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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/bedops">Debian Med / bedops</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/c4332f3e2651bbee7b1481938a89c59471479bca">c4332f3e</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-13T19:39:47Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest
For one of the tests, override with || true because although it all passes, still throws an error
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bedops/commit/5ec8b7e1b2e883f6ce9549e37c90cb88928ad68e">5ec8b7e1</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-13T19:40:49Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch for tests to use the installed binaries instead of the locally generated ones
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bedops/commit/5c41ecb8f2dd7cdd48f80c221c9aab3c9c7e2944">5c41ecb8</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-13T19:42:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Append recent changes to changelog
</pre>
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<h4>6 changed files:</h4>
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<a href="#ab7f38db9ece4375a40dfe01775538aa73a5b404">
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+
debian/bedops.install
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#e4830b70c1241fbf253115a0a0a52e982d994ee9">
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+
debian/patches/tests_use_installed_binaries.patch
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="ab7f38db9ece4375a40dfe01775538aa73a5b404">
<a href="https://salsa.debian.org/med-team/bedops/compare/c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6...5c41ecb8f2dd7cdd48f80c221c9aab3c9c7e2944#ab7f38db9ece4375a40dfe01775538aa73a5b404"><strong>debian/bedops.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">tests</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">bedops</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bedops/compare/c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6...5c41ecb8f2dd7cdd48f80c221c9aab3c9c7e2944#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -3,6 +3,9 @@ bedops (2.4.36+dfsg-2) UNRELEASED; urgency=medium</td>
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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"> * Use 2to3 to port python files from python2 to python3</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Closes: #936197</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Patch for tests to use the installed binaries instead of the locally</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> generated ones</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Write an autopkgtest</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"> -- Shayan Doust <hello@shayandoust.me> Fri, 13 Sep 2019 15:10:57 +0100</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bedops/compare/c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6...5c41ecb8f2dd7cdd48f80c221c9aab3c9c7e2944#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tests_use_installed_binaries.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_debian_libs</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">hardening.patch</span></pre>
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<li id="e4830b70c1241fbf253115a0a0a52e982d994ee9">
<a href="https://salsa.debian.org/med-team/bedops/compare/c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6...5c41ecb8f2dd7cdd48f80c221c9aab3c9c7e2944#e4830b70c1241fbf253115a0a0a52e982d994ee9"><strong>debian/patches/tests_use_installed_binaries.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/tests/starch/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/tests/starch/Makefile 2019-09-13 19:28:55.216495617 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/tests/starch/Makefile 2019-09-13 19:55:44.350045227 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,14 +1,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> APPGROUP = starch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> CWD := $(abspath $(patsubst %/,%,$(dir $(abspath $(lastword $(MAKEFILE_LIST))))))</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;">-STARCH = $(CWD)/../../bin/starch</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;">+STARCH = bedops-starch</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> STARCHBIN = starch</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-UNSTARCH = $(CWD)/../../bin/unstarch</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+UNSTARCH = unstarch</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> UNSTARCHBIN = unstarch</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-STARCHCAT = $(CWD)/../../bin/starchcat</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+STARCHCAT = starchcat</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> STARCHCATBIN = starchcat</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-STARCHSTRIP = $(CWD)/../../bin/starchstrip</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+STARCHSTRIP = starchstrip</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> STARCHSTRIPBIN = starchstrip</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SORTBED = $(CWD)/../../bin/sort-bed</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SORTBED = sort-bed</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> TMP := $(shell mktemp -d)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> DATA = $(CWD)/data</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> SHELL := /bin/bash</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -84,4 +84,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> starchstrip_prep:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> @[ -f $(STARCHSTRIP) ] || echo "Missing binary [$(STARCHSTRIP)] for build type [$(BUILDTYPE)]"</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> @echo "Writing to [$(TMP)]"</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(STARCHSTRIP) --version</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(STARCHSTRIP) --version</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/tests/bedops/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/tests/bedops/Makefile 2019-09-13 19:28:55.208495649 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/tests/bedops/Makefile 2019-09-13 19:57:07.897710316 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> APP = bedops</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> CWD := $(abspath $(patsubst %/,%,$(dir $(abspath $(lastword $(MAKEFILE_LIST))))))</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BIN = $(CWD)/../../bin/bedops</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+BIN = bedops</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> TMP := $(shell mktemp -d)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> DATA = $(CWD)/data</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> SHELL := /bin/bash</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/bedops/compare/c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6...5c41ecb8f2dd7cdd48f80c221c9aab3c9c7e2944#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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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/bedops/compare/c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6...5c41ecb8f2dd7cdd48f80c221c9aab3c9c7e2944#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>bedops</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="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="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;"># shellcheck disable=SC2064</span></span>
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/tests <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>/tests</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" 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">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.sh"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">chmod</span> +x <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Even though we get all passes for bedops, this still fails? Needs visual check.</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing bedops"</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>bedops <span class="o" style="font-weight: 600;">&&</span> make <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing starch"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../starch <span class="o" style="font-weight: 600;">&&</span> make</span></pre>
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