435 lines
14 KiB
HTML
435 lines
14 KiB
HTML
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<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8" />
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<meta name="generator" content="pandoc" />
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<meta name="author" content="Jim Hester, Hadley Wickham, Gábor Csárdi" />
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<meta name="date" content="2024-03-17" />
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<title>Dependency resolution for R package development</title>
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<script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
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// be compatible with the behavior of Pandoc < 2.8).
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document.addEventListener('DOMContentLoaded', function(e) {
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var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
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var i, h, a;
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for (i = 0; i < hs.length; i++) {
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h = hs[i];
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if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
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a = h.attributes;
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while (a.length > 0) h.removeAttribute(a[0].name);
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}
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});
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</script>
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<style type="text/css">
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code{white-space: pre-wrap;}
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span.smallcaps{font-variant: small-caps;}
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span.underline{text-decoration: underline;}
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div.column{display: inline-block; vertical-align: top; width: 50%;}
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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ul.task-list{list-style: none;}
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<style type="text/css">
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code {
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white-space: pre;
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.sourceCode {
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overflow: visible;
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}
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</style>
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<style type="text/css" data-origin="pandoc">
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pre > code.sourceCode { white-space: pre; position: relative; }
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pre > code.sourceCode > span { line-height: 1.25; }
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pre > code.sourceCode > span:empty { height: 1.2em; }
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.sourceCode { overflow: visible; }
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code.sourceCode > span { color: inherit; text-decoration: inherit; }
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div.sourceCode { margin: 1em 0; }
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pre.sourceCode { margin: 0; }
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@media screen {
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div.sourceCode { overflow: auto; }
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}
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pre > code.sourceCode { white-space: pre-wrap; }
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pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
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{ counter-reset: source-line 0; }
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pre.numberSource code > span > a:first-child::before
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{ content: counter(source-line);
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position: relative; left: -1em; text-align: right; vertical-align: baseline;
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border: none; display: inline-block;
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-webkit-touch-callout: none; -webkit-user-select: none;
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-ms-user-select: none; user-select: none;
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padding: 0 4px; width: 4em;
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color: #aaaaaa;
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}
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pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
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div.sourceCode
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{ }
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pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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}
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code span.al { color: #ff0000; font-weight: bold; }
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code span.an { color: #60a0b0; font-weight: bold; font-style: italic; }
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code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; }
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code span.do { color: #ba2121; font-style: italic; }
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code span.dt { color: #902000; }
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code span.dv { color: #40a070; }
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code span.er { color: #ff0000; font-weight: bold; }
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code span.ex { }
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code span.fl { color: #40a070; }
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code span.fu { color: #06287e; }
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code span.im { color: #008000; font-weight: bold; }
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code span.in { color: #60a0b0; font-weight: bold; font-style: italic; }
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code span.kw { color: #007020; font-weight: bold; }
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code span.op { color: #666666; }
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code span.ot { color: #007020; }
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code span.pp { color: #bc7a00; }
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code span.sc { color: #4070a0; }
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code span.ss { color: #bb6688; }
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code span.st { color: #4070a0; }
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code span.va { color: #19177c; }
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code span.vs { color: #4070a0; }
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code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; }
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</style>
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<script>
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// apply pandoc div.sourceCode style to pre.sourceCode instead
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(function() {
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var sheets = document.styleSheets;
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for (var i = 0; i < sheets.length; i++) {
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if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
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try { var rules = sheets[i].cssRules; } catch (e) { continue; }
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var j = 0;
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while (j < rules.length) {
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var rule = rules[j];
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// check if there is a div.sourceCode rule
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if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") {
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j++;
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continue;
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}
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var style = rule.style.cssText;
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// check if color or background-color is set
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if (rule.style.color === '' && rule.style.backgroundColor === '') {
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j++;
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continue;
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}
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// replace div.sourceCode by a pre.sourceCode rule
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sheets[i].deleteRule(j);
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sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
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}
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}
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})();
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</script>
