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<title>Using miniCRAN to create and maintain a local CRAN repository</title>

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</head>

<body>




<h1 class="title toc-ignore">Using miniCRAN to create and maintain a
local CRAN repository</h1>
<h4 class="author">Andrie de Vries and Alex Chubaty</h4>
<h4 class="date">March 28, 2024</h4>



<p>Start by creating the recursive dependency tree for your target
packages.</p>
<p>For example, imagine a scenario where you want to create a repository
that consists of the package <code>foreach</code> and its
dependencies.</p>
<p>Start by creating the dependency list:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">library</span>(<span class="st">&quot;miniCRAN&quot;</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co"># use Revolution Analytics CRAN mirror</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>revolution <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="at">CRAN =</span> <span class="st">&quot;https://cloud.r-project.org&quot;</span>)</span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="co"># Specify list of packages to download</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a>pkgs <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">&quot;foreach&quot;</span>)</span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a>pkgList <span class="ot">&lt;-</span> <span class="fu">pkgDep</span>(pkgs, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="st">&quot;source&quot;</span>, <span class="at">suggests =</span> <span class="cn">FALSE</span>, </span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>                  <span class="at">availPkgs =</span> cranJuly2014)</span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a>pkgList</span></code></pre></div>
<pre><code>## [1] &quot;foreach&quot;   &quot;codetools&quot; &quot;iterators&quot;</code></pre>
<p>Next, create a repository with the function <code>makeRepo()</code>.
In this example, get the required files for <code>source</code> packages
as well as windows binaries:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="co"># Create temporary folder for miniCRAN</span></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="fu">dir.create</span>(pth <span class="ot">&lt;-</span> <span class="fu">file.path</span>(<span class="fu">tempdir</span>(), <span class="st">&quot;miniCRAN&quot;</span>))</span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a><span class="co"># Make repo for source and win.binary</span></span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a><span class="fu">makeRepo</span>(pkgList, <span class="at">path =</span> pth, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="fu">c</span>(<span class="st">&quot;source&quot;</span>, <span class="st">&quot;win.binary&quot;</span>))</span></code></pre></div>
<p>Investigate the repository file structure:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="co"># List all files in miniCRAN</span></span>
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="fu">list.files</span>(pth, <span class="at">recursive =</span> <span class="cn">TRUE</span>, <span class="at">full.names =</span> <span class="cn">FALSE</span>)</span></code></pre></div>
<p>Use <code>pkgAvail</code> to list available packages in your
repository:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="co"># Check for available packages</span></span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="fu">pkgAvail</span>(<span class="at">repos =</span> pth, <span class="at">type =</span> <span class="st">&quot;win.binary&quot;</span>)[, <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="dv">5</span>)]</span></code></pre></div>
<div id="install-packages-from-your-local-repository" class="section level1">
<h1>Install packages from your local repository</h1>
<p>To install packages from a local repository, you need to use the <a href="https://en.wikipedia.org/wiki/Uniform_Resource_Identifier">Uniform
Resource Identifier</a> (URI) convention <code>file:///</code> to point
to your file location.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="fu">install.packages</span>(pkgs, </span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>                 <span class="at">repos =</span> <span class="fu">paste0</span>(<span class="st">&quot;file:///&quot;</span>, pth),</span>
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a>                 <span class="at">type =</span> <span class="st">&quot;source&quot;</span>)</span></code></pre></div>
</div>
<div id="adding-packages-to-an-existing-minicran-repository" class="section level1">
<h1>Adding packages to an existing miniCRAN repository</h1>
<div id="adding-new-packages-from-cran" class="section level2">
<h2>Adding new packages from CRAN</h2>
<p>After creating a local miniCRAN repository, additional packages and
their dependencies can easily be added. This mechanism can also be used
to re-add an existing package to the miniCRAN repo.</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Add new packages (from CRAN) to the miniCRAN repo</span></span>
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="fu">addPackage</span>(<span class="st">&quot;Matrix&quot;</span>, <span class="at">path =</span> pth, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="fu">c</span>(<span class="st">&quot;source&quot;</span>, <span class="st">&quot;win.binary&quot;</span>))</span>
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a><span class="fu">pkgAvail</span>(<span class="at">repos =</span> pth, <span class="at">type =</span> <span class="st">&quot;win.binary&quot;</span>)[, <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="dv">5</span>)]</span></code></pre></div>
<p>The value that is returned (invisibly) via <code>addPackage</code> is
the number of packages written to the index file, <em>i.e.</em>, the
total number of packages in the repo of that type.</p>
</div>
<div id="adding-an-older-version-of-a-package-from-cran" class="section level2">
<h2>Adding an older version of a package from CRAN</h2>
<p>To add a specific version of a package from CRAN (or another
CRAN-like repository), we can easily download the source packages from
the CRAN archives. Dependencies for old package versions cannot be
determined automatically and must be specified by the user.</p>
<p><em>Note:</em> in order to to add binaries of older packages, you
will need to download the source and build the binaries on the intended
platform yourself. You will need the appropriate R development tools
installed in order to build package binaries from source.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># create a data frame with the package and version info</span></span>
