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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/emboss">Debian Med / emboss</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/014d12b949756f1fcc54d8f105de0148204ff9fe">014d12b9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T02:18:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/7ab9c02643ea06e512a48b1bf1a92a3f25e76a3a">7ab9c026</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T02:24:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/c4a48e1071f3cf5e6b8158e42afbae557fc60d22">c4a48e10</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T02:24:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/b30d4be931c15f92393507b65f171901ee6eeb5e">b30d4be9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T03:00:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unused lintian-overrides
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/72975f86151f974a4e24c48e8b4418b0c6416ff6">72975f86</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T03:02:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/a12accad68280d6fb17acaf0d418915731ecd162">a12accad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T03:18:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop autotools from d/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/6e58879dc62be896e4228d9dcd0773bfca735862">6e58879d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T03:52:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Really drop autoreconf commands
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/c4a47c67185edc08d3e8802cc1fd638ef8329d7f">c4a47c67</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T03:59:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lintian override for script-with-language-extension
More verbose package descriptions for all packages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emboss/commit/1f6d29ebeaa4feb00772ffdb299402083e1c9c5b">1f6d29eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T04:19:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#3bcc3e61507d3f57348e27c43dca9b5ada1b64fa">
<span class="deleted-file">
−
debian/emboss-doc.lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#6ea2976e0d2d6f959efe039b3d5d98d3f9ecc754">
<span class="new-file">
+
debian/jemboss.lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">emboss</span> <span class="p">(</span><span class="m" style="color: #099;">6.6.0</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">7</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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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="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">debhelper</span> <span class="m" style="color: #099;">11</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" 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">
4
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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="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Point</span> <span class="n" style="color: #333;">Vcs</span> <span class="n" style="color: #333;">fields</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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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="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.1.5</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Drop</span> <span class="n" style="color: #333;">unused</span> <span class="n" style="color: #333;">lintian</span><span class="p">-</span><span class="n" style="color: #333;">overrides</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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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="LC7" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Respect</span> <span class="n" style="color: #333;">DEB_BUILD_OPTIONS</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">override_dh_auto_test</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Lintian</span> <span class="n" style="color: #333;">override</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">script</span><span class="p">-</span><span class="k" style="font-weight: 600;">with</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">-</span><span class="n" style="color: #333;">extension</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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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="LC9" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">More</span> <span class="n" style="color: #333;">verbose</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">descriptions</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">packages</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"></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="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Fri</span><span class="p">,</span> <span class="m" style="color: #099;">03</span> <span class="n" style="color: #333;">Aug</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">05</span><span class="p">:</span><span class="m" style="color: #099;">59</span><span class="p">:</span><span class="m" style="color: #099;">14</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="mosel"></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">emboss</span> <span class="p">(</span><span class="m" style="color: #099;">6.6.0</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">6</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">debhelper</span> <span class="m" style="color: #099;">10</span></span>
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<a href="https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b#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">@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># javahelper,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libx11-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> x11proto-core-dev,</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">@@ -18,16 +18,14 @@ Build-Depends: debhelper (>= 10),</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libpq-dev,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> antiword,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> sharutils,</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> autotools-dev,</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> tcsh | csh | c-shell,</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> dh-autoreconf,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"># Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> default-jdk,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> ant</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#Build-Depends-Indep: default-jdk</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">3.9.8</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/emboss.git</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/emboss.git</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">#<span class="idiff left right"> #</span>Build-Depends-Indep: default-jdk</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">4.1.5</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/emboss</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/emboss.git</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Homepage: http://emboss.sourceforge.net</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Package: emboss</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="55" 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">@@ -57,6 +55,16 @@ Package: emboss-data</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">Description: data files for the EMBOSS package</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> EMBOSS is a free Open Source software analysis package specially developed for</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> the needs of the molecular biology (e.g. EMBnet) user community. The software</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> automatically copes with data in a variety of formats and even allows</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> transparent retrieval of sequence data from the web. Also, as extensive</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> libraries are provided with the package, it is a platform to allow other</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> scientists to develop and release software in true open source spirit. EMBOSS</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> also integrates a range of currently available packages and tools for sequence</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> analysis into a seamless whole. EMBOSS breaks the historical trend towards</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> commercial software packages.</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> This package includes data files needed by EMBOSS, the European Molecular</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> Biology Open Software Suite.</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="74" 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">@@ -66,6 +74,16 @@ Section: doc</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">Suggests: evince | pdf-viewer | postscript-viewer</span>
