkIdentical(8, ifcond(2, 2))
    checkIdentical(5, ifcond(1, 2))
    checkIdentical(c(5, 8, 5), ifcond(3:1, c(2, 2, 2)))
}

test_ifcond()

## updated function:
ifcond <- function(x, y)
    ifelse(x > y, x*x - y*y, x*x + y*y)

test_ifcond()

Know your inputs

The function

## Example
distances <- function(point, pointVec) {
    x <- point[1]
    y <- point[2]
    xVec <- pointVec[,1]
    yVec <- pointVec[,2]
    dist <- sqrt((xVec - x)^2 + (yVec - y)^2)
    return(dist)
}

## Expected
x <- rnorm(5)
y <- rnorm(5)

m <- cbind(x, y)
p <- m[1, ]

distances(p, m)

## Bug!
dd <- data.frame(x, y)
q <- dd[1, ]

distances(q, dd)

A unit test and a solution

## Unit test:
library("RUnit")
test_distances <- function() {
    x <- y <- c(0, 1, 2)
    m <- cbind(x, y)
    p <- m[1, ]
    dd <- data.frame(x, y)
    q <- dd[1, ]
    expct <- c(0, sqrt(c(2, 8)))
    checkIdentical(expct, distances(p, m))
    checkIdentical(expct, distances(q, dd))
}

test_distances()

## updated function
distances <- function(point, pointVec) {
    point <- as.numeric(point)
    x <- point[1]
    y <- point[2]
    xVec <- pointVec[,1]
    yVec <- pointVec[,2]
    dist <- sqrt((xVec - x)^2 + (yVec - y)^2)
    return(dist)
}

test_distances()

Iterate on 0 length

The buggy function

## Example
sqrtabs <- function(x) {
    v <- abs(x)
    sapply(1:length(v), function(i) sqrt(v[i]))
}

## Expected
all(sqrtabs(c(-4, 0, 4)) == c(2, 0, 2))

## Bug!
sqrtabs(numeric())

A unit tests and a solution

## Unit test:
library(RUnit)
test_sqrtabs <- function() {
    checkIdentical(c(2, 0, 2), sqrtabs(c(-4, 0, 4)))
    checkIdentical(numeric(), sqrtabs(numeric()))
}
test_sqrtabs()

## updated function:
sqrtabs <- function(x) {
  v <- abs(x)
  sapply(seq_along(v), function(i) sqrt(v[i]))
}
test_sqrtabs()                          # nope!

sqrtabs <- function(x) {
  v <- abs(x)
  vapply(seq_along(v), function(i) sqrt(v[i]), 0)
}
test_sqrtabs()                          # yes!