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>oldVers <span class="ot">&lt;-</span> <span class="fu">data.frame</span>(</span>
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a>  <span class="at">package =</span> <span class="fu">c</span>(<span class="st">&quot;foreach&quot;</span>, <span class="st">&quot;codetools&quot;</span>, <span class="st">&quot;iterators&quot;</span>),</span>
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a>  <span class="at">version =</span> <span class="fu">c</span>(<span class="st">&quot;1.4.0&quot;</span>, <span class="st">&quot;0.2-7&quot;</span>, <span class="st">&quot;1.0.5&quot;</span>),</span>
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>  <span class="at">stringsAsFactors =</span> <span class="cn">FALSE</span></span>
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a>)</span>
<span id="cb8-7"><a href="#cb8-7" tabindex="-1"></a></span>
<span id="cb8-8"><a href="#cb8-8" tabindex="-1"></a><span class="co"># download old source package version and create repo index</span></span>
<span id="cb8-9"><a href="#cb8-9" tabindex="-1"></a><span class="fu">addOldPackage</span>(pkgList, <span class="at">path =</span> pth, <span class="at">vers =</span> oldVers<span class="sc">$</span>version, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="st">&quot;source&quot;</span>)</span></code></pre></div>
<p>You will get a warning whenever there are multiple versions of a
package saved in the repository. Currently, you need to manually remove
duplicate versions before rebuilding the repositoryâ€™s package index.</p>
<p>Note: This last step is important, otherwise you may end up with a
repo in an inconsistent state.</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="co"># List package versions in the miniCRAN repo (produces warning about duplicates)</span></span>
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a>pkgVersionsSrc <span class="ot">&lt;-</span> <span class="fu">checkVersions</span>(pkgList, <span class="at">path =</span> pth, <span class="at">type =</span> <span class="st">&quot;source&quot;</span>)</span>
<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a>pkgVersionsBin <span class="ot">&lt;-</span> <span class="fu">checkVersions</span>(pkgList, <span class="at">path =</span> pth, <span class="at">type =</span> <span class="st">&quot;win.binary&quot;</span>)</span>
<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a></span>
<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a><span class="co"># After inspecting package versions, remove old versions</span></span>
<span id="cb9-6"><a href="#cb9-6" tabindex="-1"></a><span class="fu">basename</span>(pkgVersionsSrc) <span class="co"># duplicate versions</span></span>
<span id="cb9-7"><a href="#cb9-7" tabindex="-1"></a><span class="fu">basename</span>(pkgVersionsBin)</span>
<span id="cb9-8"><a href="#cb9-8" tabindex="-1"></a></span>
<span id="cb9-9"><a href="#cb9-9" tabindex="-1"></a><span class="fu">file.remove</span>(pkgVersionsSrc[<span class="fu">c</span>(<span class="dv">2</span>,<span class="dv">4</span>,<span class="dv">6</span>)])</span>
<span id="cb9-10"><a href="#cb9-10" tabindex="-1"></a></span>
<span id="cb9-11"><a href="#cb9-11" tabindex="-1"></a><span class="co"># rebuild the package index after removing duplicate package versions</span></span>
<span id="cb9-12"><a href="#cb9-12" tabindex="-1"></a><span class="fu">updateRepoIndex</span>(pth, <span class="at">type =</span> <span class="fu">c</span>(<span class="st">&quot;source&quot;</span>, <span class="st">&quot;win.binary&quot;</span>))</span></code></pre></div>
<p>To see the updated list of packages available in the miniCRAN
repo:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="fu">pkgAvail</span>(pth, <span class="at">type =</span> <span class="st">&quot;source&quot;</span>)[, <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="dv">5</span>)] <span class="co"># contains the old versions</span></span>
<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="fu">pkgAvail</span>(pth, <span class="at">type =</span> <span class="st">&quot;win.binary&quot;</span>)[, <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="dv">5</span>)] <span class="co"># contains the current versions</span></span></code></pre></div>
</div>
<div id="adding-packages-from-other-sources" class="section level2">
<h2>Adding packages from other sources</h2>
<p>This feature will be implemented in a future release.</p>
</div>
</div>
<div id="updating-the-packages-in-a-minicran-repository" class="section level1">
<h1>Updating the packages in a miniCRAN repository</h1>
<p>Checking for updated versions of the packages currently stored in the
miniCRAN repository:</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="co"># Check if updated packages are available</span></span>
<span id="cb11-2"><a href="#cb11-2" tabindex="-1"></a><span class="fu">oldPackages</span>(<span class="at">path =</span> pth, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="st">&quot;source&quot;</span>)[, <span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>] <span class="co"># should need update</span></span>
<span id="cb11-3"><a href="#cb11-3" tabindex="-1"></a><span class="fu">oldPackages</span>(<span class="at">path =</span> pth, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="st">&quot;win.binary&quot;</span>)[, <span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>] <span class="co"># should be current</span></span></code></pre></div>
<p>Update the versions of the packages currently stored in the miniCRAN
repository. By default, a prompt is given to confirm the update for each
package. This prompt can be suppressed using <code>ask = FALSE</code>,
which will update all packages. Be careful using this option if you want
to keep certain packages at an older version.</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="co"># Update available packages</span></span>
<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a><span class="fu">updatePackages</span>(<span class="at">path =</span> pth, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="st">&quot;source&quot;</span>, <span class="at">ask =</span> <span class="cn">FALSE</span>) <span class="co"># should need update</span></span>
<span id="cb12-3"><a href="#cb12-3" tabindex="-1"></a><span class="fu">updatePackages</span>(<span class="at">path =</span> pth, <span class="at">repos =</span> revolution, <span class="at">type =</span> <span class="st">&quot;win.binary&quot;</span>, <span class="at">ask =</span> <span class="cn">FALSE</span>) <span class="co"># should be current</span></span></code></pre></div>
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