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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/cgview">Debian Med / cgview</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cgview/-/commit/41030c64d25965070e6ef010305585025def4d9b">41030c64</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-09T10:41:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cgview/-/commit/dd806b7c54428a07dc8dcf8dcd8bf90d7500d59b">dd806b7c</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-09T10:43:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cgview/-/commit/9c7f4c721d220475e7c991607a67a6d87aceb0f3">9c7f4c72</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-09T10:43:53+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cgview/-/commit/5d454d2fdc4318e6e6af5f478edc8b1895a1c868">5d454d2f</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-09T21:46:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add more autopkgtests
</pre>
</li>
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<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
debian/examples
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<li class="file-stats">
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debian/tests/data/README.test_data
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debian/tests/data/R_denitrificans.xml
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<a href="#ddee09162f050b1b6bc9dc1f8fb5207ae3093305">
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debian/tests/data/R_denitrificans_b.xml
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#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="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="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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<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">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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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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>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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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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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">cgview (0.0.20100111-5) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Jelmer Vernooij ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Use secure copyright file specification URI.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Jelmer Vernooij <jelmer@debian.org> Sat, 20 Oct 2018 13:37:58 +0000</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Added ref to conda</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Ooops? Adjusted ref to conda.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * d/u/metadata: yamllint</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [ Pranav Ballaney ]</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Sat, 09 May 2020 10:43:18 +0530</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">cgview (0.0.20100111-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/data/README.test_data</span></pre>
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<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</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">@@ -2,3 +2,4 @@ api_examples</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">cybercell.xml</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">example_3_features.tab</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">NC_001849.ptt</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#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/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#9400395398704fe42840ce7005f56d88482d8867"><strong>debian/tests/data/README.test_data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">The input files used for testing were generated using cgview_xml_builder.pl </span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">provided along with this package, as described in the corresponding README.</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#e408ea27c31bf911941511fe80bc5aff44fba56d"><strong>debian/tests/data/R_denitrificans.xml</strong></a>
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<li id="ddee09162f050b1b6bc9dc1f8fb5207ae3093305">
<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#ddee09162f050b1b6bc9dc1f8fb5207ae3093305"><strong>debian/tests/data/R_denitrificans_b.xml</strong></a>
The diff for this file was not included because it is too large.
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/cgview/-/compare/e3e1d985ecb5993b240ae50ba8c42b29972304ce...5d454d2fdc4318e6e6af5f478edc8b1895a1c868#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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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: #000080;">-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: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>cgview</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="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</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;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</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;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>
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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="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>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">cgview <span class="nt" style="color: #000080;">-i</span> cybercell.xml <span class="nt" style="color: #000080;">-o</span> cybercell.png <span class="nt" style="color: #000080;">-f</span> png</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">cgview <span class="nt" style="color: #000080;">-i</span> R_denitrificans.xml <span class="nt" style="color: #000080;">-o</span> R_denitrificans.png <span class="nt" style="color: #000080;">-f</span> png</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">cgview <span class="nt" style="color: #000080;">-i</span> R_denitrificans_b.xml <span class="nt" style="color: #000080;">-o</span> R_denitrificans_b.png <span class="nt" style="color: #000080;">-f</span> png </span></pre>
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