1433 lines
857 KiB
HTML
1433 lines
857 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="date" content="2024-08-27" />
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<title>Installing and Managing Bioconductor Packages</title>
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<script>/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */
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<script>/*!
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* Bootstrap v3.3.5 (http://getbootstrap.com)
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* Copyright 2011-2015 Twitter, Inc.
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* Licensed under the MIT license
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*/
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!function(a,b){function c(a,b){var c=a.createElement("p"),d=a.getElementsByTagName("head")[0]||a.documentElement;return c.innerHTML="x<style>"+b+"</style>",d.insertBefore(c.lastChild,d.firstChild)}function d(){var a=t.elements;return"string"==typeof a?a.split(" "):a}function e(a,b){var c=t.elements;"string"!=typeof c&&(c=c.join(" ")),"string"!=typeof a&&(a=a.join(" ")),t.elements=c+" "+a,j(b)}function f(a){var b=s[a[q]];return b||(b={},r++,a[q]=r,s[r]=b),b}function g(a,c,d){if(c||(c=b),l)return c.createElement(a);d||(d=f(c));var e;return e=d.cache[a]?d.cache[a].cloneNode():p.test(a)?(d.cache[a]=d.createElem(a)).cloneNode():d.createElem(a),!e.canHaveChildren||o.test(a)||e.tagUrn?e:d.frag.appendChild(e)}function h(a,c){if(a||(a=b),l)return a.createDocumentFragment();c=c||f(a);for(var e=c.frag.cloneNode(),g=0,h=d(),i=h.length;i>g;g++)e.createElement(h[g]);return e}function i(a,b){b.cache||(b.cache={},b.createElem=a.createElement,b.createFrag=a.createDocumentFragment,b.frag=b.createFrag()),a.createElement=function(c){return t.shivMethods?g(c,a,b):b.createElem(c)},a.createDocumentFragment=Function("h,f","return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&("+d().join().replace(/[\w\-:]+/g,function(a){return b.createElem(a),b.frag.createElement(a),'c("'+a+'")'})+");return n}")(t,b.frag)}function j(a){a||(a=b);var d=f(a);return!t.shivCSS||k||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),l||i(a,d),a}var k,l,m="3.7.2",n=a.html5||{},o=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,p=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,q="_html5shiv",r=0,s={};!function(){try{var a=b.createElement("a");a.innerHTML="<xyz></xyz>",k="hidden"in a,l=1==a.childNodes.length||function(){b.createElement("a");var a=b.createDocumentFragment();return"undefined"==typeof a.cloneNode||"undefined"==typeof a.createDocumentFragment||"undefined"==typeof a.createElement}()}catch(c){k=!0,l=!0}}();var t={elements:n.elements||"abbr article aside audio bdi canvas data datalist details dialog figcaption figure footer header hgroup main mark meter nav output picture progress section summary template time video",version:m,shivCSS:n.shivCSS!==!1,supportsUnknownElements:l,shivMethods:n.shivMethods!==!1,type:"default",shivDocument:j,createElement:g,createDocumentFragment:h,addElements:e};a.html5=t,j(b)}(this,document);
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|||
|
|
};
|
|||
|
|
</script>
|
|||
|
|
<script>/*! Respond.js v1.4.2: min/max-width media query polyfill * Copyright 2013 Scott Jehl
|
|||
|
|
* Licensed under https://github.com/scottjehl/Respond/blob/master/LICENSE-MIT
|
|||
|
|
* */
|
|||
|
|
|
|||
|
|
// Only run this code in IE 8
|
|||
|
|
if (!!window.navigator.userAgent.match("MSIE 8")) {
|
|||
|
|
!function(a){"use strict";a.matchMedia=a.matchMedia||function(a){var b,c=a.documentElement,d=c.firstElementChild||c.firstChild,e=a.createElement("body"),f=a.createElement("div");return f.id="mq-test-1",f.style.cssText="position:absolute;top:-100em",e.style.background="none",e.appendChild(f),function(a){return f.innerHTML='­<style media="'+a+'"> #mq-test-1 { width: 42px; }</style>',c.insertBefore(e,d),b=42===f.offsetWidth,c.removeChild(e),{matches:b,media:a}}}(a.document)}(this),function(a){"use strict";function b(){u(!0)}var c={};a.respond=c,c.update=function(){};var d=[],e=function(){var b=!1;try{b=new a.XMLHttpRequest}catch(c){b=new a.ActiveXObject("Microsoft.XMLHTTP")}return function(){return b}}(),f=function(a,b){var c=e();c&&(c.open("GET",a,!0),c.onreadystatechange=function(){4!==c.readyState||200!==c.status&&304!==c.status||b(c.responseText)},4!==c.readyState&&c.send(null))};if(c.ajax=f,c.queue=d,c.regex={media:/@media[^\{]+\{([^\{\}]*\{[^\}\{]*\})+/gi,keyframes:/@(?:\-(?:o|moz|webkit)\-)?keyframes[^\{]+\{(?:[^\{\}]*\{[^\}\{]*\})+[^\}]*\}/gi,urls:/(url\()['"]?([^\/\)'"][^:\)'"]+)['"]?(\))/g,findStyles:/@media *([^\{]+)\{([\S\s]+?)$/,only:/(only\s+)?([a-zA-Z]+)\s?/,minw:/\([\s]*min\-width\s*:[\s]*([\s]*[0-9\.]+)(px|em)[\s]*\)/,maxw:/\([\s]*max\-width\s*:[\s]*([\s]*[0-9\.]+)(px|em)[\s]*\)/},c.mediaQueriesSupported=a.matchMedia&&null!==a.matchMedia("only all")&&a.matchMedia("only all").matches,!c.mediaQueriesSupported){var g,h,i,j=a.document,k=j.documentElement,l=[],m=[],n=[],o={},p=30,q=j.getElementsByTagName("head")[0]||k,r=j.getElementsByTagName("base")[0],s=q.getElementsByTagName("link"),t=function(){var a,b=j.createElement("div"),c=j.body,d=k.style.fontSize,e=c&&c.style.fontSize,f=!1;return b.style.cssText="position:absolute;font-size:1em;width:1em",c||(c=f=j.createElement("body"),c.style.background="none"),k.style.fontSize="100%",c.style.fontSize="100%",c.appendChild(b),f&&k.insertBefore(c,k.firstChild),a=b.offsetWidth,f?k.removeChild(c):c.removeChild(b),k.style.fontSize=d,e&&(c.style.fontSize=e),a=i=parseFloat(a)},u=function(b){var c="clientWidth",d=k[c],e="CSS1Compat"===j.compatMode&&d||j.body[c]||d,f={},o=s[s.length-1],r=(new Date).getTime();if(b&&g&&p>r-g)return a.clearTimeout(h),h=a.setTimeout(u,p),void 0;g=r;for(var v in l)if(l.hasOwnProperty(v)){var w=l[v],x=w.minw,y=w.maxw,z=null===x,A=null===y,B="em";x&&(x=parseFloat(x)*(x.indexOf(B)>-1?i||t():1)),y&&(y=parseFloat(y)*(y.indexOf(B)>-1?i||t():1)),w.hasquery&&(z&&A||!(z||e>=x)||!(A||y>=e))||(f[w.media]||(f[w.media]=[]),f[w.media].push(m[w.rules]))}for(var C in n)n.hasOwnProperty(C)&&n[C]&&n[C].parentNode===q&&q.removeChild(n[C]);n.length=0;for(var D in f)if(f.hasOwnProperty(D)){var E=j.createElement("style"),F=f[D].join("\n");E.type="text/css",E.media=D,q.insertBefore(E,o.nextSibling),E.styleSheet?E.styleSheet.cssText=F:E.appendChild(j.createTextNode(F)),n.push(E)}},v=function(a,b,d){var e=a.replace(c.regex.keyframes,"").match(c.regex.media),f=e&&e.length||0;b=b.substring(0,b.lastIndexOf("/"));var g=function(a){return a.replace(c.regex.urls,"$1"+b+"$2$3")},h=!f&&d;b.length&&(b+="/"),h&&(f=1);for(var i=0;f>i;i++){var j,k,n,o;h?(j=d,m.push(g(a))):(j=e[i].match(c.regex.findStyles)&&RegExp.$1,m.push(RegExp.$2&&g(RegExp.$2))),n=j.split(","),o=n.length;for(var p=0;o>p;p++)k=n[p],l.push({media:k.split("(")[0].match(c.regex.only)&&RegExp.$2||"all",rules:m.length-1,hasquery:k.indexOf("(")>-1,minw:k.match(c.regex.minw)&&parseFloat(RegExp.$1)+(RegExp.$2||""),maxw:k.match(c.regex.maxw)&&parseFloat(RegExp.$1)+(RegExp.$2||"")})}u()},w=function(){if(d.length){var b=d.shift();f(b.href,function(c){v(c,b.href,b.media),o[b.href]=!0,a.setTimeout(function(){w()},0)})}},x=function(){for(var b=0;b<s.length;b++){var c=s[b],e=c.href,f=c.media,g=c.rel&&"stylesheet"===c.rel.toLowerCase();e&&g&&!o[e]&&(c.styleSheet&&c.styleSheet.rawCssText?(v(c.styleSheet.rawCssText,e,f),o[e]=!0):(!/^([a-zA-Z:]*\/\/)/.test(e)&&!r||e.replace(RegExp.$1,"").split("/")[0]===a.location.host)&&("//"===e.substring(0,2)&&(e=a.location.protocol+e),d.push({href:e,media:f})))}w()};x(),c.update=x,c.getEmVal
|
|||
|
|
};
|
|||
|
|
</script>
|
|||
|
|
<style>h1 {font-size: 34px;}
|
|||
|
|
h1.title {font-size: 38px;}
|
|||
|
|
h2 {font-size: 30px;}
|
|||
|
|
h3 {font-size: 24px;}
|
|||
|
|
h4 {font-size: 18px;}
|
|||
|
|
h5 {font-size: 16px;}
|
|||
|
|
h6 {font-size: 12px;}
|
|||
|
|
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
|
|||
|
|
</style>
|
|||
|
|
<script>
|
|||
|
|
|
|||
|
|
/**
|
|||
|
|
* jQuery Plugin: Sticky Tabs
|
|||
|
|
*
|
|||
|
|
* @author Aidan Lister <aidan@php.net>
|
|||
|
|
* adapted by Ruben Arslan to activate parent tabs too
|
|||
|
|
* http://www.aidanlister.com/2014/03/persisting-the-tab-state-in-bootstrap/
|
|||
|
|
*/
|
|||
|
|
(function($) {
|
|||
|
|
"use strict";
|
|||
|
|
$.fn.rmarkdownStickyTabs = function() {
|
|||
|
|
var context = this;
|
|||
|
|
// Show the tab corresponding with the hash in the URL, or the first tab
|
|||
|
|
