[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Wed Aug 19 17:47:02 BST 2015


I ran this command '../bio/scripts/project_build -b -v localhost
~/malariamine-dump' and I get the following error:



action update-publications took 284 seconds

Wed Aug 19 11:13:45 CDT 2015

starting command: ant -v -Dsource=entrez-organism


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 19 seconds
Wed Aug 19 11:15:05 CDT 2015

finished


ERROR: 256
failed with exit code 0: ant -v -Dsource=entrez-organism

check log: pbuild.log

On Wed, Aug 19, 2015 at 9:54 AM, Sofia Robb <sofia at sofiarobb.com> wrote:

> Yes, i will increase the number of connections allowed to my db, but I
> will wait for my tripal load to finish.
>
> Thanks for the info about action vs source. There is so much to learn :)
>
> Performing them separately resulted in all of the postprocesses in the
> malariamine tutorial to be successful
>
> <post-process name="create-references"/>
> <post-process name="transfer-sequences" dump="true"/>
> <post-process name="do-sources"/>
> <post-process name="summarise-objectstore"/>
> <post-process name="create-autocomplete-index"/>
> <post-process name="create-search-index"/>
>
> I will work on my webapp now.
>
> Thank you for your continued support :)
> Sofia
>
> On Wed, Aug 19, 2015 at 9:31 AM, sergio contrino <sergio at modencode.org>
> wrote:
>
>> hi sofia,
>> the bit
>>
>> Caused by: org.postgresql.util.PSQLException: FATAL: remaining connection
>> slots are reserved for non-replication superuser connections
>>
>> means that you have exhausted the db connection (at the time of running
>> the build).
>>
>> you can check how many connection are open (you can just do something
>> like ps awx| grep post | grep -c . )
>>
>> you can increase the number of connection of a db, but maybe you need to
>> wait for the other program to finish?
>>
>> but your command
>>
>> ant -v -Dsource=create-references
>>
>> should be
>>
>> ant -v -Daction=create-references
>>
>> thanks
>> sergio
>>
>>
>> On 19/08/15 16:18, Sofia Robb wrote:
>>
>>> I can connect from the command line with the user in my properties file.
>>> Did I run my ant command incorrectly?
>>>
>>> ant -v -Dsource=create-references
>>>
>>> postprocess:
>>> [postprocess] Found 6 post-processes
>>> [postprocess]  executing post process: create-references
>>> [postprocess] Performing postprocess: create-references
>>> [Finalizer] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>>> db.production is being shutdown.
>>> [postprocess]  executing post process: transfer-sequences
>>> [postprocess] Performing postprocess: transfer-sequences
>>> [postprocess]  executing post process: do-sources
>>> [postprocess] no postprocess for source: uniprot-malaria, in dir:
>>> /var/lib/pgsql/other_data/intermine/bio/sources/uniprot
>>> [postprocess] no postprocess for source: malaria-gff, in dir:
>>>
>>> /var/lib/pgsql/other_data/intermine/bio/sources/example-sources/malaria-gff
>>> [postprocess] no postprocess for source: malaria-chromosome-fasta, in
>>> dir: /var/lib/pgsql/other_data/intermine/bio/sources/fasta
>>> [postprocess] no postprocess for source: interpro, in dir:
>>> /var/lib/pgsql/other_data/intermine/bio/sources/interpro
>>> [postprocess] no postprocess for source: go, in dir:
>>> /var/lib/pgsql/other_data/intermine/bio/sources/go
>>> [postprocess] Performing postprocess on source: go-annotation, in dir:
>>> /var/lib/pgsql/other_data/intermine/bio/sources/go-annotation
>>>
>>>
>>> Also, this is in my error "Build Failed"
>>> Caused by: org.postgresql.util.PSQLException: FATAL: remaining
>>> connection slots are reserved for non-replication superuser connections
>>> Doesn't sound good. Oh, I am loading data into chado for my tripal
>>> install, maybe it has something to do with that? why does it say that no
>>> postprocess for my sources can be found?
