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Lesson11.html
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<li>
<a href="index.html">Home</a>
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<li>
<a href="Lesson1.html">Lesson 1</a>
</li>
<li>
<a href="Lesson2.html">Lesson 2</a>
</li>
<li>
<a href="Lesson3.html">Lesson 3</a>
</li>
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<a href="Lesson4.html">Lesson 4</a>
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<a href="Lesson5.html">Lesson 5</a>
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<a href="Lesson6.html">Lesson 6</a>
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<a href="Lesson7.html">Lesson 7</a>
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<a href="Lesson8.html">Lesson 8</a>
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<a href="Lesson9.html">Lesson 9</a>
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<a href="Lesson10.html">Lesson 10</a>
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<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
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<p> </p>
<!-- install packages -->
<!-- ____________________________________________________________________________ -->
<p><!-- ____________________________________________________________________________ --> <!-- ____________________________________________________________________________ --> <!-- start body --></p>
<div id="lesson-11-debugging-and-troubleshooting-in-r" class="section level1">
<h1>Lesson 11: Debugging and troubleshooting in <code>R</code></h1>
<p> </p>
<p>Functions for Lesson 11<br />
<code>debug()</code>,<code>traceback()</code>,<code>browser()</code>, <code>options()</code>, <code>test_that()</code>, <code>qq_show()</code><br />
</p>
<p>Packages for Lesson 11<br />
<code>reprex</code>, <code>rlang</code>, <code>testthat</code><br />
</p>
</div>
<div id="agenda" class="section level1">
<h1>Agenda</h1>
<!-- ----------------------- image --------------------------- -->
<div align="center">
<p><img src="https://github.com/tidyverse/rvest/raw/master/man/figures/logo.pngZZ" style=width:25%></p>
</div>
<p>Debugging with purpose in <code>R</code></p>
<p><a href="https://rvest.tidyverse.org/">Debugging in <code>R</code></a>.<br />
</p>
<div id="troubleshooting-terminology" class="section level2">
<h2>Troubleshooting terminology</h2>
<p>error<br />
debug<br />
breakpoint<br />
callstack<br />
traceback<br />
browser</p>
<div id="restart-your-r-workspace" class="section level3">
<h3>Restart your <code>R</code> workspace</h3>
<p>The blanket approach to debugging. This resets your installed packages to the version you initially loaded on your computer and into the memory in your new <code>R</code> session.</p>
</div>
</div>
<div id="common-arenas-that-breed-errors-and-issues" class="section level2">
<h2>Common arenas that breed errors and issues</h2>
<div id="working-with-many-packages-across-multiple-r-sessions" class="section level3">
<h3>Working with many packages across multiple <code>R</code> sessions</h3>
<ul>
<li>Restart <code>R</code> to reload the current package version into the <code>R</code> session memory<br />
</li>
<li>Change your <code>R</code> preferences so that your current workspace doesn't translate stored objects to any future workspaces</li>
<li>Set "Save workspace to .Rdata on exit" to 'Never'<br />
</li>
<li>Uncheck "Restore .Rdata into workspace on startup"</li>
</ul>
</div>
<div id="finding-errors-in-collaborators-code" class="section level3">
<h3>Finding errors in collaborators' code</h3>
<ul>
<li>Create a minimal reproducible example<br />
Advantages of creating minimal reproducible examples<br />
</li>
<li>Removes noise from your problem code<br />
</li>
<li>Creates a neater template for outside help e.g. StackOverflow forums - Helps you diagnose and solve your own problem<br />
</li>
<li>Feedsback to deeper understanding of root issues to simplify future troubleshooting</li>
</ul>
</div>
</div>
<div id="debug-menu" class="section level2">
<h2>Debug menu</h2>
<p>Changing the way errors are diagnosed using the Debug dropdown menu options</p>
<p>Debug > On Error > Error inspector<br />
Debug > On Error > Message only</p>
</div>
<div id="debug-function-and-using-breakpoints" class="section level2">
<h2><code>debug()</code> function and using breakpoints</h2>
<ol style="list-style-type: decimal">
<li>Insert breakpoints in RStudio IDE at specific rows</li>
</ol>
<ul>
<li>Sometimes cleaner by avoiding editing code directly</li>
</ul>
<!-- ----------------------- image --------------------------- -->
<div align="center" ;="" text-align:center="">
<p><img src="img/lesson11_breakpoint.jpg" style=width:100%></p>
</div>
<ol start="2" style="list-style-type: decimal">
<li>Run <code>debug()</code> on your erraneous function</li>
</ol>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># first insert breakpoint in code</span>
