* Package:    sci-biology/jalview-2.6.1
 * Repository: science
 * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
 * USE:        elibc_glibc kernel_linux userland_GNU x86
 * FEATURES:   distcc nostrip sandbox splitdebug
 * Using: sun-jdk-1.6
>>> Unpacking source...
>>> Unpacking jalview_2_6_1.tar.gz to /var/tmp/portage/sci-biology/jalview-2.6.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/jalview-2.6.1/work
>>> Preparing source in /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview ...
removed `./utils/castor-1.1-cycle-codegen-anttask.jar'
removed `./utils/castor-1.1-cycle-codegen.jar'
removed `./utils/jhall.jar'
removed `./utils/proguard.jar'
removed `./utils/jhindexer.jar'
removed `./utils/jalopy/lib/jalopy-ant-0.6.2.jar'
removed `./utils/jalopy/lib/jalopy-1.0b11.jar'
removed `./utils/jalopy/lib/oro-2.0.6.jar'
removed `./utils/jalopy/lib/jdom-1.0b8.jar'
removed `./utils/jalopy/lib/aelfred-1.2.jar'
removed `./utils/jalopy/lib/log4j-1.2.6.jar'
removed `./utils/jalopy/lib/sax-2.0.1.jar'
removed `./utils/jalopy/lib/jaxp-1.2.jar'
removed `./utils/wsdl4j.jar'
removed `./lib/activation.jar'
removed `./lib/min-jaba-client.jar'
removed `./lib/jhall.jar'
removed `./lib/mail.jar'
removed `./lib/xercesImpl.jar'
removed `./lib/commons-logging.jar'
removed `./lib/Jmol-12.1.13.jar'
removed `./lib/saaj.jar'
removed `./lib/castor-1.1-cycle-xml.jar'
removed `./lib/log4j-1.2.8.jar'
removed `./lib/commons-discovery.jar'
removed `./lib/wsdl4j.jar'
removed `./lib/JGoogleAnalytics-0.2.1-SNAPSHOT.jar'
removed `./appletlib/JmolApplet-12.1.13.jar'
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview ...
Rewriting attributes
Rewriting ./build.xml
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview ...
 * Disabling all optional ANT_TASKS
Buildfile: /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/build.xml

init:

clean:

distclean:
     [echo] REMOVING ALL BACKUP/AUTOSAVES!

init:

prepare:
    [mkdir] Created dir: /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/classes
     [copy] Copying 168 files to /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/classes