>>>
>>> Thanks,
>>> Sofia
>>>
>>> On Wed, Aug 19, 2015 at 9:00 AM, sergio contrino <sergio at modencode.org
>>> <mailto:sergio at modencode.org>> wrote:
>>>
>>>     hi sofia,
>>>     it seems that the connection to the database is not happening.
>>>     can you try to connect via command line? maybe you need a postgres
>>>     restart?
>>>     thanks
>>>     sergio
>>>
>>>     On 19/08/15 15:53, Sofia Robb wrote:
>>>
>>>         Hi Sergio,
>>>
>>>         I ran the first post-process 'ant -v  -Dsource=create-references'
>>>
>>>         Here is what I get.
>>>
>>>         -Sofia
>>>
>>>         ----------------
>>>
>>>         -pre-generate-retrieve:
>>>                [echo] Retrieving model from os.production...
>>>         [postprocess] Failed to retrieve metadata from db.production
>>>         (malariamine) - maybe you need to run build-db?
>>>                [null] Exiting
>>>
>>> /var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build.xml.
>>>                [null] Exiting
>>>
>>> /var/lib/pgsql/other_data/intermine/bio/sources/go-annotation/build.xml.
>>>
>>>         BUILD FAILED
>>>         /var/lib/pgsql/other_data/intermine/imbuild/postprocess.xml:31:
>>> The
>>>         following error occurred while executing this line:
>>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The
>>>         following error occurred while executing this line:
>>>         /var/lib/pgsql/other_data/intermine/imbuild/objectstore.xml:98:
>>>         java.sql.SQLException: Timeout of 30000ms encountered waiting for
>>>         connection.
>>>         at
>>>
>>> com.zaxxer.hikari.pool.HikariPool.getConnection(HikariPool.java:184)
>>>         at
>>>
>>> com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:84)
>>>         at org.intermine.sql.Database.getConnection(Database.java:163)
>>>         at
>>>
>>> org.intermine.modelproduction.MetadataManager.retrieve(MetadataManager.java:233)
>>>         at
>>>
>>> org.intermine.task.RetrieveMetadataTask.execute(RetrieveMetadataTask.java:97)
>>>         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.Dependencies.execute(Dependencies.java:304)
>>>         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.PostProcessTask.doSourcePostProcess(PostProcessTask.java:200)
>>>         at
>>>
>>> org.intermine.task.PostProcessTask.doAllSourcePostProcessing(PostProcessTask.java:155)
>>>         at
>>>
>>> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:110)
>>>         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: org.postgresql.util.PSQLException: FATAL: remaining
>>>         connection slots are reserved for non-replication superuser
>>>         connections
>>>         at
>>>
>>> org.postgresql.core.v3.ConnectionFactoryImpl.readStartupMessages(ConnectionFactoryImpl.java:574)
>>>         at
>>>
>>> org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:177)
>>>         at
>>>
>>> org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:64)
>>>         at
>>>
>>> org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:138)
>>>         at
>>>
>>> org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:29)
>>>         at
>>>
>>> org.postgresql.jdbc3g.AbstractJdbc3gConnection.<init>(AbstractJdbc3gConnection.java:21)
>>>         at
>>>
>>> org.postgresql.jdbc4.AbstractJdbc4Connection.<init>(AbstractJdbc4Connection.java:31)
>>>         at
>>>
>>> org.postgresql.jdbc4.Jdbc4Connection.<init>(Jdbc4Connection.java:24)
>>>         at org.postgresql.Driver.makeConnection(Driver.java:410)
>>>         at org.postgresql.Driver.connect(Driver.java:280)
>>>         at java.sql.DriverManager.getConnection(DriverManager.java:571)
>>>         at java.sql.DriverManager.getConnection(DriverManager.java:215)
>>>         at
>>>
>>> org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:99)
>>>         at
>>>
>>> org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:82)
>>>         at
>>>
>>> com.zaxxer.hikari.pool.HikariPool.addConnection(HikariPool.java:383)
>>>         at
>>> com.zaxxer.hikari.pool.HikariPool.access$300(HikariPool.java:54)
>>>         at
>>>
>>> com.zaxxer.hikari.pool.HikariPool$1AddConnection.run(HikariPool.java:295)
>>>         at
>>>
>>> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>>>         at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>>>         at
>>>
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>>         at
>>>
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>         at java.lang.Thread.run(Thread.java:745)
>>>
>>>         Total time: 1 minute 36 seconds
>>>         [Thread-3] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>>>         db.production is being shutdown.