<span class="kw">debug</span>(your_function) <span class="co"># run debug mode on function with error </span>
<span class="kw">debugonce</span>(your_function) <span class="co"># run debug once for first call of function </span></code></pre></div>
<p>Two options that pop up within the console:<br />
* Show/Hide traceback<br />
* Rerun with Debug</p>
<p><code>debug()</code><br />
* Useful when you have the source code for the error, i.e. it's your own function * Using breakpoints avoid editing the code directly</p>
</div>
<div id="using-traceback" class="section level2">
<h2>Using <code>traceback()</code></h2>
<ul>
<li>In-depth reporting of call stack (steps that <code>R</code> works through when running your code)<br />
</li>
<li>Read from bottom-up<br />
</li>
<li>Good for a quick snapshot of sequence to visualise code steps<br />
</li>
<li>No triage available<br />
</li>
<li>Alternative option is <code>rlang::last_trace()</code></li>
</ul>
</div>
<div id="using-optionserrorrecover" class="section level2">
<h2>Using <code>options(error=recover)</code></h2>
<ul>
<li>Run <code>R</code> commands as per usual, but with error browsing capabilities<br />
</li>
<li>Allows you to enter frames for each <code>R</code> function/step of the call stack<br />
</li>
<li>Selecting a frame will allow you to diagnose the error by showing two extra screens within the <code>R</code> Environment pane<br />
</li>
</ul>
<ol style="list-style-type: decimal">
<li>A trackback window that dives into the native functions <code>R</code> used to run your erraneous code. Here, you can select each function and see the inner workings.<br />
</li>
<li>A breakdown of each piece of the erraneous code, including values, class, and calls in the call stack, which can highlight the source of error.</li>
</ol>
<p>Depending on which call in the trackback you select, a third window as an R file tab with a spectacles logo will appear. This is the inner code of the function <code>R</code> used to run your erraneous code.</p>
<p><code>Browse[1]></code> The traceback will look like a menu with options</p>
<!-- ----------------------- image --------------------------- -->
<div align="center" ;="" text-align:center="">
<p><img src="img/lesson11_traceback.jpg" style=width:100%></p>
</div>
<ul>
<li>The 1 represents the frame number in the traceback<br />
</li>
<li><code>ls.str()</code> = Run <code>str</code> on all current objects in memory. When run with <code>Browse[1]></code>, it can identify what objects in memory could be interfering with your commands and causing the error.</li>
</ul>
</div>
<div id="using-browser" class="section level2">
<h2>Using <code>browser()</code></h2>
<p>Allows you to move incrementally through code lines to identify error location<br />
1. Insert <code>browser()</code> within code before error<br />
Chances are you're unsure of error location, so best practice is to start further up and work down.</p>
<ol start="2" style="list-style-type: decimal">
<li>Run troublesome code and enter browser mode<br />
</li>
<li>Press Next or type <code>n</code> to move down through each line<br />
</li>
<li>Once you enter the troublesome line, the <code>Browser[]></code> index will move up a number(?). Press <code>s</code> to step into code.<br />
</li>
<li>From here, you can engage with <code>R</code> objects using regular commands e.g. <code>xx %>% str(), xx %>% dims()</code><br />
</li>
<li>Change the <code>R</code> object directly within debugging mode to diagnose the issue using the newly corrected object<br />
</li>
<li>Enter <code>Q</code> or use the STOP button to exit browser<br />
</li>
<li>Use <code>undebug()</code> to stop debugging for any new errors</li>
</ol>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">xx <-<span class="st"> </span>LETTERS[<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>]
<span class="kw">browser</span>() <span class="co"># enter browsing mode before error </span>
xx <span class="op">%>%</span><span class="st"> </span><span class="kw">rowMeans</span>() <span class="co"># this is erroneous code </span></code></pre></div>
<p>Using the <code>reprex</code> package</p>
</div>
<div id="debugging-summary" class="section level2">
<h2>Debugging summary</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">last.warning
<span class="kw">geterrmessage</span>() <span class="co"># get last warning and/or error message </span>
<span class="kw">traceback</span>() <span class="co"># trace backwards in the call stack to error position</span>
<span class="kw">browser</span>() <span class="co"># move incrementally through code lines </span>
<span class="kw">rm</span>(<span class="dt">list =</span> <span class="kw">ls</span>()) <span class="co"># lists and deletes all objects in your global workspace </span>
<span class="co"># base options</span>
<span class="kw">options</span>(<span class="dt">error =</span> recover) <span class="co"># turn on r debugger </span>
<span class="kw">options</span>(<span class="dt">error =</span> <span class="ot">NULL</span>) <span class="co"># turn off debugger </span>
