Exceptions Debugging

Exceptions, debugging and getting help.

This chapter describes techniques to use when things go wrong:

• Exceptions: dealing with errors in your code

• Debugging: understanding or figuring out problems in other people's codes (debugging) The debugging techniques are also useful when you're trying to understand other people's R code, or R code that I've highlighted through out this book that you should be able to tease apart and figure out how it works.

• Getting help: what to do if you can't figure out what the problem is

As with many other parts of R, the approach to dealing with errors and exceptions comes from a LISP-heritage, and is quite different (although some of the terminology is the same) from that of languages like Java.

Interactive analysis vs. programming

There is a tension between interactive analysis and programming. When you a doing an analysis, you want R to do what you mean, and if it guesses wrong, then you'll discover it right away and can fix it. If you're creating a function, then you want to make it as robust as possible so that any problems become apparent right away (see fail fast below).

• Be explicit:

  • Be explicit about missings

  • Use TRUE and FALSE instead of T and F

  • Avoid functions that have non-standard evaluation rules (no subset, with, transform)

• Avoid functions that can return different types of objects:

  • Always use drop = FALSE

  • Don't use sapply: use vapply, or lapply plus the appropriate transformation

An example

The following function is naively written and might cause problems:

col_means <- function(df) {
  numeric <- sapply(df, is.numeric)
  numeric_cols <- df[, numeric]
  
  data.frame(lapply(numeric_cols, mean))
}

The ability to come up with a set of potential pathological inputs is a good skill to master. Common cases that I try and check are:

• dimensions of length 0
• dimensions of length 1 (in case dropping occurs)
• incorrect input types

The following code exercises some of those cases for col_means

col_means(mtcars)
col_means(mtcars[, 0])
col_means(mtcars[0, ])
col_means(mtcars[, "mpg", drop = F])
col_means(1:10)
col_means(as.matrix(mtcars))
col_means(as.list(mtcars))

mtcars2 <- mtcars
mtcars2[-1] <- lapply(mtcars2[-1], as.character)
col_means(mtcars2)

A better version of col_means might be:

col_means <- function(df) {
  numeric <- vapply(df, is.numeric, logical(1))
  numeric_cols <- df[, numeric, drop = FALSE]
  
  data.frame(lapply(numeric_cols, mean))
}

We use vapply instead of sapply, remember to use drop = FALSE. It still doesn't check that the input is correct, or coerce it to the correct format.

Debugging

To illustrate debugging techniques, we need some functions with bugs in them.

Traceback

The key function for performing a post-mortem on an error is traceback, which shows all the calls leading up to the error. Here's an example:

f <- function() g()
g <- function() h()
h <- function() i()
i <- function() "a" + 1
f()
traceback()

This is very helpful to determine exactly where in a stack of calls an error occured. However, it's not so helpful if you have a recursive function, or other situations where the same function is called in multiple places:

j <- function(i = 10) {
  if (i == 1) "a" + 1
  j(i - 1)
}
j()
traceback()

Browser

Trackback can help you figure out where the error occurred, but to understand why the error occured and to fix it, it's often easier to explore interactively. The browser function allows you to do this by pausing execution and returning you to an interactive state. Here you can run any regular R command, as well as some extra single letter commands:

• c: leave interactive debugging and continue execution

• n: execute the next step. Be careful if you have a variable named n: to print it you'll need to be explicit print(n).

• return: the default behaviour is the same as c, but this is somewhat dangerous as it makes it very easy to accidentally continue during debugging. I recommend options(browserNLdisabled = TRUE) so that return is simply ignored.

• Q: stops debugging, terminate the function and return to the global workspace

• where: prints stack trace of active calls (the interactive equivalent of traceback)

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

Browsing arbitrary R code

There are two ways to insert browser() statements in arbitrary R code:

• debug inserts a browser statement in the first line of the specified function. undebug will remove it, or you can use debugonce to insert a browser call for the next run, and have it automatically removed afterwards.

• utils::setBreakpoint does the same thing, but instead inserts browser in the function corresponding to the specified file name and line number.

These two functions are both special cases of trace(), which allows you to insert arbitrary code in any position in an existing function. The complement of trace is untrace. You can only perform one trace per function - subsequent traces will replace prior.

