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<h3>
Olivier Sallou pushed to branch master
at <a href="https://salsa.debian.org/med-team/htsjdk">Debian Med / htsjdk</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/08ecca67f07f90e257e0760aca52c835f54d1de8">08ecca67</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-04-17T08:43:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch for Java 9 support
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/2bbfe997e4c1aa12ed49f8d40ff589f8982a9bb6">2bbfe997</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-04-17T10:03:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix javadoc generation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/855b9b6a8385212bdb87c3274f27069443b05fcc">855b9b6a</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-04-17T10:06:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update modifications done and pending
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#0e145a9888f04e5bcc1b32e5ba78679670498477">
<span class="new-file">
+
debian/patches/40-fix-java9
</span>
</a>
</li>
<li class="file-stats">
<a href="#4c055fa82b51b7b5d9f9cd14eb4ec33a81b06f62">
<span class="new-file">
+
debian/patches/50-fix-javadoc
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/a49f8588499169413b73161dec26c9f293ab7db2...855b9b6a8385212bdb87c3274f27069443b05fcc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,11 +12,10 @@ htsjdk (2.14.3+dfsg-1) UNRELEASED-targeting-experimental; urgency=medium</td>
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<td class="diff-line-num old_line" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * d/rules</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> Disable unit testing due to gradle+testng errors in gradle 3.2</span>
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<td class="diff-line-num 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> gradle 3.4 will fix the problem</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Fix JDK9 with --add-modules java.xml.bind in javadoc generation</span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> * Fix javadoc generation</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> </span>
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<td class="diff-line-num old_line" data-linenumber="16" 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="18" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> [TODO - O. Sallou in progress]</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> * Fix JDK9 with --add-modules java.xml.bind in javadoc generation and test, need a new patch</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext"> * Javadoc generation failure: certainly due to openjdk issues (exits with error</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> on warnings, would need to patch a lot of files to workaround the issue or disable javadoc package)</span>
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<td class="diff-line-num old_line" data-linenumber="20" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Reintroduce unit tests now that gradle 3.4 is available in sid</span>
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<td class="diff-line-num old_line" data-linenumber="21" 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="LC20" class="line" lang="plaintext"> - new patch is needed for latest upstream, referencing junit classes</span>
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<td class="diff-line-num old_line" data-linenumber="22" 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="21" 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="LC21" class="line" lang="plaintext"> - add testng() call in build.gradle with a patch and set test call in d/rules back</span>
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</li>
<li id="0e145a9888f04e5bcc1b32e5ba78679670498477">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/a49f8588499169413b73161dec26c9f293ab7db2...855b9b6a8385212bdb87c3274f27069443b05fcc#0e145a9888f04e5bcc1b32e5ba78679670498477"><strong>debian/patches/40-fix-java9</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Subject: add support for java9</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Description: Java 9 uses modules, code makes use fo some modules,</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> need to add them</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Author: Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Last-Updated: 17-04-2018</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Forwarded: no</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">--- a/build.gradle</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">+++ b/build.gradle</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">@@ -115,6 +115,7 @@</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> if (JavaVersion.current().isJava8Compatible()) {</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> tasks.withType(Javadoc) {</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> options.addStringOption('Xdoclint:none', '-quiet')</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">+ options.addStringOption('-add-modules', 'java.xml.bind')</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> </span></pre>
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<li id="4c055fa82b51b7b5d9f9cd14eb4ec33a81b06f62">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/a49f8588499169413b73161dec26c9f293ab7db2...855b9b6a8385212bdb87c3274f27069443b05fcc#4c055fa82b51b7b5d9f9cd14eb4ec33a81b06f62"><strong>debian/patches/50-fix-javadoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Subject: javadoc exception</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Description: some exception is raised by javadoc</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> looks like an openjdk issue, this patch removes impacted</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> comments</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Author: Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Last-Updated: 2018-04-17</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Forwarded: no</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">--- a/src/main/java/htsjdk/samtools/util/MergingIterator.java</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">+++ b/src/main/java/htsjdk/samtools/util/MergingIterator.java</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">@@ -88,7 +88,6 @@</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> /**</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- * @see java.util.Iterator<T>.hasNext</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"> @Override</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> public boolean hasNext() {</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">@@ -96,7 +95,6 @@</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> }</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> /**</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- * @see java.util.Iterator<T>.next</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> */</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> @Override</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> public T next() {</span></pre>
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<a href="https://salsa.debian.org/med-team/htsjdk/compare/a49f8588499169413b73161dec26c9f293ab7db2...855b9b6a8385212bdb87c3274f27069443b05fcc#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">@@ -2,3 +2,5 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">13-skip_network_tests</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">20-fix-version.patch</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">30-disable-scalatest.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">40-fix-java9</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">50-fix-javadoc</span></pre>
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