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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/artemis">Debian Med / artemis</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/9cd5f4dc340977b9f384ab484584551ca3515e0a">9cd5f4dc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-05T12:49:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patch that prevents copying of non-existing files; d/rules: Use dh_auto_build instead of $(MAKE)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/2a678f55a2ef88e603c3915d09f2ae1ed770484b">2a678f55</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-05T14:10:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not try to install non-existing files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8">551ab850</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-05T14:23:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not mention non-existing test target
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#d868ab7f769125e66a23484c0b2cd648eeaff096">
debian/patches/jar-rules.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/artemis/compare/b62d032ad478158c5a9117a603827869e0c2bbb0...551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,6 +7,8 @@ artemis (17.0.1+dfsg-1) UNRELEASED; urgency=medium</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<td class="diff-line-num new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Standards-Version: 4.2.0</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Class FTPSeekableStream should not be excluded</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Update patch that prevents copying of non-existing files</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> * d/rules: Use dh_auto_build instead of $(MAKE)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 17 Mar 2018 11:41:38 +0100</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"></span>
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<li id="d868ab7f769125e66a23484c0b2cd648eeaff096">
<a href="https://salsa.debian.org/med-team/artemis/compare/b62d032ad478158c5a9117a603827869e0c2bbb0...551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8#d868ab7f769125e66a23484c0b2cd648eeaff096"><strong>debian/patches/jar-rules.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">@@ -4,48 +4,61 @@ Description: Leave out removed files when building jar files</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> Their absence causes "can not stat" errors, so any reference to</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> them is removed here.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">Author: Afif Elghraoui <afif@ghraoui.name></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">Forwarded: not-needed</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">Last-Update: 2015-10-22</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">Last-Update: Sun, 05 Aug 2018 07:16:40 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"></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;">--- a/Makefile</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;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -75,<span class="idiff left right">6</span> +75,7 @@ artemis.jar : $(CLASSES)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -75,<span class="idiff left right">27</span> +75,7 @@ artemis.jar : $(CLASSES)</span></span>
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12
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> mkdir -p jar_build/build</span>
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13
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> rm -f *.jar</span>
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14
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> cd jar_build/build; \</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if [ "$$BUILDSYSEM" = "not-Debian" ] ; then \</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> for fileJar in ../../lib/*.jar; do \</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> jar xvf $$fileJar; \</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> rm -rf META-INF/MANIFEST.MF; \</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -96,7 +97,11 @@ artemis.jar : $(CLASSES)</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> rm -rf META-INF/MANIFEST.MF; \</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> done; \</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap .</span></span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap . \</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else \</span></span>
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26
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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp -R ../uk ../org ../nsdb ../type ../seqdb ../etc ../images \</span></span>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
27
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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap . ; \</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fi</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fileJar in ../../lib/*.jar; do \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jar xvf $$fileJar; \</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rf META-INF/MANIFEST.MF; \</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done; \</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fileJar in ../../lib/j2ssh/*.jar; do \</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jar xvf $$fileJar; \</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rf META-INF/MANIFEST.MF; \</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done; \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fileJar in ../../lib/ibatis/*.jar; do \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jar xvf $$fileJar; \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rf META-INF/MANIFEST.MF; \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done; \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fileJar in ../../lib/batik/*.jar; do \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="30" 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">
30
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jar xvf $$fileJar; \</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rf META-INF/MANIFEST.MF; \</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done; \</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fileJar in ../../lib/picard/*.jar; do \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jar xvf $$fileJar; \</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rf META-INF/MANIFEST.MF; \</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done; \</span></span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp -R ../../uk ../../org ../../etc ../../images \</span></span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap .</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="29" 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">
29
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<td class="diff-line-num new_line" data-linenumber="40" 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">
40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> find jar_build/build -name '*.java' -print | xargs rm -f</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="30" 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">
30
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<td class="diff-line-num new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> find jar_build/build -name '.svn' -print | xargs rm -rf</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="idiff left right"> find jar_build/build -name '*.DS_Store' -print | xargs rm -rf</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">@@ -104,15 +109,15 @@ artemis.jar : $(CLASSES)</span></span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">@@ -103,16 +83,16 @@ artemis.jar : $(CLASSES)</span></span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="idiff left right"> cd jar_build/build; \</span></span>
</pre>
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33
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<td class="diff-line-num new_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">
44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> rm -rf META-INF/MANIFEST.MF; \</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="34" 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">
34
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="idiff left right"> </span> jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span> jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ jar cmf manifest-art ../artemis.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ artemis_sqlmap org uk ; \</span></span>
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38
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \</span>
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39
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> jar cmf manifest-circular ../DNAPlotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \</span>
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40
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ org uk <span class="idiff left right">com net htsjdk picard gov </span>joptsimple ngs freemarker ; \</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ org uk joptsimple ngs freemarker ; \</span></span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \</span>
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43
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE; \</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ jar cmf manifest-bamview ../bamview.jar <span class="idiff left right">META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker</span> ; \</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ jar cmf manifest-bamview ../bamview.jar <span class="idiff left right">etc org uk</span> ; \</span></span>
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45
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \</span>
</pre>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="idiff left right"> </span> jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span> jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \</span></span>
</pre>
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47
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \</span></span>
</pre>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \</span></span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ jar cmf manifest-act ../act.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \</span></span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ artemis_sqlmap org uk ; \</span></span>
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49
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> rm -rf jar_build/build;</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> </span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/artemis/compare/b62d032ad478158c5a9117a603827869e0c2bbb0...551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8#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">@@ -38,14 +38,13 @@ export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> dh $@ --with javahelper</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> $(MAKE) jar</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> # dh_auto_build -- jar # does not work since the build does not find all plain files that should be include in jar since it cds to subdir first</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> dh_auto_build -- jar</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> debian/artemis.manifest</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> convert images/helix.gif -resize 96x96\! images/helix.png</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> cd test && ant -f build-test.xml <span class="idiff left right">test-headless </span>-DEMBOSS_ROOT=/usr</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> cd test && ant -f build-test.xml -DEMBOSS_ROOT=/usr</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> dh_auto_clean</span>
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