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<h1>Reinstall Julia</h1>
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<p>A couple of days ago, I found that I <a href="https://github.com/JeffreySarnoff/ArbNumerics.jl/issues/41">could not install and compile
<code>ArbNumerics.jl</code></a>. The only options is to reinstall Julia. Fortunately, this is quite easy.</p>
<p>To be extra cautious, I started with a backup of the whole <code>~/.julia</code>. Start a terminal by typing</p>
<div class="highlight"><pre><span></span><code>cp -r ~/.julia/ ~/Downloads/
</code></pre></div>
<p>Then I removed <code>~/.julia</code> without mercy 👿.</p>
<div class="highlight"><pre><span></span><code>rm -rf ~/.julia/
</code></pre></div>
<p>This means all my previously installed Julia packages are now gone, but Julia itself (the binary and
core packages) are still there.</p>
<p>Most of my project has its own environment. In other words, there are two files <code>Project.toml</code> and
<code>Manifest.tomal</code> in the directory containing an environment. For example, to play with <code>Weave.jl</code>, I
have an environment in <code>~/Work/weave</code>. The content of <code>Project.toml</code> is quite simple,
which just indicates that this environment needs three dependencies <code>DSP</code>, <code>Plots</code> and <code>Weave</code>.</p>
<div class="highlight"><pre><span></span><code><span class="k">[deps]</span>
<span class="n">DSP</span> <span class="o">=</span> <span class="s">"717857b8-e6f2-59f4-9121-6e50c889abd2"</span>
<span class="n">Plots</span> <span class="o">=</span> <span class="s">"91a5bcdd-55d7-5caf-9e0b-520d859cae80"</span>
<span class="n">Weave</span> <span class="o">=</span> <span class="s">"44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"</span>
</code></pre></div>
<p>The content of <code>Manifest.toml</code> is a bit more complicated. The first few lines of it are like this.</p>
<div class="highlight"><pre><span></span><code><span class="c1"># This file is machine-generated - editing it directly is not advised</span>
<span class="k">[[AbstractFFTs]]</span>
<span class="n">deps</span> <span class="o">=</span> <span class="k">["LinearAlgebra"]</span>
<span class="n">git-tree-sha1</span> <span class="o">=</span> <span class="s">"051c95d6836228d120f5f4b984dd5aba1624f716"</span>
<span class="n">uuid</span> <span class="o">=</span> <span class="s">"621f4979-c628-5d54-868e-fcf4e3e8185c"</span>
<span class="n">version</span> <span class="o">=</span> <span class="s">"0.5.0"</span>
<span class="k">[[Base64]]</span>
<span class="n">uuid</span> <span class="o">=</span> <span class="s">"2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"</span>
</code></pre></div>
<p>What it does, is to indicate what exact packages are installed the last time I modified the
environment. </p>
<p>These two files allow me to install all the packages needed to run this environment. I can simply to
launch Julia <code>REPL</code> in the directly where the environment is, <code>active</code> the environment, and run the command
<code>instantiate</code>.</p>
<div class="highlight"><pre><span></span><code><span class="p">(</span><span class="nd">@v1</span><span class="o">.</span><span class="mi">4</span><span class="p">)</span> <span class="n">pkg</span><span class="o">></span> <span class="n">activate</span> <span class="o">.</span> <span class="c"># press ] to get the pkg prompt</span>
<span class="n">Activating</span> <span class="n">environment</span> <span class="n">at</span> <span class="sb">`~/Work/weave/Project.toml`</span>
<span class="p">(</span><span class="n">weave</span><span class="p">)</span> <span class="n">pkg</span><span class="o">></span> <span class="n">st</span>
<span class="n">Status</span> <span class="sb">`~/Work/weave/Project.toml`</span>
<span class="n">→</span> <span class="p">[</span><span class="mi">717857</span><span class="n">b8</span><span class="p">]</span> <span class="n">DSP</span> <span class="n">v0</span><span class="o">.</span><span class="mf">6.6</span>
<span class="p">[</span><span class="mi">91</span><span class="n">a5bcdd</span><span class="p">]</span> <span class="n">Plots</span> <span class="n">v1</span><span class="o">.</span><span class="mf">2.4</span>
<span class="n">→</span> <span class="p">[</span><span class="mi">44</span><span class="n">d3d7a6</span><span class="p">]</span> <span class="n">Weave</span> <span class="n">v0</span><span class="o">.</span><span class="mf">9.4</span>
