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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/2b92e8a8fad75915e61c9c435963025361cf293a">2b92e8a8</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-11-12T15:44:40Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adapt for openjdk 11, use jaxb-api, closes #913566
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<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/7b99008826b9ed1a6b80cc8bae6fcbfe45cf307c">7b990088</a></strong>
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<span>by Olivier Sallou</span>
<i>at 2018-11-12T15:55:20Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add jaxb impl
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<h4>5 changed files:</h4>
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<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="#ebc84475be7ad87c1e7a0caa944982aa6ab1e0cf">
debian/libhtsjdk-java.classpath
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<li class="file-stats">
<a href="#eacc88751a9dfebcbf60538e262fa864e473a2b8">
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+
debian/patches/100-fix-java11
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/e6e4faf23f72599afa4e4351af324504a0a73934...7b99008826b9ed1a6b80cc8bae6fcbfe45cf307c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">htsjdk (2.16.1+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix FTBS with OpenJDK 11 (Closes: #913566) </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Olivier Sallou <osallou@debian.org> Mon, 12 Nov 2018 15:38:32 +0000</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">htsjdk (2.16.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/e6e4faf23f72599afa4e4351af324504a0a73934...7b99008826b9ed1a6b80cc8bae6fcbfe45cf307c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,8 @@ Build-Depends: default-jdk (>= 2:1.9),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> debhelper (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libcommons-jexl2-java,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libcommons-logging-java,</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libjaxb-api-java,</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> libjaxb-java,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libsnappy-java,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libcommons-compress-java,</span>
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<td class="diff-line-num old_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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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> libxz-java (>= 1.5),</span>
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<li id="ebc84475be7ad87c1e7a0caa944982aa6ab1e0cf">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/e6e4faf23f72599afa4e4351af324504a0a73934...7b99008826b9ed1a6b80cc8bae6fcbfe45cf307c#ebc84475be7ad87c1e7a0caa944982aa6ab1e0cf"><strong>debian/libhtsjdk-java.classpath</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/share/java/htsjdk.jar /usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/snappy-java.jar /usr/share/java/commons-compress.jar /usr/share/java/xz.jar /usr/share/java/ngs-java.jar</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/java/htsjdk.jar /usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/snappy-java.jar /usr/share/java/commons-compress.jar /usr/share/java/xz.jar /usr/share/java/ngs-java.jar<span class="idiff left right"> /usr/share/java/libjaxb-api.jar /usr/share/java/jaxb-impl.jar</span></span></pre>
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<li id="eacc88751a9dfebcbf60538e262fa864e473a2b8">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/e6e4faf23f72599afa4e4351af324504a0a73934...7b99008826b9ed1a6b80cc8bae6fcbfe45cf307c#eacc88751a9dfebcbf60538e262fa864e473a2b8"><strong>debian/patches/100-fix-java11</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Subject: add jaxb-api jar for openjdk 11</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: xml.bind has been removed from openjdk 11,</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> add jaxb-api jar file to compilation and classpath</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Author: Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Last-Updated: 2018-11-12</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Forwarded: no</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build.gradle</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build.gradle</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -22,12 +22,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> compile "org.apache.commons:commons-compress:1.4.1"</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> compile "org.tukaani:xz:1.5"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> compile "gov.nih.nlm.ncbi:ngs-java:2.9.0"</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;">+ compile "javax.xml.bind:jaxb-api:debian"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> testCompile "org.scala-lang:scala-library:2.11.x"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> //testCompile "org.scalatest:scalatest_2.12:3.0.5"</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> //testRuntime 'org.pegdown:pegdown:1.6.0' // Necessary for generating HTML reports with ScalaTest</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> testCompile "org.testng:testng:debian"</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> testCompile "com.google.jimfs:jimfs:debian"</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;">+ testCompile "com.sun.xml.bind:jaxb-impl:debian"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> }</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"> sourceCompatibility = 1.8</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -93,7 +95,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> if (System.env.CI == "true") {</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> jvmArgs += '-Dsamjdk.sra_libraries_download=true'</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jvmArgs += ["--add-modules", "java.xml.bind"]</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> exclude 'htsjdk/samtools/sra/**'</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> exclude 'htsjdk/samtools/BAMFileIndexTest.java'</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -120,7 +121,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> if (JavaVersion.current().isJava8Compatible()) {</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> tasks.withType(Javadoc) {</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> options.addStringOption('Xdoclint:none', '-quiet')</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- options.addStringOption('-add-modules', 'java.xml.bind')</span></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>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/htsjdk/compare/e6e4faf23f72599afa4e4351af324504a0a73934...7b99008826b9ed1a6b80cc8bae6fcbfe45cf307c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -9,3 +9,4 @@</td>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">80-2to3.patch</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">90-disable-testftp.patch</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">92-disable-testhttp.patch</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">100-fix-java11</span></pre>
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