[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Wed Aug 19 16:18:11 BST 2015


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>
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>> 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>>>
>> 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>>>> 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>>>> 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>>>>>
>>
>>                               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>>>>
>>         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>>>> 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>>>>> 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>>>>
>>         http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>
>>                                --
>>                                sergio contrino                  InterMine,
>>                  University of
>>                           Cambridge
>>         https://sergiocontrino.github.io http://www.intermine.org
>>
>>
>>
>>                       --
>>                       sergio contrino                  InterMine,
>>         University of
>>                  Cambridge
>>         https://sergiocontrino.github.io http://www.intermine.org
>>
>>
>>
>>              --
>>              sergio contrino                  InterMine, University of
>>         Cambridge
>>         https://sergiocontrino.github.io http://www.intermine.org
>>
>>
>>
>>     --
>>     sergio contrino                  InterMine, University of Cambridge
>>     https://sergiocontrino.github.io http://www.intermine.org
>>
>>
>>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org
>
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