[InterMine Dev] git update, which branch?

sergio contrino sergio at modencode.org
Tue Aug 18 17:33:09 BST 2015


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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