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<h1 data-toc-skip>Issues</h1>
<h4 data-toc-skip class="author">Jonas Förster
&amp; Jürgen Pahle</h4>
<small class="dont-index">Source: <a href="https://github.com/jpahle/CoRC/blob/HEAD/vignettes/issues.Rmd" class="external-link"><code>vignettes/issues.Rmd</code></a></small>
<div class="hidden name"><code>issues.Rmd</code></div>
</div>
<div class="section level2">
<h2 id="initial-setup">Initial Setup<a class="anchor" aria-label="anchor" href="#initial-setup"></a>
</h2>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jpahle/CoRC" class="external-link">CoRC</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/loadExamples.html">loadExamples</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span></span>
<span><span class="co">#&gt; [[1]]</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "The Brusselator"</span></span>
<span><span class="co">#&gt; Number of compartments: 1</span></span>
<span><span class="co">#&gt; Number of species: 6</span></span>
<span><span class="co">#&gt; Number of reactions: 4</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="quicklist">Quicklist<a class="anchor" aria-label="anchor" href="#quicklist"></a>
</h2>
<p>Todo:</p>
<ul>
<li>Add more COPASI tasks</li>
<li>(Internal) Code marked with ‘TODO’ for minor problems</li>
<li>Consider only ever using setcompileflag instead of compiling</li>
<li>getListOfPossibleFunctions only returns bare pointer</li>
</ul>
<p>Issues:</p>
<ul>
<li>getwd() and copasi$getReferenceDirectory() are not in sync</li>
<li>some S3 classes should have reconstruct functions
(hadley/sloop)</li>
</ul>
</div>
<div class="section level2">
<h2 id="saving--cps-loses-experimental-data">Saving .cps loses experimental data<a class="anchor" aria-label="anchor" href="#saving--cps-loses-experimental-data"></a>
</h2>
<p>I commonly want to save a .cps to a tmp folder but when I do that
experimental data paths will fail.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Load example which has experimental data.</span></span>
<span><span class="va">datamodel</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/loadExamples.html">loadExamples</a></span><span class="op">(</span><span class="fl">4</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span>
<span></span>
<span><span class="va">fitproblem</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/methods/as.html" class="external-link">as</a></span><span class="op">(</span><span class="va">datamodel</span><span class="op">$</span><span class="fu">getTask</span><span class="op">(</span><span class="st">"Parameter Estimation"</span><span class="op">)</span><span class="op">$</span><span class="fu">getProblem</span><span class="op">(</span><span class="op">)</span>, <span class="st">"_p_CFitProblem"</span><span class="op">)</span></span>
<span><span class="va">filenames</span> <span class="op">&lt;-</span> <span class="va">fitproblem</span><span class="op">$</span><span class="fu">getExperimentSet</span><span class="op">(</span><span class="op">)</span><span class="op">$</span><span class="fu">getFileNames</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>The filenames are in the correct folder.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">filenames</span></span>
<span><span class="co">#&gt; [1] "/Users/juergen/software/R/tempfiles/Rtmpu4xZ3h/temp_libpath74864e09ff7/CoRC/extdata/test_paramest_exp_data.txt"</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/files.html" class="external-link">file.exists</a></span><span class="op">(</span><span class="va">filenames</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] TRUE</span></span></code></pre></div>
<p>Now I will save the model into a tmp folder.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">file</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempfile</a></span><span class="op">(</span>fileext <span class="op">=</span> <span class="st">".cps"</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/saveModel.html">saveModel</a></span><span class="op">(</span><span class="va">file</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="va">datamodel</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/loadModel.html">loadModel</a></span><span class="op">(</span><span class="va">file</span><span class="op">)</span></span>
<span><span class="va">fitproblem</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/methods/as.html" class="external-link">as</a></span><span class="op">(</span><span class="va">datamodel</span><span class="op">$</span><span class="fu">getTask</span><span class="op">(</span><span class="st">"Parameter Estimation"</span><span class="op">)</span><span class="op">$</span><span class="fu">getProblem</span><span class="op">(</span><span class="op">)</span>, <span class="st">"_p_CFitProblem"</span><span class="op">)</span></span>
<span><span class="va">filenames</span> <span class="op">&lt;-</span> <span class="va">fitproblem</span><span class="op">$</span><span class="fu">getExperimentSet</span><span class="op">(</span><span class="op">)</span><span class="op">$</span><span class="fu">getFileNames</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>The filenames are now supposedly in the folder where the .cps was
saved but there they don’t exist.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">filenames</span></span>
<span><span class="co">#&gt; [1] "/Users/juergen/software/R/tempfiles/Rtmpu4xZ3h/temp_libpath74864e09ff7/CoRC/extdata/test_paramest_exp_data.txt"</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/files.html" class="external-link">file.exists</a></span><span class="op">(</span><span class="va">filenames</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] TRUE</span></span></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/invisible.html" class="external-link">invisible</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/files.html" class="external-link">file.remove</a></span><span class="op">(</span><span class="va">file</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
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