<span class="kw">options</span>(<span class="dt">future.debug =</span> T) <span class="co">#</span>
<span class="kw">options</span>(<span class="dt">gargle.quiet =</span> F) <span class="co"># </span>
<span class="kw">options</span>(<span class="dt">internet.info =</span> <span class="dv">0</span>) <span class="co"># info printed with url downloads. 0 = most, 2 = minimum </span></code></pre></div>
<!-- ----------------------- image --------------------------- -->
<!-- ----------------------- image --------------------------- -->
<div align="center" ;="" text-align:center="">
<p><img src="img/lesson11_debug.jpg" style=width:100%></p>
</div>
<p><code>rlang</code> package</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(rlang)
<span class="kw">last_error</span>() <span class="co"># latest error </span>
<span class="kw">last_trace</span>() <span class="co"># traceback last error </span>
<span class="kw">qq_show</span>()</code></pre></div>
</div>
<div id="some-common-abstract-error-messages" class="section level2">
<h2>Some common abstract error messages</h2>
<div id="error-object-of-type-closure-is-not-subsettable" class="section level3">
<h3><code>Error: object of type closure is not subsettable</code></h3>
<p><strong>Meaning</strong></p>
<ul>
<li>When you try to index or subset a function<br />
</li>
<li>When you try to access a stored <code>R</code> function as a variable e.g. using <code>data</code> as a local variable</li>
</ul>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># the following are all errors</span>
sum[<span class="dv">1</span>]
sum[[<span class="dv">1</span>]]
sum<span class="op">$</span>a
data <span class="co"># this is a native r function, so avoid using it to name your own variables/functions </span></code></pre></div>
<p>In Shiny<br />
* When using a function shared across multiple packages, e.g. <code>tags()</code> is found in both <code>{htmltools}</code> and <code>{shiny}</code></p>
<p><strong>Diagnosis</strong><br />
* Avoid defining variables that share the same names as native <code>R</code> functions</p>
<p>In Shiny<br />
* Specify package for function <code>shiny::tags()</code></p>
</div>
<div id="error-in-rowmeansdata-x-must-be-an-array-of-at-least-two-dimensions" class="section level3">
<h3><code>Error in rowMeans(data): 'x' must be an array of at least two dimensions</code></h3>
<p><strong>Meaning</strong></p>
<p><strong>Diagnosis</strong></p>
</div>
</div>
<div id="debugging-commands" class="section level2">
<h2>Debugging commands</h2>
<p>Q = quit callstack traceback/browser</p>
<hr />
<p>(r package content)</p>
</div>
<div id="debugging-r-packages" class="section level2">
<h2>Debugging <code>R</code> packages</h2>
<p><code>testthat</code> package<br />
Create testable code for your own reference after diagnosing and solving a recent issue</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(testthat)
<span class="kw">require</span>(usethis)
<span class="kw">test_check</span>()
<span class="kw">use_testthat</span>() <span class="co"># creates tests/testthat.R and tests/testthat/ </span>
<span class="kw">capture_warning</span>(xx <span class="op">%>%</span><span class="st"> </span><span class="kw">rowMeans</span>()) <span class="co"># summarise warning </span>
<span class="kw">capture_error</span>(xx <span class="op">%>%</span><span class="st"> </span><span class="kw">rowMeans</span>()) <span class="co"># summarise error </span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(testthat)
<span class="kw">test_that</span>(<span class="st">"rowMeans() still shouldn't work for xx"</span>, {
<span class="kw">expect_equal</span>(<span class="st">"<code for condition 1>"</span>)
<span class="kw">expect_equal</span>(<span class="st">"<code for condition 2>"</span>)
<span class="kw">expect_equal</span>(<span class="st">"<code for condition 3>"</span>)
})</code></pre></div>
</div>
<div id="debugging-shiny-apps" class="section level2">
<h2>Debugging Shiny apps</h2>
<p>For undeployed apps</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># shows log of commands Shiny is executing on your app</span>
<span class="kw">options</span>(<span class="dt">shiny.reactlog =</span> T)
<span class="kw">showReactLog</span>()
<span class="co"># print progress statments within app</span>
<span class="kw">cat</span>(<span class="dt">file =</span> <span class="kw">stderr</span>(), <span class="st">"your message"</span>) <span class="co"># standard connection to error in console</span></code></pre></div>
<p>For deployed apps<br />
<strong>Option 1</strong><br />
1. Keep <code>cat(file=stderr(), "your message")</code> statements in Shiny code<br />
2. In your Shiny.io app page, click on Logs and view your <code>cat()</code> outputs</p>
<p><strong>Option 2</strong><br />
Set <code>rsconnect::showLogs(steaming = T)</code> in app code to stream log within the RStudio IDE and interact with app log in real time.</p>
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