postprocess GeneFlankingRegion error

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postprocess GeneFlankingRegion error

Sofia Robb-4
when I run `ant -v -Daction=create-references` I get these errors. I updated from 1.6 to 1.6.1 and ` ant clean build-db`  to make sure this wasn't corrected in the newest version.

Thank you, thank you, thank you for your continued support!
Sofia

[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:26: error: cannot find symbol
[dependencies] import org.intermine.model.bio.GeneFlankingRegion;
[dependencies]                               ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: package org.intermine.model.bio
[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:164: error: cannot find symbol
[dependencies]                     GeneFlankingRegion region = (GeneFlankingRegion) DynamicUtil
[dependencies]                     ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: class CreateFlankingRegions
[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:164: error: cannot find symbol
[dependencies]                     GeneFlankingRegion region = (GeneFlankingRegion) DynamicUtil
[dependencies]                                                  ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: class CreateFlankingRegions
[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:165: error: cannot find symbol
[dependencies]                     .createObject(Collections.singleton(GeneFlankingRegion.class));
[dependencies]                                                         ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: class CreateFlankingRegions
[dependencies] Note: Some input files use unchecked or unsafe operations.
[dependencies] Note: Recompile with -Xlint:unchecked for details.
[dependencies] 4 errors
[dependencies] 1 warning
     [null] Exiting /var/lib/pgsql/other_data/intermine/bio/postprocess/main/build.xml.

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:117: 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.
at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1174)
at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:930)
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.taskdefs.Sequential.execute(Sequential.java:68)
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.taskdefs.MacroInstance.execute(MacroInstance.java:396)
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.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)

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Re: postprocess GeneFlankingRegion error

Sofia Robb-4
I got it worked out. Before I updated to 1.6.1, I could not build my db model if I included genomic_additions.xml. So I commented it out so I could test load some data. I forgot I commented it out. Now that I updated, I included it, and now my error is gone. Sorry about that.

Thanks!
Sofia

On Wed, Nov 11, 2015 at 3:59 PM, Sofia Robb <[hidden email]> wrote:
when I run `ant -v -Daction=create-references` I get these errors. I updated from 1.6 to 1.6.1 and ` ant clean build-db`  to make sure this wasn't corrected in the newest version.

Thank you, thank you, thank you for your continued support!
Sofia

[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:26: error: cannot find symbol
[dependencies] import org.intermine.model.bio.GeneFlankingRegion;
[dependencies]                               ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: package org.intermine.model.bio
[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:164: error: cannot find symbol
[dependencies]                     GeneFlankingRegion region = (GeneFlankingRegion) DynamicUtil
[dependencies]                     ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: class CreateFlankingRegions
[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:164: error: cannot find symbol
[dependencies]                     GeneFlankingRegion region = (GeneFlankingRegion) DynamicUtil
[dependencies]                                                  ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: class CreateFlankingRegions
[dependencies] /var/lib/pgsql/other_data/intermine/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java:165: error: cannot find symbol
[dependencies]                     .createObject(Collections.singleton(GeneFlankingRegion.class));
[dependencies]                                                         ^
[dependencies]   symbol:   class GeneFlankingRegion
[dependencies]   location: class CreateFlankingRegions
[dependencies] Note: Some input files use unchecked or unsafe operations.
[dependencies] Note: Recompile with -Xlint:unchecked for details.
[dependencies] 4 errors
[dependencies] 1 warning
     [null] Exiting /var/lib/pgsql/other_data/intermine/bio/postprocess/main/build.xml.

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:117: 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.
at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1174)
at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:930)
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.taskdefs.Sequential.execute(Sequential.java:68)
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.taskdefs.MacroInstance.execute(MacroInstance.java:396)
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.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)


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