build:
    [javac] Compiling 509 source files to /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/classes
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ext/jmol/JalviewJmolBinding.java:1380: cannot find symbol
    [javac] symbol  : class JmolAppConsoleInterface
    [javac] location: class jalview.ext.jmol.JalviewJmolBinding
    [javac]   protected abstract JmolAppConsoleInterface createJmolConsole(
    [javac]                      ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ext/jmol/JalviewJmolBinding.java:1383: cannot find symbol
    [javac] symbol  : class JmolAppConsoleInterface
    [javac] location: package org.jmol.api
    [javac]   protected org.jmol.api.JmolAppConsoleInterface console = null;
    [javac]                         ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/AppJmol.java:43: package org.openscience.jmol.app.jmolpanel does not exist
    [javac] import org.openscience.jmol.app.jmolpanel.AppConsole;
    [javac]                                          ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/AppJmolBinding.java:33: cannot find symbol
    [javac] symbol  : class JmolAppConsoleInterface
    [javac] location: package org.jmol.api
    [javac] import org.jmol.api.JmolAppConsoleInterface;
    [javac]                    ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/AppJmolBinding.java:36: package org.openscience.jmol.app.jmolpanel does not exist
    [javac] import org.openscience.jmol.app.jmolpanel.AppConsole;
    [javac]                                          ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/AppJmolBinding.java:190: cannot find symbol
    [javac] symbol  : class JmolAppConsoleInterface
    [javac] location: class jalview.gui.AppJmolBinding
    [javac]   protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
    [javac]             ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:86: package compbio.metadata does not exist
    [javac] import compbio.metadata.Argument;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:87: package compbio.metadata does not exist
    [javac] import compbio.metadata.Option;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:88: package compbio.metadata does not exist
    [javac] import compbio.metadata.Parameter;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:89: package compbio.metadata does not exist
    [javac] import compbio.metadata.Preset;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:90: package compbio.metadata does not exist
    [javac] import compbio.metadata.PresetManager;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:91: package compbio.metadata does not exist
    [javac] import compbio.metadata.RunnerConfig;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:92: package compbio.metadata does not exist
    [javac] import compbio.metadata.ValueConstrain;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:93: package compbio.metadata does not exist
    [javac] import compbio.metadata.WrongParameterException;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:94: package compbio.metadata.ValueConstrain does not exist
    [javac] import compbio.metadata.ValueConstrain.Type;
    [javac]                                       ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:49: package compbio.data.msa does not exist
    [javac] import compbio.data.msa.MsaWS;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:50: package compbio.metadata does not exist
    [javac] import compbio.metadata.Option;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:51: package compbio.metadata does not exist
    [javac] import compbio.metadata.Preset;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:52: package compbio.metadata does not exist
    [javac] import compbio.metadata.PresetManager;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:53: package compbio.metadata does not exist
    [javac] import compbio.metadata.RunnerConfig;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:54: package compbio.ws.client does not exist
    [javac] import compbio.ws.client.Jws2Client;
    [javac]                         ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:55: package compbio.ws.client does not exist
    [javac] import compbio.ws.client.Services;
    [javac]                         ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:178: cannot find symbol
    [javac] symbol  : class RunnerConfig
    [javac] location: class jalview.gui.WsJobParameters
    [javac]   RunnerConfig serviceOptions;
    [javac]   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:200: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.gui.WsJobParameters
    [javac]           WsParamSetI preset, List<Argument> jobArgset)
    [javac]                                    ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:214: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.gui.WsJobParameters
    [javac]           Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
    [javac]                                                          ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/gui/WsJobParameters.java:512: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.gui.WsJobParameters
    [javac]           List<Argument> jabajobArgset)
    [javac]                ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/params/ParameterI.java:22: package compbio.metadata does not exist
    [javac] import compbio.metadata.ValueConstrain;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:210: cannot find symbol
    [javac] symbol  : class Services
    [javac] location: class jalview.ws.jws2.Jws2Discoverer
    [javac]   synchronized void addService(String jwsservers, Services srv,
    [javac]                                                   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:211: cannot find symbol
    [javac] symbol  : class MsaWS
    [javac] location: class jalview.ws.jws2.Jws2Discoverer
    [javac]           MsaWS service2)
    [javac]           ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:234: cannot find symbol
    [javac] symbol  : class MsaWS
    [javac] location: class jalview.ws.jws2.Jws2Discoverer.Jws2Instance
    [javac]     public MsaWS service;
    [javac]            ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:236: cannot find symbol
    [javac] symbol  : class MsaWS
    [javac] location: class jalview.ws.jws2.Jws2Discoverer.Jws2Instance
    [javac]     public Jws2Instance(String hosturl, String serviceType, MsaWS service)
    [javac]                                                             ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:244: cannot find symbol
    [javac] symbol  : class PresetManager
    [javac] location: class jalview.ws.jws2.Jws2Discoverer.Jws2Instance
    [javac]     PresetManager presets = null;
    [javac]     ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaParamStore.java:29: package compbio.metadata does not exist
    [javac] import compbio.metadata.Argument;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaParamStore.java:30: package compbio.metadata does not exist
    [javac] import compbio.metadata.Option;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaParamStore.java:31: package compbio.metadata does not exist
    [javac] import compbio.metadata.Parameter;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaParamStore.java:32: package compbio.metadata does not exist