Locating warnings is a little trickier. The easiest way to turn it in an error with options(warn = 2) and then use the standard functions described above. Turn back to default behaviour with options(warn = 0).

Browsing on error

It's also possible to start browser automatically when an error occurs, by setting options(error = browser). This will start the interactive debugger in the environment in which the error occurred. Other functions that you can supply to error are:

• recover: a step up from browser, as it allows you to drill down into any of the calls in the call stack. This is useful because often the cause of the error is a number of calls back - you're just seeing the consequences. This is the result of "fail-slow" code

• dump.frames: an equivalent to recover for non-interactive code. Will save an rdata file containing the nested environments where the error occurred. This allows you to later use debugger to re-create the error as if you had called recover from where the error occurred

  options(error = quote({dump.frames(to.file = TRUE); q()}))
  
  # Saves debugging info to file last.dump.rda
  
  # Then in an interactive R session:
  print(load("last.dump.rda"))
  debugger("last.dump")
  

• NULL: the default. Prints an error message and stops function execution. Use this to reset back to the regular behaviour.

Warnings are harder to track down because they don't provide any information about where they occured. One way to make them easier to detect is to convert them to errors with options(warn = 2). Another way is to use function to trigger special behaviour. We can use withCallingHandlers (explained below) to set up something similar for warnings. The following function will call the specified action when a warning is generated. The code is slightly tricky because we need to find the right environment to evaluate the action - it should be the function that calls warning.

on_warning <- function(action, code) {
  q_action <- substitute(action)
  
  withCallingHandlers(code, warning = function(c) {
    for(i in seq_len(sys.nframe())) {
      f <- as.character(sys.call(i)[[1]])
      if (f == "warning") break;
    }
    
    eval(q_action, sys.frame(i - 1))
  })
}

x <- 1
f <- function() {
  x <- 2
  g()
}
g <- function() {
  x <- 3
  warning("Leaving g")
}
on_warning(browser(), f())
on_warning(recover(), f())

Creative uses of trace

Trace is a useful debugging function that along with some of our computing on the language tools can be used to set up warnings on a large number of functions at a time. This is useful if you for automatically detecting some of the potential problems described above. The 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)

Next, we write a version of trace that is vectorised over the function name, and then use that function to add a warning to every function that we found above.

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

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

pmin(1:10, 1:10)
# Error in eval(expr, envir, enclos) : na.rm not set
pmin(1:10, 1:10, na.rm = T)
# [1]  1  2  3  4  5  6  7  8  9 10

One problem of this approach is that we don't automatically pick up any primitive functions, because these functions don't have formal arguments.

Exceptions

Defensive programming is the art of making code fail in a well-defined manner even when something unexpected occurs. There are two components of this art related to exceptions: raising exceptions as soon as you notice something has gone wrong, and responding to errors as cleanly as possible.

A general principle for errors is to "fail fast" - as soon as you figure out something as wrong, and your inputs are not as expected, you should raise an error. This is more work for you as the function author, but will make it easier for the user to debug because they get errors early on, not after unexpected input has passed through several functions and caused a problem.

Creating

There are a number of options for letting the user know when something has gone wrong:

• 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 were used if not specified, and plyr::join, which informs which variables were used to join the two tables. You can suppress messages with suppressMessages.

• use warning() for unexpected problems that aren't show stoppers. options(warn = 2) will turn warnings into errors. Warnings are often more appropriate for vectorised functions when a single value in the vector is incorrect, e.g. log(-1:2) and sqrt(-1:2). You can suppress warnings with suppressWarnings

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

• stopifnot() is a quick and dirty way of checking that pre-conditions for your function are met. The problem with stopifnot is that if they aren't met, it will display the test code as an error, not a more informative message. Checking pre-conditions with stopifnot is better than nothing, but it's better still to check the condition yourself and return an informative message with stop()

Handling

Error handling is performed with the try and tryCatch functions. try is a simpler version, so we'll start with that first. The try functions allows execution to continue even if an exception occurs, and is particularly useful when operating on elements in a loop. The silent argument controls whether or not the error is still printed.