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<style type="text/css">body {
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background-color: #fff;
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margin: 1em auto;
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max-width: 700px;
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overflow: visible;
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padding-left: 2em;
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padding-right: 2em;
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font-family: "Open Sans", "Helvetica Neue", Helvetica, Arial, sans-serif;
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font-size: 14px;
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line-height: 1.35;
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}
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#TOC {
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clear: both;
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margin: 0 0 10px 10px;
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padding: 4px;
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width: 400px;
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border: 1px solid #CCCCCC;
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border-radius: 5px;
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background-color: #f6f6f6;
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font-size: 13px;
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line-height: 1.3;
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}
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#TOC .toctitle {
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font-weight: bold;
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font-size: 15px;
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margin-left: 5px;
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}
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#TOC ul {
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padding-left: 40px;
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margin-left: -1.5em;
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margin-top: 5px;
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margin-bottom: 5px;
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}
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#TOC ul ul {
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margin-left: -2em;
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}
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#TOC li {
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line-height: 16px;
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}
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table {
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margin: 1em auto;
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border-width: 1px;
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border-color: #DDDDDD;
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border-style: outset;
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border-collapse: collapse;
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}
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table th {
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border-width: 2px;
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padding: 5px;
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border-style: inset;
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}
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table td {
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border-width: 1px;
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border-style: inset;
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line-height: 18px;
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padding: 5px 5px;
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}
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table, table th, table td {
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border-left-style: none;
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border-right-style: none;
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}
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table thead, table tr.even {
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background-color: #f7f7f7;
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}
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p {
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margin: 0.5em 0;
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}
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blockquote {
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background-color: #f6f6f6;
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padding: 0.25em 0.75em;
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}
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hr {
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border-style: solid;
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border: none;
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border-top: 1px solid #777;
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margin: 28px 0;
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}
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dl {
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margin-left: 0;
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}
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dl dd {
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margin-bottom: 13px;
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margin-left: 13px;
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}
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dl dt {
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font-weight: bold;
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}
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ul {
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margin-top: 0;
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}
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ul li {
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list-style: circle outside;
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}
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ul ul {
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margin-bottom: 0;
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}
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pre, code {
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background-color: #f7f7f7;
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border-radius: 3px;
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color: #333;
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white-space: pre-wrap;
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}
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pre {
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border-radius: 3px;
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margin: 5px 0px 10px 0px;
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padding: 10px;
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}
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pre:not([class]) {
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background-color: #f7f7f7;
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}
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code {
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font-family: Consolas, Monaco, 'Courier New', monospace;
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font-size: 85%;
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}
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p > code, li > code {
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padding: 2px 0px;
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}
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div.figure {
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text-align: center;
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}
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img {
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background-color: #FFFFFF;
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padding: 2px;
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border: 1px solid #DDDDDD;
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border-radius: 3px;
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border: 1px solid #CCCCCC;
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margin: 0 5px;
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}
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h1 {
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margin-top: 0;
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font-size: 35px;
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line-height: 40px;
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}
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h2 {
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border-bottom: 4px solid #f7f7f7;
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padding-top: 10px;
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padding-bottom: 2px;
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font-size: 145%;
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}
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h3 {
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border-bottom: 2px solid #f7f7f7;
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padding-top: 10px;
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font-size: 120%;