<span class="n">┌</span> <span class="n">Warning</span><span class="o">:</span> <span class="n">Some</span> <span class="n">packages</span> <span class="p">(</span><span class="n">indicated</span> <span class="n">with</span> <span class="n">a</span> <span class="n">red</span> <span class="n">arrow</span><span class="p">)</span> <span class="n">are</span> <span class="n">not</span> <span class="n">downloaded</span><span class="p">,</span> <span class="n">use</span> <span class="sb">`instantiate`</span> <span class="n">to</span> <span class="n">instantiate</span> <span class="n">the</span> <span class="n">current</span> <span class="n">environment</span>
<span class="n">└</span> <span class="err">@</span> <span class="n">Pkg</span><span class="o">.</span><span class="kt">Display</span> <span class="o">/</span><span class="n">buildworker</span><span class="o">/</span><span class="n">worker</span><span class="o">/</span><span class="n">package_linux64</span><span class="o">/</span><span class="n">build</span><span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">share</span><span class="o">/</span><span class="n">julia</span><span class="o">/</span><span class="n">stdlib</span><span class="o">/</span><span class="n">v1</span><span class="o">.</span><span class="mi">4</span><span class="o">/</span><span class="n">Pkg</span><span class="o">/</span><span class="n">src</span><span class="o">/</span><span class="kt">Display</span><span class="o">.</span><span class="n">jl</span><span class="o">:</span><span class="mi">238</span>
<span class="p">(</span><span class="n">weave</span><span class="p">)</span> <span class="n">pkg</span><span class="o">></span> <span class="n">instantiate</span>
<span class="n">Updating</span> <span class="n">registry</span> <span class="n">at</span> <span class="sb">`~/.julia/registries/General`</span>
<span class="n">Updating</span> <span class="n">git</span><span class="o">-</span><span class="n">repo</span> <span class="sb">`https://github.com/JuliaRegistries/General.git`</span>
<span class="n">Installed</span> <span class="n">AbstractFFTs</span> <span class="n">────────────────</span> <span class="n">v0</span><span class="o">.</span><span class="mf">5.0</span>
<span class="n">Installed</span> <span class="n">Parsers</span> <span class="n">─────────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">0.3</span>
<span class="n">Installed</span> <span class="n">Tables</span> <span class="n">──────────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">0.4</span>
<span class="n">Installed</span> <span class="n">SpecialFunctions</span> <span class="n">────────────</span> <span class="n">v0</span><span class="o">.</span><span class="mf">10.0</span>
<span class="n">Installed</span> <span class="n">Weave</span> <span class="n">───────────────────────</span> <span class="n">v0</span><span class="o">.</span><span class="mf">9.4</span>
<span class="n">Installed</span> <span class="n">DataStructures</span> <span class="n">──────────────</span> <span class="n">v0</span><span class="o">.</span><span class="mf">17.15</span>
<span class="n">Installed</span> <span class="n">Plots</span> <span class="n">───────────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">2.4</span>
<span class="n">Installed</span> <span class="n">DSP</span> <span class="n">─────────────────────────</span> <span class="n">v0</span><span class="o">.</span><span class="mf">6.6</span>
<span class="n">Installed</span> <span class="n">IteratorInterfaceExtensions</span> <span class="n">─</span> <span class="n">v1</span><span class="o">.</span><span class="mf">0.0</span>
<span class="n">Installed</span> <span class="n">TableTraits</span> <span class="n">─────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">0.0</span>
<span class="n">Installed</span> <span class="n">PlotUtils</span> <span class="n">───────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">0.2</span>
<span class="n">Installed</span> <span class="n">Mustache</span> <span class="n">────────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">0.2</span>
<span class="n">Installed</span> <span class="n">DataValueInterfaces</span> <span class="n">─────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">0.0</span>
<span class="n">Installed</span> <span class="n">FFTW</span> <span class="n">────────────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">2.1</span>