elements <- list(1:10, c(-1, 10), c(T, F), letters)
results <- lapply(elements, log)
results <- lapply(elements, function(x) try(log(x)))

If code fails, try invisibly returns an object of class try-error. There isn't a built in function for testing for this class, so we'll define one. Then we can easily strip all errors out of a list with Filter:

is.error <- function(x) inherits(x, "try-error")
successful <- Filter(Negate(is.error), results)

Or if we want to know where the successes and failures were, when can use sapply or vapply:

vapply(results, is.error, logical(1))
sapply(results, is.error)

# (Aside: vapply is preferred when you're writing a function because
# it guarantees you'll always get a logical vector as a result, even if
# you list has length zero)
sapply(NULL, is.error)
vapply(NULL, is.error, logical(1))    

If we wanted to avoid the anonymous function call, we could create our own function to automatically wrap a call in a try:

try_to <- function(f, silent = FALSE) {
  function(...) try(f(...), silent = silent)
}
results <- lapply(elements, try_to(log))

tryCatch gives more control than try, but to understand how it works, we first need to learn a little about conditions, the S3 objects that represent errors, warnings and messages.

is.condition <- function(x) inherits(x, "condition")

There are three convenience methods for creating errors, warnings and messages. All take two arguments: the message to display, and an optional call indicating where the condition was created

e <- simpleError("My error", quote(f(x = 71)))
w <- simpleWarning("My warning")
m <- simpleMessage("My message")

There is one class of conditions that can't be directly: interrupts, which occur when the user presses Ctrl + Break, Escape, or Ctrl + C (depending on the platform) to terminate execution.

The components of a condition can be extracted with conditionMessage and conditionCall:

conditionMessage(e)
conditionCall(e)

Conditions can be signalled using signalCondition. By default, no one is listening, so this doesn't do anything.

signalCondition(e)
signalCondition(w)
signalCondition(m)

To listen to signals, we have two tools: tryCatch and withCallingHandlers.
tryCatch is an exiting handler: it catches the condition, but the rest of the code after the exception is not run. withCallingHandlers sets up calling handlers: it catches the condition, and then resumes execution of the code. We will focus first on tryCatch.

The tryCatch call has three arguments:

• expr: the code to run.

• ...: a set of named arguments setting up error handlers. If an error occurs, tryCatch will call the first handler whose name matches one of the classes of the condition. The only useful names for built-in conditions are interrupt, error, warning and message.

• finally: code to run regardless of whether expr succeeds or fails. This is useful for clean up, as described below. All handlers have been turned off by the time the finally code is run, so errors will propagate as usual.

The following examples illustrate the basic properties of tryCatch:

# Handlers are passed a single argument
tryCatch(stop("error"), 
  error = function(...) list(...)
)
# This argument is the signalled condition, so we'll call
# it c for short.

# If multiple handlers match, the first is used
tryCatch(stop("error"), 
  error = function(c) "a",
  error = function(c) "b"
)

# If multiple signals are nested, the the most internal is used first.
tryCatch(
  tryCatch(stop("error"), error = function(c) "a"),
  error = function(c) "b"
)

# Uncaught signals propagate outwards. 
tryCatch(
  tryCatch(stop("error")),
  error = function(c) "b"
)

# The first handler that matches a class of the condition is used, 
# not the "best" match:
a <- structure(list(message = "my error", call = quote(a)), 
  class = c("a", "error", "condition"))

tryCatch(stop(a), 
  error = function(c) "error",
  a = function(c) "a"
)
tryCatch(stop(a), 
  a = function(c) "a",
  error = function(c) "error"
)

# No matter what happens, finally is run:
tryCatch(stop("error"), 
  finally = print("Done."))
tryCatch(a <- 1, 
  finally = print("Done."))
  
# Any errors that occur in the finally block are handled normally
a <- 1
tryCatch(a <- 2, 
  finally = stop("Error!"))

What can handler functions do?

• Return a value.

• Pass the condition along, by re-signalling the error with stop(c), or signalCondition(c) for non-error conditions.

