iCode_debug/iCode_debug.qmd at main · gpatoine/iCode_debug · GitHub

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---
title: "Debugging"
title-slide-attributes:
  data-background-image: fig/iCode_logo_simple.png
  data-background-size: contain
  data-background-opacity: "0.2"
format:
  revealjs:
    theme: default
editor: visual
author: Guillaume Patoine
logo: fig/iCode_logo_simple.png
footer: "iCode Seminar Series"
toc: true
toc-title: Contents
preview-links: true
---

## When it breaks


![](fig/bug_meme.jpg){height=450}
![](fig/debug_docu_meme.jpeg){height=450}


# 1.Manual debugging

## Finding the error(s)

When you encounter an error

::: {.alert .alert-info style="text-align: center; max-width: 800; margin: auto; border: 3px solid black; padding: 10px;"}
Finding your bug is a process of confirming the many things that you believe are true — until you find one which is not true.

—Norm Matloff
:::


## Accessing source code

- F1 for documentation
- print (no comment)
- F2 (no comment)
- check source code (Github/CRAN)


## View traceback

![](fig/callstack.png){height=300  fig-align="center"}

- traceback()
- rlang::last_trace()


## View traceback {.unnumbered .unlisted}

```{r, echo=TRUE, error=TRUE}
f <- function(a) g(a)
g <- function(b) h(b)
h <- function(c) i(c)
i <- function(d) {
  if (!is.numeric(d)) {
    stop("`d` must be numeric", call. = FALSE)
  }
  d + 10
}

f("a")

```

```
> traceback()
5: stop("`d` must be numeric", call. = FALSE) at #3
4: i(c) at #1
3: h(b) at #1
2: g(a) at #1
1: f("a")

```


## Tips and tricks

- Can you reproduce it?
- Simplify the problem, make a reprex

**Run the function line by line in the global environment**

- Input argument values
- Add `print()` calls
- Check expected results along way


# 2. Advanced tools to dive/dig into the function

## Interactive debugger interface (browser mode)

![](fig/debug_interface.png){fig-align="center"}

## Exercise 1: How to use debugger

- interactive "Rerun with debug"
- `browser()`: in code, when run
- breakpoints: in IDE, when line reached
- recover: set in options, starts at time of error
- `debug()`: run with function name as arguments

Exercise 1: (https://github.com/gpatoine/iCode_debug/sample_script.R)


## Exercise 2: Error of your choice

Pick a function to look into, or try to resolve an error that you had.

Examples: `sample()`, `lm()`, `ggplot`, `gptools::coldesc()`

Look into how the functions are built, you can relate to the function writing guidelines from the function iCode series. Are checks performed.

Break the functions and see how errors are handled?


# Sources and references

- Advanced R book: Debugging chapter <br>
<https://adv-r.hadley.nz/debugging.html>
- Jenny Brian talk <br>
<https://www.youtube.com/watch?v=vgYS-F8opgE)>

![](fig/closure_talk.PNG){height="280"}
![](fig/closure_summary_slide.PNG){height="280"}