[InterMine Dev] Snp fails due to name change

Vallejos, Andrew avallejos at mcw.edu
Thu Aug 6 16:31:01 BST 2009


I tried changing the same from EnsemblSNP to Snp and now building the
database fails with the following error.  I have looked everywhere I can
think of, and I cannot figure out where this is failing.

 

-Andrew

 

BUILD FAILED

/usr/local/intermine/dev/imbuild/objectstore.xml:51: The following error
occurred while executing this line:

/usr/local/intermine/dev/imbuild/task.xml:188:
java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong name:
org/intermine/model/bio/Snp)

            at
org.apache.tools.ant.ProjectHelper.addLocationToBuildException(ProjectHe
lper.java:541)

            at
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
94)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at org.apache.tools.ant.Target.execute(Target.java:357)

            at org.apache.tools.ant.Target.performTasks(Target.java:385)

            at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)

            at
org.apache.tools.ant.Project.executeTarget(Project.java:1298)

            at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)

            at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)

            at org.apache.tools.ant.Main.runBuild(Main.java:698)

            at org.apache.tools.ant.Main.startAnt(Main.java:199)

            at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)

            at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

Caused by: /usr/local/intermine/dev/imbuild/task.xml:188:
java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong name:
org/intermine/model/bio/Snp)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
15)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at
org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:62)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
91)

            ... 16 more

Caused by: java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP
(wrong name: org/intermine/model/bio/Snp)

            at java.lang.ClassLoader.defineClass1(Native Method)

            at java.lang.ClassLoader.defineClass(ClassLoader.java:675)

            at
org.apache.tools.ant.AntClassLoader.defineClassFromData(AntClassLoader.j
ava:1130)

            at
org.apache.tools.ant.AntClassLoader.getClassFromStream(AntClassLoader.ja
va:1307)

            at
org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader
.java:1371)

            at
org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1324)

            at
org.apache.tools.ant.AntClassLoader.loadClass(AntClassLoader.java:1072)

            at java.lang.ClassLoader.loadClass(ClassLoader.java:251)

            at
java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)

            at java.lang.Class.forName0(Native Method)

            at java.lang.Class.forName(Class.java:164)

            at
org.intermine.metadata.ClassDescriptor.getType(ClassDescriptor.java:145)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
elOutput.java:196)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
elOutput.java:121)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.process(TorqueMode
lOutput.java:82)

            at
org.intermine.objectstore.intermine.TorqueModelOutputTask.execute(Torque
ModelOutputTask.java:122)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            ... 25 more

--- Nested Exception ---

/usr/local/intermine/dev/imbuild/task.xml:188:
java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong name:
org/intermine/model/bio/Snp)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
15)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at
org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:62)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
91)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at org.apache.tools.ant.Target.execute(Target.java:357)

            at org.apache.tools.ant.Target.performTasks(Target.java:385)

            at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)

            at
org.apache.tools.ant.Project.executeTarget(Project.java:1298)

            at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)

            at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)

            at org.apache.tools.ant.Main.runBuild(Main.java:698)

            at org.apache.tools.ant.Main.startAnt(Main.java:199)

            at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)

            at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

Caused by: java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP
(wrong name: org/intermine/model/bio/Snp)

            at java.lang.ClassLoader.defineClass1(Native Method)

            at java.lang.ClassLoader.defineClass(ClassLoader.java:675)

            at
org.apache.tools.ant.AntClassLoader.defineClassFromData(AntClassLoader.j
ava:1130)

            at
org.apache.tools.ant.AntClassLoader.getClassFromStream(AntClassLoader.ja
va:1307)

            at
org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader
.java:1371)

            at
org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1324)

            at
org.apache.tools.ant.AntClassLoader.loadClass(AntClassLoader.java:1072)

            at java.lang.ClassLoader.loadClass(ClassLoader.java:251)

            at
java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)

            at java.lang.Class.forName0(Native Method)

            at java.lang.Class.forName(Class.java:164)

            at
org.intermine.metadata.ClassDescriptor.getType(ClassDescriptor.java:145)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
elOutput.java:196)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
elOutput.java:121)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.process(TorqueMode
lOutput.java:82)

            at
org.intermine.objectstore.intermine.TorqueModelOutputTask.execute(Torque
ModelOutputTask.java:122)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            ... 25 more

--- Nested Exception ---

java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong name:
org/intermine/model/bio/Snp)

            at java.lang.ClassLoader.defineClass1(Native Method)

            at java.lang.ClassLoader.defineClass(ClassLoader.java:675)

            at
org.apache.tools.ant.AntClassLoader.defineClassFromData(AntClassLoader.j
ava:1130)

            at
org.apache.tools.ant.AntClassLoader.getClassFromStream(AntClassLoader.ja
va:1307)

            at
org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader
.java:1371)

            at
org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1324)

            at
org.apache.tools.ant.AntClassLoader.loadClass(AntClassLoader.java:1072)

            at java.lang.ClassLoader.loadClass(ClassLoader.java:251)

            at
java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)

            at java.lang.Class.forName0(Native Method)

            at java.lang.Class.forName(Class.java:164)

            at
org.intermine.metadata.ClassDescriptor.getType(ClassDescriptor.java:145)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
elOutput.java:196)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
elOutput.java:121)

            at
org.intermine.objectstore.intermine.TorqueModelOutput.process(TorqueMode
lOutput.java:82)

            at
org.intermine.objectstore.intermine.TorqueModelOutputTask.execute(Torque
ModelOutputTask.java:122)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at
org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:62)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
91)

            at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

            at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
Source)

            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)

            at java.lang.reflect.Method.invoke(Method.java:585)

            at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)

            at org.apache.tools.ant.Task.perform(Task.java:348)

            at org.apache.tools.ant.Target.execute(Target.java:357)

            at org.apache.tools.ant.Target.performTasks(Target.java:385)

            at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)

            at
org.apache.tools.ant.Project.executeTarget(Project.java:1298)

            at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)

            at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)

            at org.apache.tools.ant.Main.runBuild(Main.java:698)

            at org.apache.tools.ant.Main.startAnt(Main.java:199)

            at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)

            at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

 

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

avallejos at mcw.edu

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.intermine.org/pipermail/dev/attachments/20090806/3759eaf8/attachment-0001.htm>


More information about the dev mailing list