Exceptions Debugging

Dealing with errors and exceptions

Exceptions

Creating

• don't use cat() or print(), except for print methods, or for optional debugging information.

• use message() to inform the user about something expected - I often do this when filling in important missing arguments that have a non-trivial computation or impact. Two examples are reshape2::melt package which informs the user what melt and id variables where used if not specific, and plyr::join which informs which variables where used to join the two tables.

• use warning() for unexpected problems that aren't show stoppers

• use stop() when the problem is so big you can't continue

Handling

• try
• tryCatch

Examples:

• capturing all messages or warnings produced by a function
• capturing user interrupts: Ctrl + C

suppressWarnings, suppressMessages

Debugging

• traceback: show where error occurred
• browser: interact inside function environment. c, n, return, Q, where
• debug/undebug, debugonce: automatically inserts browser
• trace, untrace: automatically inserts any code
• recover, options(error = recover): automatic traceback + browser on error

If you're trying to track down where a warning occurs, it can be useful to turn it into an error with options(warn = 2). Turn back to default behaviour with options(warn = 0).

Don't forget that you can combine if statements with browser() to only debug when a certain situation occurs.

Trace

Our first step is to find all functions that have a na.rm argument. We'll do this by first building a list of all functions in base and stats, then inspecting their formals.

objs <- c(ls("package:base", "package:stats")) has_missing_arg <- function(name) { x <- get(name) if (!is.function(x)) return(FALSE)

args <- names(formals(x))
"na.rm" %in% args

} f_miss <- Filter(has_missing_arg, objs)

trace_all <- function(fs, tracer) { sapply(fs, trace, tracer = tracer, print = FALSE) return() }

trace_all(f_miss, quote(if(missing(na.rm)) stop("na.rm not set")))

But misses primitives

pmin(1:10, 1:10)

Error in eval(expr, envir, enclos) : na.rm not set

pmin(1:10, 1:10, na.rm = T)

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Exercises

1. Write a function that walks the code tree to find all functions that are missing an explicit drop argument that need them.