Hi Florian Can you try to install it outside eclipse first so we can tackle one problem at a time?
a Sent from my BlackBerry® smartphone on O2 -----Original Message----- From: "Florian Huber" <[email protected]> Sender: [email protected] Date: Mon, 25 Jun 2012 17:41:01 To: Die Biomart Mailing List<[email protected]> Subject: [BioMart Users] Installation problem Dear all I tried installing BioMart version 0.8 as specified in the user documentation at www.biomart.org. Everything seems to have worked until step 3 (compile and build Biomart) where I got the following output. I'm quite new to database searching and computing so the error might be a trivial one. I'm trying to do the installation on a Linux machine, Ubuntu version 10.04. Many thanks! Here the shell output: lab@lab10:~/bin/release-0_8-candidate_6$ ant Buildfile: build.xml -load.properties: -init: compile.main: [javac] Compiling 528 source files to /home/lab/bin/release-0_8-candidate_6/build/classes/main [javac] failed to read ecj.jar (reconfigure with --with-ecj-jar): /usr/share/java/eclipse-ecj.jar [javac] failed to load org.eclipse.jdt.internal.compiler.batch.Main from ecj.jar: /usr/share/java/eclipse-ecj.jar [javac] java.lang.ClassNotFoundException: org.eclipse.jdt.internal.compiler.batch.Main not found in java.net.URLClassLoader{urls=[file:/usr/share/java/eclipse-ecj.jar], parent=gnu.gcj.runtime.SystemClassLoader{urls=[file:/usr/share/ant/lib/ant-launcher.jar,file:/usr/share/java/xmlParserAPIs.jar,file:/usr/share/java/xercesImpl.jar], parent=gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}} [javac] at java.net.URLClassLoader.findClass(libgcj.so.10) [javac] at java.lang.ClassLoader.loadClass(libgcj.so.10) [javac] at java.lang.ClassLoader.loadClass(libgcj.so.10) [javac] at com.sun.tools.javac.Main.<clinit>(Main.java:91) [javac] at java.lang.Class.initializeClass(libgcj.so.10) [javac] at java.lang.Class.forName(libgcj.so.10) [javac] at org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.doesModernCompilerExist(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.getCompiler(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.taskdefs.Javac.compile(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.taskdefs.Javac.execute(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.UnknownElement.execute(ant-1.7.1.jar.so) [javac] at java.lang.reflect.Method.invoke(libgcj.so.10) [javac] at org.apache.tools.ant.dispatch.DispatchUtils.execute(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Task.perform(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Target.execute(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Target.performTasks(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Project.executeSortedTargets(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Project.executeTarget(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Project.executeTargets(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Main.runBuild(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.Main.startAnt(ant-1.7.1.jar.so) [javac] at org.apache.tools.ant.launch.Launcher.run(ant-launcher-1.7.1.jar.so) [javac] at org.apache.tools.ant.launch.Launcher.main(ant-launcher-1.7.1.jar.so) BUILD FAILED java.lang.ExceptionInInitializerError at java.lang.Class.initializeClass(libgcj.so.10) at java.lang.Class.forName(libgcj.so.10) at org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.doesModernCompilerExist(ant-1.7.1.jar.so) at org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.getCompiler(ant-1.7.1.jar.so) at org.apache.tools.ant.taskdefs.Javac.compile(ant-1.7.1.jar.so) at org.apache.tools.ant.taskdefs.Javac.execute(ant-1.7.1.jar.so) at org.apache.tools.ant.UnknownElement.execute(ant-1.7.1.jar.so) at java.lang.reflect.Method.invoke(libgcj.so.10) at org.apache.tools.ant.dispatch.DispatchUtils.execute(ant-1.7.1.jar.so) at org.apache.tools.ant.Task.perform(ant-1.7.1.jar.so) at org.apache.tools.ant.Target.execute(ant-1.7.1.jar.so) at org.apache.tools.ant.Target.performTasks(ant-1.7.1.jar.so) at org.apache.tools.ant.Project.executeSortedTargets(ant-1.7.1.jar.so) at org.apache.tools.ant.Project.executeTarget(ant-1.7.1.jar.so) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(ant-1.7.1.jar.so) at org.apache.tools.ant.Project.executeTargets(ant-1.7.1.jar.so) at org.apache.tools.ant.Main.runBuild(ant-1.7.1.jar.so) at org.apache.tools.ant.Main.startAnt(ant-1.7.1.jar.so) at org.apache.tools.ant.launch.Launcher.run(ant-launcher-1.7.1.jar.so) at org.apache.tools.ant.launch.Launcher.main(ant-launcher-1.7.1.jar.so) Caused by: java.lang.NullPointerException at com.sun.tools.javac.Main.<clinit>(Main.java:106) at java.lang.Class.initializeClass(libgcj.so.10) ...19 more Total time: 0 seconds _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
