[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Tue Aug 18 16:55:35 BST 2015


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/objectstore/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-browse-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> 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>
>  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>> 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>
>>>         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
>>
>
>
On Tue, Aug 18, 2015 at 2:47 AM, sergio contrino <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>> 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>
>>         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
>
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