>>>         [Thread-13] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP
>>> pool
>>>         db.production is being shutdown.
>>>         [Thread-9] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>>>         db.production is being shutdown.
>>>
>>>         On Wed, Aug 19, 2015 at 7:41 AM, sergio contrino
>>>         <sergio at modencode.org <mailto:sergio at modencode.org>
>>>         <mailto:sergio at modencode.org <mailto:sergio at modencode.org>>>
>>> wrote:
>>>
>>>              dear sofia,
>>>              could you try to run the post processes one by one and let
>>>         us know
>>>              which one fails? and can you try to release your webapp
>>> even if
>>>              you've got a failed post process?
>>>              thanks
>>>              sergio
>>>
>>>
>>>              On 18/08/15 20:32, Sofia Robb wrote:
>>>
>>>                  Hi Sergio,
>>>
>>>                  Ok, the clean checkout worked!  I have gotten through
>>>         much of the
>>>                  tutorial, but now have another error in post
>>>         processing: It said no
>>>                  source was set to try ant -Dsource=all. I tried this
>>>         and got the
>>>                  next error
>>>
>>>                  Thanks,
>>>                  Sofia
>>>
>>>                  Postprocessing 1st error:
>>>
>>>                  BUILD FAILED
>>>
>>>         /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: no
>>>                  source
>>>                  set, try "ant -Dsource=all" or "ant
>>>         -Dsource=source1,source2"
>>>                  at
>>> org.intermine.task.Integrate.execute(Integrate.java:86)
>>>                  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)
>>>
>>>                  Total time: 14 seconds
>>>                  [Thread-1] INFO com.zaxxer.hikari.pool.HikariPool -
>>>         HikariCP pool
>>>                  db.production is being shutdown.
>>>
>>>
>>>                  Postprocessing 2nd error after ant -v -Dsource=all:
>>>
>>>                  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.RuntimeException: Exception while dataloading
>>>         - to allow
>>>                  multiple errors, set the property
>>>                  "dataLoader.allowMultipleErrors" to true
>>>                  Problem while loading item identifier 1_1 because
>>>                  There is already an equivalent in the database from
>>>         this source
>>>                  (<Source: name="uniprot-malaria", type="uniprot",
>>>                  skeleton=false>) from
>>>                  a *previous* run; object from source in this run:
>>>         "DataSource
>>>                  [description=null, id=4, name="UniProt", url=null]",
>>>         object from
>>>                  database: "DataSource [description=null, id=1000001,
>>>         name="UniProt",
>>>                  url=null]"; noticed problem while merging field "name"
>>>                  originally read
>>>                  from source: <Source: name="uniprot-malaria",
>>>         type="uniprot",
>>>                  skeleton=false>
>>>                  at
>>>
>>>
>>> org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:165)
>>>                  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: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: There is
>>>         already an
>>>                  equivalent in the database from this source (<Source:
>>>                  name="uniprot-malaria", type="uniprot",
>>>         skeleton=false>) from a
>>>                  *previous* run; object from source in this run:
>>> "DataSource
>>>                  [description=null, id=4, name="UniProt", url=null]",
>>>         object from
>>>                  database: "DataSource [description=null, id=1000001,
>>>         name="UniProt",
>>>                  url=null]"; noticed problem while merging field "name"
>>>                  originally read
>>>                  from source: <Source: name="uniprot-malaria",
>>>         type="uniprot",
>>>                  skeleton=false>
>>>                  at
>>>
>>>
>>> org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:372)
>>>                  at
>>>
>>>
>>> org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
>>>                  at
>>>
>>>
>>> org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:147)
>>>                  ... 33 more
>>>
>>>                  Total time: 1 minute 20 seconds
>>>                  [Thread-7] INFO com.zaxxer.hikari.pool.HikariPool -
>>>         HikariCP pool
>>>                  db.common-tgt-items is being shutdown.
