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<h3>
Emmanuel Bourg pushed to branch master
at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</a>
</h3>
<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/9359e09f6df2c08b2f2ec3269c9243b8ef06c449">9359e09f</a></strong>
<div>
<span>by Emmanuel Bourg</span>
<i>at 2018-11-30T12:29:23Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed the build failure with Java 11
</pre>
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<h4>2 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="#e186644cad34bbb8e38eb75706855e6cd177ad48">
debian/patches/10-build.xml.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/picard-tools/commit/9359e09f6df2c08b2f2ec3269c9243b8ef06c449#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">picard-tools (2.18.14+dfsg-2) UNRELEASED; 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"> * Team upload.</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"> * Fixed the build failure with Java 11</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Emmanuel Bourg <ebourg@apache.org> Fri, 30 Nov 2018 13:28:52 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">picard-tools (2.18.14+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version</span>
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<li id="e186644cad34bbb8e38eb75706855e6cd177ad48">
<a href="https://salsa.debian.org/med-team/picard-tools/commit/9359e09f6df2c08b2f2ec3269c9243b8ef06c449#e186644cad34bbb8e38eb75706855e6cd177ad48"><strong>debian/patches/10-build.xml.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" 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="99" 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">@@ -99,16 +99,15 @@ Last-Updated: 2016-07-07</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> logger.info("build for version:" + version)</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"> group = 'com.github.broadinstitute'</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -166,6 +171,<span class="idiff left right">8</span> @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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="LC102" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -166,6 +171,<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="diff"> tasks.withType(Javadoc) {</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="diff"> // do this for all javadoc tasks, including gatkDoc</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="diff"> options.addStringOption('Xdoclint:none')</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addStringOption('XDignore.symbol.file')</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addStringOption('-add-modules', 'java.xml.bind')</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"> javadoc {</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -192,7 +19<span class="idiff left right">9</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -192,7 +19<span class="idiff left right">8</span>,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"> // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="diff"> // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,7 +117,7 @@ Last-Updated: 2016-07-07</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> options.docletpath = classpath.asType(List)</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> options.doclet = "picard.util.help.PicardHelpDoclet"</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -279,6 +28<span class="idiff left right">7</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -279,6 +28<span class="idiff left right">6</span>,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" 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="126" 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">@@ -127,7 +126,7 @@ Last-Updated: 2016-07-07</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"> // set heap size for the test JVM(s)</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"> minHeapSize = "1G"</span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"> maxHeapSize = "2G"</span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -415,6 +42<span class="idiff left right">5</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -415,6 +42<span class="idiff left right">4</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> into "$htmlDir/picarddoc"</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,7 +134,7 @@ Last-Updated: 2016-07-07</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> task updateGhPages(dependsOn: ['copyJavadoc', 'copyPicardDoc']){</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> outputs.dir htmlDir</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -430,3 +44<span class="idiff left right">1</span>,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -430,3 +44<span class="idiff left right">0</span>,4 @@</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="diff"> into 'newdocs'</span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="diff"> }</span>
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