Debugging

Shannon Pileggi

Agenda

Getting started

Troubleshooting

Moving on

Debugging your code

Debugging in RStudio

Debugging their code

Special cases

Read the source

Getting started

Licensing

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA4.0).

Checklist

R installed? Pretty recent?

     Recommended R ≥ 4.2.0

RStudio installed?

     I’m on 2022.02.3+492

Ready to build packages?

     devtools::has_devel()
     Your system is ready to build packages!

Additional resources

• WTF Ch 11 Debugging R code
  https://rstats.wtf/debugging-r-code.html

• Advanced R Ch 22 Debugging
  https://adv-r.hadley.nz/debugging.html

• Jenny Bryan 2020 RStudio Conf Keynote Object of type closure is not subsettable
  https://github.com/jennybc/debugging#readme

• Amanda Gadrow 2018 Webinar Debugging techniques in RStudio
  https://www.rstudio.com/resources/webinars/debugging-techniques-in-rstudio/

• Jim Hester 2019 Introduction to debugging in R and RStudio
  https://www.jimhester.com/talk/2019-crug-debugging/

• Maëlle Salmon 2021 How to become a better R code detective?
  https://masalmon.eu/2021/07/13/code-detective/

• Kara Woo 2019 RStudio Conf Box plots A case study in debugging and perseverance https://www.rstudio.com/resources/rstudioconf-2019/box-plots-a-case-study-in-debugging-and-perseverance/

Troubleshooting

1. SEARCH
   Teach Me How To Google, Samantha Csik (2022)
   slides, recording

2. RESET
   Restart R, especially when things get weird.

3. REPREX
   https://reprex.tidyverse.org/
   make a reprex….. please, Sharla Gelfand (2021)
   slides, recording

Reset - details

Have you tried turning it OFF and ON again?

Session -> Restart R or

• Ctrl + Shift + F10 (Windows),

• Cmd + Shift + 0 / Cmd + Shift + F10 (Mac)

Tools -> Global Options -> Workspace

Why reset?

Which persist after rm(list = ls())?

Option	Persists?
A. library(dplyr)
B. summary <- head
C. options(stringsAsFactors = FALSE)
D. Sys.setenv(LANGUAGE = “fr”)
E. x <- 1:5
F. attach(iris)

02:00

Why reset?

Which persist after rm(list = ls())?

Option	Persists?
A. library(dplyr)
B. summary <- head
C. options(stringsAsFactors = FALSE)
D. Sys.setenv(LANGUAGE = “fr”)
E. x <- 1:5
F. attach(iris)

Your turn, exercise 00

Either on your Posit cloud workspace or your personal computer…

Set your Workspace options as shown.

Tools -> Global Options -> Workspace

02:00

But what if

Moving on

from troubleshooting to…

formal debugging techniques.

Key concepts

traceback

   location where did the error occur

interactive debugger

   context why did the error occur

your code   vs   their code

interactive debugging: pause the execution of a function and launch environment where you can interactively explore what’s happening

Debugging tools

source for image in google slides at

https://docs.google.com/presentation/d/14mqGirw4TnblqSFY0Tk30YrxkAwIrz1xo4nMIwgqk_o/edit?u sp=sharing

This is a lot.

These tools achieve similar objectives slightly differently.

People don’t generally use all of these tools at once. They pick and choose the ones they like.

Debugging your code

Debugging your code

Sourcing

⚠️ name your script with functions

⚠️ source your script with functions

for the best debugging experience 😎

Set up

f <- function(x) {
  x + 1
}

g <- function(x) f(x)

g("a")

Error in x + 1: non-numeric argument to binary operator

traceback()

source("demo/my_functions.R")
g("a")
traceback()

shows the sequence of calls that lead to the error.

used interactively in console, called for last error observed

Richer traceback

source("demo/my_functions.R")
options(error = rlang::entrace) 
g("a")
rlang::last_trace()

options(error = rlang::entrace)
could go in your .Rprofile

traceback vs rlang functions

Numbering and ordering differs between traceback() and rlang functions.

browser()

f <- function(x) {
  browser()
  x + 1
}

g <- function(x) f(x)

browser() opens the interactive debugger.

1. Modify the function by inserting a browser() statement.

2. Source the function.

3. Execute the function.

Interactive debugger

Interactive debugger tips

Investigate objects

Control execution

ls(), ls.str(),
str(), print()

command	operation
n	next statement
c	continue (leave interactive debugging)
s	step into function call
f	finish loop / function
where	show previous calls
Q	quit debugger

Debugging your code

Your turn, exercise 01

Enter Posit cloud or work locally via usethis::use_course("rstats-wtf/wtf-debugging") (https://github.com/rstats-wtf/wtf-debugging)

Complete 01_exercise to practice debugging your own code.

Check out the README.md for some getting started tips!

