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Build Error: GATK Framework

ramanibkramanibk IndiMember
edited September 2015 in Ask the GATK team

I'm trying to install mutect, and as directed in the README.md, I've git cloned gatk-protected and tried to do 'mvn -Ddisable.queue install'. But I get the following issue. I've java 1.7 and maven 3.3.3.

[INFO] -------------------------------------------------------------
[WARNING] COMPILATION WARNING :
[INFO] -------------------------------------------------------------
[WARNING] /home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadEfficiencyMonitor.java: Some input files use or override a deprecated API.
[WARNING] /home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadEfficiencyMonitor.java: Recompile with -Xlint:deprecation for details.
[WARNING] /home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java: Some input files use unchecked or unsafe operations.
[WARNING] /home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java: Recompile with -Xlint:unchecked for details.
[WARNING] Some messages have been simplified; recompile with -Xdiags:verbose to get full output
[INFO] 5 warnings
[INFO] -------------------------------------------------------------
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
    method java.util.Collection.add(T) is not applicable
      (argument mismatch; java.lang.Object cannot be converted to T)
    method java.util.List.add(T) is not applicable
      (argument mismatch; java.lang.Object cannot be converted to T)
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Sting Root ......................................... SUCCESS [  0.455 s]
[INFO] Sting Aggregator ................................... SUCCESS [  0.185 s]
[INFO] Sting GSALib ....................................... SUCCESS [  0.447 s]
[INFO] Sting Utils ........................................ SUCCESS [  0.698 s]
[INFO] GATK Framework ..................................... FAILURE [  4.181 s]
[INFO] GATK Protected ..................................... SKIPPED
[INFO] GATK Package ....................................... SKIPPED
[INFO] Sting Public ....................................... SKIPPED
[INFO] Sting Protected .................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 6.134 s
[INFO] Finished at: 2015-09-16T14:27:14+05:30
[INFO] Final Memory: 44M/1583M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (compile-java) on project gatk-framework: Compilation failure
[ERROR] /home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
[ERROR] method java.util.Collection.add(T) is not applicable
[ERROR] (argument mismatch; java.lang.Object cannot be converted to T)
[ERROR] method java.util.List.add(T) is not applicable
[ERROR] (argument mismatch; java.lang.Object cannot be converted to T)
[ERROR] -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (compile-java) on project gatk-framework: Compilation failure
/home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
    method java.util.Collection.add(T) is not applicable
      (argument mismatch; java.lang.Object cannot be converted to T)
    method java.util.List.add(T) is not applicable
      (argument mismatch; java.lang.Object cannot be converted to T)

        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
        at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
        at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
        at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
        at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
        at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
        at org.apache.maven.cli.MavenCli.execute(MavenCli.java:862)
        at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:286)
        at org.apache.maven.cli.MavenCli.main(MavenCli.java:197)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
        at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
        at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
        at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.compiler.CompilationFailureException: Compilation failure
/home/krb/Ramani/MUTECT/gatk-protected/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
    method java.util.Collection.add(T) is not applicable
      (argument mismatch; java.lang.Object cannot be converted to T)
    method java.util.List.add(T) is not applicable
      (argument mismatch; java.lang.Object cannot be converted to T)

        at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:858)
        at org.apache.maven.plugin.compiler.CompilerMojo.execute(CompilerMojo.java:129)
        at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
        ... 20 more
[ERROR]
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :gatk-framework

I'm not able to understand how to resolve the issue. Could anybody please help me with it?

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