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">Description: documentation for EMBOSS</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> EMBOSS is a free Open Source software analysis package specially developed for</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> the needs of the molecular biology (e.g. EMBnet) user community. The software</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> automatically copes with data in a variety of formats and even allows</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> transparent retrieval of sequence data from the web. Also, as extensive</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> libraries are provided with the package, it is a platform to allow other</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> scientists to develop and release software in true open source spirit. EMBOSS</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> also integrates a range of currently available packages and tools for sequence</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> analysis into a seamless whole. EMBOSS breaks the historical trend towards</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> commercial software packages.</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> This package includes non-essential user documentation for EMBOSS, the</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> European Molecular Biology Open Software Suite.</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></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">@@ -76,6 +94,16 @@ Depends: ${misc:Depends}</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">Recommends: tcsh | csh | c-shell</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">Suggests: valgrind</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">Description: test files for the EMBOSS package</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> EMBOSS is a free Open Source software analysis package specially developed for</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> the needs of the molecular biology (e.g. EMBnet) user community. The software</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> automatically copes with data in a variety of formats and even allows</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> transparent retrieval of sequence data from the web. Also, as extensive</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> libraries are provided with the package, it is a platform to allow other</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> scientists to develop and release software in true open source spirit. EMBOSS</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> also integrates a range of currently available packages and tools for sequence</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> analysis into a seamless whole. EMBOSS breaks the historical trend towards</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> commercial software packages.</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> This package includes test files for EMBOSS, the European Molecular Biology</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> Open Software Suite.</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> .</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">@@ -121,5 +149,15 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> default-jre</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"># libgnujaf-java</span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">Description: graphical user interface to EMBOSS</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> EMBOSS is a free Open Source software analysis package specially developed for</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> the needs of the molecular biology (e.g. EMBnet) user community. The software</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> automatically copes with data in a variety of formats and even allows</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> transparent retrieval of sequence data from the web. Also, as extensive</span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> libraries are provided with the package, it is a platform to allow other</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> scientists to develop and release software in true open source spirit. EMBOSS</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> also integrates a range of currently available packages and tools for sequence</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> analysis into a seamless whole. EMBOSS breaks the historical trend towards</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> commercial software packages.</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"> Jemboss is a Graphical User Interface (GUI) to EMBOSS, the European Molecular</span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext"> Biology Open Software Suite. It is part of the EMBOSS distribution.</span></pre>
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<a href="https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b#3bcc3e61507d3f57348e27c43dca9b5ada1b64fa"><strong>debian/emboss-doc.lintian-overrides</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># false positives: These files are just carbon copies of the files in upstream tarball</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/manuals/adminguide.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/manuals/program.ps.gz</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/tutorials/emboss_tut.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b#6ea2976e0d2d6f959efe039b3d5d98d3f9ecc754"><strong>debian/jemboss.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">jemboss: script-with-language-extension usr/bin/runJemboss.sh</span></pre>
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<a href="https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" 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">@@ -10,7 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#export CLASSPATH=/usr/share/java/activation.jar:</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">%:</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with autotools-dev,autoreconf</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">VERSION := $(shell dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">RENAMED := cons pscan</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">@@ -37,7 +37,6 @@ DEB_LDFLAGS += $(shell dpkg-buildflags --get LDFLAGS)</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">#DEB_LDFLAGS += $(shell pg_config | grep LIBS | cut -f2 -d=)</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> dh_autotools-dev_updateconfig</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> dh_auto_configure -- $(CONFFLAGS)</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">override_dh_auto_build:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,7 +46,6 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> cd jemboss && jar uf lib/jemboss.jar resources/version resources/*.properties</span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>
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49
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">override_dh_clean:</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> dh_autotools-dev_restoreconfig</span>
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51
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> rm -rf debian/emboss_tmp</span>
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52
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> find jemboss/ -type f -name "*.class" -delete</span>
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53
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<td class="diff-line-num new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> [ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv debian/testbackup test )</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" 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">@@ -107,6 +105,7 @@ override_dh_auto_install-indep:</td>
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107
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<td class="diff-line-num new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> find debian/emboss-test/usr/share/EMBOSS/test -type f -name .cvsignore -delete</span>
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108
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<td class="diff-line-num new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="109" 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">
109
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">override_dh_auto_test:</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<td class="diff-line-num old_line" data-linenumber="110" 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">
110
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> $(RM) test-stamp</span>
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<td class="diff-line-num old_line" data-linenumber="111" 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">
111
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<td class="diff-line-num new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> [ -d debian/testbackup ] || cp -a test debian/testbackup</span>
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<td class="diff-line-num old_line" data-linenumber="112" 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">
112
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> sed -i "/SET emboss_tempdata/cSET emboss_tempdata $(CURDIR)/test" test/.embossrc</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="114" 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">@@ -115,6 +114,7 @@ override_dh_auto_test:</td>
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115
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> echo "SET emboss_data $(CURDIR)/emboss/data" >> test/.embossrc</span>
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<td class="diff-line-num old_line" data-linenumber="116" 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">
116
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> echo "SET emboss_docroot $(CURDIR)/doc" >> test/.embossrc</span>
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<td class="diff-line-num old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
117
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">endif</span>
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<td class="diff-line-num old_line" data-linenumber="118" 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">
118
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<td class="diff-line-num new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="119" 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">
119
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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<td class="diff-line-num old_line" data-linenumber="120" 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">
120
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<td class="diff-line-num new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> dh_installchangelogs -k ChangeLog</span>
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