• 01_debugging_spartan.R (directions to explore without suggested code)

• 01_debugging_comfy.R (directions to explore with suggested code)

• 01_debugging_solution.R (directions to explore with code solutions)

15:00

Debugging in RStudio

Debugging in the RStudio IDE

Editor breakpoints

red circle = breakpoint = browser()

(but you don’t have to change your code)

Set / re-set an editor breakpoint:

• click to the left of the line number in the source file

• press Shift+F9 with your cursor on the line

Editor breakpoints

red circle = breakpoint = browser()

(but you don’t have to change your code)

To activate, either

• click IDE Source button, or

• debugSource(“demo/my_functions.R”)

Debugging console

IDE on error

Automatically invoke actions on error.

New set up for demonstration.

f <- function(x) { strsplit(x, ",") }
g <- function(x) { f(x) }
g("a,b")

[[1]]
[1] "a" "b"

g(factor("a,b"))

Error in strsplit(x, ","): non-character argument

IDE message only

IDE error inspector

IDE break in code

Error inspector

# IDE Error Inspector not triggered
f <- function(x) x + 1
g <- function(x) f(x)
g("a")

# IDE Error Inspector not triggered
strsplit(factor("a,b"), ",")

# IDE Error Inspector not triggered
f <- function(x) strsplit(x, ",")
f(factor("a,b"))

# IDE Error Inspector yes triggered
g <- function(x) f(x)
g(factor("a,b"))

The error inspector is only invoked if your code is involved.

Debugging in the RStudio IDE

Your turn, exercise 02

Complete 02_exercise to practice debugging a slightly different version of your own code, using features from the RStudio IDE.

07:00

Debugging their code

Debugging their code

debug()

debug() = browser()/ breakpoint in first line of function

# source if code is yours, otherwise not necessary
source("demo/my_functions.R")
# set debugging flag
debug("g")
g("a")
# turn off debugging flag
undebug("g")

• interactive debugger is initiated every time g() is executed, until undebug("g")

• depending on function internals, this can… trap you in the debugger 😬

debugonce()

debugonce() = browser()/ breakpoint in first line of function

# source if code is yours, otherwise not necessary
source("demo/my_functions.R")
# set debugging flag
debugonce("g")
g("a")

• one time only!

• interactive debugger initiated a single time when g() is executed

options(error = recover)

we already discussed
options(error = rlang::entrace)
for a richer traceback on error

🤠 options(error = recover)

1. displays an interactive prompt with frames

2. you select the frame to enter the debugger

recover example

source("demo/my_functions.R")
options(error = recover)
g("a")
options(error = NULL)

trace() overview

trace(what = fun, tracer = browser)
is equivalent to

• inserting browser() in first line of function

• debug(fun)

you an also insert any code at any location in function

• trace(what = fun, tracer = browser, at = 2)
  inserts browser() at second step of fun

untrace(fun) cancels the tracing

trace() is a more flexible version of debug()

⚠️ trace() requires { in function definition

trace() without a specified step

trace(what = colSums, tracer = browser)
colSums(1:3)
# ls.str() in browser
untrace(colSums)

trace(what = colSums, tracer = browser)
is equivalent to

• inserting browser() in first line of colSums
  if we had the source code

• debug(colSums)

navigating function steps

investigate 🧐 the function with as.list() + body()

x <- as.list(body(colSums))
View(x)

identify function step

trace() at specified step

# identify spot to insert code
as.list(x[[3]][[1]])
# equivalent notation
as.list(x[[c(3, 1)]])

# insert browser at step 3.1
trace(colSums, browser, at = list(c(3, 1)))
# execute function
colSums(1:3)
# ls.str() handy in browser
# cancel tracing
untrace(colSums)

Debugging their code

Your turn, exercise 03

# already installed in the Posit Cloud work space
# install.packages("devtools")
# devtools::install_github("rstats-wtf/wtfdbg")

Complete 03_exercise to practice debugging others’ code.

10:00

Special cases

Rmarkdown

Troubleshooting:

1. rmarkdown chunk option error = TRUE enables knitting with errors

2. insert knitr::knit_exit() and interactively work through .Rmd

. . .

Debugging:

1. Adv R Ch 22.5.3 RMarkdown https://adv-r.hadley.nz/debugging.html#rmarkdown

2. WTF Ch 11.4 Debugging in Rmarkdown documents https://rstats.wtf/debugging-r-code.html#debugging-in-r-markdown-documents

Piped expressions

tracebacks can be verbose with pipes

options(error = rlang::entrace, rlang_backtrace_on_error = "branch")

gives trimmed tracebacks when using pipes

• more contributed answers on RStudio Community

• Matt Dray 2019 blog post Fix leaky pipes in R

Warnings

If you want to dig deeper into a warning, you can convert them to errors to initiate debugging tools.

?options
options(warn = 0) # default, stores warnings until top-level function returns
options(warn = 1) # warnings are printed as they occur
options(warn = 2) # upgrades warnings to errors


# initiate recover on warning
options(warn = 2, error = recover)
# restore original settings
options(warn = 0, error = NULL)

Debugging special cases

Wrap up

Pick your favorite

Go forth,
and learn from your bugs!

traceback

interactive debugger

your code   vs  
their code