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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/beast2-mcmc">Debian Med / beast2-mcmc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast2-mcmc/commit/88b19c13a1a60d7c86f435a16ee1e2212c584915">88b19c13</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-09T13:06:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Its fest-util.jar rather than fest.jar
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast2-mcmc/commit/5125f32e55a60a45a9bcac30235e70ad2f1e6e0e">5125f32e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-09T13:06:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Comment out ineffective attempt to set CLASSPATH
</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#60bc9af5ec216f8a84f4c14ada50ecf18d619e42">
debian/patches/fix_classpath_in_build_xml.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="60bc9af5ec216f8a84f4c14ada50ecf18d619e42">
<a href="https://salsa.debian.org/med-team/beast2-mcmc/compare/e27a222ff58ddca384ce3d5782bb68b5c593e7ef...5125f32e55a60a45a9bcac30235e70ad2f1e6e0e#60bc9af5ec216f8a84f4c14ada50ecf18d619e42"><strong>debian/patches/fix_classpath_in_build_xml.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">@@ -25,12 +25,14 @@ Forwarded: no</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff">     <property name="main_class_BEAST" value="beast.app.beastapp.BeastMain" /></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff">     <property name="report" value="build/junitreport" /></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -23,8 +23,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -22,9 +22,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff">         <fileset dir="${lib}" includes="beagle.jar"/></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff">         <fileset dir="${lib}" includes="jam.jar"/></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff">         <fileset dir="${lib}" includes="colt.jar"/></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="idiff left right"> </span>        <fileset dir="${lib}" includes="fest.jar"/></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>        <fileset dir="${lib}" includes="fest.jar"/></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <fileset dir="${lib}" includes="junit-4.8.2.jar"/></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <fileset dir="${lib}" includes="antlr-runtime-4.7.jar"/></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <fileset dir="${lib}" includes="fest-util.jar"/></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <fileset dir="${lib}" includes="junit4.jar"/></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <fileset dir="${lib}" includes="antlr4-runtime.jar"/></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff">     </path></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/beast2-mcmc/compare/e27a222ff58ddca384ce3d5782bb68b5c593e7ef...5125f32e55a60a45a9bcac30235e70ad2f1e6e0e#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -11,7 +11,9 @@ PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: teal;">JAVA_HOME</span>  <span class="o" style="font-weight: 600;">:=</span> /usr/lib/jvm/default-java</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nv" style="color: teal;">DEBJAR</span>    <span class="o" style="font-weight: 600;">:=</span> /usr/share/java</span>
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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC14" class="line" lang="make"><span class="nv" style="color: teal;">CLASS_PATH</span> <span class="o" style="font-weight: 600;">:=</span> /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/antlr4-runtime.jar:<span class="nv" style="color: teal;">$(JAVA_HOME)</span>/lib/tools.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/beagle.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/mpj.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/org.boehn.kmlframework.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/itext1-1.4.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/junit4.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/figtree.jar:lib/colt.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/options.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/mtj.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/jam.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/jdom1.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/jebl.jar:<span class="nv" style="color: teal;">$(DEBJAR)</span>/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># This does not seem to have any effect at all.  The only way to add</span></span>
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<td class="diff-line-num new old_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="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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># CLASSPATH relieably is editing build.xml</span></span>
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<td class="diff-line-num new old_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="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="make"><span class="c" style="color: #998; font-style: italic;"># CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(DEBJAR)/antlr4-runtime.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:$(DEBJAR)/colt.jar:$(DEBJAR)/fest-util.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"></span>
</pre>
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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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># to run the test suite</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="17" 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="LC19" class="line" lang="make"><span class="nv" style="color: teal;">JAVA</span>       <span class="o" style="font-weight: 600;">:=</span> <span class="nv" style="color: teal;">$(JAVA_HOME)</span>/bin/java</span>
</pre>
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