[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Fri Aug 21 14:54:11 BST 2015


Hi Sergio,

Yes, that is the step I am on.

Sofia

On Fri, Aug 21, 2015 at 4:33 AM, sergio contrino <sergio at modencode.org>
wrote:

> hi sofia,
> are you running the 'Build complete MalariaMine' step from the tutorial?
> thanks
> sergio
>
>
> On 20/08/15 17:48, Sofia Robb wrote:
>
>> Sergio and Vivek,
>>
>> I followed the documentation and changed the encoding. The create db
>> errors while running project_build are gone but I still have my
>> objectStore errors. Any ideas?
>>
>> Thanks,
>> Sofia
>>
>> ​BUILD FAILED
>> /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
>> following error occurred while executing this line:
>> /var/lib/pgsql/other_data/intermine/imbuild/source.xml:330:
>> java.lang.reflect.InvocationTargetException
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>>
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>> at
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:606)
>> at
>>
>> org.intermine.objectstore.ObjectStoreFactory.getObjectStore(ObjectStoreFactory.java:61)
>> at
>>
>> org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.java:128)
>> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> at
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:606)
>> 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:435)
>> at org.apache.tools.ant.Target.performTasks(Target.java:456)
>> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>> at
>>
>> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>> at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
>> 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:292)
>> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> at
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:606)
>> 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:435)
>> at org.apache.tools.ant.Target.performTasks(Target.java:456)
>> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>> at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
>> at
>>
>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>> at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>> at org.apache.tools.ant.Main.runBuild(Main.java:851)
>> at org.apache.tools.ant.Main.startAnt(Main.java:235)
>> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>> Caused by: java.lang.IllegalArgumentException: ObjectStore
>> 'os.common-translated-std' not found in properties
>> at
>>
>> org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.getInstance(ObjectStoreFastCollectionsForTranslatorImpl.java:97)
>> ... 37 more
>> Caused by: java.lang.reflect.InvocationTargetException
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>>
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>> at
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:606)
>> at
>>
>> org.intermine.objectstore.ObjectStoreFactory.getObjectStore(ObjectStoreFactory.java:61)
>> at
>>
>> org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.getInstance(ObjectStoreFastCollectionsForTranslatorImpl.java:90)
>> ... 37 more
>> Caused by: java.lang.IllegalArgumentException: Unable to get
>> sub-ObjectStore for Translating ObjectStore (check properties file)
>> at
>>
>> org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.getInstance(ObjectStoreTranslatingImpl.java:87)
>> ... 43 more
>>
>> Total time: 1 minute 28 seconds
>> Thu Aug 20 11:43:42 CDT 2015
>>
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org
>
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