debian/patches/fix_classpath_in_build_xml.patch

@@ -25,12 +25,14 @@ Forwarded: no
  
      <property name="main_class_BEAST" value="beast.app.beastapp.BeastMain" />
      <property name="report" value="build/junitreport" />
-@@ -23,8 +23,8 @@
+@@ -22,9 +22,9 @@
+         <fileset dir="${lib}" includes="beagle.jar"/>
          <fileset dir="${lib}" includes="jam.jar"/>
          <fileset dir="${lib}" includes="colt.jar"/>
-         <fileset dir="${lib}" includes="fest.jar"/>
+-        <fileset dir="${lib}" includes="fest.jar"/>
 -        <fileset dir="${lib}" includes="junit-4.8.2.jar"/>
 -        <fileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
++        <fileset dir="${lib}" includes="fest-util.jar"/>
 +        <fileset dir="${lib}" includes="junit4.jar"/>
 +        <fileset dir="${lib}" includes="antlr4-runtime.jar"/>
      </path>

debian/rules

@@ -11,7 +11,9 @@ PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
 JAVA_HOME  := /usr/lib/jvm/default-java
 
 DEBJAR    := /usr/share/java
-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:lib/colt.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
+# This does not seem to have any effect at all.  The only way to add
+# CLASSPATH relieably is editing build.xml
+# 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
 
 # to run the test suite
 JAVA       := $(JAVA_HOME)/bin/java