var showStuffFromHash = function() {
|
|||
|
|
var hash = window.location.hash;
|
|||
|
|
var selector = hash ? 'a[href="' + hash + '"]' : 'li.active > a';
|
|||
|
|
var $selector = $(selector, context);
|
|||
|
|
if($selector.data('toggle') === "tab") {
|
|||
|
|
$selector.tab('show');
|
|||
|
|
// walk up the ancestors of this element, show any hidden tabs
|
|||
|
|
$selector.parents('.section.tabset').each(function(i, elm) {
|
|||
|
|
var link = $('a[href="#' + $(elm).attr('id') + '"]');
|
|||
|
|
if(link.data('toggle') === "tab") {
|
|||
|
|
link.tab("show");
|
|||
|
|
}
|
|||
|
|
});
|
|||
|
|
}
|
|||
|
|
};
|
|||
|
|
|
|||
|
|
|
|||
|
|
// Set the correct tab when the page loads
|
|||
|
|
showStuffFromHash(context);
|
|||
|
|
|
|||
|
|
// Set the correct tab when a user uses their back/forward button
|
|||
|
|
$(window).on('hashchange', function() {
|
|||
|
|
showStuffFromHash(context);
|
|||
|
|
});
|
|||
|
|
|
|||
|
|
// Change the URL when tabs are clicked
|
|||
|
|
$('a', context).on('click', function(e) {
|
|||
|
|
history.pushState(null, null, this.href);
|
|||
|
|
showStuffFromHash(context);
|
|||
|
|
});
|
|||
|
|
|
|||
|
|
return this;
|
|||
|
|
};
|
|||
|
|
}(jQuery));
|
|||
|
|
|
|||
|
|
window.buildTabsets = function(tocID) {
|
|||
|
|
|
|||
|
|
// build a tabset from a section div with the .tabset class
|
|||
|
|
function buildTabset(tabset) {
|
|||
|
|
|
|||
|
|
// check for fade and pills options
|
|||
|
|
var fade = tabset.hasClass("tabset-fade");
|
|||
|
|
var pills = tabset.hasClass("tabset-pills");
|
|||
|
|
var navClass = pills ? "nav-pills" : "nav-tabs";
|
|||
|
|
|
|||
|
|
// determine the heading level of the tabset and tabs
|
|||
|
|
var match = tabset.attr('class').match(/level(\d) /);
|
|||
|
|
if (match === null)
|
|||
|
|
return;
|
|||
|
|
var tabsetLevel = Number(match[1]);
|
|||
|
|
var tabLevel = tabsetLevel + 1;
|
|||
|
|
|
|||
|
|
// find all subheadings immediately below
|
|||
|
|
var tabs = tabset.find("div.section.level" + tabLevel);
|
|||
|
|
if (!tabs.length)
|
|||
|
|
return;
|
|||
|
|
|
|||
|
|
// create tablist and tab-content elements
|
|||
|
|
var tabList = $('<ul class="nav ' + navClass + '" role="tablist"></ul>');
|
|||
|
|
$(tabs[0]).before(tabList);
|
|||
|
|
var tabContent = $('<div class="tab-content"></div>');
|
|||
|
|
$(tabs[0]).before(tabContent);
|
|||
|
|
|
|||
|
|
// build the tabset
|
|||
|
|
var activeTab = 0;
|
|||
|
|
tabs.each(function(i) {
|
|||
|
|
|
|||
|
|
// get the tab div
|
|||
|
|
var tab = $(tabs[i]);
|
|||
|
|
|
|||
|
|
// get the id then sanitize it for use with bootstrap tabs
|
|||
|
|
var id = tab.attr('id');
|
|||
|
|
|
|||
|
|
// see if this is marked as the active tab
|
|||
|
|
if (tab.hasClass('active'))
|
|||
|
|
activeTab = i;
|
|||
|
|
|
|||
|
|
// remove any table of contents entries associated with
|
|||
|
|
// this ID (since we'll be removing the heading element)
|
|||
|
|
$("div#" + tocID + " li a[href='#" + id + "']").parent().remove();
|
|||
|
|
|
|||
|
|
// sanitize the id for use with bootstrap tabs
|
|||
|
|
id = id.replace(/[.\/?&!#<>]/g, '').replace(/\s/g, '_');
|
|||
|
|
tab.attr('id', id);
|
|||
|
|
|
|||
|
|
// get the heading element within it, grab it's text, then remove it
|
|||
|
|
var heading = tab.find('h' + tabLevel + ':first');
|
|||
|
|
var headingText = heading.html();
|
|||
|
|
heading.remove();
|
|||
|
|
|
|||
|
|
// build and append the tab list item
|
|||
|
|
var a = $('<a role="tab" data-toggle="tab">' + headingText + '</a>');
|
|||
|
|
a.attr('href', '#' + id);
|
|||
|
|
a.attr('aria-controls', id);
|
|||
|
|
var li = $('<li role="presentation"></li>');
|
|||
|
|
li.append(a);
|
|||
|
|
tabList.append(li);
|
|||
|
|
|
|||
|
|
// set it's attributes
|
|||
|
|
tab.attr('role', 'tabpanel');
|
|||
|
|
tab.addClass('tab-pane');
|
|||
|
|
tab.addClass('tabbed-pane');
|
|||
|
|
if (fade)
|
|||
|
|
tab.addClass('fade');
|
|||
|
|
|
|||
|
|
// move it into the tab content div
|
|||
|
|
tab.detach().appendTo(tabContent);
|
|||
|
|
});
|
|||
|
|
|
|||
|
|
// set active tab
|
|||
|
|
$(tabList.children('li')[activeTab]).addClass('active');
|
|||
|
|
var active = $(tabContent.children('div.section')[activeTab]);
|
|||
|
|
active.addClass('active');
|
|||
|
|
if (fade)
|
|||
|
|
active.addClass('in');
|
|||
|
|
|
|||
|
|
if (tabset.hasClass("tabset-sticky"))
|
|||
|
|
tabset.rmarkdownStickyTabs();
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
// convert section divs with the .tabset class to tabsets
|
|||
|
|
var tabsets = $("div.section.tabset");
|
|||
|
|
tabsets.each(function(i) {
|
|||
|
|
buildTabset($(tabsets[i]));
|
|||
|
|
});
|
|||
|
|
};
|
|||
|
|
|
|||
|
|
</script>
|
|||
|
|
<style type="text/css">.hljs-literal {
|
|||
|
|
color: #990073;
|
|||
|
|
}
|
|||
|
|
.hljs-number {
|
|||
|
|
color: #099;
|
|||
|
|
}
|
|||
|
|
.hljs-comment {
|
|||
|
|
color: #998;
|
|||
|
|
font-style: italic;
|
|||
|
|
}
|
|||
|
|
.hljs-keyword {
|
|||
|
|
color: #900;
|
|||
|
|
font-weight: bold;
|
|||
|
|
}
|
|||
|
|
.hljs-string {
|
|||
|
|
color: #d14;
|
|||
|
|
}
|
|||
|
|
</style>
|
|||
|
|
<script src="data:application/javascript;base64,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
|
|||
|
|
|
|||
|
|
<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;}</style>
|
|||
|
|
<script type="text/javascript">
|
|||
|
|
if (window.hljs) {
|
|||
|
|
hljs.configure({languages: []});
|
|||
|
|
hljs.initHighlightingOnLoad();
|
|||
|
|
if (document.readyState && document.readyState === "complete") {
|
|||
|
|
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<style type="text/css">body {
|
|||
|
|
margin: 0px auto;
|
|||
|
|
max-width: 1134px;
|
|||
|
|
font-family: sans-serif;
|
|||
|
|
font-size: 10pt;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
div#TOC ul {
|
|||
|
|
padding: 0px 0px 0px 45px;
|
|||
|
|
list-style: none;
|
|||
|
|
background-image: none;
|
|||
|
|
background-repeat: none;
|
|||
|
|
background-position: 0;
|
|||
|
|
font-size: 10pt;
|
|||
|
|
font-family: Helvetica, Arial, sans-serif;
|
|||
|
|
}
|
|||
|
|
div#TOC > ul {
|
|||
|
|
padding: 0px 150px 0px 65px;
|
|||
|
|
font-size: 12pt;
|
|||
|
|
}
|
|||
|
|
div#TOC > ul > li {
|
|||
|
|
padding: 5px 0px 0px 0px;
|
|||
|
|
}
|
|||
|
|
div#TOC ul ul {
|
|||
|
|
font-size: 11pt;
|
|||
|
|
}
|
|||
|
|
div#TOC.tocify ul {
|
|||
|
|
padding: 0px;
|
|||
|
|
font-size: inherit;
|
|||
|
|
font-family: inherit;
|
|||
|
|
}
|
|||
|
|
div#TOC.tocify li {
|
|||
|
|
padding: 5px;
|
|||
|
|
font-size: inherit;
|
|||
|
|
font-family: inherit;
|
|||
|
|
}
|
|||
|
|
p, dl {
|
|||
|
|
padding: 0px 150px 0px 65px;
|
|||
|
|
text-align: justify;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
p, img, table {
|
|||
|
|
margin-top: 10px;
|
|||
|
|
margin-bottom: 10px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
ol, ul {
|
|||
|
|
padding: 0px 150px 0px 100px;
|
|||
|
|
list-style: square;
|
|||
|
|
}
|
|||
|
|
li ol, li ul {
|
|||
|
|
padding: 0px 0px 0px 35px;
|
|||
|
|
}
|
|||
|
|
li p {
|
|||
|
|
padding: 0;
|
|||
|
|
}
|
|||
|
|
pre {
|
|||
|
|
margin: 0em 150px 0.5em 0em;
|
|||
|
|
padding: 0px 0px 0px 65px;
|
|||
|
|
border: 0px none;
|
|||
|
|
background-color: #f0f0f0;
|
|||
|
|
white-space: pre;
|
|||
|
|
overflow-x: auto;
|
|||
|
|
font-size: 90%;
|
|||
|
|
}
|
|||
|
|
li pre {
|
|||
|
|
margin: 0em 0px 0.5em -65px;
|
|||
|
|
padding: 0px 0px 0px 65px;
|
|||
|
|
}
|
|||
|
|
pre code {
|
|||
|
|
background-color: inherit;
|
|||
|
|
display: block;
|
|||
|
|
padding: 10px 10px 10px 0px;
|
|||
|
|
white-space: pre;
|
|||
|
|
overflow-x: inherit;
|
|||
|
|
font-size: 100%;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
pre code[class] {
|
|||
|
|
background-color: inherit;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
pre[class] code {
|
|||
|
|
background-color: inherit;
|
|||
|
|
}
|
|||
|
|
tt, code, pre {
|
|||
|
|
font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace;
|
|||
|
|
}
|
|||
|
|
h1, h2, h3, h4, h5, h6 {
|
|||
|
|
font-family: Helvetica, Arial, sans-serif;
|
|||
|
|
margin: 1.2em 150px 0.6em 0em;
|
|||
|
|
|
|||
|
|
padding-left: 65px;
|
|||
|
|
text-indent: -65px;
|
|||
|
|
}
|
|||
|
|
h1.title {
|
|||
|
|
color: #87b13f;
|
|||
|
|
line-height: 1.1em;
|
|||
|
|
margin-top: 25px;
|
|||
|
|
border-bottom: 0px;
|
|||
|
|
}
|
|||
|
|
h1 {
|
|||
|
|
line-height: 1.4em;
|
|||
|
|
border-bottom: 1px #1a81c2 solid;
|
|||
|
|
}
|
|||
|
|
h1, h2, h3 {
|
|||
|
|
color: #1a81c2;
|
|||
|
|
}
|
|||
|
|
h1 {
|
|||
|
|
font-size: 18.0pt;
|
|||
|
|
}
|
|||
|
|
h2 {
|
|||
|
|
