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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/simka">Debian Med / simka</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/commit/c1cb069486ba11ac26a151ba6b9c8312a79b609b">c1cb0694</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-13T05:26:21Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First section of autopkgtest
Tests simka but need to also test simkaMin
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#9aeb3f33ba7407966ded6269d14de4bad9117663">
debian/patches/fix_test_path.patch
</a>
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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="9aeb3f33ba7407966ded6269d14de4bad9117663">
<a href="https://salsa.debian.org/med-team/simka/commit/c1cb069486ba11ac26a151ba6b9c8312a79b609b#9aeb3f33ba7407966ded6269d14de4bad9117663"><strong>debian/patches/fix_test_path.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,8 @@ Last-Update: 2019-09-13</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">Index: simka/tests/simkaMin/test_simkaMin.py</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 0<span class="idiff left right">4:26:28.362188349</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 0<span class="idiff left right">4:26:28.358188366</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 0<span class="idiff left right">6:19:47.190416943</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 0<span class="idiff left right">6:19:47.186416959</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> for nb_reads in NB_READS:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> for nb_kmers in NB_KMERS:</span>
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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">@@ -74,8 +74,8 @@ Index: simka/tests/simkaMin/test_simkaMin.py</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/tests/simple_test.py</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simple_test.py 2019-09-13 0<span class="idiff left right">4:26:28.362188349</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simple_test.py 2019-09-13 0<span class="idiff left right">4:26:28.358188366</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simple_test.py 2019-09-13 0<span class="idiff left right">6:19:47.190416943</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simple_test.py 2019-09-13 0<span class="idiff left right">6:19:47.186416959</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"><span class="p">@@ -91,7 +91,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> #test k=31 t=0</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> clear()</span>
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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">@@ -126,9 +126,9 @@ Index: simka/tests/simple_test.py</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/example/simple_test.sh</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/example/simple_test.sh 2019-09-1<span class="idiff left right">2 22:31:11.297235515</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/example/simple_test.sh 2019-09-13 0<span class="idiff left right">4:27:15.069993869</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="p">@@ -3,1<span class="idiff left right">7 +3,17</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/example/simple_test.sh 2019-09-1<span class="idiff left right">3 06:19:47.190416943</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/example/simple_test.sh 2019-09-13 0<span class="idiff left right">6:20:36.106219416</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="p">@@ -3,1<span class="idiff left right">9 +3,19</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"> # look for simka binary. In devel mode, it's in ../build/bin directory.</span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> # In production mode, it's in ../bin directory.</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="155" 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">@@ -155,5 +155,8 @@ Index: simka/example/simple_test.sh</td>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#fi</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bindir="/usr/bin"</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="diff"> # run simka</span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command="$bindir/simka -in simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"</span></span>
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159
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"> #printf "$command\n\n"</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> # DO NOT add lines between '$command' exec and 'var...' !</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/simka/commit/c1cb069486ba11ac26a151ba6b9c8312a79b609b#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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<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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<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><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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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><span class="idiff left right">simka</span></span>
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5
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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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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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="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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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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10
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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11
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/example<span class="idiff left right">s</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/example/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="k" style="font-weight: 600;">*</span>.gz</span>
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17
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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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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#do_stuff_to_test_package#</span></span></span></pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="idiff left right">bash simple_test.sh</span></span></pre>
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