>>>                  [Thread-18] INFO com.zaxxer.hikari.pool.HikariPool -
>>>         HikariCP pool
>>>                  db.common-tgt-items is being shutdown.
>>>                  [Thread-18] INFO com.zaxxer.hikari.pool.HikariPool -
>>>         HikariCP pool
>>>                  db.production is being shutdown.
>>>
>>>
>>>                  On Tue, Aug 18, 2015 at 10:33 AM, sergio contrino
>>>                  <sergio at modencode.org <mailto:sergio at modencode.org>
>>>         <mailto:sergio at modencode.org <mailto:sergio at modencode.org>>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>> wrote:
>>>
>>>                       hi sofia,
>>>                       could you try a fresh checkout?
>>>                       where are you running your build from? i would
>>>         suggest some
>>>                       directory like ~/git/intermine/..
>>>                       thanks
>>>                       sergio
>>>
>>>
>>>
>>>                       On 18/08/15 16:55, Sofia Robb wrote:
>>>
>>>                           Hi Sergio,
>>>
>>>                           I tried the clean and the rm the build dir. I
>>>         get this
>>>                  error:
>>>
>>>                           Sofia
>>>
>>>                           BUILD FAILED
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build.xml:6:
>>>                           taskdef class
>>> org.intermine.bio.task.SOToModelTask
>>>                  cannot be found
>>>                              using the classloader
>>>
>>>
>>>
>>> AntClassLoader[/var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build/model:/var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build/main:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/antlr-2.7.6-caching.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/asm-4.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/asm-util-4.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/cglib-3.1.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/commons-collections-3.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/commons-io-1.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/commons-lang-2.6.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/json20110106.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/log4j.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/HikariCP-1.3.8.jar:/var/lib/pgsql/other_data/intermine/interm
>>>
>>
>>
>>>
>>>
>>>              ine/obje
>>>
>>>
>>>
>>>
>>>
>>> ctstore/main/lib/ant-1.6.5.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/base64.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/commons-beanutils-1.6.1.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/commons-digester-2.1.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/commons-logging-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/javassist-3.18.2.GA.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/jaxrpc.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/libreadline-java.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/ojdbc14.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/opencsv-2.3.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/postgresql-9.3-1101.jdbc4.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/saaj.jar:/var/lib/p
>>>
>>
>>
>>>     gsql
>>>
>>>
>>>              /other
>>>
>>>
>>>
>>>
>>> _data/intermine/intermine/objectstore/main/lib/slf4j-api-1.7.7.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/slf4j-simple-1.7.7.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/torque-3.2-dev.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/torque-gen-3.2-dev.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/velocity-1.3.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/xercesImpl-2.9.1.jar:/var/lib/pgsql/other_data/intermine/intermine/integrate/main/lib/mysql-connector-java-5.1.26-bin.jar:/var/lib/pgsql/other_data/intermine/intermine/integrate/main/lib/stax-api-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/integrate/main/lib/stax-ri-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/pathquery/main/lib/stax-api-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/pathquery/main/lib/stax-ri-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/li
>>>
>>
>>
>>>     b/bo
>>>
>>>
>>>              bo-bro
>>>
>>>
>>>
>>>
>>> wse-2.5.1.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/fastutil.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/kamikaze-2.0.0.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-core-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-highlighter-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-queries-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-snowball-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/xalan.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/bbop.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/biojava-1.7.1.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/jakarta-regexp-1.4.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/jena.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/obo.jar:/var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build/classes]
>>>
>>>
>>>                           On Tue, Aug 18, 2015 at 9:53 AM, Sofia Robb
>>>                  <sofia2341 at gmail.com <mailto:sofia2341 at gmail.com>
>>>         <mailto:sofia2341 at gmail.com <mailto:sofia2341 at gmail.com>>
>>>                           <mailto:sofia2341 at gmail.com
>>>         <mailto:sofia2341 at gmail.com> <mailto:sofia2341 at gmail.com
>>>         <mailto:sofia2341 at gmail.com>>>
>>>                           <mailto:sofia2341 at gmail.com