font-size: 14.5pt;
|
|||
|
|
}
|
|||
|
|
h3, h4 {
|
|||
|
|
font-size: 12pt;
|
|||
|
|
}
|
|||
|
|
span.header-section-number {
|
|||
|
|
float: left;
|
|||
|
|
width: 65px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
p.author-name {
|
|||
|
|
font-size: 14.5pt;
|
|||
|
|
font-weight: bold;
|
|||
|
|
font-style: italic;
|
|||
|
|
text-align: left;
|
|||
|
|
}
|
|||
|
|
.date {
|
|||
|
|
text-indent: 0px;
|
|||
|
|
font-weight: bold;
|
|||
|
|
}
|
|||
|
|
.abstract, .package {
|
|||
|
|
font-weight: bold;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
code {
|
|||
|
|
background-color: #f0f0f0;
|
|||
|
|
color: #404040;
|
|||
|
|
font-size: 90%;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.figure {
|
|||
|
|
margin: 0em 0px 0.5em;
|
|||
|
|
}
|
|||
|
|
img {
|
|||
|
|
max-width: 100%;
|
|||
|
|
display: block;
|
|||
|
|
padding: 0px 150px 0px 130px;
|
|||
|
|
}
|
|||
|
|
p > img {
|
|||
|
|
padding-left: 65px;
|
|||
|
|
padding-right: 0px;
|
|||
|
|
}
|
|||
|
|
td > img {
|
|||
|
|
padding: 0px;
|
|||
|
|
max-width: 100%;
|
|||
|
|
display: inline;
|
|||
|
|
}
|
|||
|
|
img.smallfigure {
|
|||
|
|
padding-left: 195px;
|
|||
|
|
padding-right: 280px;
|
|||
|
|
}
|
|||
|
|
p > img.smallfigure {
|
|||
|
|
padding-left: 130px;
|
|||
|
|
padding-right: 130px;
|
|||
|
|
}
|
|||
|
|
img.widefigure {
|
|||
|
|
padding-left: 65px;
|
|||
|
|
padding-right: 85px;
|
|||
|
|
margin-right: -65px;
|
|||
|
|
}
|
|||
|
|
p > img.widefigure {
|
|||
|
|
padding-left: 0px;
|
|||
|
|
padding-right: 0px;
|
|||
|
|
margin-right: -65px;
|
|||
|
|
}
|
|||
|
|
p.caption, caption {
|
|||
|
|
color: inherit;
|
|||
|
|
font-size: 8pt;
|
|||
|
|
}
|
|||
|
|
p.caption {
|
|||
|
|
padding-left: 130px;
|
|||
|
|
padding-right: 85px;
|
|||
|
|
margin-bottom: 20px;
|
|||
|
|
}
|
|||
|
|
caption {
|
|||
|
|
padding: 0px;
|
|||
|
|
margin-bottom: 10px;
|
|||
|
|
min-width: 583;
|
|||
|
|
}
|
|||
|
|
span.caption-title {
|
|||
|
|
color: #1a81c2;
|
|||
|
|
font-weight: bold;
|
|||
|
|
}
|
|||
|
|
span.caption-label {
|
|||
|
|
font-weight: bold;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
table {
|
|||
|
|
margin-left: 130px;
|
|||
|
|
margin-right: 85px;
|
|||
|
|
}
|
|||
|
|
.table {
|
|||
|
|
max-width: 518px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
dd {
|
|||
|
|
margin-left: 65px;
|
|||
|
|
margin-bottom: 10px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.code-folding-btn {
|
|||
|
|
position: relative;
|
|||
|
|
margin-top: -26px;
|
|||
|
|
top: 26px;
|
|||
|
|
}
|
|||
|
|
.col-md-12 {
|
|||
|
|
min-height: 0px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.sidenote {
|
|||
|
|
float: right;
|
|||
|
|
clear: right;
|
|||
|
|
margin-right: -150px;
|
|||
|
|
width: 130px;
|
|||
|
|
margin-top: 0;
|
|||
|
|
margin-bottom: 1rem;
|
|||
|
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|
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|
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|
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|
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@media screen and (max-width: 767px) {
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|||
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|
|||
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|
|||
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|
|||
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|
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|
|||
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|
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|
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|
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|
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|
|||
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|
|||
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|
|||
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|
|||
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|
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|
|||
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|
|||
|
|
</head>
|
|||
|
|
|
|||
|
|
<body>
|
|||
|
|
|
|||
|
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|
|||
|
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|
|||
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|
|||
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|
|||
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|
|||
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|
|
|||
|
|
<div id="header">
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<h1 class="title toc-ignore">Installing and Managing <em>Bioconductor</em> Packages</h1>
|
|||
|
|
<p class="author-name">Marcel Ramos<span class="affil-mark">1</span> and Martin Morgan<span class="affil-mark">1</span></p>
|
|||
|
|
<p class="author-affiliation"><span class="affil-mark">1</span>Roswell Park Comprehensive Cancer Center, Buffalo, NY</p>
|
|||
|
|
<h4 class="date">27 August 2024</h4>
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<h1>Contents</h1>
|
|||
|
|
<div id="TOC">
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="#introduction" id="toc-introduction"><span class="toc-section-number">1</span> Introduction</a></li>
|
|||
|
|
<li><a href="#basic-use" id="toc-basic-use"><span class="toc-section-number">2</span> Basic use</a>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="#installing-r" id="toc-installing-r"><span class="toc-section-number">2.1</span> Installing <em>R</em></a></li>
|
|||
|
|
<li><a href="#installing-biocmanager" id="toc-installing-biocmanager"><span class="toc-section-number">2.2</span> Installing <em>BiocManager</em></a></li>
|
|||
|
|
<li><a href="#installing-bioconductor-cran-or-github-packages" id="toc-installing-bioconductor-cran-or-github-packages"><span class="toc-section-number">2.3</span> Installing <em>Bioconductor</em>, <em>CRAN</em>, or GitHub packages</a></li>
|
|||
|
|
<li><a href="#previous-releases" id="toc-previous-releases"><span class="toc-section-number">2.4</span> Previous releases</a></li>
|
|||
|
|
<li><a href="#version-and-validity-of-installations" id="toc-version-and-validity-of-installations"><span class="toc-section-number">2.5</span> Version and validity of installations</a></li>
|
|||
|
|
<li><a href="#available-packages" id="toc-available-packages"><span class="toc-section-number">2.6</span> Available packages</a></li>
|
|||
|
|
<li><a href="#updating-old-packages" id="toc-updating-old-packages"><span class="toc-section-number">2.7</span> Updating old packages</a>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="#rationale" id="toc-rationale"><span class="toc-section-number">2.7.1</span> Rationale</a></li>
|
|||
|
|
<li><a href="#pros-of-updating" id="toc-pros-of-updating"><span class="toc-section-number">2.7.2</span> Pros of updating</a></li>
|
|||
|
|
<li><a href="#cons-of-updating" id="toc-cons-of-updating"><span class="toc-section-number">2.7.3</span> Cons of updating</a></li>
|
|||
|
|
<li><a href="#balancing-the-decision" id="toc-balancing-the-decision"><span class="toc-section-number">2.7.4</span> Balancing the Decision</a></li>
|
|||
|
|
</ul></li>
|
|||
|
|
<li><a href="#archived-cran-packages" id="toc-archived-cran-packages"><span class="toc-section-number">2.8</span> Archived CRAN packages</a></li>
|
|||
|
|
</ul></li>
|
|||
|
|
<li><a href="#advanced-use" id="toc-advanced-use"><span class="toc-section-number">3</span> Advanced use</a>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="#changing-version" id="toc-changing-version"><span class="toc-section-number">3.1</span> Changing version</a></li>
|
|||
|
|
<li><a href="#unsupported-r-bioconductor-versions" id="toc-unsupported-r-bioconductor-versions"><span class="toc-section-number">3.2</span> Unsupported <em>R</em> / <em>Bioconductor</em> versions</a></li>
|
|||
|
|
<li><a href="#multiple-versions" id="toc-multiple-versions"><span class="toc-section-number">3.3</span> Managing multiple versions</a></li>
|
|||
|
|
<li><a href="#offline-use" id="toc-offline-use"><span class="toc-section-number">3.4</span> Offline use</a>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="#offline-config.yaml" id="toc-offline-config.yaml"><span class="toc-section-number">3.4.1</span> Offline config.yaml</a></li>
|
|||
|
|
</ul></li>
|
|||
|
|
</ul></li>
|
|||
|
|
<li><a href="#how-it-works" id="toc-how-it-works"><span class="toc-section-number">4</span> How it works</a></li>
|
|||
|
|
