BiomedEngX/CircosHeatmap-aardio
2
1
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 3 Wiki Activity
CircosHeatmap-aardio/dist/lib/r-library/lifecycle/doc/manage.html

218 lines
19 KiB
HTML
Raw Normal View History

首次上传
2025-01-12 00:52:51 +08:00
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Manage lifecycle changes in functions you use</title>
<script src="data:application/javascript;base64,Ly8gUGFuZG9jIDIuOSBhZGRzIGF0dHJpYnV0ZXMgb24gYm90aCBoZWFkZXIgYW5kIGRpdi4gV2UgcmVtb3ZlIHRoZSBmb3JtZXIgKHRvCi8vIGJlIGNvbXBhdGlibGUgd2l0aCB0aGUgYmVoYXZpb3Igb2YgUGFuZG9jIDwgMi44KS4KZG9jdW1lbnQuYWRkRXZlbnRMaXN0ZW5lcignRE9NQ29udGVudExvYWRlZCcsIGZ1bmN0aW9uKGUpIHsKICB2YXIgaHMgPSBkb2N1bWVudC5xdWVyeVNlbGVjdG9yQWxsKCJkaXYuc2VjdGlvbltjbGFzcyo9J2xldmVsJ10gPiA6Zmlyc3QtY2hpbGQiKTsKICB2YXIgaSwgaCwgYTsKICBmb3IgKGkgPSAwOyBpIDwgaHMubGVuZ3RoOyBpKyspIHsKICAgIGggPSBoc1tpXTsKICAgIGlmICghL15oWzEtNl0kL2kudGVzdChoLnRhZ05hbWUpKSBjb250aW51ZTsgIC8vIGl0IHNob3VsZCBiZSBhIGhlYWRlciBoMS1oNgogICAgYSA9IGguYXR0cmlidXRlczsKICAgIHdoaWxlIChhLmxlbmd0aCA+IDApIGgucmVtb3ZlQXR0cmlidXRlKGFbMF0ubmFtZSk7CiAgfQp9KTsK"></script>
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">
code {
white-space: pre;
}
.sourceCode {
overflow: visible;
}
</style>
<style type="text/css" data-origin="pandoc">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
<script>
// apply pandoc div.sourceCode style to pre.sourceCode instead
(function() {
var sheets = document.styleSheets;
for (var i = 0; i < sheets.length; i++) {
if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
try { var rules = sheets[i].cssRules; } catch (e) { continue; }
var j = 0;
while (j < rules.length) {
var rule = rules[j];
// check if there is a div.sourceCode rule
if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") {
j++;
continue;
}
var style = rule.style.cssText;
// check if color or background-color is set
if (rule.style.color === '' && rule.style.backgroundColor === '') {
j++;
continue;
}
// replace div.sourceCode by a pre.sourceCode rule
sheets[i].deleteRule(j);
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
}
}
})();
</script>
<link rel="stylesheet" href="data:text/css,body%20%7B%0Abackground%2Dcolor%3A%20%23fff%3B%0Amargin%3A%201em%20auto%3B%0Amax%2Dwidth%3A%20700px%3B%0Aoverflow%3A%20visible%3B%0Apadding%2Dleft%3A%202em%3B%0Apadding%2Dright%3A%202em%3B%0Afont%2Dfamily%3A%20%22Open%20Sans%22%2C%20%22Helvetica%20Neue%22%2C%20Helvetica%2C%20Arial%2C%20sans%2Dserif%3B%0Afont%2Dsize%3A%2014px%3B%0Aline%2Dheight%3A%201%2E35%3B%0A%7D%0A%23TOC%20%7B%0Aclear%3A%20both%3B%0Amargin%3A%200%200%2010px%2010px%3B%0Apadding%3A%204px%3B%0Awidth%3A%20400px%3B%0Aborder%3A%201px%20solid%20%23CCCCCC%3B%0Aborder%2Dradius%3A%205px%3B%0Abackground%2Dcolor%3A%20%23f6f6f6%3B%0Afont%2Dsize%3A%2013px%3B%0Aline%2Dheight%3A%201%2E3%3B%0A%7D%0A%23TOC%20%2Etoctitle%20%7B%0Afont%2Dweight%3A%20bold%3B%0Afont%2Dsize%3A%2015px%3B%0Amargin%2Dleft%3A%205px%3B%0A%7D%0A%23TOC%20ul%20%7B%0Apadding%2Dleft%3A%2040px%3B%0Amargin%2Dleft%3A%20%2D1%2E5em%3B%0Amargin%2Dtop%3A%205px%3B%0Amargin%2Dbottom%3A%205px%3B%0A%7D%0A%23TOC%20ul%20ul%20%7B%0Amargin%2Dleft%3A%20%2D2em%3B%0A%7D%0A%23TOC%20li%20%7B%0Aline%2Dheight%3A%2016px%3B%0A%7D%0Atable%20%7B%0Amargin%3A%201em%20auto%3B%0Aborder%2Dwidth%3A%201px%3B%0Aborder%2Dcolor%3A%20%23DDDDDD%3B%0Aborder%2Dstyle%3A%20outset%3B%0Aborder%2Dcollapse%3A%20collapse%3B%0A%7D%0Atable%20th%20%7B%0Aborder%2Dwidth%3A%202px%3B%0Apadding%3A%205px%3B%0Aborder%2Dstyle%3A%20inset%3B%0A%7D%0Atable%20td%20%7B%0Aborder%2Dwidth%3A%201px%3B%0Aborder%2Dstyle%3A%20inset%3B%0Aline%2Dheight%3A%2018px%3B%0Apadding%3A%205px%205px%3B%0A%7D%0Atable%2C%20table%20th%2C%20table%20td%20%7B%0Aborder%2Dleft%2Dstyle%3A%20none%3B%0Aborder%2Dright%2Dstyle%3A%20none%3B%0A%7D%0Atable%20thead%2C%20table%20tr%2Eeven%20%7B%0Abackground%2Dcolor%3A%20%23f7f7f7%3B%0A%7D%0Ap%20%7B%0Amargin%3A%200%2E5em%200%3B%0A%7D%0Ablockquote%20%7B%0Abackground%2Dcolor%3A%20%23f6f6f6%3B%0Apadding%3A%200%2E25em%200%2E75em%3B%0A%7D%0Ahr%20%7B%0Aborder%2Dstyle%3A%20solid%3B%0Aborder%3A%20none%3B%0Aborder%2Dtop%3A%201px%20solid%20%23777%3B%0Amargin%3A%2028px%200%3B%0A%7D%0Adl%20%7B%0Amargin%2Dleft%3A%200%3B%0A%7D%0Adl%20dd%20%7B%0Amargin%2Dbottom%3A%2013px%3B%0Amargin%2Dleft%3A%2013px%3B%0A%7D%0Adl%20dt%20%7B%0Afont%2Dweight%3A%20bold%3B%0A%7D%0Aul%20%7B%0Amargin%2Dtop%3A%200%3B%0A%7D%0Aul%20li%20%7B%0Alist%2Dstyle%3A%20circle%20outside%3B%0A%7D%0Aul%20ul%20%7B%0Amargin%2Dbottom%3A%200%3B%0A%7D%0Apre%2C%20code%20%7B%0Abackground%2Dcolor%3A%20%23f7f7f7%3B%0Aborder%2Dradius%3A%203px%3B%0Acolor%3A%20%23333%3B%0Awhite%2Dspace%3A%20pre%2Dwrap%3B%20%0A%7D%0Apre%20%7B%0Aborder%2Dradius%3A%203px%3B%0Amargin%3A%205px%200px%2010px%200px%3B%0Apadding%3A%2010px%3B%0A%7D%0Apre%3Anot%28%5Bclass%5D%29%20%7B%0Abackground%2Dcolor%3A%20%23f7f7f7%3B%0A%7D%0Acode%20%7B%0Afont%2Dfamily%3A%20Consolas%2C%20Monaco%2C%20%27Courier%20New%27%2C%20monospace%3B%0Afont%2Dsize%3A%2085%25%3B%0A%7D%0Ap%20%3E%20code%2C%20li%20%3E%20code%20%7B%0Apadding%3A%202px%200px%3B%0A%7D%0Adiv%2Efigure%20%7B%0Atext%2Dalign%3A%20center%3B%0A%7D%0Aimg%20%7B%0Abackground%2Dcolor%3A%20%23FFFFFF%3B%0Apadding%3A%202px%3B%0Aborder%3A%201px%20solid%20%23DDDDDD%3B%0Aborder%2Dradius%3A%203px%3B%0Aborder%3A%201px%20solid%20%23CCCCCC%3B%0Amargin%3A%200%205px%3B%0A%7D%0Ah1%20%7B%0Amargin%2Dtop%3A%200%3B%0Afont%2Dsize%3A%2035px%3B%0Aline%2Dheight%3A%2040px%3B%0A%7D%0Ah2%20%7B%0Aborder%2Dbottom%3A%204px%20solid%20%23f7f7f7%3B%0Apadding%2Dtop%3A%2010px%3B%0Apadding%2Dbottom%3A%202px%3B%0Afont%2Dsize%3A%20145%25%3B%0A%7D%0Ah3%20%7B%0Aborder%2Dbottom%3A%202px%20solid%20%23f7f7f7%3B%0Apadding%2Dtop%3A%2010px%3B%0Afont%2Dsize%3A%20120%25%3B%0A%7D%0Ah4%20%7B%0Aborder%2Dbottom%3A%201px%20solid%20%23f7f7f7%3B%0Amargin%2Dleft%3A%208px%3B%0Afont%2Dsize%3A%20105%25%3B%0A%7D%0Ah5%2C%20h6%20%7B%0Aborder%2Dbottom%3A%201px%20solid%20%23ccc%3B%0Afont%2Dsize%3A%20105%25%3B%0A%7D%0Aa%20%7B%0Acolor%3A%20%230033dd%3B%0Atext%2Ddecoration%3A%20none%3B%0A%7D%0Aa%3Ahover%20%7B%0Acolor%3A%20%236666ff%3B%20%7D%0Aa%3Avisited%20%7B%0Acolor%3A%20%23800080%3B%20%7D%0Aa%3Avisited%3Ahover%20%7B%0Acolor%3A%20%23BB00BB%3B%20%7D%0Aa%5Bhref%5E%3D%22http%3A%22%5D%20%7B%0Atext%2Ddecoration%3A%20underline%
</head>
<body>
<h1 class="title toc-ignore">Manage lifecycle changes in functions you use</h1>
<p>The lifecycle package uses warnings to tell you about deprecated functions. Deprecated functions will be removed in a future release, so it’s good practice to eliminate the warnings as soon as you see them.</p>
