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<h3>
Graham Inggs pushed to branch master
at <a href="https://salsa.debian.org/med-team/uc-echo">Debian Med / uc-echo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/-/commit/508261d3846510f05e0ffb10839701d27108d6cb">508261d3</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2021-11-07T13:19:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not build 32-bit binaries for the wrong architecture
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/-/commit/83acbd1269081c834df7e1a9f0c996f545f849cf">83acbd12</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2021-11-07T13:19:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depend on python3 instead of python3-all-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/-/commit/304eafb5e52695c42f3d9ea000093c4dce15aef2">304eafb5</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2021-11-07T13:19:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switch to debhelper 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/-/commit/9427024b8f2f16c33bbcfd3f8bc3c2f9093932cb">9427024b</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2021-11-07T13:19:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Test the installed binaries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/-/commit/c69179a3c0a89b7042aa3e73549f4893904c8765">c69179a3</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2021-11-07T13:19:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/-/commit/e79f0dc8217c09b85af011099832f777b17e59b5">e79f0dc8</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2021-11-07T13:21:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepare for upload to unstable
</pre>
</li>
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<h4>6 changed files:</h4>
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<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
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−
debian/README.Debian
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<a href="#d74521e38fd108bcbeb3c8673510b9b3edc4d00c">
debian/tests/runtest
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/uc-echo/-/compare/f5b2c0f54177e2d60d74fbfb623fbc27ff8002a3...e79f0dc8217c09b85af011099832f777b17e59b5#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">According to upstream this program needs lots of RAM and thus for i386/amd64</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">the compiler flag -m64 is needed. </span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Unfortunately this is not supported on all architectures. So on some (like</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">mips, mipsel, kfreebsd-i386, hurd-i386, armel, armhf), that have no 64-bit</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">mode implemented, only a 32bit version is built. </span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Apart from the number of data that can be processed, this has no influence</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">on the results.</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/uc-echo/-/compare/f5b2c0f54177e2d60d74fbfb623fbc27ff8002a3...e79f0dc8217c09b85af011099832f777b17e59b5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">uc-echo (1.12-16) unstable; 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"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Do not build 32-bit binaries for the wrong architecture</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Build-Depend on python3 instead of python3-all-dev</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Switch to debhelper 13</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Test the installed binaries</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Bump Standards-Version to 4.6.0, no changes</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"> -- Graham Inggs <ginggs@debian.org> Sun, 07 Nov 2021 11:20:37 +0000</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">uc-echo (1.12-15) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Using int and not char for storing offsets</span>
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<a href="https://salsa.debian.org/med-team/uc-echo/-/compare/f5b2c0f54177e2d60d74fbfb623fbc27ff8002a3...e79f0dc8217c09b85af011099832f777b17e59b5#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">@@ -6,13 +6,12 @@ Uploaders: Thorsten Alteholz <debian@alteholz.de>,</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Pierre Gruet <pgtdebian@free.fr></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python3<span class="idiff left right">-all-dev</span>:any,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3:any,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-scipy:native,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-numpy:native,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> g++-multilib [i386 powerpc sparc x32]</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/uc-echo</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/uc-echo.git</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://uc-echo.sourceforge.net/</span>
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<a href="https://salsa.debian.org/med-team/uc-echo/-/compare/f5b2c0f54177e2d60d74fbfb623fbc27ff8002a3...e79f0dc8217c09b85af011099832f777b17e59b5#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -6,10 +6,6 @@ include /usr/share/dpkg/architecture.mk</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">LIBRARY_PATH=/usr/lib/$(DEB_HOST_MULTIARCH)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">CPATH=/usr/include/$(DEB_HOST_MULTIARCH)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export LIBRARY_PATH CPATH</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">ADDCXXFLAGS = -m64</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),mips mipsel mipsn32 mipsn32el mips64 mips64el hppa kfreebsd-i386 hurd-i386 armel armhf arm64 ia64 sh4 powerpcspe m68k))</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">ADDCXXFLAGS =</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">endif</span>
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9
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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">CXXFLAGS += $(ADDCXXFLAGS)</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/uc-echo/-/compare/f5b2c0f54177e2d60d74fbfb623fbc27ff8002a3...e79f0dc8217c09b85af011099832f777b17e59b5#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: runtest</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @<span class="idiff left right">, build-essential</span></span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span></pre>
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<a href="https://salsa.debian.org/med-team/uc-echo/-/compare/f5b2c0f54177e2d60d74fbfb623fbc27ff8002a3...e79f0dc8217c09b85af011099832f777b17e59b5#d74521e38fd108bcbeb3c8673510b9b3edc4d00c"><strong>debian/tests/runtest</strong></a>
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1
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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="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'make to get required binaries'</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell">make</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test for sample data'</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="idiff left right">python3 ./ErrorCorrection.py</span> <span class="nt" style="color: #000080;">-o</span> output/sample_data.fastq sample_data.txt</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="idiff left right">uc-echo</span> <span class="nt" style="color: #000080;">-o</span> output/sample_data.fastq sample_data.txt</span>
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9
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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10
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Run with 4 threads'</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="idiff left right">python3 ./ErrorCorrection.py</span> <span class="nt" style="color: #000080;">--ncpu</span> 4 <span class="nt" style="color: #000080;">-o</span> output/sample_data.fastq sample_data.txt</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="idiff left right">uc-echo</span> <span class="nt" style="color: #000080;">--ncpu</span> 4 <span class="nt" style="color: #000080;">-o</span> output/sample_data.fastq sample_data.txt</span>
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12
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'cleaning up ...'</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell">make clean</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;">rm</span> <span class="nt" style="color: #000080;">-rf</span> tmp/ log/ output/ </span></pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> tmp/ log/ output/</span></pre>
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