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GitLab

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<h3>

Pierre Gruet pushed to branch master

at <a href="https://salsa.debian.org/med-team/biojava4-live">Debian Med / biojava4-live</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/edd0b3c916640c9246057374ab85e2f93fa1443a">edd0b3c9</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2021-10-13T17:58:54+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing obsolete patches

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/cf559b2121348b8ea45c8ade4b54daa9a5044980">cf559b21</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2021-10-13T18:00:00+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Stopping symlinking jquery-* files as it causes broken symlinks

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/e322622473407b5b34152360bb7c425482e226f2">e3226224</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2021-10-13T18:00:33+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding a Lintian override for the resulting warning about embedded JS copies

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/bc7351de7c508ab6ed18b81445679eab4ad0fc59">bc7351de</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2021-10-13T18:00:43+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/6ea5ecb247ea1e7f69d9848466f33049770178f3">6ea5ecb2</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2021-10-13T20:14:56+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#8a9496039b15763a770ac83149bf756928e59284">

<span class="new-file">

+

debian/libbiojava4-java-doc.lintian-overrides

</span>

</a>

</li>

<li class="file-stats">

<a href="#92bd46c229a10b0625513e7630f258b5ed6feee4">

<span class="deleted-file">

−

debian/patches/fix_code_to_support_latest_jmol

</span>

</a>

</li>

<li class="file-stats">

<a href="#1158dc93240f5f211001b47cf9b79b3924774c78">

<span class="deleted-file">

−

debian/patches/fix_uselog4j1

</span>

</a>

</li>

<li class="file-stats">

<a href="#8eff31f13b9dc98b089c30739f46f28faad111bc">

<span class="deleted-file">

−

debian/patches/java8_compatibility.patch

</span>

</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/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<td class="new_line diff-line-num new" 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;">biojava4</span><span class="p">-</span><span class="n" style="color: #333;">live</span> <span class="p">(</span><span class="m" style="color: #099;">4.2.12</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">5</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="new_line diff-line-num new" 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="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel">  <span class="p">*</span> <span class="n" style="color: #333;">Team</span> <span class="n" style="color: #333;">upload</span><span class="p">.</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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" 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;">Stopping</span> <span class="n" style="color: #333;">symlinking</span> <span class="n" style="color: #333;">jquery</span><span class="p">*</span> <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">default</span><span class="p">-</span><span class="n" style="color: #333;">jdk</span><span class="p">-</span><span class="n" style="color: #333;">doc</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">ones</span> <span class="n" style="color: #333;">we</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel">    <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">symlinks</span> <span class="k" style="font-weight: 600;">break</span> <span class="n" style="color: #333;">each</span> <span class="n" style="color: #333;">time</span> <span class="n" style="color: #333;">default</span><span class="p">-</span><span class="n" style="color: #333;">jdk</span><span class="p">-</span><span class="n" style="color: #333;">doc</span> <span class="n" style="color: #333;">evolves</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">988846</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel">  <span class="p">*</span> <span class="n" style="color: #333;">Adding</span> <span class="n" style="color: #333;">a</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;">the</span> <span class="n" style="color: #333;">resulting</span> <span class="n" style="color: #333;">warning</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">embedded</span> <span class="n" style="color: #333;">JS</span> <span class="n" style="color: #333;">copies</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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;">Removing</span> <span class="n" style="color: #333;">obsolete</span> <span class="n" style="color: #333;">patches</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Pierre</span> <span class="n" style="color: #333;">Gruet</span> <span class="p"><</span><span class="n" style="color: #333;">pgt</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;">Wed</span><span class="p">,</span> <span class="m" style="color: #099;">13</span> <span class="n" style="color: #333;">Oct</span> <span class="m" style="color: #099;">2021</span> <span class="m" style="color: #099;">18</span><span class="p">:</span><span class="m" style="color: #099;">00</span><span class="p">:</span><span class="m" style="color: #099;">50</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>

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<td class="new_line diff-line-num new" 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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"></span>

</pre>

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1

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<td class="new_line diff-line-num" data-linenumber="12" 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="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">biojava4</span><span class="p">-</span><span class="n" style="color: #333;">live</span> <span class="p">(</span><span class="m" style="color: #099;">4.2.12</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">4</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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"></span>

