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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/figtree">Debian Med / figtree</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/-/commit/f2c8c875b13ff032f12f58a8fa8c3341e7792407">f2c8c875</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-05T18:59:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix FTBFS with new jebl2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/-/commit/44800651f6a640f3805ff10d5755a2f6f2d5222b">44800651</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-05T18:59:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/-/commit/0db783e50b52a1a586e5420608264f57fc498218">0db783e5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-05T18:59:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/-/commit/fbd778d12fb404070ce4e97da8e026f1f49268d2">fbd778d1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-05T18:59:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/-/commit/9839d4c4bda286300ad4c8e49c8670482e538d55">9839d4c4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-05T18:59:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/-/commit/0d74461fd7f687431d8e432c6febf48b759922ce">0d74461f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-05T18:59:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/-/commit/d8141b70fca82fc6dc84e34303f3fa76d28c7389">d8141b70</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-05T19:02:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#27232acb36b723c9f89acbc2a2ae946bb6145ee5">
<span class="new-file">
+
debian/patches/fix_ftbfs.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">figtree (1.4.4-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Sudip Mukherjee ]</span>
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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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix FTBFS with new jebl2</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #966878</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</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">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 05 Aug 2020 18:59:52 +0200</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">figtree (1.4.4-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * Do not Build-Depend libfreehep-graphics*</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389#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">@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> javahelper,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> default-jdk,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> ant,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -14,10 +14,11 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libjam-java (>= 0.1.20140824),</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libtrove-java,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libitext5-java</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/figtree</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/figtree.git</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: http://tree.bio.ed.ac.uk/software/figtree/</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Package: figtree</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: all</span>
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<li id="27232acb36b723c9f89acbc2a2ae946bb6145ee5">
<a href="https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389#27232acb36b723c9f89acbc2a2ae946bb6145ee5"><strong>debian/patches/fix_ftbfs.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix FTBFS</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The recent update of jebl2 removed the 'IOException' and has also added</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> close() which needs to be overriden.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Author: Sudip Mukherjee <sudipm.mukherjee@gmail.com></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/966878</span></span>
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7
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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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">--- figtree-1.4.4.orig/src/figtree/application/JSONTreeExporter.java</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ figtree-1.4.4/src/figtree/application/JSONTreeExporter.java</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -80,13 +80,13 @@</span> public class JSONTreeExporter implements</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> * @throws java.io.IOException</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void exportTree(Tree tree) throws IOException {</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;">+ public void exportTree(Tree tree) {</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> java.util.List<Tree> trees = new ArrayList<Tree>();</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> trees.add(tree);</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> exportTrees(trees);</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- private void writeTrees(Collection<? extends Tree> trees) throws IOException {</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ private void writeTrees(Collection<? extends Tree> trees) {</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> int indent = 0;</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> int treeCount = 0;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -178,10 +178,15 @@</span> public class JSONTreeExporter implements</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void exportTrees(Collection<? extends Tree> trees) throws IOException {</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void exportTrees(Collection<? extends Tree> trees) {</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> writeTrees(trees);</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Override</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void close() {</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ close();</span></span>
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<pre style="margin: 0;">+<span id="LC41" 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="LC42" 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="LC43" class="line" lang="diff"> final private String nameRegex = "^(\\w|-)+$";</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,3 +4,4 @@ fix_classpath_in_build_xml.patch</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">fix_itext_api_change.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">fix_jebl.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">0009-add-batik-all.jar.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">fix_ftbfs.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/rambaut/figtree/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/rambaut/figtree/issues/new</span>
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1
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Entry: SCR_008515</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,5 +9,5 @@ Registry:</td>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> Entry: OMICS_04268</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> Entry: figtree</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Repository: https://github.com/rambaut/figtree</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Repository: https://github.com/rambaut/figtree<span class="idiff left right">.git</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Repository-Browse: https://github.com/rambaut/figtree</span></pre>
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