<p>For example, lets imagine your code uses <code>tibble::data_frame()</code>, which was deprecated in favour of <code>tibble()</code> in version 1.1.0. <code>data_frame()</code> now looks something like this:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>data_frame <span class="ot">&lt;-</span> <span class="cf">function</span>(...) {</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> lifecycle<span class="sc">::</span><span class="fu">deprecate_warn</span>(<span class="st">&quot;1.1.0&quot;</span>, <span class="st">&quot;data_frame()&quot;</span>, <span class="st">&quot;tibble()&quot;</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> tibble<span class="sc">::</span><span class="fu">tibble</span>(...)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>}</span></code></pre></div>
<p>That means if you use <code>data_frame()</code> in your own code you’ll get a warning:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>df1 <span class="ot">&lt;-</span> <span class="fu">data_frame</span>(<span class="at">x =</span> <span class="dv">1</span>, <span class="at">y =</span> <span class="dv">2</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: `data_frame()` was deprecated in tibble 1.1.0.</span></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ℹ Please use `tibble()` instead.</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Call `lifecycle::last_lifecycle_warnings()` to see where this warning was</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; generated.</span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; This warning is displayed once every 8 hours.</span></span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.</span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>df2 <span class="ot">&lt;-</span> <span class="fu">data_frame</span>(<span class="at">a =</span> <span class="st">&quot;apple&quot;</span>, <span class="at">b =</span> <span class="st">&quot;banana&quot;</span>)</span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: `data_frame()` was deprecated in tibble 1.1.0.</span></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ℹ Please use `tibble()` instead.</span></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Call `lifecycle::last_lifecycle_warnings()` to see where this warning was</span></span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; generated.</span></span></code></pre></div>
<p>You’ll notice that the warning only appears the first time we call it — lifecycle only notifies you every 8 hours so it’s not overly disruptive if you’ve used a deprecated function in many places.</p>
<p>So how do you track down exactly where the warning came from? Firstly, you might notice the deprecation warning message includes the advice to call <code>lifecycle::last_lifecycle_warnings()</code>. That’ll give you a list of all the deprecation warnings that have happened recently:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>lifecycle<span class="sc">::</span><span class="fu">last_lifecycle_warnings</span>()</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [[1]]</span></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;deprecated&gt;</span></span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; message: `data_frame()` was deprecated in tibble 1.1.0.</span></span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Please use `tibble()` instead.</span></span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Backtrace:</span></span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1. global::data_frame(x = 1)</span></span></code></pre></div>