    [javac] import compbio.metadata.Preset;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaParamStore.java:33: package compbio.metadata does not exist
    [javac] import compbio.metadata.PresetManager;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaParamStore.java:34: package compbio.metadata does not exist
    [javac] import compbio.metadata.RunnerConfig;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:254: cannot find symbol
    [javac] symbol  : class PresetManager
    [javac] location: class jalview.ws.jws2.Jws2Discoverer.Jws2Instance
    [javac]     public PresetManager getPresets()
    [javac]            ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/Jws2Discoverer.java:297: cannot find symbol
    [javac] symbol  : class RunnerConfig
    [javac] location: class jalview.ws.jws2.Jws2Discoverer.Jws2Instance
    [javac]     public RunnerConfig getRunnerConfig()
    [javac]            ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/params/ValueConstrainI.java:20: package compbio.metadata.ValueConstrain does not exist
    [javac] import compbio.metadata.ValueConstrain.Type;
    [javac]                                       ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaWsParamSet.java:27: package compbio.metadata does not exist
    [javac] import compbio.metadata.Argument;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaWsParamSet.java:28: package compbio.metadata does not exist
    [javac] import compbio.metadata.Option;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaParamStore.java:52: cannot find symbol
    [javac] symbol  : class RunnerConfig
    [javac] location: class jalview.ws.jws2.JabaParamStore
    [javac]   private RunnerConfig serviceOptions;
    [javac]           ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaPreset.java:26: package compbio.metadata does not exist
    [javac] import compbio.metadata.Preset;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/params/ValueConstrainI.java:30: cannot find symbol
    [javac] symbol  : class Type
    [javac] location: interface jalview.ws.params.ValueConstrainI
    [javac]   Type getType();
    [javac]   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaWsParamSet.java:41: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.dm.JabaWsParamSet
    [javac]   List<Option> jabaArguments;
    [javac]        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaWsParamSet.java:194: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.dm.JabaWsParamSet
    [javac]   public List<Option> getjabaArguments()
    [javac]               ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaWsParamSet.java:199: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.dm.JabaWsParamSet
    [javac]   public void setjabaArguments(List<Option> args)
    [javac]                                     ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaPreset.java:30: cannot find symbol
    [javac] symbol  : class Preset
    [javac] location: class jalview.ws.jws2.JabaPreset
    [javac]   Preset p = null;
    [javac]   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaPreset.java:34: cannot find symbol
    [javac] symbol  : class Preset
    [javac] location: class jalview.ws.jws2.JabaPreset
    [javac]   public JabaPreset(Jws2Instance svc, Preset preset)
    [javac]                                       ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JWs2Job.java:20: package compbio.metadata does not exist
    [javac] import compbio.metadata.JobStatus;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JWs2Job.java:32: cannot find symbol
    [javac] symbol  : class JobStatus
    [javac] location: class jalview.ws.jws2.JWs2Job
    [javac]   JobStatus status = null;
    [javac]   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JWs2Job.java:34: cannot find symbol
    [javac] symbol  : class JobStatus
    [javac] location: class jalview.ws.jws2.JWs2Job
    [javac]   public void setjobStatus(JobStatus jobStatus)
    [javac]                            ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaWsServerQuery.java:22: package compbio.data.msa does not exist
    [javac] import compbio.data.msa.MsaWS;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaWsServerQuery.java:23: package compbio.ws.client does not exist
    [javac] import compbio.ws.client.Jws2Client;
    [javac]                         ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/JabaWsServerQuery.java:24: package compbio.ws.client does not exist
    [javac] import compbio.ws.client.Services;
    [javac]                         ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:29: package compbio.data.msa does not exist
    [javac] import compbio.data.msa.MsaWS;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:30: package compbio.metadata does not exist
    [javac] import compbio.metadata.Argument;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:31: package compbio.metadata does not exist
    [javac] import compbio.metadata.Option;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:32: package compbio.metadata does not exist
    [javac] import compbio.metadata.Preset;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:33: package compbio.metadata does not exist
    [javac] import compbio.metadata.PresetManager;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:49: cannot find symbol
    [javac] symbol  : class MsaWS
    [javac] location: class jalview.ws.jws2.MsaWSClient
    [javac]   MsaWS server;
    [javac]   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:55: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.ws.jws2.MsaWSClient
    [javac]   private List<Argument> paramset;
    [javac]                ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSClient.java:94: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.ws.jws2.MsaWSClient
    [javac]           List<Argument> arguments, boolean editParams, String altitle,
    [javac]                ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:22: package compbio.data.msa does not exist
    [javac] import compbio.data.msa.MsaWS;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:23: package compbio.data.sequence does not exist
    [javac] import compbio.data.sequence.AlignmentMetadata;
    [javac]                             ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:24: package compbio.data.sequence does not exist
    [javac] import compbio.data.sequence.Program;
    [javac]                             ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:25: package compbio.metadata does not exist
    [javac] import compbio.metadata.Argument;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:26: package compbio.metadata does not exist
    [javac] import compbio.metadata.ChunkHolder;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:27: package compbio.metadata does not exist
    [javac] import compbio.metadata.JobStatus;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:28: package compbio.metadata does not exist
    [javac] import compbio.metadata.Preset;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:448: cannot find symbol
    [javac] symbol  : class MsaWS
    [javac] location: class jalview.ws.jws2.MsaWSThread
    [javac]   MsaWS server = null;
    [javac]   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:458: cannot find symbol
