Re: dev Digest, Vol 20, Issue 2

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Re: dev Digest, Vol 20, Issue 2

kkarra@stanford.edu

Adding  cglib-full-2.0.1-patched.jar (/intermine/objectstore/main/lib/) explicitly to the CLASSPATH solved the NoSuchMethodError issue..

> /data/tools/intermine/dev/intermine_0_94_1/imbuild/source.xml:330: java.lang.NoSuchMethodError: org.objectweb.asm.ClassVisitor.visit(ILjava/lang/String;Ljava/lang/String;[Ljava/lang/String;Ljava/lang/String;)V




On Jan 5, 2011, at 4:00 AM, [hidden email] wrote:

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> Today's Topics:
>
>   1. asm cglib error on linux RHEL 5.5 (Kalpana Karra)
>   2. intermine.log files missing (Kalpana Karra)
>   3. Re: intermine.log files missing (Richard Smith)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 Jan 2011 12:30:30 -0800
> From: Kalpana Karra <[hidden email]>
> Subject: [InterMine Dev] asm cglib error on linux RHEL 5.5
> To: Intermine <[hidden email]>
> Cc: Stuart Miyasato <[hidden email]>, Benjamin Hitz
> <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
>
> I am running into this error when I try to integrate go-slim as a source on our new linux build machine  (sgd and go sources build successfully).
>
> Wondering if anyone else has experienced this issue.
>
> Thanks,
> -Kalpana
>
>
> BUILD FAILED
> /data/tools/intermine/dev/intermine_0_94_1/imbuild/integrate.xml:54: The following error occurred while executing this line:
> /data/tools/intermine/dev/intermine_0_94_1/imbuild/source.xml:330: java.lang.NoSuchMethodError: org.objectweb.asm.ClassVisitor.visit(ILjava/lang/String;Ljava/lang/String;[Ljava/lang/String;Ljava/lang/String;)V
> at net.sf.cglib.core.ClassEmitter.begin_class(ClassEmitter.java:101)
> at net.sf.cglib.core.KeyFactory$Generator.generateClass(KeyFactory.java:205)
> at net.sf.cglib.core.DefaultGeneratorStrategy.generate(DefaultGeneratorStrategy.java:63)
> at net.sf.cglib.core.AbstractClassGenerator.create(AbstractClassGenerator.java:192)
> at net.sf.cglib.core.KeyFactory$Generator.create(KeyFactory.java:177)
> at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:149)
> at net.sf.cglib.proxy.Enhancer.<clinit>(Enhancer.java:103)
> at org.intermine.util.DynamicBean.create(DynamicBean.java:62)
> at org.intermine.util.DynamicUtil.createObject(DynamicUtil.java:113)
> at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:283)
> at org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
> at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:146)
> at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)
> at org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.java:128)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:390)
> at org.apache.tools.ant.Target.performTasks(Target.java:411)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
> at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
> at org.intermine.task.Integrate.performAction(Integrate.java:136)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:390)
> at org.apache.tools.ant.Target.performTasks(Target.java:411)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
> at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
> at org.apache.tools.ant.Main.runBuild(Main.java:801)
> at org.apache.tools.ant.Main.startAnt(Main.java:218)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 4 Jan 2011 12:50:29 -0800
> From: Kalpana Karra <[hidden email]>
> Subject: [InterMine Dev] intermine.log files missing
> To: Intermine <[hidden email]>
> Cc: Stuart Miyasato <[hidden email]>, Benjamin Hitz
> <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
>
> Again, on our new linux build machines, when I run build-db or any other ant task in any one of the 4 directories, I don't see _intermine.log_ file being generated. No error either.
>
> -Kalpana
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 05 Jan 2011 09:35:52 +0000
> From: Richard Smith <[hidden email]>
> Subject: Re: [InterMine Dev] intermine.log files missing
> To: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Kalpana,
> This may be that there is log4j.properties found on the classpath before
> the InterMine log4j.properties files.  Can you check what your classpath
> is on the new machines and see if it points to other directories?  This
> should be $CLASSPATH.
>
> The asm cglib error may be caused by the same thing.  Sierra had a
> similar problem running on a machine with Hibernate and Spring installed
> but I can't find what the eventual fix was.  Looking for any other
> asm.jar files or cglib jars would be a start.
>
> You could also run ant clean-all in the intermine directories before
> running a normal command to see if that helps.
>
> Cheers,
> Richard.
>
>
>
>
> On 04/01/2011 20:50, Kalpana Karra wrote:
>> Hi,
>>
>> Again, on our new linux build machines, when I run build-db or any other ant task in any one of the 4 directories, I don't see _intermine.log_ file being generated. No error either.
>>
>> -Kalpana
>>
>>
>> _______________________________________________
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>
>
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>
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> End of dev Digest, Vol 20, Issue 2
> **********************************


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