[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Tue Aug 18 20:32:24 BST 2015


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>
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/intermine/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/bobo-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>> 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>> 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>>>
>>
>>             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>>
>>             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>> 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>>>
>> 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>>
>>         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
>
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