    [javac] symbol  : class MsaWS
    [javac] location: class jalview.ws.jws2.MsaWSThread
    [javac]   MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
    [javac]               ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:482: cannot find symbol
    [javac] symbol  : class MsaWS
    [javac] location: class jalview.ws.jws2.MsaWSThread
    [javac]   MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
    [javac]               ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:482: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.ws.jws2.MsaWSThread
    [javac]   MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
    [javac]                                                       ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:76: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.ws.jws2.MsaWSThread.MsaWSJob
    [javac]     List<Argument> arguments = null;
    [javac]          ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:81: package compbio.data.sequence does not exist
    [javac]     ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
    [javac]                                    ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:86: package compbio.data.sequence does not exist
    [javac]     compbio.data.sequence.Alignment alignment;
    [javac]                          ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:384: cannot find symbol
    [javac] symbol  : class Argument
    [javac] location: class jalview.ws.jws2.MsaWSThread.MsaWSJob
    [javac]     public List<Argument> getJabaArguments()
    [javac]                 ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/MsaWSThread.java:435: cannot find symbol
    [javac] symbol  : class Preset
    [javac] location: class jalview.ws.jws2.MsaWSThread.MsaWSJob
    [javac]     public Preset getServerPreset()
    [javac]            ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:27: package compbio.metadata does not exist
    [javac] import compbio.metadata.*;
    [javac] ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:31: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static List<String> writeParameterSet(List<Option> optSet,
    [javac]                                                     ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:59: cannot find symbol
    [javac] symbol  : class RunnerConfig
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]           RunnerConfig options, String pseparator)
    [javac]           ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:58: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static List<Option> processParameters(List<String> params,
    [javac]                      ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:121: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static Option copyOption(Option option)
    [javac]                                   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:121: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static Option copyOption(Option option)
    [javac]                 ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:128: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static void setOptionFrom(Option copy, Option option)
    [javac]                                    ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:128: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static void setOptionFrom(Option copy, Option option)
    [javac]                                                 ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:161: cannot find symbol
    [javac] symbol  : class ValueConstrain
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static ValueConstrain copyValueConstrain(ValueConstrain vc)
    [javac]                                                   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:161: cannot find symbol
    [javac] symbol  : class ValueConstrain
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static ValueConstrain copyValueConstrain(ValueConstrain vc)
    [javac]                 ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:187: cannot find symbol
    [javac] symbol  : class Parameter
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static Parameter copyParameter(Parameter parameter)
    [javac]                                         ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/ParameterUtils.java:187: cannot find symbol
    [javac] symbol  : class Parameter
    [javac] location: class jalview.ws.jws2.ParameterUtils
    [javac]   public static Parameter copyParameter(Parameter parameter)
    [javac]                 ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaOption.java:26: package compbio.metadata does not exist
    [javac] import compbio.metadata.Option;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaOption.java:30: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.dm.JabaOption
    [javac]   public JabaOption(Option rg)
    [javac]                     ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaOption.java:35: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.dm.JabaOption
    [javac]   Option opt;
    [javac]   ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaOption.java:100: cannot find symbol
    [javac] symbol  : class Option
    [javac] location: class jalview.ws.jws2.dm.JabaOption
    [javac]   public Option getOption()
    [javac]          ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaParameter.java:23: package compbio.metadata does not exist
    [javac] import compbio.metadata.Argument;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaParameter.java:24: package compbio.metadata does not exist
    [javac] import compbio.metadata.Parameter;
    [javac]                        ^
    [javac] /var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/src/jalview/ws/jws2/dm/JabaParameter.java:25: package compbio.metadata does not exist
    [javac] import compbio.metadata.ValueConstrain;
    [javac]                        ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 100 errors

BUILD FAILED
/var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview/build.xml:141: Compile failed; see the compiler error output for details.

Total time: 18 seconds
 * ERROR: sci-biology/jalview-2.6.1 failed:
 *   eant failed
 * 
 * Call stack:
 *     ebuild.sh, line   56:  Called src_compile
 *   environment, line 4444:  Called java-pkg-2_src_compile
 *   environment, line 2441:  Called eant 'distclean' 'makedist' '-f' 'build.xml'
 *   environment, line  959:  Called die
 * The specific snippet of code:
 *       ant ${antflags} "${@}" || die "eant failed"
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/jalview-2.6.1',
 * the complete build log and the output of 'emerge -pqv =sci-biology/jalview-2.6.1'.
 * This ebuild is from an overlay named 'science': '/home/mmokrejs/proj/sci/'
!!! When you file a bug report, please include the following information:
GENTOO_VM=sun-jdk-1.6  CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.23"
JAVACFLAGS="-source 1.5 -target 1.5" COMPILER="javac"
and of course, the output of emerge --info
 * The complete build log is located at '/var/tmp/portage/sci-biology/jalview-2.6.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/jalview-2.6.1/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/jalview-2.6.1/work/jalview'