<li><a href="#troubleshooting" id="toc-troubleshooting"><span class="toc-section-number">5</span> Troubleshooting</a>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="#package-not-available" id="toc-package-not-available"><span class="toc-section-number">5.1</span> Package not available</a></li>
|
|||
|
|
<li><a href="#cannot-load-biocmanager" id="toc-cannot-load-biocmanager"><span class="toc-section-number">5.2</span> Cannot load <em>BiocManager</em></a></li>
|
|||
|
|
<li><a href="#timeout-during-package-download" id="toc-timeout-during-package-download"><span class="toc-section-number">5.3</span> Timeout during package download</a></li>
|
|||
|
|
<li><a href="#multiple-biocversion-installations" id="toc-multiple-biocversion-installations"><span class="toc-section-number">5.4</span> Multiple <code>BiocVersion</code> installations</a></li>
|
|||
|
|
<li><a href="#errors-determining-bioconductor-version" id="toc-errors-determining-bioconductor-version"><span class="toc-section-number">5.5</span> Errors determining <em>Bioconductor</em> version</a></li>
|
|||
|
|
</ul></li>
|
|||
|
|
<li><a href="#session-information" id="toc-session-information"><span class="toc-section-number">6</span> Session information</a></li>
|
|||
|
|
</ul>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<div id="introduction" class="section level1" number="1">
|
|||
|
|
<h1><span class="header-section-number">1</span> Introduction</h1>
|
|||
|
|
<p>Use the <a href="https://cran.r-project.org/package=BiocManager">BiocManager</a> package to install and manage packages from the
|
|||
|
|
<em><a href="https://bioconductor.org">Bioconductor</a></em> project for the statistical analysis and comprehension of
|
|||
|
|
high-throughput genomic data.</p>
|
|||
|
|
<p>Current <em>Bioconductor</em> packages are available on a ‘release’ version intended
|
|||
|
|
for every-day use, and a ‘devel’ version where new features are introduced. A
|
|||
|
|
new release version is created every six months. Using the <a href="https://cran.r-project.org/package=BiocManager">BiocManager</a>
|
|||
|
|
package helps users install packages from the same release.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="basic-use" class="section level1" number="2">
|
|||
|
|
<h1><span class="header-section-number">2</span> Basic use</h1>
|
|||
|
|
<div id="installing-r" class="section level2" number="2.1">
|
|||
|
|
<h2><span class="header-section-number">2.1</span> Installing <em>R</em></h2>
|
|||
|
|
<p>We recommend using the current ‘release’ version of <em>R</em>. <a href="https://cran.R-project.org/">Follow
|
|||
|
|
instructions</a> for installing <em>R</em>.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="installing-biocmanager" class="section level2" number="2.2">
|
|||
|
|
<h2><span class="header-section-number">2.2</span> Installing <em>BiocManager</em></h2>
|
|||
|
|
<p>Use standard <em>R</em> installation procedures to install the
|
|||
|
|
<a href="https://cran.r-project.org/package=BiocManager">BiocManager</a> package. This command is requried only once per <em>R</em>
|
|||
|
|
installation.</p>
|
|||
|
|
<pre class="r"><code>install.packages("BiocManager", repos = "https://cloud.r-project.org")</code></pre>
|
|||
|
|
</div>
|
|||
|
|
<div id="installing-bioconductor-cran-or-github-packages" class="section level2" number="2.3">
|
|||
|
|
<h2><span class="header-section-number">2.3</span> Installing <em>Bioconductor</em>, <em>CRAN</em>, or GitHub packages</h2>
|
|||
|
|
<p>Install <em>Bioconductor</em> (or CRAN) packages with</p>
|
|||
|
|
<pre class="r"><code>BiocManager::install(c("GenomicRanges", "Organism.dplyr"))</code></pre>
|
|||
|
|
<p>Installed packages can be updated to their current version with</p>
|
|||
|
|
<pre class="r"><code>BiocManager::install()</code></pre>
|
|||
|
|
</div>
|
|||
|
|
<div id="previous-releases" class="section level2" number="2.4">
|
|||
|
|
<h2><span class="header-section-number">2.4</span> Previous releases</h2>
|
|||
|
|
<p>To install CRAN package versions consistent with previous releases of
|
|||
|
|
Bioconductor, use the <a href="https://github.com/Bioconductor/BiocArchive">BiocArchive</a> package. BiocArchive enables
|
|||
|
|
contemporary installations of CRAN packages with out-of-date <em>Bioconductor</em>
|
|||
|
|
releases using <a href="https://packagemanager.posit.co/">Posit Public Package Manager</a>.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="version-and-validity-of-installations" class="section level2" number="2.5">
|
|||
|
|
<h2><span class="header-section-number">2.5</span> Version and validity of installations</h2>
|
|||
|
|
<p>Use <code>version()</code> to discover the version of <em>Bioconductor</em> currently in
|
|||
|
|
use.</p>
|
|||
|
|
<pre class="r"><code>BiocManager::version()</code></pre>
|
|||
|
|
<p><em>Bioconductor</em> packages work best when they are all from the same release. Use
|
|||
|
|
<code>valid()</code> to identify packages that are out-of-date or from unexpected
|
|||
|
|
versions.</p>
|
|||
|
|
<pre class="r"><code>BiocManager::valid()</code></pre>
|
|||
|
|
<p><code>valid()</code> returns an object that can be queried for detailed
|
|||
|
|
information about invalid packages, as illustrated in the following
|
|||
|
|
screen capture</p>
|
|||
|
|
<pre><code>> v <- valid()
|
|||
|
|
Warning message:
|
|||
|
|
6 packages out-of-date; 0 packages too new
|
|||
|
|
> names(v)
|
|||
|
|
[1] "out_of_date" "too_new"
|
|||
|
|
> head(v$out_of_date, 2)
|
|||
|
|
Package LibPath
|
|||
|
|
bit "bit" "/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.8"
|
|||
|
|
ff "ff" "/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.8"
|
|||
|
|
Installed Built ReposVer Repository
|
|||
|
|
bit "1.1-12" "3.5.0" "1.1-13" "https://cloud.r-project.org/src/contrib"
|
|||
|
|
ff "2.2-13" "3.5.0" "2.2-14" "https://cloud.r-project.org/src/contrib"
|
|||
|
|
></code></pre>
|
|||
|
|
</div>
|
|||
|
|
<div id="available-packages" class="section level2" number="2.6">
|
|||
|
|
<h2><span class="header-section-number">2.6</span> Available packages</h2>
|
|||
|
|
<p>Packages available for your version of <em>Bioconductor</em> can be
|
|||
|
|
discovered with <code>available()</code>; the first argument can be used to
|
|||
|
|
filter package names based on a regular expression, e.g., ‘BSgenome’
|
|||
|
|
package available for <em>Homo sapiens</em></p>
|
|||
|
|
<pre class="r"><code>avail <- BiocManager::available()
|
|||
|
|
length(avail) # all CRAN & Bioconductor packages
|
|||
|
|
BiocManager::available("BSgenome.Hsapiens") # BSgenome.Hsapiens.* packages</code></pre>
|
|||
|
|
<p>Questions about installing and managing <em>Bioconductor</em> packages should
|
|||
|
|
be addressed to the <a href="https://support.bioconductor.org"><em>Bioconductor</em> support site</a>.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="updating-old-packages" class="section level2" number="2.7">
|
|||
|
|
<h2><span class="header-section-number">2.7</span> Updating old packages</h2>
|
|||
|
|
<p>The user can often get an update packages prompt similar to:</p>
|
|||
|
|
<pre><code>> BiocManager::install("AnVIL")
|
|||
|
|
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
|
|||
|
|
Old packages: 'AnnotationDbi', 'arrow', 'basilisk.utils', 'beachmat',
|
|||
|
|
'BiocParallel', 'BiocSingular', 'biocthis', 'Biostrings', 'bluster',
|
|||
|
|
'DelayedArray', 'downlit', 'edgeR', 'GenomeInfoDb', 'GenomicFeatures',
|
|||
|
|
'IRanges', 'limma', 'pkgbuild', 'pkgload', 'processx', 'RcppSpdlog', 'rhdf5',
|
|||
|
|
'rstudioapi', 'SingleR', 'testthat', 'usethis', 'xml2', 'KernSmooth',
|
|||
|
|
'Matrix', 'mgcv'
|
|||
|
|
Update all/some/none? [a/s/n]:</code></pre>
|
|||
|
|
<p>A decision should be made regarding updating packages. In the following section
|
|||
|
|
we will detail the rationale, pros, and cons of updating packages.</p>
|
|||
|
|
<p>(An initial draft of this section was produced by ChatGPT on 28 August 2023)</p>
|
|||
|
|
<div id="rationale" class="section level3" number="2.7.1">
|
|||
|
|
<h3><span class="header-section-number">2.7.1</span> Rationale</h3>
|
|||
|
|
<p>Package updates often include bug fixes, improvements in functionality, and
|
|||
|
|
optimizations. By updating, the user can ensure that they are benefiting from
|
|||
|
|
the latest enhancements and fixes in the packages they use.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="pros-of-updating" class="section level3" number="2.7.2">
|
|||
|
|
<h3><span class="header-section-number">2.7.2</span> Pros of updating</h3>
|
|||
|
|
<ul>
|
|||
|
|
