debugging.R

# print() is the simplest debugging technique

myFunction <- function()
{
  #...possibly buggy code...
    print("here i am")
  #...more possibly buggy code...
  print("here i am 2")
}

# a buggy function

buggyFunc <- function()
{
    for (i in 1:2)
    {
        if (i == 2)
            stop("Pretend I am a bug.") 
    }
}


# traceback() - where was the last error?

buggyFunc()
traceback()

# debug() - interactive debugging


debug(buggyFunc)
buggyFunc()

?debug

undebug(buggyFunc)

# debug tip #1 - debugging a nested function

buggyFunc2 <- function()
{
    nestedBuggyFunction <- function()
    {
        stop("Pretend I am a bug")
    }
    nestedBuggyFunction()
}

debug(nestedBuggyFunction)

debug(buggyFunc2)
buggyFunc2()

# debug tip #2 - debugging a method

library(GenomicRanges)
example(GRanges)
x <- selectMethod("seqinfo", "GRanges")
debug(x)
seqinfo(gr)

# browser()

browserDemo <- function()
{
    browser()
}

browserDemo()

# trace - in its simplest form, just prints out a line when a function is invoked

trace(sum)
sum(1,2)
trace: sum(1, 2)


untrace(sum) # turn off trace
trace(sum)
sum(1, 3)

# trace, for those hard-to-reach places

buggyFunc3 <- function()
{
   for (i in 1:10000)
   {
        if (i == 7777)
            stop("Found a bug!")   
   }
}

# find R's notion of the line number where the problem occurs

l <- as.list(body(buggyFunc3))
l

as.list(l[[2]])

trace(buggyFunc3, at=list(c(2,4,2,3,2)), tracer=browser)
buggyFunc3()

# conditional trace, if we know a function has trouble with
# certain values

buggyFunc4 <- function(x)
{
  if (x >= 10 && x <= 20) stop("I can't deal with x!")
}

trace(buggyFunc4, quote(if (x >= 10 && x <= 20) browser()))

buggyFunc4(14)

buggyFunc4(24)

# a tracer can be anything, not just browser()

trace(buggyFunc4,
    quote(if (x >= 10 && x <= 20)
        print(sprintf("Tracer says that x is %s", x))))

buggyFunc4(24)
buggyFunc4(14)