[InterMine Dev] git update, which branch?

Sofia Robb sofia2341 at gmail.com
Wed Aug 19 18:51:43 BST 2015


Thanks for the help Vivek. While rerunning like you suggested (I am still
getting the objectStore error, also as you saw) I noticed some other errors
that I did not see before.

There seems to be an issue with the encoding.


making db copy: createdb -E SQL_ASCII -U intermine -h localhost -T
malariamine malariamine:malaria-chromosome-fasta

createdb: database creation failed: ERROR:  encoding "SQL_ASCII" does not
match locale "en_US.UTF-8"
DETAIL:  The chosen LC_CTYPE setting requires encoding "UTF8".
Wed Aug 19 12:33:00 CDT 2015

making db copy: createdb -E SQL_ASCII -U intermine -h localhost -T
malariamine malariamine:go-annotation

createdb: database creation failed: ERROR:  encoding "SQL_ASCII" does not
match locale "en_US.UTF-8"
DETAIL:  The chosen LC_CTYPE setting requires encoding "UTF8".
Wed Aug 19 12:40:18 CDT 2015


On Wed, Aug 19, 2015 at 11:31 AM, Krishnakumar, Vivek <vKrishna at jcvi.org>
wrote:

> Hi Sofia,
>
> Actually, I take back what I said. After looking at your error stack trace
> a but closer, the failure of your MalariaMine build is not due to the
> Entrez eutils web services, but rather due to some issues with the
> InterMine ObjectStore.
>
> Sorry for the confusion.
>
> Thank you.
> Vivek
>
> On Aug 19, 2015, at 1:25 PM, Vivek Krishnakumar <vkrishna at jcvi.org> wrote:
>
> Hi Sofia,
>
> Just wanted to chime in on this thread since our most recent development
> build of ThaleMine (InterMine for Arabidopsis,
> https://apps.araport.org/thalemine/) failed at the same step as yours,
> i.e. entrez-organism.
>
> This failure has nothing to do with InterMine itself, but because the
> remote Entrez eutils services might have been unavailable while your build
> was running.
>
> The web service call is structured something like this:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&retmode=xml&id=10090,10116,7227,9606,4932,6239,3702,7955,
> where the ids in this list correspond to the organisms you are loading into
> your mine.
>
> However, as of writing this email, I can see that the eutils web services
> are back up online.
>
> As such, I would urge you to please try rebuilding MalariaMine again.
>
> Thank you.
>
> Regards,
> Vivek
>
> On Aug 19, 2015, at 12:47 PM, Sofia Robb <sofia at sofiarobb.com> wrote:
>
> 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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