<li><strong>Bug Fixes</strong>: Updating packages can resolve known issues and bugs present in
|
|||
|
|
older versions. This can lead to more accurate and reliable analyses.</li>
|
|||
|
|
<li><strong>Performance</strong>: Package updates might come with performance optimizations
|
|||
|
|
that can lead to faster execution of code and analyses.</li>
|
|||
|
|
<li><strong>New Features</strong>: Updated packages might introduce new features, functions,
|
|||
|
|
and capabilities that can enhance your workflow and analysis options.</li>
|
|||
|
|
<li><strong>Compatibility</strong>: Newer packages are often developed with compatibility in
|
|||
|
|
mind. Using outdated packages might lead to compatibility issues with other
|
|||
|
|
packages or R itself.</li>
|
|||
|
|
<li><strong>Security</strong>: In some cases, package updates address security
|
|||
|
|
vulnerabilities. Keeping packages up to date can help maintain the security of
|
|||
|
|
the computational environment.</li>
|
|||
|
|
<li><strong>Documentation</strong>: Newer versions of packages might come with updated
|
|||
|
|
documentation that reflects recent changes and improvements in package
|
|||
|
|
functionality.</li>
|
|||
|
|
</ul>
|
|||
|
|
</div>
|
|||
|
|
<div id="cons-of-updating" class="section level3" number="2.7.3">
|
|||
|
|
<h3><span class="header-section-number">2.7.3</span> Cons of updating</h3>
|
|||
|
|
<ul>
|
|||
|
|
<li><strong>Code Breakage</strong>: Updates can introduce changes in package behavior,
|
|||
|
|
function signatures, or syntax. This can potentially break existing code if it
|
|||
|
|
relies on the previous behavior.</li>
|
|||
|
|
<li><strong>Version Conflicts</strong>: Updates to one package might trigger dependencies on
|
|||
|
|
updated versions of other packages. This can lead to conflicts if those updated
|
|||
|
|
versions are not compatible with other parts of your workflow.</li>
|
|||
|
|
<li><strong>Workflow Disruption</strong>: When you update packages, you might need to retest
|
|||
|
|
and validate your analyses to ensure that the changes in package behavior don’t
|
|||
|
|
affect your results.</li>
|
|||
|
|
<li><strong>Learning Curve</strong>: New features and changes introduced in updated packages
|
|||
|
|
might require you to invest time in understanding how to use them effectively.</li>
|
|||
|
|
<li><strong>Temporary Instability</strong>: Right after a major update, the new version might
|
|||
|
|
not be as stable as the previous one, leading to unexpected behavior.</li>
|
|||
|
|
</ul>
|
|||
|
|
</div>
|
|||
|
|
<div id="balancing-the-decision" class="section level3" number="2.7.4">
|
|||
|
|
<h3><span class="header-section-number">2.7.4</span> Balancing the Decision</h3>
|
|||
|
|
<ul>
|
|||
|
|
<li>Consider how critical the package is to your analysis. If a package is central
|
|||
|
|
to your workflow, updating might be more important.</li>
|
|||
|
|
<li>Read the release notes of the package to understand what changes are
|
|||
|
|
introduced in the update.</li>
|
|||
|
|
<li>Consider using a separate environment (e.g., Docker container) for testing
|
|||
|
|
updates before applying them to the main analysis environment.</li>
|
|||
|
|
<li>Make sure to backup code and data before performing updates.</li>
|
|||
|
|
<li>Check if there are any compatibility issues with other packages you are using.</li>
|
|||
|
|
</ul>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
<div id="archived-cran-packages" class="section level2" number="2.8">
|
|||
|
|
<h2><span class="header-section-number">2.8</span> Archived CRAN packages</h2>
|
|||
|
|
<p>In the event that a package is no longer available on CRAN, it may be
|
|||
|
|
desirable to install an archived package, especially if it is assumed that the
|
|||
|
|
package will return to an unarchived state at a later date. Users who wish to
|
|||
|
|
protect their systems from the consequences of these state changes can
|
|||
|
|
install archived packages by using the <a href="https://www.cranhaven.org/">CRANhaven</a> repository. This repository
|
|||
|
|
contains archived versions of CRAN packages for up to five weeks or until
|
|||
|
|
they are unarchived on CRAN. To enable archived CRAN package installations, the
|
|||
|
|
user can run the following command:</p>
|
|||
|
|
<pre class="r"><code>options(
|
|||
|
|
repos = c(
|
|||
|
|
getOption("repos"),
|
|||
|
|
CRANhaven = "https://cranhaven.r-universe.dev"
|
|||
|
|
)
|
|||
|
|
)
|
|||
|
|
BiocManager::install('archivedPackage')</code></pre>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
<div id="advanced-use" class="section level1" number="3">
|
|||
|
|
<h1><span class="header-section-number">3</span> Advanced use</h1>
|
|||
|
|
<div id="changing-version" class="section level2" number="3.1">
|
|||
|
|
<h2><span class="header-section-number">3.1</span> Changing version</h2>
|
|||
|
|
<p>Use the <code>version=</code> argument to update all packages to a specific <em>Bioconductor</em>
|
|||
|
|
version</p>
|
|||
|
|
<pre class="r"><code>BiocManager::install(version="3.7")</code></pre>
|
|||
|
|
<p><em>Bioconductor</em> versions are associated with specific <em>R</em> versions, as
|
|||
|
|
summarized <a href="https://bioconductor.org/about/release-announcements/">here</a>. Attempting to install a version of
|
|||
|
|
<em>Bioconductor</em> that is not supported by the version of <em>R</em> in use
|
|||
|
|
leads to an error; using the most recent version of <em>Bioconductor</em> may
|
|||
|
|
require installing a new version of <em>R</em>.</p>
|
|||
|
|
<pre><code>> BiocManager::install(version="3.9")
|
|||
|
|
Error: Bioconductor version '3.9' requires R version '3.6'; see
|
|||
|
|
https://bioconductor.org/install</code></pre>
|
|||
|
|
<p>A special version, <code>version="devel"</code>, allows use of <em>Bioconductor</em>
|
|||
|
|
packages that are under development.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="unsupported-r-bioconductor-versions" class="section level2" number="3.2">
|
|||
|
|
<h2><span class="header-section-number">3.2</span> Unsupported <em>R</em> / <em>Bioconductor</em> versions</h2>
|
|||
|
|
<p>The main purpose of BiocManager is to ensure that users install the
|
|||
|
|
version of <em>Bioconductor</em> appropriate for their version of <em>R</em>. Use
|
|||
|
|
the environment variable <code>R_BIOC_VERSION</code> to install any version of
|
|||
|
|
<em>Bioconductor</em> on any version of <em>R</em>. Thus <em>R</em> version 4.3.0 and
|
|||
|
|
<em>Bioconductor</em> version 3.19 are not compatible…</p>
|
|||
|
|
<pre><code>> BiocManager::install(version = "3.19")
|
|||
|
|
Error: Bioconductor version '3.19' requires R version '4.4'; use
|
|||
|
|
`version = '3.18'` with R version 4.3; see
|
|||
|
|
https://bioconductor.org/install</code></pre>
|
|||
|
|
<p>…but the version can be forced with</p>
|
|||
|
|
<pre><code>> Sys.setenv(R_BIOC_VERSION="3.19")
|
|||
|
|
> BiocManager::install(version = "3.19")
|
|||
|
|
...
|
|||
|
|
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.3.0 (2023-04-21)</code></pre>
|
|||
|
|
<p><strong>Note</strong>. Compatibility of Bioconductor with a mismatched version of R
|
|||
|
|
is not guaranteed and support is not provided for such installations.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="multiple-versions" class="section level2" number="3.3">
|
|||
|
|
<h2><span class="header-section-number">3.3</span> Managing multiple versions</h2>
|
|||
|
|
<p>It is possible to have multiple versions of <em>Bioconductor</em> installed on the
|
|||
|
|
same computer. A best practice is to <a href="https://cran.R-project.org/">create an initial <em>R</em> installation</a>.
|
|||
|
|
Then create and use a library for each version of <em>Bioconductor</em>. The library
|
|||
|
|
will contain all <em>Bioconductor</em>, CRAN, and other packages for that version of
|
|||
|
|
<em>Bioconductor</em>. We illustrate the process assuming use of <em>Bioconductor</em>
|
|||
|
|
version 3.7, available using <em>R</em> version 3.5</p>
|
|||
|
|
<p>Create a directory to contain the library (replace <code>USER_NAME</code> with your user
|
|||
|
|
name on Windows)</p>
|
|||
|
|
<ul>
|
|||
|
|
<li>Linux: <code>~/R/3.5-Bioc-3.7</code></li>
|
|||
|
|
<li>macOS: <code>~/Library/R/3.5-Bioc-3.7/library</code></li>
|
|||
|
|
<li>Windows: <code>C:\Users\USER_NAME\Documents\R\3.5-Bioc-3.7</code></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>Set the environment variable <code>R_LIBS_USER</code> to this directory, and invoke <em>R</em>.
