[InterMine Dev] git update, which branch?

Krishnakumar, Vivek vKrishna at jcvi.org
Wed Aug 19 19:12:43 BST 2015


Hi Sofia,

When running createdb, by default, it uses the postgres `template1`database as a reference to instantiate an empty DB.

While setting up postgres, did you happen to follow the documentation here (http://intermine.readthedocs.org/en/latest/system-requirements/software/postgres/postgres/#character-set-encoding), which shows how to alter the `template1` database with the required SQL_ASCII encoding, and Locale settings?

Thank you.
Vivek

On Aug 19, 2015, at 1:52 PM, Sofia Robb <sofia at sofiarobb.com<mailto:sofia at sofiarobb.com>> wrote:

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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>
<mailto: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>>
        <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 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>>>
                 <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:

                      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>>>>
                          <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<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>>>>
                          <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,
                                   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>>>>>
                                       <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<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.



                            _______________________________________________
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        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>>>
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                 <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<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/>
                                       <https://sergiocontrino.github.io/>
        http://www.intermine.org<http://www.intermine.org/>
                                       <http://www.intermine.org/>



                                   --
                                   sergio contrino
        InterMine,
                 University
                          of Cambridge
        https://sergiocontrino.github.io<https://sergiocontrino.github.io/>
                                   <https://sergiocontrino.github.io/>
        http://www.intermine.org<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>>>>
                          <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,
                               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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