<span class="n">Installed</span> <span class="n">IntelOpenMP_jll</span> <span class="n">─────────────</span> <span class="n">v2018</span><span class="o">.</span><span class="mf">0.3</span><span class="o">+</span><span class="mi">0</span>
<span class="n">Installed</span> <span class="n">Polynomials</span> <span class="n">─────────────────</span> <span class="n">v0</span><span class="o">.</span><span class="mf">8.0</span>
<span class="n">Installed</span> <span class="n">IterTools</span> <span class="n">───────────────────</span> <span class="n">v1</span><span class="o">.</span><span class="mf">3.0</span>
<span class="n">Installed</span> <span class="n">FFTW_jll</span> <span class="n">────────────────────</span> <span class="n">v3</span><span class="o">.</span><span class="mf">3.9</span><span class="o">+</span><span class="mi">5</span>
<span class="n">Installed</span> <span class="n">MKL_jll</span> <span class="n">─────────────────────</span> <span class="n">v2019</span><span class="o">.</span><span class="mf">0.117</span><span class="o">+</span><span class="mi">2</span>
<span class="n">Installed</span> <span class="n">YAML</span> <span class="n">────────────────────────</span> <span class="n">v0</span><span class="o">.</span><span class="mf">4.0</span>
<span class="n">Building</span> <span class="n">Plots</span> <span class="n">→</span> <span class="sb">`~/.julia/packages/Plots/zOV0T/deps/build.log`</span>
<span class="n">Building</span> <span class="n">FFTW</span> <span class="n">─→</span> <span class="sb">`~/.julia/packages/FFTW/5DZuu/deps/build.log`</span>
<span class="n">Downloading</span> <span class="n">artifact</span><span class="o">:</span> <span class="n">IntelOpenMP</span>
<span class="c">######################################################################## 100.0%##O=# # Downloading artifact: FFTW</span>
<span class="c">######################################################################## 100.0%##O=# # </span>
</code></pre></div>
<p>To test, I load <code>Weave</code> into the <code>REPL</code>.</p>
<div class="highlight"><pre><span></span><code><span class="n">julia</span><span class="o">></span> <span class="k">using</span> <span class="n">Weave</span>
<span class="p">[</span> <span class="n">Info</span><span class="o">:</span> <span class="n">Precompiling</span> <span class="n">Weave</span> <span class="p">[</span><span class="mi">44</span><span class="n">d3d7a6</span><span class="o">-</span><span class="mi">8</span><span class="n">a23</span><span class="o">-</span><span class="mi">5</span><span class="n">bf8</span><span class="o">-</span><span class="mi">98</span><span class="n">c5</span><span class="o">-</span><span class="n">b353f8df5ec9</span><span class="p">]</span>
</code></pre></div>
<p>Everything seems to be fine. 😄</p>
<p>Now if you check, you will see a <code>~/.julia</code> has been recreated.</p>
<div class="highlight"><pre><span></span><code><span class="n">shell</span><span class="o">></span> <span class="n">ls</span> <span class="o">~/.</span><span class="n">julia</span> <span class="c"># Press ; to get shell prompt</span>
<span class="n">artifacts</span> <span class="n">compiled</span> <span class="n">conda</span> <span class="n">environments</span> <span class="n">logs</span> <span class="n">packages</span> <span class="n">prefs</span> <span class="n">registries</span>
</code></pre></div>
<p>So one last thing is to do is to restore my <code>config</code> folder by.</p>
<div class="highlight"><pre><span></span><code><span class="n">shell</span><span class="o">></span> <span class="n">cp</span> <span class="o">-</span><span class="n">r</span> <span class="o">~/</span><span class="n">Downloads</span><span class="o">/.</span><span class="n">julia</span><span class="o">/</span><span class="n">config</span><span class="o">/</span> <span class="o">~/.</span><span class="n">julia</span>
</code></pre></div>
<p>and remove the backup</p>
<div class="highlight"><pre><span></span><code><span class="n">shell</span><span class="o">></span> <span class="n">rm</span> <span class="o">-</span><span class="n">rf</span> <span class="o">~/</span><span class="n">Downloads</span><span class="o">/.</span><span class="n">julia</span><span class="o">/</span><span class="n">config</span><span class="o">/</span>
</code></pre></div>
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