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<!DOCTYPE html>
<html>
<head>
<title>Debugging</title>
<meta charset="utf-8">
<meta name="description" content="Debugging">
<meta name="author" content="Roger D. Peng, Associate Professor of Biostatistics">
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<slides class="layout-widescreen">
<!-- LOGO SLIDE -->
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<slide class="title-slide segue nobackground">
<aside class="gdbar">
<img src="../../assets/img/bloomberg_shield.png">
</aside>
<hgroup class="auto-fadein">
<h1>Debugging</h1>
<h2></h2>
<p>Roger D. Peng, Associate Professor of Biostatistics<br/>Johns Hopkins Bloomberg School of Public Health</p>
</hgroup>
</slide>
<!-- SLIDES -->
<slide class="" id="slide-1" style="background:;">
<hgroup>
<h2>Something’s Wrong!</h2>
</hgroup>
<article>
<p>Indications that something’s not right</p>
<ul>
<li><code>message</code>: A generic notification/diagnostic message produced by the <code>message</code> function; execution of the function continues</li>
<li><code>warning</code>: An indication that something is wrong but not necessarily fatal; execution of the function continues; generated by the <code>warning</code> function</li>
<li><code>error</code>: An indication that a fatal problem has occurred; execution stops; produced by the <code>stop</code> function</li>
<li><code>condition</code>: A generic concept for indicating that something unexpected can occur; programmers can create their own conditions</li>
</ul>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-2" style="background:;">
<hgroup>
<h2>Something’s Wrong!</h2>
</hgroup>
<article>
<p>Warning</p>
<pre><code class="r">log(-1)
</code></pre>
<pre><code>## Warning: NaNs produced
</code></pre>
<pre><code>## [1] NaN
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-3" style="background:;">
<hgroup>
<h2>Something’s Wrong</h2>
</hgroup>
<article>
<pre><code class="r">printmessage <- function(x) {
if(x > 0)
print("x is greater than zero")
else
print("x is less than or equal to zero")
invisible(x)
}
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-4" style="background:;">
<hgroup>
<h2>Something’s Wrong</h2>
</hgroup>
<article>
<pre><code class="r">printmessage <- function(x) {
if (x > 0)
print("x is greater than zero") else print("x is less than or equal to zero")
invisible(x)
}
printmessage(1)
</code></pre>
<pre><code>## [1] "x is greater than zero"
</code></pre>
<pre><code class="r">printmessage(NA)
</code></pre>
<pre><code>## Error: missing value where TRUE/FALSE needed
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-5" style="background:;">
<hgroup>
<h2>Something’s Wrong!</h2>
</hgroup>
<article>
<pre><code class="r">printmessage2 <- function(x) {
if(is.na(x))
print("x is a missing value!")
else if(x > 0)
print("x is greater than zero")
else
print("x is less than or equal to zero")
invisible(x)
}
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-6" style="background:;">
<hgroup>
<h2>Something’s Wrong!</h2>
</hgroup>
<article>
<pre><code class="r">printmessage2 <- function(x) {
if (is.na(x))
print("x is a missing value!") else if (x > 0)
print("x is greater than zero") else print("x is less than or equal to zero")
invisible(x)
}
x <- log(-1)
</code></pre>
<pre><code>## Warning: NaNs produced
</code></pre>
<pre><code class="r">printmessage2(x)
</code></pre>
<pre><code>## [1] "x is a missing value!"
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-7" style="background:;">
<hgroup>
<h2>Something’s Wrong!</h2>
</hgroup>
<article>
<p>How do you know that something is wrong with your function? </p>
<ul>
<li>What was your input? How did you call the function?</li>
<li>What were you expecting? Output, messages, other results? </li>
<li>What did you get?</li>
<li>How does what you get differ from what you were expecting? </li>
<li>Were your expectations correct in the first place?</li>
<li>Can you reproduce the problem (exactly)?</li>
</ul>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-8" style="background:;">
<hgroup>
<h2>Debugging Tools in R</h2>
</hgroup>
<article>
<p>The primary tools for debugging functions in R are</p>
<ul>
<li><code>traceback</code>: prints out the function call stack after an error occurs; does nothing if there’s no error</li>
<li><code>debug</code>: flags a function for “debug” mode which allows you to step through execution of a function one line at a time</li>
<li><code>browser</code>: suspends the execution of a function wherever it is called and puts the function in debug mode</li>
<li><code>trace</code>: allows you to insert debugging code into a function a specific places </li>
<li><code>recover</code>: allows you to modify the error behavior so that you can browse the function call stack</li>
</ul>
<p>These are interactive tools specifically designed to allow you to pick through a function. There’s also the more blunt technique of inserting print/cat statements in the function.</p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-9" style="background:;">
<hgroup>
<h2>traceback</h2>
</hgroup>
<article>
<pre><code class="r">> mean(x)
Error in mean(x) : object 'x' not found
> traceback()
1: mean(x)
>
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-10" style="background:;">
<hgroup>
<h2>traceback</h2>
</hgroup>
<article>
<pre><code class="r">> lm(y ~ x)
Error in eval(expr, envir, enclos) : object ’y’ not found
> traceback()
7: eval(expr, envir, enclos)
6: eval(predvars, data, env)
5: model.frame.default(formula = y ~ x, drop.unused.levels = TRUE)
4: model.frame(formula = y ~ x, drop.unused.levels = TRUE)
3: eval(expr, envir, enclos)
2: eval(mf, parent.frame())
1: lm(y ~ x)
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-11" style="background:;">
<hgroup>
<h2>debug</h2>
</hgroup>
<article>
<pre><code class="r">> debug(lm)
> lm(y ~ x)
debugging in: lm(y ~ x)
debug: {
ret.x <- x
ret.y <- y
cl <- match.call()
...
if (!qr)
z$qr <- NULL
z
}
Browse[2]>
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-12" style="background:;">
<hgroup>
<h2>debug</h2>
</hgroup>
<article>
<pre><code class="r">Browse[2]> n
debug: ret.x <- x
Browse[2]> n
debug: ret.y <- y
Browse[2]> n
debug: cl <- match.call()
Browse[2]> n
debug: mf <- match.call(expand.dots = FALSE)
Browse[2]> n
debug: m <- match(c("formula", "data", "subset", "weights", "na.action",
"offset"), names(mf), 0L)
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-13" style="background:;">
<hgroup>
<h2>recover</h2>
</hgroup>
<article>
<pre><code class="r">> options(error = recover)
> read.csv("nosuchfile")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file ’nosuchfile’: No such file or directory
Enter a frame number, or 0 to exit
1: read.csv("nosuchfile")
2: read.table(file = file, header = header, sep = sep, quote = quote, dec =
3: file(file, "rt")
Selection:
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-14" style="background:;">
<hgroup>
<h2>Debugging</h2>
</hgroup>
<article>
<p>Summary</p>
<ul>
<li>There are three main indications of a problem/condition: <code>message</code>, <code>warning</code>, <code>error</code>
<ul>
<li>only an <code>error</code> is fatal</li>
</ul></li>
<li>When analyzing a function with a problem, make sure you can reproduce the problem, clearly state your expectations and how the output differs from your expectation</li>
<li>Interactive debugging tools <code>traceback</code>, <code>debug</code>, <code>browser</code>, <code>trace</code>, and <code>recover</code> can be used to find problematic code in functions</li>
<li>Debugging tools are not a substitute for thinking!</li>
</ul>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="backdrop"></slide>
</slides>
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