Printing stack trace and continuing after error occurs in R

Question

I\'m writing some R code that calls other code that may fail. If it does, I want to print a stack trace (to track down what went wrong), then carry on regardless. However, t

Answer 1

This is a followup to @chrispy's answer above where he presented a withJavaLogging function. I commented that his solution is inspirational, but for me, is marred by some output at the start of the stack trace that I do not want to see.

To illustrate, consider this code:

f1 = function() {
        # line #2 of the function definition; add this line to confirm that the stack trace line number for this function is line #3 below
        catA("f2 = ", f2(), "\n", sep = "")
    }

    f2 = function() {
        # line #2 of the function definition; add this line to confirm that the stack trace line number for this function is line #4 below
        # line #3 of the function definition; add this line to confirm that the stack trace line number for this function is line #4 below
        stop("f2 always causes an error for testing purposes")
    }

If I execute the line withJavaLogging( f1() ) I get the output

2017-02-17 17:58:29.556 FATAL f2 always causes an error for testing purposes
      at .handleSimpleError(function (obj) 
    {
        level = sapply(class(obj), switch, debug = "DEBUG", message = "INFO", warning = "WARN", caughtError = "ERROR", error = if (stopIsFatal) 
            "FATAL"
        else "ERROR", "")
        level = c(level[level != ""], "ERROR")[1]
        simpleMessage = switch(level, DEBUG = , INFO = TRUE
      at #4: stop("f2 always causes an error for testing purposes")
      at f2()
      at catA.R#8: cat(...)
      at #3: catA("f2 = ", f2(), "\n", sep = "")
      at f1()
      at withVisible(expr)
      at #43: withCallingHandlers(withVisible(expr), debug = logger, message = logger, warning = logger, caughtError = logger, error = logger)
      at withJavaLogging(f1())
    Error in f2() : f2 always causes an error for testing purposes

I do not want to see that at .handleSimpleError(function (obj) line followed by the source code of the logger function defined inside the withJavaLogging function. I commented above that I could suppress that undesired output by changing trace = trace[length(trace):1] to trace = trace[(length(trace) - 1):1]

For the convenience of anyone else reading this, here is a complete version of the function that I now use (renamed from withJavaLogging to logFully, and slightly reformatted to fit my readability preferences):

logFully = function(expr, silentSuccess = FALSE, stopIsFatal = TRUE) {
    hasFailed = FALSE
    messages = list()
    warnings = list()

    logger = function(obj) {
        # Change behaviour based on type of message
        level = sapply(
            class(obj),
            switch,
            debug = "DEBUG",
            message = "INFO",
            warning = "WARN",
            caughtError = "ERROR",
            error = if (stopIsFatal) "FATAL" else "ERROR",
            ""
        )
        level = c(level[level != ""], "ERROR")[1]
        simpleMessage = switch(level, DEBUG = TRUE, INFO = TRUE, FALSE)
        quashable = switch(level, DEBUG = TRUE, INFO = TRUE, WARN = TRUE, FALSE)

        # Format message
        time = format(Sys.time(), "%Y-%m-%d %H:%M:%OS3")
        txt = conditionMessage(obj)
        if (!simpleMessage) txt = paste(txt, "\n", sep = "")
        msg = paste(time, level, txt, sep = " ")
        calls = sys.calls()
        calls = calls[1:length(calls) - 1]
        trace = limitedLabels(c(calls, attr(obj, "calls")))
        if (!simpleMessage && length(trace) > 0) {
            trace = trace[(length(trace) - 1):1]
            msg = paste(msg, "  ", paste("at", trace, collapse = "\n  "), "\n", sep = "")
        }

        # Output message
        if (silentSuccess && !hasFailed && quashable) {
            messages <<- append(messages, msg)
            if (level == "WARN") warnings <<- append(warnings, msg)
        } else {
            if (silentSuccess && !hasFailed) {
                cat(paste(messages, collapse = ""))
                hasFailed <<- TRUE
            }
            cat(msg)
        }

        # Muffle any redundant output of the same message
        optionalRestart = function(r) { res = findRestart(r); if (!is.null(res)) invokeRestart(res) }
        optionalRestart("muffleMessage")
        optionalRestart("muffleWarning")
    }

    vexpr = withCallingHandlers( withVisible(expr), debug = logger, message = logger, warning = logger, caughtError = logger, error = logger )

    if (silentSuccess && !hasFailed) {
        cat(paste(warnings, collapse = ""))
    }

    if (vexpr$visible) vexpr$value else invisible(vexpr$value)
}

If I execute the line logFully( f1() ) I get the output I desire, which is simply

2017-02-17 18:05:05.778 FATAL f2 always causes an error for testing purposes
  at #4: stop("f2 always causes an error for testing purposes")
  at f2()
  at catA.R#8: cat(...)
  at #3: catA("f2 = ", f2(), "\n", sep = "")
  at f1()
  at withVisible(expr)
  at logFully.R#110: withCallingHandlers(withVisible(expr), debug = logger, message = logger, warning = logger, caughtError = logger, error = logger)
  at logFully(f1())
Error in f2() : f2 always causes an error for testing purposes