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<h3>
Olivier Sallou pushed to branch master
at <a href="https://salsa.debian.org/med-team/igv">Debian Med / igv</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/commit/14eb6c5fbe6ac7df0c6b64bdc4f94f824df9c7f6">14eb6c5f</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-10-15T14:06:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add log4j to log4j2 bridge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/commit/7ffc6e7c35c48e6fd70e548827667069c72b856d">7ffc6e7c</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-10-15T14:07:10Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixes to compile, but more issues....
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/commit/5efcfda62531713f5125221f98cbee66210337f6">5efcfda6</a></strong>
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<span>by Olivier Sallou</span>
<i>at 2018-10-15T14:07:26Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of salsa.debian.org:med-team/igv
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#37e490b5584c8e52c9983093facdd5c4adde4c25">
debian/patches/fix_gradle.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/igv/compare/9b46e631cc0b6f5732987c6979f1f90cc46c8fc4...5efcfda62531713f5125221f98cbee66210337f6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<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">@@ -13,8 +13,9 @@ igv (2.4.14+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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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"> [ Olivier Sallou]</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * d/patches/fix_gradle.patch: adapt build to Debian</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> // TODO there is still an issue with log4j, Logger class is not found</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> though modules and libraries are loaded in classpath</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> // TODO there is still an issue with batik:</span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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"> if defined, there are some conflicts</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> for other libs, they are found but marked as not visible....</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 01 Oct 2018 21:14:39 +0200</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<li id="37e490b5584c8e52c9983093facdd5c4adde4c25">
<a href="https://salsa.debian.org/med-team/igv/compare/9b46e631cc0b6f5732987c6979f1f90cc46c8fc4...5efcfda62531713f5125221f98cbee66210337f6#37e490b5584c8e52c9983093facdd5c4adde4c25"><strong>debian/patches/fix_gradle.patch</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">@@ -34,10 +34,17 @@ Forwarded: no</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> sourceSets {</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> main {</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> java {</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -45,6 +54,2<span class="idiff left right">0</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -45,6 +54,2<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> dependencies {</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> // Use the newer JIDE lib for Java 9 builds</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> compile fileTree(dir: 'lib', include: '*.jar', exclude: 'jide-oss-3.5.5.jar') + fileTree(dir: 'lib_java9', include: '*.jar')</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;">+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-graphics/debian/javafx-graphics-debian-linux.jar")</span></span>
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<td class="diff-line-num new old_line" data-linenumber="41" 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="diff-line-num new new_line" data-linenumber="42" 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">
42
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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="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-controls/debian/javafx-controls-debian-linux.jar")</span></span>
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<td class="diff-line-num new old_line" data-linenumber="41" 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="diff-line-num new new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-base/debian/javafx-base-debian-linux.jar")</span></span>
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<td class="diff-line-num new old_line" data-linenumber="41" 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="diff-line-num new new_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-swing/debian/javafx-swing-debian-linux.jar")</span></span>
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<td class="diff-line-num new old_line" data-linenumber="41" 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="diff-line-num new new_line" data-linenumber="45" 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">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-fxml/debian/javafx-fxml-debian-linux.jar")</span></span>
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<td class="diff-line-num new old_line" data-linenumber="41" 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="diff-line-num new new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //compile "org.apache.xmlgraphics:batik-dom:debian"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //compile "org.apache.xmlgraphics:batik-svggen:debian"</span></span>
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<td class="diff-line-num old_line" data-linenumber="41" 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">
41
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<td class="diff-line-num new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile "com.google.guava:guava:debian"</span></span>
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<td class="diff-line-num old_line" data-linenumber="42" 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">
42
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<td class="diff-line-num new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile "commons-io:commons-io:debian"</span></span>
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<td class="diff-line-num old_line" data-linenumber="43" 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">
43
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile "org.apache.commons:commons-math:debian"</span></span>
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