R Programming week 3-Debugging


Something’s Wrong!

Indications that something’s not right

message: A generic notification/diagnostic message produced by the message function;execution of the function continues

warning: An indication that something is wrong but not necessarily fatal; execution of thefunction continues; generated by the warning function

error: An indication that a fatal problem has occurred; execution stops; produced by the stop function

condition: A generic concept for indicating that something unexpected can occur; programmers can create their own conditions

How do you know that something is wrong with your function?

What was your input?

How did you call the function?

What were you expecting? Output, messages, other results?

What did you get?

How does what you get differ from what you were expecting?

Were your expectations correct in the first place?

Can you reproduce the problem (exactly)?

Debugging Tools in R

The primary tools for debugging functions in R are:

traceback: prints out the function call stack after an error occurs; does nothing if there’s no error

debug: flags a function for “debug” mode which allows you to step through execution of a function one line at a time

browser: suspends the execution of a function wherever it is called and puts the function in debug mode

trace: allows you to insert debugging code into a function a specific places

recover: allows you to modify the error behavior so that you can browse the function call stack

These are interactive tools specifically designed to allow you to pick through a function. There’s also the more blunt technique of inserting print/cat statements in the function.


> lm(y ~ x)

Error in eval(expr, envir, enclos) : object ’y’ not found

> traceback()

7: eval(expr, envir, enclos)

6: eval(predvars, data, env)

5: model.frame.default(formula = y ~ x, drop.unused.levels = TRUE)

4: model.frame(formula = y ~ x, drop.unused.levels = TRUE)

3: eval(expr, envir, enclos)

2: eval(mf, parent.frame())

1: lm(y ~ x)


> debug(lm)

> lm(y ~ x)

debugging in: lm(y ~ x)

debug: {

ret.x <- x

ret.y <- y

cl <- match.call()


if (!qr)

z$qr <- NULL





Browse[2]> n

debug: ret.x <- x

Browse[2]> n

debug: ret.y <- y

Browse[2]> n

debug: cl <- match.call()

Browse[2]> n

debug: mf <- match.call(expand.dots = FALSE)

Browse[2]> n

debug: m <- match(c("formula", "data", "subset", "weights", "na.action",

"offset"), names(mf), 0L)


> options(error = recover)

> read.csv("nosuchfile")

Error in file(file, "rt") : cannot open the connection

In addition: Warning message:

In file(file, "rt") :

cannot open file ’nosuchfile’: No such file or directory

Enter a frame number, or 0 to exit

1: read.csv("nosuchfile")

2: read.table(file = file, header = header, sep = sep, quote = quote, dec =

3: file(file, "rt")



There are three main indications of a problem/condition: message, warning, error- only an error is fatal

When analyzing a function with a problem, make sure you can reproduce the problem, clearly state your expectations and how the output differs from your expectation

Interactive debugging tools traceback, debug, browser, trace, and recover can be used to find problematic code in functions

Debugging tools are not a substitute for thinking!