JAL-2232 some fix / partial fix of failing tests

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index d3685dd..184596c 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -302,7 +302,7 @@
     </testng>
   </target>
 
-  <target name="buildindices" depends="init, prepare,linkcheck" unless="help.uptodate">
+  <target name="buildindices" depends="init, prepare" unless="help.uptodate">
     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
       <arg line="html" />
     </java>
@@ -521,7 +521,7 @@
   </axis-wsdl2java>
 </target>
 
-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
   <!-- make the package jar if not already existing -->
   <mkdir dir="${packageDir}" />
   <!-- clean dir if it already existed -->
@@ -616,16 +616,16 @@
     <pathelement location="appletlib/${jsoup}" />
     <pathelement location="appletlib/${jsonSimple}" />
     <pathelement location="appletlib/${javaJson}" />
-       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
+    <fileset dir="${java.home}/lib">
+      <include name="plugin.jar" />
     </fileset>
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
   <proguard verbose="true" >
-    <injar file="in.jar" />    
-    <outjar file="${jalviewLiteJar}" />    
-    <libraryjar refid="obfuscateDeps.path" />    
+    <injar file="in.jar" />
+    <outjar file="${jalviewLiteJar}" />
+    <libraryjar refid="obfuscateDeps.path" />
     <dontwarn />
     <keep access="public" type="class" name="jalview.bin.JalviewLite">
       <field access="public" />
@@ -642,7 +642,7 @@
       <constructor/>
       <method name="*"/>
     </keep>
-   
+
     <keep access="public" type="class" name="MCview.PDBfile">
       <field access="public" />
       <method access="public" />
@@ -654,14 +654,14 @@
       <method access="public" />
       <constructor access="public" />
     </keep>
-    
+
     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
       <field access="public" />
       <method access="public" />
       <constructor access="public" />
     </keep>
-    
-    
+
+
     <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -926,11 +926,10 @@
     </packageset>
   </javadoc>
 </target>
-<target name="linkcheck">
-  <!-- finally, publish the help files -->
+<target name="linkcheck" depends="init,prepare">
   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
-  <java fork="true" dir="help" classpath="utils" classname="HelpLinksChecker" failonerror="true">
-    <arg file="help"/>
+  <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+    <arg file="${helpDir}"/>
     <arg value="-nointernet"/>
   </java>
 </target>