Debugging

Diagnosing the problem

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

  Warning

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>log(-1)
  ## Warning: NaNs produced
  ## [1] NaN

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>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 <- 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

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)?

Basic Tools

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

traceback

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

> 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

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> 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]>
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

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> 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:

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!

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