[InterMine Dev] dbmodel/intermine.log

Quang Trinh quang.trinh at gmail.com
Mon Oct 24 00:42:07 BST 2011


Hi,
  After running "ant clean build-db" in malariamine/dbmodel, I see a
log file called 'intermine.log'.  When looking at its contents, I see
lots of warnings like the following:

2011-10-23 19:25:33 INFO   org.intermine.bio.ontology.OboParser     -
default-namespace is "sequence"
2011-10-23 19:25:33 WARN   org.intermine.bio.ontology.OboParser     -
Failed to parse def of term SO:0000004 def: null
2011-10-23 19:25:33 WARN   org.intermine.bio.ontology.OboParser     -
Failed to parse def of term SO:0000010 def: null

  I also see this error message in intermine.log:

2011-10-23 19:26:11 WARN
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl     -
Database os.production doesn't have bioseg
org.postgresql.util.PSQLException: ERROR: function
bioseg_create(integer, integer) does not exist
  Hint: No function matches the given name and argument types. You
might need to add explicit type casts.
  Position: 8
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2079)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1812)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:366)
        at sun.reflect.GeneratedMethodAccessor28.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.postgresql.ds.jdbc23.AbstractJdbc23PooledConnection$StatementHandler.invoke(AbstractJdbc23PooledConnectio
        at $Proxy3.execute(Unknown Source)
        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.getInstance(ObjectStoreInterMineImpl.java:406)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.intermine.objectstore.ObjectStoreFactory.getObjectStore(ObjectStoreFactory.java:61)
        at org.intermine.task.CreateIndexesTask.setUp(CreateIndexesTask.java:138)
        at org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:161)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
        at sun.reflect.GeneratedMethodAccessor2.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:105)
        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(DefaultExecutor.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)

   Do I need to install bioseg or  can I just ignore these for now?

Thanks,

Q



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