|
|||
|
|
Command line examples for Linux are</p>
|
|||
|
|
<ul>
|
|||
|
|
<li>Linux: <code>R_LIBS_USER=~/R/3.5-Bioc-3.7 R</code></li>
|
|||
|
|
<li>macOS: <code>R_LIBS_USER=~/Library/R/3.5-Bioc-3.7/library R</code></li>
|
|||
|
|
<li>Windows: <code>cmd /C "set R_LIBS_USER=C:\Users\USER_NAME\Documents\R\3.5-Bioc-3.7 && R"</code></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>Once in <em>R</em>, confirm that the version-specific library path has been set</p>
|
|||
|
|
<pre class="r"><code>.libPaths()</code></pre>
|
|||
|
|
<p>On Linux and macOS, create a bash alias to save typing, e.g.,</p>
|
|||
|
|
<ul>
|
|||
|
|
<li>Linux: <code>alias Bioc3.7='R_LIBS_USER=~/R/3.5-Bioc-3.7 R'</code></li>
|
|||
|
|
<li>macOS: <code>alias Bioc3.7='R_LIBS_USER=~/Library/R/3.5-Bioc-3.7/library R'</code></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>Invoke these from the command line as <code>Bioc3.7</code>.</p>
|
|||
|
|
<p>On Windows, create a shortcut. Go to My Computer and navigate to a directory
|
|||
|
|
that is in your PATH. Then right-click and choose New->Shortcut.
|
|||
|
|
In the “type the location of the item” box, put:</p>
|
|||
|
|
<pre><code>cmd /C "set R_LIBS_USER=C:\Users\USER_NAME\Documents\R\3.5-Bioc-3.7 && R"</code></pre>
|
|||
|
|
<p>Click “Next”. In the “Type a name for this shortcut” box, type <code>Bioc-3.7</code>.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="offline-use" class="section level2" number="3.4">
|
|||
|
|
<h2><span class="header-section-number">3.4</span> Offline use</h2>
|
|||
|
|
<p>Offline use of <em>BiocManager</em> is possible for organizations and users that would
|
|||
|
|
like to provide access to internal repositories of <em>Bioconductor</em> packages
|
|||
|
|
while enforcing appropriate version checks between Bioconductor and R.
|
|||
|
|
For offline use, organizations and users require the following steps:</p>
|
|||
|
|
<ol style="list-style-type: decimal">
|
|||
|
|
<li><p>Use <code>rsync</code> to create local repositories of <a href="https://cran.r-project.org/mirror-howto.html">CRAN</a> and
|
|||
|
|
<a href="https://bioconductor.org/about/mirrors/mirror-how-to/">Bioconductor</a>. Tell <em>R</em> about these repositories using (e.g.,
|
|||
|
|
in a site-wide <code>.Rprofile</code>, see <code>?.Rprofile</code>).</p>
|
|||
|
|
<pre class="r"><code>options(
|
|||
|
|
repos = c(CRAN_mirror = "file:///path/to/CRAN-mirror"),
|
|||
|
|
BioC_mirror = "file:///path/to/Bioc-mirror"
|
|||
|
|
)</code></pre>
|
|||
|
|
<p>Validate repository setting by reviewing the output of <code>repositories()</code>.</p></li>
|
|||
|
|
<li><p>Create an environment variable or option, e.g.,</p>
|
|||
|
|
<pre class="r"><code>options(
|
|||
|
|
BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE
|
|||
|
|
)</code></pre></li>
|
|||
|
|
<li><p>Use <code>install.packages()</code> to bootstrap the BiocManager installation.</p>
|
|||
|
|
<pre class="r"><code>install.package(c("BiocManager", "BiocVersion"))</code></pre></li>
|
|||
|
|
</ol>
|
|||
|
|
<p>BiocManager can then be used for subsequent installations, e.g.,
|
|||
|
|
<code>BiocManager::install(c("ggplot2", "GenomicRanges"))</code>.</p>
|
|||
|
|
<div id="offline-config.yaml" class="section level3" number="3.4.1">
|
|||
|
|
<h3><span class="header-section-number">3.4.1</span> Offline config.yaml</h3>
|
|||
|
|
<p><em>BiocManager</em> also expects to reference an online configuration yaml
|
|||
|
|
file for <em>Bioconductor</em> version validation at
|
|||
|
|
<a href="https://bioconductor.org/config.yaml" class="uri">https://bioconductor.org/config.yaml</a>. With offline use, users are
|
|||
|
|
expected to either host this file locally or provide their
|
|||
|
|
<code>config.yaml</code> version. The package allows either an environment
|
|||
|
|
variable or R-specific option to locate this file, e.g.,</p>
|
|||
|
|
<pre><code>```r
|
|||
|
|
options(
|
|||
|
|
BIOCONDUCTOR_CONFIG_FILE = "file:///path/to/config.yaml"
|
|||
|
|
)
|
|||
|
|
```</code></pre>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
<div id="how-it-works" class="section level1" number="4">
|
|||
|
|
<h1><span class="header-section-number">4</span> How it works</h1>
|
|||
|
|
<p>BiocManager’s job is to make sure that all packages are installed from
|
|||
|
|
the same <em>Bioconductor</em> version, using compatible <em>R</em> and <em>CRAN</em>
|
|||
|
|
packages. However, <em>R</em> has an annual release cycle, whereas
|
|||
|
|
<em>Bioconductor</em> has a twice-yearly release cycle. Also, <em>Bioconductor</em>
|
|||
|
|
has a ‘devel’ branch where new packages and features are introduced,
|
|||
|
|
and a ‘release’ branch where bug fixes and relative stability are
|
|||
|
|
important; <em>CRAN</em> packages do not distinguish between devel and
|
|||
|
|
release branches.</p>
|
|||
|
|
<p>In the past, one would install a <em>Bioconductor</em> package by evaluating
|
|||
|
|
the command <code>source("https://.../biocLite.R")</code> to read a file from the
|
|||
|
|
web. The file contained an installation script that was smart enough
|
|||
|
|
to figure out what version of <em>R</em> and <em>Bioconductor</em> were in use or
|
|||
|
|
appropriate for the person invoking the script. Sourcing an executable
|
|||
|
|
script from the web is an obvious security problem.</p>
|
|||
|
|
<p>Our solution is to use a CRAN package BiocManager, so that users
|
|||
|
|
install from pre-configured CRAN mirrors rather than typing in a URL
|
|||
|
|
and sourcing from the web.</p>
|
|||
|
|
<p>But how does a CRAN package know what version of <em>Bioconductor</em> is in
|
|||
|
|
use? Can we use BiocManager? No, because we don’t have enough control
|
|||
|
|
over the version of BiocManager available on CRAN, e.g., everyone using
|
|||
|
|
the same version of <em>R</em> would get the same version of BiocManager and
|
|||
|
|
hence of <em>Bioconductor</em>. But there are two <em>Bioconductor</em> versions per R
|
|||
|
|
version, so that does not work!</p>
|
|||
|
|
<p>BiocManager could write information to a cache on the user disk, but
|
|||
|
|
this is not a robust solution for a number of reasons. Is there any
|
|||
|
|
other way that <em>R</em> could keep track of version information? Yes, by
|
|||
|
|
installing a <em>Bioconductor</em> package (BiocVersion) whose sole purpose is
|
|||
|
|
to indicate the version of <em>Bioconductor</em> in use.</p>
|
|||
|
|
<p>By default, BiocManager installs the BiocVersion package corresponding
|
|||
|
|
to the most recent released version of <em>Bioconductor</em> for the version
|
|||
|
|
of <em>R</em> in use. At the time this section was written, the most recent
|
|||
|
|
version of R is R-3.6.1, associated with <em>Bioconductor</em> release
|
|||
|
|
version 3.9. Hence on first use of <code>BiocManager::install()</code> we see
|
|||
|
|
BiocVersion version 3.9.0 being installed.</p>
|
|||
|
|
<pre><code>> BiocManager::install()
|
|||
|
|
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 Patched (2019-07-06
|
|||
|
|
r76792)
|
|||
|
|
Installing package(s) 'BiocVersion'
|
|||
|
|
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/\
|
|||
|
|
BiocVersion_3.9.0.tar.gz'
|
|||
|
|
...</code></pre>
|
|||
|
|
<p>Requesting a specific version of <em>Bioconductor</em> updates, if possible,
|
|||
|
|
the BiocVersion package.</p>
|
|||
|
|
<pre><code>> ## 3.10 is available for R-3.6
|
|||
|
|
> BiocManager::install(version="3.10")
|
|||
|
|
Upgrade 3 packages to Bioconductor version '3.10'? [y/n]: y
|
|||
|
|
Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.1 Patched (2019-07-06
|
|||
|
|
r76792)
|
|||
|
|
Installing package(s) 'BiocVersion'
|
|||
|
|
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/\
|
|||
|
|
BiocVersion_3.10.1.tar.gz'
|
|||
|
|
...
|
|||
|
|
> ## back down again...
