[InterMine Dev] dbmodel/intermine.log

Julie Sullivan julie at flymine.org
Mon Oct 24 08:28:00 BST 2011


You can safely ignore those warnings.

Your InterMine should work correctly without bioseg, although I think the region 
search depends on it.

Here are the installation instructions:

http://intermine.org/wiki/BiosegInstallation

On 24/10/11 00:42, Quang Trinh wrote:
> 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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