>>>         <mailto:sofia2341 at gmail.com>
>>>                  <mailto:sofia2341 at gmail.com
>>>         <mailto:sofia2341 at gmail.com>> <mailto:sofia2341 at gmail.com
>>>         <mailto:sofia2341 at gmail.com>
>>>                  <mailto:sofia2341 at gmail.com
>>>         <mailto:sofia2341 at gmail.com>>>>> wrote:
>>>
>>>                                I tried the clean and rm the build dir. I
>>>         get this
>>>                  error:
>>>
>>>
>>>                                On Tue, Aug 18, 2015 at 2:47 AM, sergio
>>>         contrino
>>>                                <sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>
>>>                           <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>>> wrote:
>>>
>>>                                    dear sofia,
>>>                                    could you try a
>>>                                    ant clean-all build-db
>>>                                    or, failing this, to remove manually
>>>         the dist
>>>                  and build
>>>                           directories
>>>                                    (something like rm -rf build in
>>>                  malariamine/dbmodel)
>>>                                    please let us know if this does not
>>> help
>>>                                    thanks
>>>                                    sergio
>>>
>>>
>>>                                    On 17/08/15 20:01, Sofia Robb wrote:
>>>
>>>                                        Hello Sergio,
>>>
>>>                                        I updated with  'git pull
>>>         upstream master'
>>>                  and it
>>>                           seemed to
>>>                                        be successful.
>>>
>>>                                        I am running through the
>>> malariamine
>>>                  tutorial to
>>>                           make sure
>>>                                        all is in
>>>                                        working order, when i try this I
>>>         get an error:
>>>
>>>                                        *]ant clean build-db
>>>                                        ...
>>>                                             [depend] The class
>>>
>>>         org.intermine.metadata.MetaDataException
>>>                  in file
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/metadata/MetaDataException.class
>>>                                        is out of date due to
>>>
>>>         org.intermine.metadata.MetaDataException
>>>                  but has
>>>                                        not been deleted because its
>>>         source file
>>>                  could not
>>>                           be determined
>>>                                             [depend] The class
>>>
>>>
>>>
>>>
>>> org.intermine.modelproduction.xml.InterMineModelParser$SkeletonClass
>>>                                        in
>>>                                        file
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/modelproduction/xml/InterMineModelParser$SkeletonClass.class
>>>                                        is out of date due to
>>>
>>>
>>>           org.intermine.modelproduction.xml.InterMineModelParser but
>>>                                        has not been
>>>                                        deleted because its source file
>>>         could not
>>>                  be determined
>>>                                             [depend] The class
>>>                           org.intermine.model.ShadowClass in file
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/model/ShadowClass.class
>>>                                        is out of date due to
>>>                           org.intermine.model.ShadowClass but
>>>                                        has not been
>>>                                        deleted because its source file
>>>         could not
>>>                  be determined
>>>                                             [depend] Deleted 1 out of
>>>         date files
>>>                  in 0 seconds
>>>                                              [javac] Compiling 204
>>>         source files to
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes
>>>                                        [dependencies] warning: [options]
>>>                  bootstrap class
>>>                           path not
>>>                                        set in
>>>                                        conjunction with -source 1.6
>>>                                        [dependencies]
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/src/org/intermine/codegen/JavaModelOutput.java:512:
>>>                                        error: cannot find symbol
>>>                                        [dependencies]
>>>               if
>>>                           (attr.isPrimitive() ||
>>>                                        attr.isNumeric()) {
>>>                                        [dependencies]
>>>                                                  ^
>>>                                        [dependencies]   symbol:   method
>>>         isNumeric()
>>>                                        [dependencies]   location:
>>>         variable attr
>>>                  of type
>>>                                        AttributeDescriptor
>>>                                        [dependencies] Note:
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/src/org/intermine/objectstore/query/QueryField.java
>>>                                        uses or overrides a deprecated
>>> API.
