[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Wed Aug 19 15:53:12 BST 2015


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>
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>> 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/pgsql
>>
> /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/lib/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>>> 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>>>
>> 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>>>>
>>
>>                      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
>> >>>
>>         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>>>
>> 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>>>> 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>>>
>>         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
>
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