MuTect 安装：GATK 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 git 克隆了受 gatk 保护并尝试执行 'mvn -Ddisable.queue install'。但是我遇到以下问题。我有 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)

我遵循了现有的自述文件 here. 谁能帮忙解决这个问题？

Answer 1

在堆栈跟踪中查看此部分：

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) 无法应用于 Object。

Answer 2

mutect 的 README.md 指示 gatk-protected 文件夹中的 git reset --hard 3.1。我撤消了这个操作，我猜这会导致使用最新的受 GATK 保护的版本。因此，在我使用 git reflog 取消重置命令后，程序恢复并且 mutect jar 文件也成功构建。

MuTect 安装：GATK 保护：maven：Java-编译错误

MuTect install: GATK-protected: maven: Java-compile-error

java

maven-3

gatk