</pre>

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3

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel">  <span class="p">*</span> <span class="n" style="color: #333;">Team</span> <span class="n" style="color: #333;">upload</span><span class="p">.</span></span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="31" 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">@@ -31,8 +31,7 @@ Build-Depends-Indep: libcommons-dbcp-java,</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">                     libjaxb-api-java,</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" 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="LC32" class="line" lang="plaintext">                     libjaxb-java,</span>

</pre>

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33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">                     libnetx-java,</span>

</pre>

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34

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">                     default-jdk-doc,</span>

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35

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">                     rdfind</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">                     default-jdk-doc</span>

</pre>

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36

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35

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Standards-Version: 4.6.0</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" 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">

37

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/biojava4-live</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="38" 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">

38

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/biojava4-live.git</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8a9496039b15763a770ac83149bf756928e59284">

<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3#8a9496039b15763a770ac83149bf756928e59284"><strong>debian/libbiojava4-java-doc.lintian-overrides</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># It would be too complicated to remove the javascript that is included in</span>

</pre>

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<td class="new_line diff-line-num new" 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="plaintext"># javadocs, see the discussion on Debian Java mailing list starting at </span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># https://lists.debian.org/debian-java/2018/06/msg00020.html.</span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># See also https://bugs.debian.org/988846</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">embedded-javascript-library usr/share/doc/libbiojava4-java/api/jquery/*</span></pre>

</td>

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</table>

<br>

</li>

<li id="92bd46c229a10b0625513e7630f258b5ed6feee4">

<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3#92bd46c229a10b0625513e7630f258b5ed6feee4"><strong>debian/patches/fix_code_to_support_latest_jmol</strong>

deleted

</a>

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1

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC1" class="line" lang="diff"><span class="p">Subject: Latest JMOL library requires mode method definition</span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Author: Olivier Sallou <osallou@irisa.fr></span></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Add required interface method from latest JMOL library definition</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last--Updated: 2012-05-29</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -42,7 +42,17 @@</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">   public void setTextField (JTextField statusField) {</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">          status = statusField;</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">  }</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public void resizeInnerPanel(java.lang.String arg0) {</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;">+        }</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public boolean notifyEnabled(org.jmol.constant.EnumCallback callback) {</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;">+   return false;</span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        }</span></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</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;">+ public void notifyCallback(EnumCallback type, Object[] data) {</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff">  public String createImage(String arg0, String arg1, Object arg2, int arg3) {</span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff">          // TODO Auto-generated method stub</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">          return null;</span></pre>

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<br>

</li>

<li id="1158dc93240f5f211001b47cf9b79b3924774c78">

<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3#1158dc93240f5f211001b47cf9b79b3924774c78"><strong>debian/patches/fix_uselog4j1</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Subject: use log4j v1.X</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: upstream use log4j v2.X which is not yet available in Debian.</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">There is no specific v2 API usage, so applying a patch to use the log4j </span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">version available in Debian waiting for new version availability.</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Author: Olivier Sallou <osallou@debian.org></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">Last-Updated: 2014-02-01</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava3-structure/pom.xml</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;">+++ b/biojava3-structure/pom.xml</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -29,9 +29,9 @@</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">          </dependency></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">          <dependency></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;">-                 <groupId>org.apache.logging.log4j</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                 <artifactId>log4j-core</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                 <version>2.0-beta7</version></span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <groupId>log4j</groupId></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;">+                 <artifactId>log4j</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <version>1.2.17</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff">          </dependency></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff">          </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC22" class="line" lang="diff">          <!-- <dependency> <groupId>org.biojava</groupId> <artifactId>biojava3-core</artifactId> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC25" class="line" lang="diff"><span class="p">@@ -23,8 +23,8 @@</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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"> import java.io.InputStream;</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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"> import java.net.URL;</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC28" class="line" lang="diff"> </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.LogManager;</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.Logger;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.LogManager;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.Logger;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC33" class="line" lang="diff"> import org.w3c.dom.Element;</span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> import org.w3c.dom.NodeList;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC38" class="line" lang="diff"><span class="p">@@ -25,8 +25,8 @@</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC39" class="line" lang="diff"> import java.util.ArrayList;</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="40" 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">

40

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC40" class="line" lang="diff"> import java.util.List;</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="41" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC41" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="42" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.LogManager;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="43" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.Logger;</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.LogManager;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="45" 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">