>>>                                        [dependencies] Note: Recompile
>>> with
>>>                           -Xlint:deprecation for
>>>                                        details.
>>>                                        [dependencies] Note: Some input
>>>         files use
>>>                  unchecked or
>>>                                        unsafe operations.
>>>                                        [dependencies] Note: Recompile
>>> with
>>>                           -Xlint:unchecked for
>>>                                        details.
>>>                                        [dependencies] 1 error
>>>                                        [dependencies] 1 warning
>>>
>>>                                        BUILD FAILED
>>>
>>>
>>>
>>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The
>>>                                        following error occurred while
>>>         executing
>>>                  this line:
>>>
>>>
>>>
>>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:109: The
>>>                                        following error occurred while
>>>         executing
>>>                  this line:
>>>
>>>
>>>
>>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:257:
>>>                                        Compile
>>>                                        failed; see the compiler error
>>>         output for
>>>                  details.
>>>
>>>                                        Total time: 14 seconds
>>>
>>>
>>>                                        Thanks,
>>>                                        Sofia
>>>
>>>
>>>                                        On Mon, Aug 17, 2015 at 9:43 AM,
>>>         sergio
>>>                  contrino
>>>                                        <sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>
>>>                           <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>>
>>>                                        <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org <mailto:
>>> sergio at modencode.org>>
>>>                           <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org <mailto:
>>> sergio at modencode.org>>
>>>                           <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>>>>
>>>
>>>                                        wrote:
>>>
>>>                                             dear sofia,
>>>                                             we are working on beta,
>>>         while you can
>>>                  update
>>>                           to the
>>>                                        latest release
>>>                                             (1.5.6) using the master
>>> branch.
>>>                                             thanks!
>>>                                             sergio
>>>
>>>
>>>
>>>                                             On 17/08/15 16:38, Sofia
>>>         Robb wrote:
>>>
>>>                                                 Hello,
>>>
>>>                                                 I would like to update my
>>>                  intermine. Which
>>>                           branch
>>>                                        is the best
>>>                                                 for me to use?
>>>
>>>                                                 Thanks,
>>>                                                 Sofia
>>>
>>>                                                    *]git pull upstream
>>>
>>>                                                 remote: Counting
>>>         objects: 5382, done.
>>>                                                 remote: Compressing
>>>         objects: 100%
>>>                  (4/4), done.
>>>                                                 remote: Total 5382
>>>         (delta 1958),
>>>                  reused
>>>                           1962 (delta
>>>                                        1958),
>>>                                                 pack-reused 3420
>>>                                                 Receiving objects: 100%
>>>                  (5382/5382), 6.57
>>>                           MiB |
>>>                                        4.48 MiB/s, done.
>>>                                                 Resolving deltas: 100%
>>>         (3021/3021),
>>>                           completed with
>>>                                        620 local
>>>                                                 objects.
