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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mindthegap">Debian Med / mindthegap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/c6b03820c4252e7703eada31b5bade3ddb54dd66">c6b03820</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-11T07:11:48Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Latest push with respect to testing
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#80e4eaa371fd96762163b4f21798615b8b94124c">
debian/mindthegap-examples.install
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<li class="file-stats">
<a href="#994c38d628af0182d7d5e6a5b5a27ed310b621d1">
debian/mindthegap.install
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="80e4eaa371fd96762163b4f21798615b8b94124c">
<a href="https://salsa.debian.org/med-team/mindthegap/commit/c6b03820c4252e7703eada31b5bade3ddb54dd66#80e4eaa371fd96762163b4f21798615b8b94124c"><strong>debian/mindthegap-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">test</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">data</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">scripts</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">scripts</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vde</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"></span></pre>
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<li id="994c38d628af0182d7d5e6a5b5a27ed310b621d1">
<a href="https://salsa.debian.org/med-team/mindthegap/commit/c6b03820c4252e7703eada31b5bade3ddb54dd66#994c38d628af0182d7d5e6a5b5a27ed310b621d1"><strong>debian/mindthegap.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">README</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">README</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">reads</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">references</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">truths</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">sh</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">eval</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">fasta</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">info</span><span class="o" style="font-weight: 600;">.</span><span class="nx">txt</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/*</span><span class="nx">gfa</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nb" style="color: #0086b3;">log</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">fasta</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">breakpoints</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">output</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span><span class="o" style="font-weight: 600;">/*.*.</span><span class="nx">vcf</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="php"><span class="nx">data</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">CHANGELOG</span><span class="o" style="font-weight: 600;">.</span><span class="nx">md</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">README</span><span class="o" style="font-weight: 600;">.</span><span class="nx">md</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">MindTheGap</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/mindthegap/commit/c6b03820c4252e7703eada31b5bade3ddb54dd66#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,18 +5,13 @@ pkg=mindthegap</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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11
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-r</span> /usr/share/mindthegap/test <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-r</span> /usr/share/mindthegap/data <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-r</span> /usr/share/doc/mindthegap/examples <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/test</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/<span class="idiff left right">examples/</span>test</span>
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18
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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20
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking simple_test.sh:"</span></span>
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21
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell">bash simple_test.sh</span>
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22
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking simple_full_test.sh:"</span></span>
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