<p>Each warning comes with a back trace that shows you the full sequence of calls that lead to the deprecated function.</p>
<p>Alternatively, if you’re ready to spend some time tracking down all your uses of deprecated functions, you can use the <code>lifecycle_verbosity</code> option to make deprecated functions warn every time:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">options</span>(<span class="at">lifecycle_verbosity =</span> <span class="st">&quot;warning&quot;</span>)</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>df1 <span class="ot">&lt;-</span> <span class="fu">data_frame</span>(<span class="at">x =</span> <span class="dv">1</span>, <span class="at">y =</span> <span class="dv">2</span>)</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: `data_frame()` was deprecated in tibble 1.1.0.</span></span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ℹ Please use `tibble()` instead.</span></span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Call `lifecycle::last_lifecycle_warnings()` to see where this warning was</span></span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; generated.</span></span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>df2 <span class="ot">&lt;-</span> <span class="fu">data_frame</span>(<span class="at">a =</span> <span class="st">&quot;apple&quot;</span>, <span class="at">b =</span> <span class="st">&quot;banana&quot;</span>)</span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: `data_frame()` was deprecated in tibble 1.1.0.</span></span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ℹ Please use `tibble()` instead.</span></span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Call `lifecycle::last_lifecycle_warnings()` to see where this warning was</span></span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; generated.</span></span></code></pre></div>
<p>Then use <code>lifecycle::last_lifecycle_warnings()</code> to track down the source.</p>
<p>Alternatively, if you want to be really strict, you can turn all deprecation warnings into errors, forcing you to deal with them immediately:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">options</span>(<span class="st">&quot;lifecycle_verbosity&quot;</span> <span class="ot">=</span> <span class="st">&quot;error&quot;</span>)</span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>df1 <span class="ot">&lt;-</span> <span class="fu">data_frame</span>(<span class="at">x =</span> <span class="dv">1</span>, <span class="at">y =</span> <span class="dv">2</span>)</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Error:</span></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ! `data_frame()` was deprecated in tibble 1.1.0.</span></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ℹ Please use `tibble()` instead.</span></span></code></pre></div>
<!-- code folding -->
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>
Reference in New Issue Copy Permalink