Hi everyone Thanks for your help. It turned out that some Java packages were not installed even though I thought there were.
Cheers Flo On Mo, 25.06.2012, 17:57, arek kasprzyk wrote: > 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 > -- Florian Huber PhD Student Michael Jantsch Group MFPL, University of Vienna Dr.-Bohr-Gasse 1 1030 Vienna, AUSTRIA +43 1 4277 56231 _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