45

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.Logger;</span></span>

</pre>

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46

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC46" class="line" lang="diff"> import org.w3c.dom.Element;</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="47" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC47" class="line" lang="diff"> import org.w3c.dom.NodeList;</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC48" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="49" 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="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC51" class="line" lang="diff"><span class="p">@@ -31,8 +31,8 @@</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="52" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC52" class="line" lang="diff"> import javax.xml.parsers.DocumentBuilderFactory;</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC53" class="line" lang="diff"> import javax.xml.parsers.ParserConfigurationException;</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="55" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.LogManager;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="56" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.Logger;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="57" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.LogManager;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="58" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.Logger;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="59" 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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<td class="new_line diff-line-num old" data-linenumber="0" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> import org.w3c.dom.Document;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> import org.w3c.dom.Node;</span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> import org.w3c.dom.NodeList;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="p">@@ -28,8 +28,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> import java.util.Set;</span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> import java.util.TreeSet;</span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.LogManager;</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.logging.log4j.Logger;</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.LogManager;</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.log4j.Logger;</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> /**</span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff">  * Provides programmatic access to ASTRAL representative sets. See the paper by <a</span></pre>

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<br>

</li>

<li id="8eff31f13b9dc98b089c30739f46f28faad111bc">

<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3#8eff31f13b9dc98b089c30739f46f28faad111bc"><strong>debian/patches/java8_compatibility.patch</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix a test failure with Java 8</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Author: Emmanuel Bourg <ebourg@apache.org></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -108,7 +108,7 @@</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">         this.circular = circular;</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">         this.betweenCompounds = betweenCompounds;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">         this.accession = accession;</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        this.subLocations = Collections.unmodifiableList(subLocations);</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        this.subLocations = subLocations != null ? Collections.unmodifiableList(subLocations) : Collections.<Location>emptyList();</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff">         assertLocation();</span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">     }</span></pre>

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<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6613e194ca2a2f567f25cebbb94f91d3a14e8c57...6ea5ecb247ea1e7f69d9848466f33049770178f3#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" 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="67" 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">@@ -67,17 +67,6 @@ override_dh_auto_build:</td>

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67

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="make">  <span class="nb" style="color: #0086b3;">cd </span>biojavadoc <span class="o" style="font-weight: 600;">&&</span> ant javadocs</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="68" 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="LC68" class="line" lang="make">  <span class="c" style="color: #998; font-style: italic;"># rm -rf biojavadoc</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="make"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="make"><span class="nl">override_jh_installjavadoc</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="make">  jh_installjavadoc</span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="make">  rdfind <span class="nt" style="color: #000080;">-makesymlinks</span> <span class="nb" style="color: #0086b3;">true</span> <span class="nt" style="color: #000080;">-followsymlinks</span> <span class="nb" style="color: #0086b3;">true</span> <span class="se" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="make">          <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$</span><span class="o" style="font-weight: 600;">(</span>dpkg <span class="nt" style="color: #000080;">-L</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$</span><span class="o" style="font-weight: 600;">(</span>apt-cache show default-jdk-doc | <span class="nb" style="color: #0086b3;">grep </span>Depends <span class="se" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="make">                        | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{print $$2}'</span><span class="o" style="font-weight: 600;">)</span> | <span class="nb" style="color: #0086b3;">grep</span> /usr/share/doc/ <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="70" 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="LC75" class="line" lang="make">             | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="o" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="70" 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="LC76" class="line" lang="make">          debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/</span>

</pre>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(DH_VERBOSE),1)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="78" 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">

78

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<td class="new_line diff-line-num old" data-linenumber="70" 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="LC78" class="line" lang="make">  <span class="nb" style="color: #0086b3;">cat </span>results.txt <span class="o" style="font-weight: 600;">||</span> /bin/true<span class="p">;</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> results.txt</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="79" 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">

79

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<td class="new_line diff-line-num old" data-linenumber="70" 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="LC79" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="80" 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">

80

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<td class="new_line diff-line-num old" data-linenumber="70" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC80" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="81" 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">

81

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<td class="new_line diff-line-num" data-linenumber="70" 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">

70

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"><span class="nl">override_dh_auto_test</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="82" 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">

82

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<td class="new_line diff-line-num" data-linenumber="71" 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">

71

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="83" 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">

83

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<td class="new_line diff-line-num" data-linenumber="72" 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">

72

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC72" class="line" lang="make">  <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'*********************************************************************************'</span></span>

</pre>

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