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title Debugging
subtitle
author Roger D. Peng, Associate Professor of Biostatistics
job Johns Hopkins Bloomberg School of Public Health
logo bloomberg_shield.png
framework io2012
highlighter highlight.js
hitheme tomorrow
url
lib assets
../../libraries
../../assets
widgets
mathjax
mode selfcontained

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 the function 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

Something’s Wrong!

Warning

log(-1)
## Warning: NaNs produced

## [1] NaN

Something’s Wrong

printmessage <- function(x) {
        if(x > 0)
                print("x is greater than zero")
        else
                print("x is less than or equal to zero")
        invisible(x)
}

Something’s Wrong

printmessage <- function(x) {
    if (x > 0) 
        print("x is greater than zero") else print("x is less than or equal to zero")
    invisible(x)
}
printmessage(1)
## [1] "x is greater than zero"

printmessage(NA)
## Error: missing value where TRUE/FALSE needed

Something’s Wrong!

printmessage2 <- function(x) {
        if(is.na(x))
                print("x is a missing value!")
        else if(x > 0)
                print("x is greater than zero")
        else
                print("x is less than or equal to zero")
        invisible(x)
}

Something’s Wrong!

printmessage2 <- function(x) {
    if (is.na(x)) 
        print("x is a missing value!") else if (x > 0) 
        print("x is greater than zero") else print("x is less than or equal to zero")
    invisible(x)
}
x <- log(-1)
## Warning: NaNs produced

printmessage2(x)
## [1] "x is a missing value!"

Something’s Wrong!

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.

traceback

> mean(x)
Error in mean(x) : object 'x' not found
> traceback()
1: mean(x)
>

traceback

> 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

> 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 
    z
} 
Browse[2]>

debug

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)

recover

> 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")

Selection:

Debugging

Summary

  • 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!