The document discusses various debugging tools in R including writing small testable functions, traceback(), browser(), recover(), and options(error). It emphasizes that these tools should only be used when needed, and the best approach is to write modular code with isolated functions. Browser() allows dropping into an interactive session within a function to inspect values, while recover() and options(error) allow navigating the call stack to find the source of errors.

1. Stat405 Debugging
Hadley Wickham
Monday, 23 November 2009

2. Pop quiz
Which is the best way to solve a problem?
Write a giant function that tries to do
everything, and then when it doesn’t work
you have no idea where the problem is.
Write small functions that each do a single
task and can be tested easily. If there is a
problem, you can localise it to a few lines
of code
Monday, 23 November 2009

3. Tools of
last resort
Monday, 23 November 2009

4. If you’re using
them all the time,
something is
wrong with your
basic approach
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5. traceback()
browser()
recover()
options(error)
Monday, 23 November 2009

6. f <- function(x) {
h(x)
i(x)
}
g <- function(x) {
a <- 10
x
}
h <- function(x) {
i(x)
i(x)
}
i <- function(x) {
if (sample(5, 1) == 1) stop("This is an error!")
}
f()
traceback() # This is the call stack
Monday, 23 November 2009

7. Browser
Creates an interactive prompt in a function’s
environment
Four special commands (no brackets):
n = next line
c = continue (or just press return)
where = where am I in the call stack?
Q = quit
Can also use any regular R function
Monday, 23 November 2009

8. j <- function(x, y = 10) {
k(x, y)
}
k <- function(x, y) {
z <- 3
browser()
x + y
}
j(10)
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9. Your turn
Familiarise yourself with browser()
Try using ls() while you are browsing.
What do you see?
Try modifying the values inside the
function. What happens to the result?
Monday, 23 November 2009

10. Browser
debug(f) automatically adds a browser
statement to the start of f, undebug(f)
removes it.
debugonce(f) automatically removes it after
f is run for the first time
If the error occurs only under some
conditions you might want to put browser()
inside an if statement.
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11. Recover
Works like browser(), but lets you jump
anywhere in the call stack
Most usefully:
options(error = recover)
Monday, 23 November 2009

12. # Can change the default behaviour when an error occurs
options(error = recover)
f()
# Set to NULL to return to the default (i.e. do nothing)
options(error = NULL)
# Another useful option: turn warnings into errors
options(warn = 2)
# and turn them back
options(warn = 0)
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13. Your turn
Use options(error = recover) and
explore the call stack of f.
Use ls() to explore what variables are
defined in each environment
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14. # Your turn
# Use the tools you have just learned about to debug
# this function and create a version that works
larger <- function(x, y) {
y.is.bigger <- y > x
x[y.is.bigger] <- y[y.is.bigger]
x
}
larger(c(1, 5, 10), c(2, 4, 11))
larger(c(1, 5, 10), 6)
larger(c(1, 5, 10), c(2, 4, NA))
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15. Learn more
http://www.biostat.jhsph.edu/~rpeng/
docs/R-debug-tools.pdf
Monday, 23 November 2009