• Kill the function completely and return to the top-level with invokeRestart("abort")

A common use for try and tryCatch is to set a default value if a condition fails. The easiest way to do this is to assign within the try:

success <- FALSE
try({
  # Do something that might fail
  success <- TRUE
})

An alternative idiom is

success <- tryCatch({
  # Do something that might fail
  success <- TRUE      
}, error = function(e) FALSE)

We can write a simple version of try using tryCatch. The real version of try is considerably more complicated to preserve the usual error behaviour.

try <- function(code, silent = FALSE) {
  tryCatch(code, error = function(c) {
    if (!silent) message("Error:", conditionMessage(c))
    invisible(structure(conditionMessage(c), class = "try-error"))
  })
} 
try(1)
try(stop("Hi"))
try(stop("Hi"), silent = TRUE)

rm(try)

withCallingHandlers({
  a <- 1
  stop("Error")
  a <- 2
}, error = function(c) {})

Using tryCatch

With the basics in place, we'll next develop some useful tools based the ideas we just learned about.

The finally argument to tryCatch is particularly useful for clean up, because it is always called, regardless of whether the code executed successfully or not. This is useful when you have:

• modified options, par or locale
• opened connections, or created temporary files and directories
• opened graphics devices
• changed the working directory
• modified environment variables

The following function changes the working directory, executes some code, and always resets the working directory back to what it was before, even if the code raises an error.

in_dir <- function(path, code) {
  cur_dir <- getwd()
  tryCatch({
    setwd(path)
    force(code)
  }, finally = setwd(cur_dir))
}

getwd()
in_dir(R.home(), dir())
getwd()
in_dir(R.home(), stop("Error!"))
getwd()

Another more casual way of cleaning up is the on.exit function, which is called when the function terminates. It's not as fine grained as tryCatch, but it's a bit less typing.

in_dir <- function(path, code) {
  cur_dir <- getwd()
  on.exit(setwd(cur_dir))

  force(code)
}

If you're using multiple on.exit calls, make sure to set add = TRUE, otherwise they will replace the previous call.

Getting help

Currently, there are two main venues to get help when you are stuck and can't figure out what's causing the problem: stackoverflow and the R-help mailing list. You can get fantastic help in both venues, but they do have their own culture and expectations. It's usually a good idea to spend a little time lurking, and learning about community expectations before your first post.

Some good general advice:

• Make sure you have the latest version of R, and the package (or packages) you are having problems with. It may be that your problem is the result of a bug that has been fixed recently.

• If it's not clear where the problem is, include the results of sessionInfo() so others can see your R setup.

• Spend some time creating a reproducible example, as described below. This is often a useful process in its own right, because in the course of making the problem reproducible you figure out what's causing the problem.

How to write a reproducible example.

You are most likely to get good help with your R problem if you provide a reproducible example. A reproducible example allows someone else to recreate your problem by just copying and pasting R code.

There are four things you need to include to make your example reproducible: required packages, data, code, and a description of your R environment.

• Packages should be loaded at the top of the script, so it's easy to see which ones the example needs.

• The easiest way to include data in an email is to use dput() to generate the R code to recreate it. For example, to recreate the mtcars dataset in R, I'd perform the following steps:

  1. Run dput(mtcars) in R
  2. Copy the output
  3. In my reproducible script, type mtcars <- then paste.

• Spend a little bit of time ensuring that your code is easy for others to read:

  • make sure you've used spaces and your variable names are concise, but informative

  • use comments to indicate where your problem lies

  • do your best to remove everything that is not related to the problem.
    The shorter your code is, the easier it is to understand.

• Include the output of sessionInfo() as a comment. This summarises your R environment and makes it easy to check if you're using an out-of-date package, or a non-standard locale.

You can check you have actually made a reproducible example by starting up a fresh R session and pasting your script in.

Before putting all of your code in an email, consider putting it in a gist. It will give your code nice syntax highlighting, and you don't have to worry about anything getting mangled by the email system.

Exercises

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

2. Write a function that takes code as an argument and runs that code with options(warn = 2) and returns options back to their previous values on exit (either from an exception or a normal exit).

3. Write a function that opens a graphics device, runs the supplied code, and closes the graphics device (always, regardless of whether or not the plotting code worked).