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404.html

@@ -118,7 +118,7 @@ <h1>Page not found<a class="anchor" aria-label="anchor" href="#page-not-found"><
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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bioconductor-package-submissions.html

@@ -521,7 +521,7 @@ <h2>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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booknews.html

@@ -154,7 +154,7 @@ <h2>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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branch-rename-faqs.html

@@ -348,7 +348,7 @@ <h2>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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c-fortran.html

@@ -183,7 +183,7 @@ <h3>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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citation.html

@@ -140,7 +140,7 @@ <h1>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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cmavericks-best-practices.html

@@ -764,7 +764,7 @@ <h4>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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conclusion.html

@@ -139,7 +139,7 @@ <h1>
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   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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data.html

@@ -161,7 +161,7 @@ <h3>
 <p>For packages that need to use documented data within a function, we recommend
 creating an environment for holding the data to avoid polluting the
 global environment when using <code><a href="https://rdrr.io/r/utils/data.html">data()</a></code>.</p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_env</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/environment.html">new.env</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/environment.html">emptyenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/data.html">data</a></span><span class="op">(</span><span class="st">"mydata"</span>, envir <span class="op">=</span> <span class="va">data_env</span>, package <span class="op">=</span> <span class="st">"mypackage"</span><span class="op">)</span></span>
 <span><span class="va">mydata</span> <span class="op">&lt;-</span> <span class="va">data_env</span><span class="op">[[</span><span class="st">"mydata"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
@@ -240,7 +240,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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debugging-cc-code.html

@@ -334,7 +334,7 @@ <h2>
 players) because it is the least tested of the code. We could be
 wrong, of course… After many iterations, my colleague arrived at
 buggy24.R:</p>
-<div class="sourceCode" id="cb188"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb189"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va">RCurl</span><span class="op">)</span></span>
 <span></span>
 <span><span class="va">foo</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span></span>
@@ -493,7 +493,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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deprecation.html

@@ -355,7 +355,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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description.html

@@ -357,7 +357,7 @@ <h2>
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   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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develop-overview.html

@@ -129,7 +129,7 @@ <h1>Overview<a class="anchor" aria-label="anchor" href="#develop-overview"><i cl
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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docs.html

@@ -158,6 +158,19 @@ <h2>
     toc: true
     toc_depth: 2
 </code></pre>
+<p>If you want to write more than one vignette, you may want to control
+the order that they are displayed on the package homepage and when the
+<code><a href="https://rdrr.io/r/utils/browseVignettes.html">browseVignettes()</a></code> function is called. Vignettes will show up in
+alphabetical order, which may not be a logical ordering without
+further specification. One approach to controlling the order of the
+vignettes is to use a number in the <code>VignettteIndexEntry</code> setting,
+e.g. using numbers <code>1-9</code>, if you have a single digit number of
+vignettes, or <code>01-99</code> if you have ten or more vignettes. For example,
+the first vignette could specify in the header:</p>
+<pre><code>vignette: &gt;
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteIndexEntry{1. Quick start to MyPackage}
+  %\VignetteEncoding{UTF-8}</code></pre>
 <p>Some best practices and requirements for writing <em>Bioconductor</em> vignettes are
 detailed in the following sections.</p>
 <div id="vignette-introduction" class="section level3" number="12.2.1">
@@ -336,7 +349,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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general.html

@@ -248,7 +248,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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git-version-control.html

@@ -1550,7 +1550,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
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gitignore.html

@@ -109,7 +109,7 @@ <h1>
 be excluded from the Git repository which is possible by including a
 <code>.gitignore</code> file.</p>
 <p>The following are files that are checked by <em><a href="https://bioconductor.org/packages/3.20/BiocCheck">BiocCheck</a></em> and flagged as unacceptable:</p>
-<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">hidden_file_ext</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span></span>
 <span>    <span class="st">".renviron"</span>, <span class="st">".rprofile"</span>, <span class="st">".rproj"</span>, <span class="st">".rproj.user"</span>, <span class="st">".rhistory"</span>,</span>
 <span>    <span class="st">".rapp.history"</span>, <span class="st">".o"</span>, <span class="st">".sl"</span>, <span class="st">".so"</span>, <span class="st">".dylib"</span>, <span class="st">".a"</span>, <span class="st">".dll"</span>,</span>
@@ -144,7 +144,7 @@ <h1>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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important-bioconductor-package-development-features.html

@@ -293,7 +293,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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index.html

@@ -156,7 +156,7 @@ <h2>Contribute<a class="anchor" aria-label="anchor" href="#contribute"><i class=
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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license.html

@@ -140,7 +140,7 @@ <h1>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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long-tests.html

@@ -195,7 +195,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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man-links.html

@@ -187,7 +187,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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namespace.html

@@ -161,7 +161,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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news.html

@@ -213,7 +213,7 @@ <h1>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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non-software.html

@@ -339,7 +339,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-06.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2024-05-07.</p>
   </div>
 
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