[InterMine Dev] git update, which branch?

sergio contrino sergio at modencode.org
Wed Aug 19 16:00:48 BST 2015


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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