|
|||
|
|
> BiocManager::install(version="3.9")
|
|||
|
|
Downgrade 3 packages to Bioconductor version '3.9'? [y/n]: y
|
|||
|
|
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 Patched (2019-07-06
|
|||
|
|
r76792)
|
|||
|
|
Installing package(s) 'BiocVersion'
|
|||
|
|
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/\
|
|||
|
|
BiocVersion_3.9.0.tar.gz'
|
|||
|
|
...</code></pre>
|
|||
|
|
<p>Answering <code>n</code> to the prompt to up- or downgrade packages leaves the
|
|||
|
|
installation unchanged, since this would immediately create an
|
|||
|
|
inconsistent installation.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="troubleshooting" class="section level1" number="5">
|
|||
|
|
<h1><span class="header-section-number">5</span> Troubleshooting</h1>
|
|||
|
|
<div id="package-not-available" class="section level2" number="5.1">
|
|||
|
|
<h2><span class="header-section-number">5.1</span> Package not available</h2>
|
|||
|
|
<p>(An initial draft of this section was produced by ChatGPT on 25 May 2023)</p>
|
|||
|
|
<p>A user failed to install the ‘celldex’ package on 25 May 2023. A
|
|||
|
|
transcript of the <em>R</em> session is as follows:</p>
|
|||
|
|
<pre><code>> BiocManager::version()
|
|||
|
|
[1] '3.18'
|
|||
|
|
> BiocManager::install("celldex")
|
|||
|
|
Bioconductor version 3.18 (BiocManager 1.30.20), R 4.3.0 Patched (2023-05-01
|
|||
|
|
r84362)
|
|||
|
|
Installing package(s) 'celldex'
|
|||
|
|
Warning message:
|
|||
|
|
package 'celldex' is not available for Bioconductor version '3.18'
|
|||
|
|
|
|||
|
|
A version of this package for your version of R might be available elsewhere,
|
|||
|
|
see the ideas at
|
|||
|
|
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages</code></pre>
|
|||
|
|
<p>The availability of specific packages within <em>Bioconductor</em> can depend
|
|||
|
|
on various factors, including simple errors in entering the package
|
|||
|
|
name, the package’s development status, maintenance, and compatibility
|
|||
|
|
with the latest version of <em>Bioconductor</em>, as well as the availability
|
|||
|
|
of CRAN packages that the <em>Bioconductor</em> package depends on.</p>
|
|||
|
|
<p>Package Name: <em>R</em> package names are case sensitive and must be spelt
|
|||
|
|
correctly, so using <code>BiocManager::install("Celldex")</code> (with a capital
|
|||
|
|
<code>C</code>) or <code>BiocManager::install("celdex")</code> (with only one <code>l</code>) would
|
|||
|
|
both fail to install <code>celldex</code>; <em>R</em> will sometimes suggest the correct
|
|||
|
|
name.</p>
|
|||
|
|
<p><em>CRAN</em> Packages: <code>BiocManager::install()</code> tries to install packages
|
|||
|
|
from CRAN and from <em>Bioconductor</em>. Check that the package is not a CRAN
|
|||
|
|
package by trying to visit the CRAN ‘landing page’</p>
|
|||
|
|
<ul>
|
|||
|
|
<li><code>https://cran.R-project.org/package=celldex</code></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>If this page is found, then the package is a CRAN package; see the
|
|||
|
|
<a href="https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages">R-admin</a> manual section on troubleshooting CRAN package
|
|||
|
|
installations.</p>
|
|||
|
|
<p>Check also that the package is not a CRAN package that has been
|
|||
|
|
‘archived’ and no longer available by trying to visit</p>
|
|||
|
|
<ul>
|
|||
|
|
<li><code>https://cran.R-project.org/src/contrib/Archive/celldex/</code></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>If this page exists but the ‘landing page’ does not, this means that
|
|||
|
|
the package has been removed from CRAN. While it is possible to
|
|||
|
|
install archived packages, usually the best course of action is to
|
|||
|
|
identify alternative packages to accomplish the task you are
|
|||
|
|
interested in. This is especially true if the ‘Last modified’ date of
|
|||
|
|
the most recent archived package is more than several months ago.</p>
|
|||
|
|
<p>Compatibility: A <em>Bioconductor</em> package must be available for the
|
|||
|
|
specific version of <em>Bioconductor</em> you are using. Try visiting the
|
|||
|
|
‘landing page’ of the package for your version of <em>Bioconductor</em>,
|
|||
|
|
e.g., for <em>Bioconductor</em> version 3.18 and package celldex</p>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="https://bioconductor.org/packages/3.18/celldex" class="uri">https://bioconductor.org/packages/3.18/celldex</a></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>If this landing page does not exist, then the package is not available
|
|||
|
|
for your version of <em>Bioconductor</em>.</p>
|
|||
|
|
<p>Users may sometimes have an out-of-date version of <em>R</em> or
|
|||
|
|
<em>Bioconductor</em> installed; this may be intentional (e.g., to ensure
|
|||
|
|
reproducibility of existing analyses) or simply because <em>Bioconductor</em>
|
|||
|
|
has not yet been updated. Try visiting the current release landing
|
|||
|
|
page</p>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="https://bioconductor.org/packages/release/celldex" class="uri">https://bioconductor.org/packages/release/celldex</a></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>If the release landing page exists, and it is not important that you
|
|||
|
|
continue using the out-of-date version of <em>Bioconductor</em>, consider
|
|||
|
|
updating <em>R</em> (if necessary) and <em>Bioconductor</em> to the current release
|
|||
|
|
versions using instructions at the top of this document.</p>
|
|||
|
|
<p>Packages recently contributed to <em>Bioconductor</em> are added to the
|
|||
|
|
‘devel’ branch, whereas most users are configured to use the ‘release’
|
|||
|
|
branch. Try visiting the ‘devel’ landing page</p>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="https://bioconductor.org/packages/devel/celldex" class="uri">https://bioconductor.org/packages/devel/celldex</a></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>If only the devel landing page exists, then consider updating your
|
|||
|
|
installation to use the development version of <em>Bioconductor</em>. Note
|
|||
|
|
that the development version is not as stable as the release version,
|
|||
|
|
so should not be used for time-critical or ‘production’ analysis.</p>
|
|||
|
|
<p>It may be that the package you are interested in has been removed from
|
|||
|
|
<em>Bioconductor</em>. Check this by visiting</p>
|
|||
|
|
<ul>
|
|||
|
|
<li><a href="https://bioconductor.org/about/removed-packages/" class="uri">https://bioconductor.org/about/removed-packages/</a></li>
|
|||
|
|
</ul>
|
|||
|
|
<p>If the package has been removed, the best course of action is to
|
|||
|
|
identify alternative packages to accomplish the task you are
|
|||
|
|
interested in.</p>
|
|||
|
|
<p>Maintenance and Operating System Availability: A package may be
|
|||
|
|
included in the release or devel version of <em>Bioconductor</em>, but
|
|||
|
|
currently unavailable because it requires maintenance. This might be
|
|||
|
|
indicated by a red ‘build’ badge as in the image below (details of the
|
|||
|
|
build problem are available by clicking on the badge). The build error
|
|||
|
|
usually requires that the package maintainer correct an issue with
|
|||
|
|
their package; the maintainer and email address are listed on the
|
|||
|
|
package landing page.</p>
|
|||
|
|
<p><img src="data:image/png;base64,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
|
|||
|
|
<p>A small number of <em>Bioconductor</em> packages are not available on all
|
|||
|
|
operating systems. An orange ‘platforms’ badge indicates this. Click
|
|||
|
|
on the badge to be taken to the ‘Package Archives’ section of the
|
|||
|
|
landing page; BGmix is not supported on Windows, and not available on
|
|||
|
|
‘Intel’ macOS because of build-related errors. Consider using an
|
|||
|
|
alternative operating system if the package is essential to your work</p>
|
|||
|
|
<p><img src="data:image/png;base64,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
|
|||
|
|
<p>Packages with landing pages from older releases but not available for
|
|||
|
|
your operating system cannot be updated by the maintainer. If the
|
|||
|
|
package is available in the current release and for your operating
|
|||
|
|
system, consider updating to the current release of <em>Bioconductor</em>.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="cannot-load-biocmanager" class="section level2" number="5.2">
|
|||
|
|
<h2><span class="header-section-number">5.2</span> Cannot load <em>BiocManager</em></h2>
|
|||
|
|
<p>After updating <em>R</em> (e.g., from <em>R</em> version 3.5.x to <em>R</em> version 3.6.x
|
|||
|
|
at the time of writing this) and trying to load <code>BiocManager</code>, <em>R</em>
|
|||
|
|
replies</p>
|
|||
|
|
<pre><code>Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
|
|||
|
|
call: NULL
|
|||
|
|
error: Bioconductor version '3.8' requires R version '3.5'; see
|
|||
|
|
https://bioconductor.org/install</code></pre>
|
|||
|
|
<p>This problem arises because <code>BiocManager</code> uses a second package,
|
|||
|
|
<code>BiocVersion</code>, to indicate the version of <em>Bioconductor</em> in use. In
|
|||
|
|
the original installation, <code>BiocManager</code> had installed <code>BiocVersion</code>
|
|||
|
|
appropriate for <em>R</em> version 3.5. With the update, the version of
|
|||
|
|
<em>Bioconductor</em> indicated by <code>BiocVersion</code> is no longer valid – you’ll
|
|||
|
|
need to update <code>BiocVersion</code> and all <em>Bioconductor</em> packages to the
|
|||
|
|
most recent version available for your new version of <em>R</em>.</p>
|
|||
|
|
<p>The recommended practice is to maintain a separate library for each
|
|||
|
|
<em>R</em> and <em>Bioconductor</em> version. So instead of installing packages into
|
|||
|
|
<em>R</em>’s system library (e.g., as ‘administrator’), install only base <em>R</em>
|
|||
|
|
into the system location. Then use aliases or other approaches to
|
|||
|
|
create <em>R</em> / <em>Bioconductor</em> version-specific installations. This is
|
|||
|
|
described in the section on <a href="#multiple-versions">maintaining multiple
|
|||
|
|
versions</a> of <em>R</em> and <em>Bioconductor</em>.</p>
|
|||
|
|
<p>Alternatively, one could update all <em>Bioconductor</em> packages in the
|
|||
|
|
previous installation directory. The problem with this is that the
|
|||
|
|
previous version of <em>Bioconductor</em> is removed, compromising the
|
|||
|
|
ability to reproduce earlier results. Update all <em>Bioconductor</em>
|
|||
|
|
packages in the previous installation directory by removing <em>all</em>
|
|||
|
|
versions of <code>BiocVersion</code></p>
|
|||
|
|
<pre><code>remove.packages("BiocVersion") # repeat until all instances removed</code></pre>
|
|||
|
|
<p>Then install the updated <code>BiocVersion</code>, and update all <em>Bioconductor</em>
|
|||
|
|
packages; answer ‘yes’ when you are asked to update a potentially
|
|||
|
|
large number of <em>Bioconductor</em> packages.</p>
|
|||
|
|
<pre class="r"><code>BiocManager::install()</code></pre>
|
|||
|
|
<p>Confirm that the updated <em>Bioconductor</em> is valid for your version of
|
|||
|
|
<em>R</em></p>
|
|||
|
|
<pre class="r"><code>BiocManager::valid()</code></pre>
|
|||
|
|
</div>
|
|||
|
|
<div id="timeout-during-package-download" class="section level2" number="5.3">
|
|||
|
|
<h2><span class="header-section-number">5.3</span> Timeout during package download</h2>
|
|||
|
|
<p>Large packages can take a long time to downloaded over poor internet
|
|||
|
|
connects. The BiocManager package sets the time limit to 300 seconds,
|
|||
|
|
using <code>options(timeout = 300)</code>. Only part of a package may download,
|
|||
|
|
e.g., only 15.1 of 79.4 MB in the example below</p>
|
|||
|
|
<pre><code>trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/org.Hs.eg.db_3.12.0.tar.gz'
|
|||
|
|
Content type 'application/x-gzip' length 83225518 bytes (79.4 MB)
|
|||
|
|
=========
|
|||
|
|
downloaded 15.1 MB</code></pre>
|
|||
|
|
<p>or perhaps with a warning (often difficult to see in the output)</p>
|
|||
|
|
<pre><code>Error in download.file(url, destfile, method, mode = "wb", ...) :
|
|||
|
|
...