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}
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h4 {
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border-bottom: 1px solid #f7f7f7;
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margin-left: 8px;
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font-size: 105%;
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}
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h5, h6 {
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border-bottom: 1px solid #ccc;
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font-size: 105%;
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}
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a {
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color: #0033dd;
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text-decoration: none;
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}
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a:hover {
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color: #6666ff; }
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a:visited {
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color: #800080; }
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a:visited:hover {
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color: #BB00BB; }
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a[href^="http:"] {
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text-decoration: underline; }
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a[href^="https:"] {
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text-decoration: underline; }
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code > span.kw { color: #555; font-weight: bold; }
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code > span.dt { color: #902000; }
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code > span.dv { color: #40a070; }
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code > span.bn { color: #d14; }
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code > span.fl { color: #d14; }
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code > span.ch { color: #d14; }
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code > span.st { color: #d14; }
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code > span.co { color: #888888; font-style: italic; }
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code > span.ot { color: #007020; }
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code > span.al { color: #ff0000; font-weight: bold; }
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code > span.fu { color: #900; font-weight: bold; }
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code > span.er { color: #a61717; background-color: #e3d2d2; }
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</style>
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</head>
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<body>
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<h1 class="title toc-ignore">Dependency resolution for R package
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development</h1>
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<h4 class="author">Jim Hester, Hadley Wickham, Gábor Csárdi</h4>
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<h4 class="date">2024-03-17</h4>
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<div id="package-remotes" class="section level1">
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<h1>Package remotes</h1>
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<p>Remotes, just like devtools, supports package dependency installation
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for packages not yet in a standard package repository such as <a href="https://cran.r-project.org">CRAN</a> or <a href="https://bioconductor.org">Bioconductor</a>.</p>
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<p>You can mark any regular dependency defined in the
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|||
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<code>Depends</code>, <code>Imports</code>, <code>Suggests</code> or
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|||
|
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<code>Enhances</code> fields as being installed from a remote location
|
|||
|
|
by adding the remote location to <code>Remotes</code> in your
|
|||
|
|
<code>DESCRIPTION</code> file. This will cause remotes to download and
|
|||
|
|
install them from the specified location, instead of CRAN.</p>
|
|||
|
|
<p>The remote dependencies specified in <code>Remotes</code> should be
|
|||
|
|
described in the following form.</p>
|
|||
|
|
<pre><code>Remotes: [type::]<Repository>, [type2::]<Repository2></code></pre>
|
|||
|
|
<p>The <code>type</code> is an optional parameter. If the type is
|
|||
|
|
missing the default is to install from GitHub. Additional remote
|
|||
|
|
dependencies should be separated by commas, just like normal
|
|||
|
|
dependencies elsewhere in the <code>DESCRIPTION</code> file.</p>
|
|||
|
|
<div id="github" class="section level3">
|
|||
|
|
<h3>GitHub</h3>
|
|||
|
|
<p>Because GitHub is the most commonly used unofficial package
|
|||
|
|
distribution in R, it’s the default:</p>
|
|||
|
|
<div class="sourceCode" id="cb2"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> r-lib/testthat</span></span></code></pre></div>
|
|||
|
|
<p>You can also specify a specific hash, tag, or pull request (using the
|
|||
|
|
same syntax as <code>install_github()</code> if you want a particular
|
|||
|
|
commit. Otherwise the latest commit on the default branch is used.</p>
|
|||
|
|
<div class="sourceCode" id="cb3"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> r-lib/httr@v0.4,</span></span>
|
|||
|
|
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="at"> klutometis/roxygen</span><span class="co">#142,</span></span>
|
|||
|
|
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a><span class="at"> r-lib/testthat@c67018fa4970</span></span></code></pre></div>
|
|||
|
|
<p>The special <code>@*release</code> syntax will install the latest
|
|||
|
|
release:</p>
|
|||
|
|
<div class="sourceCode" id="cb4"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> r-lib/testthat@*release</span></span></code></pre></div>
|
|||
|
|
<p>A type of ‘github’ can be specified, but is not required</p>
|
|||
|
|
<div class="sourceCode" id="cb5"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> github::tidyverse/ggplot2</span></span></code></pre></div>
|
|||
|
|
</div>
|
|||
|
|
<div id="other-sources" class="section level3">
|
|||
|
|
<h3>Other sources</h3>
|
|||
|
|
<p>All of the currently supported install sources are available, see the
|
|||
|
|
‘See Also’ section in <code>?install_github</code> for a complete
|
|||
|
|
list.</p>
|
|||
|
|
<div class="sourceCode" id="cb6"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co"># GitLab</span></span>
|
|||
|
|
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> gitlab::jimhester/covr</span></span>
|
|||
|
|
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a></span>
|
|||
|
|
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="co"># Git</span></span>
|
|||
|
|
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> git::git@bitbucket.org:djnavarro/lsr.git,</span></span>
|
|||
|
|
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="at"> git::https://github.com/igraph/rigraph.git@main</span></span>
|
|||
|
|
<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a></span>
|
|||
|
|
<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a><span class="co"># Bitbucket</span></span>
|
|||
|
|
<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> bitbucket::sulab/mygene.r@default, djnavarro/lsr</span></span>
|
|||
|
|
<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a></span>
|
|||
|
|
<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a><span class="co"># Bioconductor</span></span>
|
|||
|
|
<span id="cb6-12"><a href="#cb6-12" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> bioc::3.3/SummarizedExperiment</span><span class="co">#117513, bioc::release/Biobase</span></span>
|
|||
|
|
<span id="cb6-13"><a href="#cb6-13" tabindex="-1"></a></span>
|
|||
|
|
<span id="cb6-14"><a href="#cb6-14" tabindex="-1"></a><span class="co"># SVN</span></span>
|
|||
|
|
<span id="cb6-15"><a href="#cb6-15" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> svn::https://github.com/tidyverse/stringr</span></span>
|
|||
|
|
<span id="cb6-16"><a href="#cb6-16" tabindex="-1"></a></span>
|
|||
|
|
<span id="cb6-17"><a href="#cb6-17" tabindex="-1"></a><span class="co"># URL</span></span>
|
|||
|
|
<span id="cb6-18"><a href="#cb6-18" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> url::https://github.com/tidyverse/stringr/archive/HEAD.zip</span></span>
|
|||
|
|
<span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a></span>
|
|||
|
|
<span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a><span class="co"># Local</span></span>
|
|||
|
|
<span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="fu">Remotes</span><span class="kw">:</span><span class="at"> local::/pkgs/testthat</span></span></code></pre></div>
|
|||
|
|
</div>
|
|||
|
|
<div id="cran-submission" class="section level3">
|
|||
|
|
<h3>CRAN submission</h3>
|
|||
|
|
<p>When you submit your package to CRAN, all of its dependencies must
|
|||
|
|
also be available on CRAN. For this reason,
|
|||
|
|
<code>devtools::release()</code> will warn you if you try to release a
|
|||
|
|
package with a <code>Remotes</code> field.</p>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
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