>>>                                                   From
>>>         github.com:intermine/intermine
>>>                                                    * [new branch]
>>>         1.5.1-rc   ->
>>>                           upstream/1.5.1-rc
>>>                                                      898cce9..1137c13
>>>         beta       ->
>>>                           upstream/beta
>>>                                                    * [new branch]
>>>                  biogrid-detail-dupes ->
>>>
>>>           upstream/biogrid-detail-dupes
>>>                                                    + 37b68d5...11e56dc
>>>         dev        ->
>>>                           upstream/dev
>>>                                        (forced update)
>>>                                                    * [new branch]
>>>                  dynamic-objects ->
>>>                                        upstream/dynamic-objects
>>>                                                    * [new branch]
>>>         gradle     ->
>>>                           upstream/gradle
>>>                                                      787829e..0a759cf
>>>                  human-identifiers ->
>>>
>>> upstream/human-identifiers
>>>                                                      d10b7bd..0e77615
>>>         i169       ->
>>>                           upstream/i169
>>>                                                      60eb6eb..9324602
>>>         i797       ->
>>>                           upstream/i797
>>>                                                    * [new branch]
>>>                  keyword-fail-loudly ->
>>>
>>> upstream/keyword-fail-loudly
>>>                                                      c01ea52..7fff99c
>>>         like       ->
>>>                           upstream/like
>>>                                                      b8133ad..9848015
>>>         master     ->
>>>                           upstream/master
>>>                                                    * [new branch]
>>>                  new-class-key ->
>>>                                        upstream/new-class-key
>>>                                                    * [new branch]
>>>                  new_jsp_jars ->
>>>                                        upstream/new_jsp_jars
>>>                                                    * [new branch]
>>>                  panther-config-fix ->
>>>
>>> upstream/panther-config-fix
>>>                                                      3e88474..6a29469
>>>                  protein-interactions ->
>>>
>>>           upstream/protein-interactions
>>>                                                    * [new branch]
>>>                  rm-onto-pubs ->
>>>                                        upstream/rm-onto-pubs
>>>                                                    * [new tag]
>>>                    intermine-1.5.1 ->
>>>                                        intermine-1.5.1
>>>                                                    * [new tag]
>>>                    intermine-1.5.5 ->
>>>                                        intermine-1.5.5
>>>                                                    * [new tag]
>>>                    intermine-1.5.6 ->
>>>                                        intermine-1.5.6
>>>                                                   From
>>>         github.com:intermine/intermine
>>>                                                    * [new tag]
>>>                    intermine-1.4.2 ->
>>>                                        intermine-1.4.2
>>>                                                    * [new tag]
>>>                    intermine-1.5 ->
>>>                           intermine-1.5
>>>                                                    * [new tag]
>>>                    intermine-1.5.3 ->
>>>                                        intermine-1.5.3
>>>                                                    * [new tag]
>>>                    intermine-1.5.4 ->
>>>                                        intermine-1.5.4
>>>                                                 You asked to pull from
>>>         the remote
>>>                           'upstream', but
>>>                                        did not specify
>>>                                                 a branch. Because this
>>>         is not the
>>>                  default
>>>                                        configured remote
>>>                                                 for your current branch,
>>>         you must
>>>                  specify
>>>                           a branch
>>>                                        on the
>>>                                                 command line.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>>                                                 dev mailing list
>>>         dev at intermine.org <mailto:dev at intermine.org>
>>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>
>>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>>>
>>>                                        <mailto:dev at intermine.org
>>>         <mailto:dev at intermine.org>
>>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>>                           <mailto:dev at intermine.org
>>>         <mailto:dev at intermine.org> <mailto:dev at intermine.org
>>>         <mailto:dev at intermine.org>>>>
>>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>
>>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>>                           <mailto:dev at intermine.org
>>>         <mailto:dev at intermine.org> <mailto:dev at intermine.org
>>>         <mailto:dev at intermine.org>>>
>>>                                        <mailto:dev at intermine.org
>>>         <mailto:dev at intermine.org>
>>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>
