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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/cct">Debian Med / cct</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612">e66803a6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-30T13:19:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest to find out the broken parts
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#5c73063cce379eff0039ea18dc1cb5429483efff">
<span class="new-file">
+
debian/cct-examples.install
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</li>
<li class="file-stats">
<a href="#5920ca13bc40e8a1cdb771f6537c9c8349038a0d">
<span class="new-file">
+
debian/cct.docs
</span>
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</li>
<li class="file-stats">
<a href="#9c6a2afe7e632a7329aaaaacffa5a403bfa93fe2">
debian/install
→
debian/cct.install
</a>
</li>
<li class="file-stats">
<a href="#63ec8605f389b503319174c57ff7c1eb47c46912">
debian/manpages
→
debian/cct.manpages
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
debian/createmanpages
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">installing</span> <span class="nx">the</span> <span class="nx">package</span> <span class="nx">cct</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span> <span class="k" style="font-weight: 600;">and</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<br>
</li>
<li id="5c73063cce379eff0039ea18dc1cb5429483efff">
<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#5c73063cce379eff0039ea18dc1cb5429483efff"><strong>debian/cct-examples.install</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
1
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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">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">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">cct</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">sample_projects</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">cct</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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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<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">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><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">cct</span></span></pre>
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<li id="5920ca13bc40e8a1cdb771f6537c9c8349038a0d">
<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#5920ca13bc40e8a1cdb771f6537c9c8349038a0d"><strong>debian/cct.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span></pre>
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<li id="9c6a2afe7e632a7329aaaaacffa5a403bfa93fe2">
<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#9c6a2afe7e632a7329aaaaacffa5a403bfa93fe2"><strong>debian/install</strong>
→
<strong>debian/cct.install</strong>
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<li id="63ec8605f389b503319174c57ff7c1eb47c46912">
<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#63ec8605f389b503319174c57ff7c1eb47c46912"><strong>debian/manpages</strong>
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<strong>debian/cct.manpages</strong>
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<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~)</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.2.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.2.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/cct</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/cct.git</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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">...</td>
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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">@@ -32,3 +32,30 @@ Description: visually comparing bacterial, plasmid, chloroplast, or mitochondria</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> setup, a CCT virtual machine that includes all dependencies preinstalled</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> is available. Detailed tutorials illustrating the use of CCT are</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> included with the CCT documentation.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Package: cct-examples</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Depends: ${perl:Depends},</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> bioperl,</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> cgview</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Description: example data for testing the package cct</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> The CGView Comparison Tool (CCT) is a package for visually comparing</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> bacterial, plasmid, chloroplast, or mitochondrial sequences of interest</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> to existing genomes or sequence collections. The comparisons are</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> conducted using BLAST, and the BLAST results are presented in the form</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> of graphical maps that can also show sequence features, gene and protein</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> names, COG category assignments, and sequence composition</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> characteristics. CCT can generate maps in a variety of sizes, including</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> 400 Megapixel maps suitable for posters. Comparisons can be conducted</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> within a particular species or genus, or all available genomes can be</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> used. The entire map creation process, from downloading sequences to</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> redrawing zoomed maps, can be completed easily using scripts included</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> with the CCT. User-defined features or analysis results can be included</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> on maps, and maps can be extensively customized. To simplify program</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> setup, a CCT virtual machine that includes all dependencies preinstalled</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> is available. Detailed tutorials illustrating the use of CCT are</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> included with the CCT documentation.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> This package provides the data which can be used as example. These are</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> the same data as used in autopkgtest.</span></pre>
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<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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">...</td>
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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">@@ -74,7 +74,7 @@ echo $AUTHOR >> $MANDIR/${progname}.1</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/perl \([^ ]\+\)\.pl/\1/'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/\.pl / /'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/\.sh / /'</span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/<span class="idiff left right">cct.</span>manpages</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/cct/commit/e66803a67b8f7d6cbd822c36f295e8c56e2d1612#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>cct</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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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="nv" style="color: teal;">$AUTOPKGTEST_TMP</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: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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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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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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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: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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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="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nv" style="color: teal;">CCT_HOME</span><span class="o" style="font-weight: 600;">=</span>/usr/share/cct ./test.sh</span></pre>
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