MuTect安装:GATK-受保护: maven: Java-编译-错误

Question

我正在尝试安装mutect，并且按照README.md中的指示，我已经克隆了gatk，并尝试执行'mvn -Ddisable.queue安装‘。但我得到了以下问题。我已经有了java 1.7和maven 3.3.3。

     1.[INFO] -------------------------------------------------------------
     2.[ERROR] COMPILATION ERROR :
     3.[INFO] -------------------------------------------------------------
     4.[ERROR] /home/krb/.../annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
     5.method java.util.Collection.add(T) is not applicable
     6.  (argument mismatch; java.lang.Object cannot be converted to T)
     7.method java.util.List.add(T) is not applicable
     8.  (argument mismatch; java.lang.Object cannot be converted to T)
     9.[INFO] 1 error
    10.[INFO] -------------------------------------------------------------
    11.[INFO] ------------------------------------------------------------------------ 
    12.[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (compile-java) on project gatk-framework: Compilation failure
    13.[ERROR] /home/krb/.../annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
    14.[ERROR] method java.util.Collection.add(T) is not applicable
    15.[ERROR] (argument mismatch; java.lang.Object cannot be converted to T)
    16.[ERROR] method java.util.List.add(T) is not applicable
    17.[ERROR] (argument mismatch; java.lang.Object cannot be converted to T)
    18.[ERROR] -> [Help 1]
    19.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
    20./home/krb/.../annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
    21.method java.util.Collection.add(T) is not applicable
    22. (argument mismatch; java.lang.Object cannot be converted to T)
    23.method java.util.List.add(T) is not applicable
    24.  (argument mismatch; java.lang.Object cannot be converted to T)

我跟随自述文件提交给这里。，有人能帮我解决这个问题吗？

Answer 1

mutect的README.md指示gatk-protected文件夹中的git reset --hard 3.1。我撤销了这一行为，我猜想，这导致了最新的GATK保护版本的使用。因此，在我使用git reflog撤消该重置命令之后，该过程继续进行，mutect jar文件也被成功构建。

Answer 2

在堆栈跟踪中看到此部分：

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)

Collection.add(T)不能应用于Object。