>>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org
>>> >>>>>
>>>         http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>>
>>>                                             --
>>>                                             sergio contrino
>>>                  InterMine,
>>>                           University
>>>                                        of Cambridge
>>>         https://sergiocontrino.github.io
>>>                                        <
>>> https://sergiocontrino.github.io/>
>>>         http://www.intermine.org
>>>                                        <http://www.intermine.org/>
>>>
>>>
>>>
>>>                                    --
>>>                                    sergio contrino
>>>         InterMine,
>>>                  University
>>>                           of Cambridge
>>>         https://sergiocontrino.github.io
>>>                                    <https://sergiocontrino.github.io/>
>>>         http://www.intermine.org
>>>                                    <http://www.intermine.org/>
>>>
>>>
>>>
>>>                           On Tue, Aug 18, 2015 at 2:47 AM, sergio
>>> contrino
>>>                           <sergio at modencode.org
>>>         <mailto:sergio at modencode.org> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>
>>>                           <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>
>>>                  <mailto:sergio at modencode.org
>>>         <mailto:sergio at modencode.org>>>>> wrote:
>>>
>>>                                dear sofia,
>>>                                could you try a
>>>                                ant clean-all build-db
>>>                                or, failing this, to remove manually the
>>>         dist and
>>>                  build
>>>                           directories
>>>                                (something like rm -rf build in
>>>         malariamine/dbmodel)
>>>                                please let us know if this does not help
>>>                                thanks
>>>                                sergio
>>>
>>>
>>>                                On 17/08/15 20:01, Sofia Robb wrote:
>>>
>>>                                    Hello Sergio,
>>>
>>>                                    I updated with  'git pull upstream
>>>         master' and it
>>>                           seemed to be
>>>                                    successful.
>>>
>>>                                    I am running through the malariamine
>>>         tutorial
>>>                  to make
>>>                           sure all is in
>>>                                    working order, when i try this I get
>>>         an error:
>>>
>>>                                    *]ant clean build-db
>>>                                    ...
>>>                                         [depend] The class
>>>                           org.intermine.metadata.MetaDataException
>>>                                    in file
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/metadata/MetaDataException.class
>>>                                    is out of date due to
>>>                           org.intermine.metadata.MetaDataException
>>>                                    but has
>>>                                    not been deleted because its source
>>>         file could
>>>                  not be
>>>                           determined
>>>                                         [depend] The class
>>>
>>>
>>>
>>>
>>> org.intermine.modelproduction.xml.InterMineModelParser$SkeletonClass
>>>                                    in
>>>                                    file
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/modelproduction/xml/InterMineModelParser$SkeletonClass.class
>>>                                    is out of date due to
>>>
>>>                    org.intermine.modelproduction.xml.InterMineModelParser
>>>                           but has
>>>                                    not been
>>>                                    deleted because its source file could
>>>         not be
>>>                  determined
>>>                                         [depend] The class
>>>                  org.intermine.model.ShadowClass
>>>                           in file
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/model/ShadowClass.class
>>>                                    is out of date due to
>>>                  org.intermine.model.ShadowClass
>>>                           but has
>>>                                    not been
>>>                                    deleted because its source file could
>>>         not be
>>>                  determined
>>>                                         [depend] Deleted 1 out of date
>>>         files in 0
>>>                  seconds
>>>                                          [javac] Compiling 204 source
>>>         files to
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes
>>>                                    [dependencies] warning: [options]
>>>         bootstrap
>>>                  class path
>>>                           not set in
>>>                                    conjunction with -source 1.6
>>>                                    [dependencies]
>>>
>>>
>>>
>>>
>>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/src/org/intermine/codegen/JavaModelOutput.java:512:
>>>                                    error: cannot find symbol
>>>                                    [dependencies]
>>>  if
>>>                           (attr.isPrimitive() ||
>>>                                    attr.isNumeric()) {
>>>                                    [dependencies]
>>>                                          ^
>>
>>
>
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