[InterMine Dev] git update, which branch?

sergio contrino sergio at modencode.org
Tue Aug 18 09:47:37 BST 2015


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 is out of date due to org.intermine.metadata.MetaDataException but has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 is out of date due to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 is out of date due to org.intermine.model.ShadowClass but has not been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     [depend] Deleted 1 out of date files in 0 seconds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



More information about the dev mailing list