[InterMine Dev] git update, which branch?

sergio contrino sergio at modencode.org
Fri Aug 21 11:33:44 BST 2015


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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