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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pairix">Debian Med / python-pairix</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pairix/-/commit/aa926c7c46b0be60d6f99045aba6079ac65de196">aa926c7c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-02T21:20:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix missing copyright statements
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pairix/-/commit/b897e47cd58b0915a775ddb1b95433c16d35a3da">b897e47c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-02T21:21:30+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix binary package name of examples according to ftpmaster advise
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pairix/-/commit/0ab67b2d7d9fa7880f65e06103d9e81b8dca68ce">0ab67b2d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-02T21:47:26+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix installation
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-pairix/-/commit/727c61fab22830f3d665c286b1e9220b02b1f39c">727c61fa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-02T22:23:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Its to hard to preserve all the gz compressed versus non-gz compressed files and restore these after dh_compress has done its job. Thus create a tar archive and unpack it later
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<a href="#10b4d8d818b5c9958bca30cceb373442d9b50c03">
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+
debian/python-pairix-examples.install
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<a href="#ad3274941586f62e8bfdc6b0af9ce14ea03f23c7">
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−
debian/python3-pairix-examples.install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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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="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-pairix/-/compare/ee0a6d59642417f26d7a95aaba45781b9287da2d...727c61fab22830f3d665c286b1e9220b02b1f39c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" 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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,7 @@ Description: 1D/2D indexing and querying with a pair of genomic coordinates</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> uses it to access the file from a relevant position by taking advantage</span>
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<td class="diff-line-num old_line" data-linenumber="39" 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">
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<td class="diff-line-num new_line" data-linenumber="39" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> of bgzf compression, allowing for a fast query on large files.</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Package: python<span class="idiff left right">3</span>-pairix-examples</span>
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<td class="diff-line-num new old_line" data-linenumber="42" 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="LC41" class="line" lang="plaintext">Package: python-pairix-examples</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Architecture: all</span>
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<td class="diff-line-num old_line" data-linenumber="43" 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">
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<td class="diff-line-num old_line" data-linenumber="44" 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">
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Enhances: python3-pairix</span>
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<br>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/python-pairix/-/compare/ee0a6d59642417f26d7a95aaba45781b9287da2d...727c61fab22830f3d665c286b1e9220b02b1f39c#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -7,11 +7,18 @@ Copyright: 2016 Soo Lee</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> 2008-2009 Genome Research Ltd (GRL)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: MIT</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">Files: src/bgzf.c</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Files: src/bgzf.*</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> src/bgzip.c</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> src/knetfile.c</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> src/ksort.h</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Copyright: 2008 Broad Institute / Massachusetts Institute of Technology</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> 2011 Attractive Chaos <attractor@live.co.uk></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">License: MIT</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">Files: src/pairixmodule.c</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Copyright: 2011 Seoul National University</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Files: src/pairix.h</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Copyright: 2009 Genome Research Ltd (GRL), 2010 Broad Institute</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">License: MIT</span>
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<a href="https://salsa.debian.org/med-team/python-pairix/-/compare/ee0a6d59642417f26d7a95aaba45781b9287da2d...727c61fab22830f3d665c286b1e9220b02b1f39c#10b4d8d818b5c9958bca30cceb373442d9b50c03"><strong>debian/python-pairix-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">python3</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pairix</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">samples</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">tar</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">xz</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">python3</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pairix</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="no" style="color: #008080;">VERSION</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">txt</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">python3</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pairix</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">examples</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pairix/-/compare/ee0a6d59642417f26d7a95aaba45781b9287da2d...727c61fab22830f3d665c286b1e9220b02b1f39c#ad3274941586f62e8bfdc6b0af9ce14ea03f23c7"><strong>debian/python3-pairix-examples.install</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">python3</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pairix</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">examples</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pairix/-/compare/ee0a6d59642417f26d7a95aaba45781b9287da2d...727c61fab22830f3d665c286b1e9220b02b1f39c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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">@@ -9,10 +9,8 @@ export PYBUILD_BEFORE_TEST=cp -a $(CURDIR)/samples {build_dir}; cp -a $(CURDIR)/</td>
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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"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">override_dh_installexamples:</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> dh_installexamples</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> mkdir -p debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> mv debian/python3-$(PYBUILD_NAME)/usr/lib/python`py3versions -d -v`/dist-packages/samples debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> cd debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples && tar caf samples.tar.xz samples && rm -rf samples</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> mv debian/python3-$(PYBUILD_NAME)/usr/lib/python`py3versions -d -v`/dist-packages/VERSION.txt debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> find debian -name VERSION.txt -delete</span></pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">override_dh_install:</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> tar caf samples.tar.xz samples</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> dh_install</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> find debian/python3-$(PYBUILD_NAME)/usr/lib -name samples -type d | xargs rm -rf</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> find debian/*/usr/lib -name VERSION.txt -delete</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/python-pairix/-/compare/ee0a6d59642417f26d7a95aaba45781b9287da2d...727c61fab22830f3d665c286b1e9220b02b1f39c#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">@@ -6,7 +6,7 @@ pkg=python3-pairix</td>
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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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