|
|||
|
|
...: Timeout of 300 seconds was reached
|
|||
|
|
...</code></pre>
|
|||
|
|
<p>Try increasing the download timeout, e.g, <code>options(timeout = 600)</code>.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="multiple-biocversion-installations" class="section level2" number="5.4">
|
|||
|
|
<h2><span class="header-section-number">5.4</span> Multiple <code>BiocVersion</code> installations</h2>
|
|||
|
|
<p>One potential problem occurs when there are two or more <code>.libPaths()</code>,
|
|||
|
|
with more than one BiocVersion package installed. This might occur for
|
|||
|
|
instance if a ‘system administrator’ installed BiocVersion, and then a
|
|||
|
|
user installed their own version. In this circumstance, it seems
|
|||
|
|
appropriate to standardize the installation by repeatedly calling
|
|||
|
|
<code>remove.packages("BiocVersion")</code> until all versions are removed, and
|
|||
|
|
then installing the desired version.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="errors-determining-bioconductor-version" class="section level2" number="5.5">
|
|||
|
|
<h2><span class="header-section-number">5.5</span> Errors determining <em>Bioconductor</em> version</h2>
|
|||
|
|
<p>An essential task for <em>BiocManager</em> is to determine that the version
|
|||
|
|
of <em>Bioconductor</em> is appropriate for the version of <em>R</em>. Several
|
|||
|
|
errors can occur when this task fails.</p>
|
|||
|
|
<ul>
|
|||
|
|
<li><p>Bioconductor version cannot be determined; no internet connection?
|
|||
|
|
When the <em>Bioconductor</em> version cannot be obtained from the version
|
|||
|
|
map hosted at <a href="https://bioconductor.org/config.yaml" class="uri">https://bioconductor.org/config.yaml</a>, this error will
|
|||
|
|
occur. It may be a result of poor internet connectivity or offline
|
|||
|
|
use. See the <a href="#offline-config.yaml">offline config.yaml</a> section
|
|||
|
|
above.</p></li>
|
|||
|
|
<li><p>Bioconductor version cannot be validated; no internet connection?
|
|||
|
|
Usually occurs when the map is unable to be downloaded possibly due
|
|||
|
|
to a missing <code>BIOCONDUCTOR_CONFIG_FILE</code>. For offline use, a copy of
|
|||
|
|
the configuration file should be downloaded and its address set to
|
|||
|
|
the environment variable or option.</p></li>
|
|||
|
|
<li><p>Bioconductor version map cannot be validated; is it misconfigured?
|
|||
|
|
On <em>rare</em> occasion, the version map hosted at
|
|||
|
|
<a href="https://bioconductor.org/config.yaml" class="uri">https://bioconductor.org/config.yaml</a> may be misconfigured. The check
|
|||
|
|
ensures that all the version name tags, i.e., out-of-date, release,
|
|||
|
|
devel, and future are in the map.</p></li>
|
|||
|
|
<li><p>Bioconductor version cannot be validated; is type input
|
|||
|
|
mis-specified? The type input refers to the version name inputs,
|
|||
|
|
mainly release and devel. This error is chiefly due to internal
|
|||
|
|
logic and is not due to user error. Please open a <a href="https://github.com/Bioconductor/BiocManager/issues">GitHub
|
|||
|
|
issue</a>.</p></li>
|
|||
|
|
</ul>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
<div id="session-information" class="section level1" number="6">
|
|||
|
|
<h1><span class="header-section-number">6</span> Session information</h1>
|
|||
|
|
<pre class="r"><code>sessionInfo()</code></pre>
|
|||
|
|
<pre><code>## R Under development (unstable) (2024-08-21 r87038)
|
|||
|
|
## Platform: x86_64-pc-linux-gnu
|
|||
|
|
## Running under: Ubuntu 22.04.4 LTS
|
|||
|
|
##
|
|||
|
|
## Matrix products: default
|
|||
|
|
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
|
|||
|
|
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
|
|||
|
|
##
|
|||
|
|
## locale:
|
|||
|
|
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
|
|||
|
|
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
|
|||
|
|
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
|
|||
|
|
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
|
|||
|
|
## [9] LC_ADDRESS=C LC_TELEPHONE=C
|
|||
|
|
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
|
|||
|
|
##
|
|||
|
|
## time zone: America/New_York
|
|||
|
|
## tzcode source: system (glibc)
|
|||
|
|
##
|
|||
|
|
## attached base packages:
|
|||
|
|
## [1] stats graphics grDevices utils datasets methods base
|
|||
|
|
##
|
|||
|
|
## other attached packages:
|
|||
|
|
## [1] BiocStyle_2.32.1
|
|||
|
|
##
|
|||
|
|
## loaded via a namespace (and not attached):
|
|||
|
|
## [1] digest_0.6.35 R6_2.5.1 bookdown_0.39
|
|||
|
|
## [4] fastmap_1.1.1 xfun_0.43 cachem_1.0.8
|
|||
|
|
## [7] knitr_1.46 htmltools_0.5.8.1 rmarkdown_2.26
|
|||
|
|
## [10] lifecycle_1.0.4 cli_3.6.2 sass_0.4.9
|
|||
|
|
## [13] jquerylib_0.1.4 compiler_4.5.0 highr_0.10
|
|||
|
|
## [16] tools_4.5.0 evaluate_0.23 bslib_0.7.0
|
|||
|
|
## [19] yaml_2.3.8 BiocManager_1.30.25 jsonlite_1.8.8
|
|||
|
|
## [22] rlang_1.1.3</code></pre>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<script>
|
|||
|
|
|
|||
|
|
// add bootstrap table styles to pandoc tables
|
|||
|
|
function bootstrapStylePandocTables() {
|
|||
|
|
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
|
|||
|
|
}
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
bootstrapStylePandocTables();
|
|||
|
|
});
|
|||
|
|
|
|||
|
|
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- tabsets -->
|
|||
|
|
|
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|
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<script>
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
window.buildTabsets("TOC");
|
|||
|
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});
|
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|
|||
|
|
$(document).ready(function () {
|
|||
|
|
$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
|||
|
|
$(this).parent().toggleClass('nav-tabs-open');
|
|||
|
|
});
|
|||
|
|
});
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- code folding -->
|
|||
|
|
|
|||
|
|
|
|||
|
|
<script type="text/x-mathjax-config">
|
|||
|
|
MathJax.Hub.Config({
|
|||
|
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"HTML-CSS": {
|
|||
|
|
styles: {
|
|||
|
|
".MathJax_Display": {
|
|||
|
|
"text-align": "center",
|
|||
|
|
padding: "0px 150px 0px 65px",
|
|||
|
|
margin: "0px 0px 0.5em"
|
|||
|
|
},
|
|||
|
|
"@media screen and (max-width: 991px)": {
|
|||
|
|
".MathJax_Display": {
|
|||
|
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"text-align": "center",
|
|||
|
|
padding: "0 0 0 0"
|
|||
|
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}
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
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|
|||
|
|
</script>
|
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|
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<!-- dynamically load mathjax for compatibility with self-contained -->
|
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<script>
|
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(function () {
|
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var script = document.createElement("script");
|
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script.type = "text/javascript";
|
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script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
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document.getElementsByTagName("head")[0].appendChild(script);
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|
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<script type="text/javascript">
|
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|
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|
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if (e.key === "Enter") {
|
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$(this).trigger("click");
|
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|
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|
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|
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|
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var toc_items = document.querySelectorAll(".tocify-item");
|
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for (var i = 0; i < toc_items.length; i++) {
|
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// The link role tells screen readers this is for navigation
|
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|
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toc_items.item(i).setAttribute("role", "link");
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// tabindex = 0 allows selection via keyboard tab presses
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|
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toc_items.item(i).setAttribute("tabindex", "0");
|
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|
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// Listen for "Enter" keypress when item is selected
|
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|
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toc_items.item(i).addEventListener("keydown", navigateLink);
|
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|
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|
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|
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|
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|
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|
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|
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|
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</html>
|