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Thread: Taverna Workbench 1.3.1

  1. #1
    Member AljoshaNL's Avatar
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    Taverna Workbench 1.3.1

    Hello,

    Me and my mother are trying to install Taverna Workbench on a Fedora Core 4 machine. When we run runme.sh we get a splash screen, but it crashes with the folowing output:

    Code:
    [jdmitrie@thestral taverna-workbench-1.3.1]$ ./runme.sh
    java.util.ConcurrentModificationException
       at java.util.HashMap$HashIterator.hasNext() (/usr/lib/libgcj.so.6.0.0)
       at java.awt.image.BufferedImage$1.startProduction(java.awt.image.ImageConsumer) (/usr/lib/libgcj.so.6.0.0)
       at gnu.java.awt.peer.gtk.GtkToolkit.createImage(java.awt.image.ImageProducer) (/usr/lib/lib-gnu-java-awt-peer-gtk.so.6.0.0)
       at javax.swing.ImageIcon.ImageIcon(java.awt.Image, java.lang.String) (/usr/lib/libgcj.so.6.0.0)
       at javax.swing.ImageIcon.ImageIcon(java.awt.Image) (/usr/lib/libgcj.so.6.0.0)
       at org.embl.ebi.escience.scuflui.ScuflIcons.<clinit>() (Unknown Source)
       at java.lang.Class.initializeClass() (/usr/lib/libgcj.so.6.0.0)
       at org.embl.ebi.escience.scuflui.AdvancedModelExplorer.getIcon() (Unknown Source)
       at org.embl.ebi.escience.scuflui.UIComponentRegistry.loadInstances(java.lang.ClassLoader) (Unknown Source)
       at org.embl.ebi.escience.scuflui.UIComponentRegistry.instance() (Unknown Source)
       at org.embl.ebi.escience.scuflui.workbench.Workbench.main(java.lang.String[]) (Unknown Source)
       at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/usr/lib/libgcj.so.6.0.0)
       at org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher.main(java.lang.String[]) (Unknown Source)
       at gnu.java.lang.MainThread.call_main() (/usr/lib/libgcj.so.6.0.0)
       at gnu.java.lang.MainThread.run() (/usr/lib/libgcj.so.6.0.0)
    java.util.ConcurrentModificationException
    Found auth = www.mygrid.org.uk for ns = dataprovenance
    Found auth = www.mygrid.org.uk for ns = person
    Found auth = www.mygrid.org.uk for ns = formaloutputparameter
    Found auth = www.mygrid.org.uk for ns = documentcollection
    Found auth = www.mygrid.org.uk for ns = affiliationepisode
    Found auth = www.mygrid.org.uk for ns = lsdocument
    Found auth = www.mygrid.org.uk for ns = experimentinstance
    Found auth = www.mygrid.org.uk for ns = creationtype
    Found auth = www.mygrid.org.uk for ns = address
    Found auth = www.mygrid.org.uk for ns = servicedescription
    Found auth = www.mygrid.org.uk for ns = programme
    Found auth = www.mygrid.org.uk for ns = experimentdesign
    Found auth = www.mygrid.org.uk for ns = study
    Found auth = www.mygrid.org.uk for ns = operationtype
    Found auth = www.mygrid.org.uk for ns = operation
    Found auth = www.mygrid.org.uk for ns = labbookview
    Found auth = www.mygrid.org.uk for ns = datatype
    Found auth = www.mygrid.org.uk for ns = actualoutputparameter
    Found auth = www.mygrid.org.uk for ns = formalinputparameter
    Found auth = www.mygrid.org.uk for ns = operationtrace
    Found auth = www.mygrid.org.uk for ns = format
    Found auth = www.mygrid.org.uk for ns = operationcontent
    Found auth = www.mygrid.org.uk for ns = scuflworkflowtrace
    Found auth = www.mygrid.org.uk for ns = actualinputparameter
    Found auth = www.mygrid.org.uk for ns = studyparticipationepisode
    Found auth = www.mygrid.org.uk for ns = organization
    Exception in thread "main" java.lang.reflect.InvocationTargetException
       at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/usr/lib/libgcj.so.6.0.0)
       at org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher.main(java.lang.String[]) (Unknown Source)
       at gnu.java.lang.MainThread.call_main() (/usr/lib/libgcj.so.6.0.0)
       at gnu.java.lang.MainThread.run() (/usr/lib/libgcj.so.6.0.0)
    Caused by: java.util.regex.PatternSyntaxException: At position 4 in regular expression pattern:
    attempted to repeat a token that is already repeated
            \w++
                ^
       at java.util.regex.Pattern.Pattern(java.lang.String, int) (/usr/lib/libgcj.so.6.0.0)
       at java.util.regex.Pattern.compile(java.lang.String, int) (/usr/lib/libgcj.so.6.0.0)
       at java.util.regex.Pattern.compile(java.lang.String) (/usr/lib/libgcj.so.6.0.0)
       at java.util.regex.Pattern.matches(java.lang.String, java.lang.CharSequence) (/usr/lib/libgcj.so.6.0.0)
       at org.embl.ebi.escience.scufl.Processor.Processor(org.embl.ebi.escience.scufl.ScuflModel, java.lang.String) (Unknown Source)
       at org.embl.ebi.escience.scufl.InternalSinkPortHolder.InternalSinkPortHolder(org.embl.ebi.escience.scufl.ScuflModel) (Unknown Source)
       at org.embl.ebi.escience.scufl.ScuflModel.ScuflModel() (Unknown Source)
       at org.embl.ebi.escience.scuflui.workbench.Workbench.Workbench() (Unknown Source)
       at org.embl.ebi.escience.scuflui.workbench.Workbench.main(java.lang.String[]) (Unknown Source)
       at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/usr/lib/libgcj.so.6.0.0)
    At first, when we ran runme.sh it gave out the java help screen. We altered the command a bit, after that we got the output. We also installed some compatiblity gcj libraries, and after that we restored the command found in the runme.sh script to what is was. Here is the runme.sh script:

    Code:
    #!/bin/sh
    
    ## resolve links - $0 may be a symlink
    PRG="$0"
    progname=`basename "$0"`
    saveddir=`pwd`
    
    # need this for relative symlinks
    cd `dirname "$PRG"`
      
    while [ -h "$PRG" ] ; do
        ls=`ls -ld "$PRG"`
        link=`expr "$ls" : '.*-> \(.*\)$'`
        if expr "$link" : '.*/.*' > /dev/null; then
        PRG="$link"
        else
        PRG=`dirname "$PRG"`"/$link"
        fi
    done
    
    TAVERNA_HOME=`dirname "$PRG"`
    
    cd "$saveddir"
    
    # make it fully qualified
    TAVERNA_HOME=`cd "$TAVERNA_HOME" && pwd`
    
    
    CLASSP=$TAVERNA_HOME/resources:$TAVERNA_HOME/conf:$TAVERNA_HOME/taverna-1.3.1-launcher.jar
    
    for i in $TAVERNA_HOME/libext/*.jar
    do
      CLASSP=$CLASSP:$i
    done
    
    case "`uname`" in
      CYGWIN*) CLASSP=`cygpath --path --type windows $CLASSP`;;
    esac
    
    # echo "java -classpath" $CLASSP "-Djava.protocol.handler.pkgs=uk.ac.rdg.resc.jstyx.client -Dtaverna.home=$TAVERNA_HOME -ea" "org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher"
    
    java -classpath $CLASSP -Djava.protocol.handler.pkgs=uk.ac.rdg.resc.jstyx.client -Dtaverna.home=$TAVERNA_HOME -ea org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher
    Help is very much appreciated, were sitting here already for some hours, we really dont know what to try next.

    Aljosha and Julia
    Eat your l33t skillz!
    My home page: http://www.inter.nl.net/users/alexeif/

  2. #2
    Mentor jro's Avatar
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    Without looking at the source directly it looks like a syntax error in one of the Regular Expressions in this file:
    org.embl.ebi.escience.scufl.Processor.Processor

    Did you try adding some stuff or are there optional modules that are included? If so try compiling without them.
    jro - http://jeff.robbins.ws
    Linux counter#:213782
    GnuPG ID: 406238E7

  3. #3
    Member AljoshaNL's Avatar
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    I think I'm e-mailing the guys who made Taverna. It really ain't for humans. The only documentation I found didn't work, on 2 (totally) different distros.
    Eat your l33t skillz!
    My home page: http://www.inter.nl.net/users/alexeif/

  4. #4
    Mentor jro's Avatar
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    That would probably be my next course of action. Either that or post the error to the programs discussion board or mailing list. It didn't appear to be a problem on your end.
    jro - http://jeff.robbins.ws
    Linux counter#:213782
    GnuPG ID: 406238E7

  5. #5
    Member AljoshaNL's Avatar
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    I needed to get sun's java. Now it works. They promised to make it clearer in the manual
    Eat your l33t skillz!
    My home page: http://www.inter.nl.net/users/alexeif/

  6. #6
    Mentor jro's Avatar
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    Ah ha, I looked right over the fact that you were compiling with gcj. Glad you got it working.
    jro - http://jeff.robbins.ws
    Linux counter#:213782
    GnuPG ID: 406238E7

  7. #7
    Member AljoshaNL's Avatar
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    Here a short tutorial how to install J2RE on a debian (-based) system:

    1) Go to http://java.sun.com and look for java J2RE
    2) Meanwhile get these dependencies with apt-get : fakeroot java-package java-common
    Important: NO! Do NOT (!) use sudo instead of fakeroot! It really ain't the same!
    3) Make a .deb archive of the java package you downloaded:
    fakeroot make-jpkg jre-<thing you downloaded>
    4) Install the package: sudo dpkg -i sun-j2re1.5_1.5.0+update05_i386.deb
    5) Select Sun's java as the default java compiler and bytecode interpreter:
    sudo update-alternatives --config java

    Done this, you should be able to use Taverna Workbench
    Eat your l33t skillz!
    My home page: http://www.inter.nl.net/users/alexeif/

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