java.lang.AssertionError: assertion failed: Tried to find 'samtools' in '/home/project/avocado/avocado-core/target/scala-2.10.3/classes/htsjdk' but it is not a directory

Google Groups | Unknown author | 2 years ago
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    Avocado-core does not build

    Google Groups | 2 years ago | Unknown author
    java.lang.AssertionError: assertion failed: Tried to find 'samtools' in '/home/project/avocado/avocado-core/target/scala-2.10.3/classes/htsjdk' but it is not a directory

    Root Cause Analysis

    1. java.lang.AssertionError

      assertion failed: Tried to find 'samtools' in '/home/project/avocado/avocado-core/target/scala-2.10.3/classes/htsjdk' but it is not a directory

      at scala.reflect.io.AbstractFile.subdirectoryNamed()
    2. Scala
      AbstractFile.subdirectoryNamed
      1. scala.reflect.io.AbstractFile.subdirectoryNamed(AbstractFile.scala:254)
      1 frame
    3. Scala Compiler
      Global$Run.compile
      1. scala.tools.nsc.backend.jvm.BytecodeWriters$class.getFile(BytecodeWriters.scala:31)
      2. scala.tools.nsc.backend.jvm.BytecodeWriters$class.scala$tools$nsc$backend$jvm$BytecodeWriters$$getFile(BytecodeWriters.scala:37)
      3. scala.tools.nsc.backend.jvm.BytecodeWriters$ClassBytecodeWriter$class.writeClass(BytecodeWriters.scala:89)
      4. scala.tools.nsc.backend.jvm.GenASM$AsmPhase$$anon$4.writeClass(GenASM.scala:67)
      5. scala.tools.nsc.backend.jvm.GenASM$JBuilder.writeIfNotTooBig(GenASM.scala:458)
      6. scala.tools.nsc.backend.jvm.GenASM$JPlainBuilder.genClass(GenASM.scala:1402)
      7. scala.tools.nsc.backend.jvm.GenASM$AsmPhase.run(GenASM.scala:119)
      8. scala.tools.nsc.Global$Run.compileUnitsInternal(Global.scala:1583)
      9. scala.tools.nsc.Global$Run.compileUnits(Global.scala:1557)
      10. scala.tools.nsc.Global$Run.compileSources(Global.scala:1553)
      11. scala.tools.nsc.Global$Run.compile(Global.scala:1662)
      11 frames
    4. SBT
      CompilerInterface.run
      1. xsbt.CachedCompiler0.run(CompilerInterface.scala:123)
      2. xsbt.CachedCompiler0.run(CompilerInterface.scala:99)
      3. xsbt.CompilerInterface.run(CompilerInterface.scala:27)
      3 frames
    5. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:606)
      4 frames
    6. SBT
      AggressiveCompile.compile1
      1. sbt.compiler.AnalyzingCompiler.call(AnalyzingCompiler.scala:102)
      2. sbt.compiler.AnalyzingCompiler.compile(AnalyzingCompiler.scala:48)
      3. sbt.compiler.AnalyzingCompiler.compile(AnalyzingCompiler.scala:41)
      4. sbt.compiler.AggressiveCompile$$anonfun$3$$anonfun$compileScala$1$1.apply$mcV$sp(AggressiveCompile.scala:99)
      5. sbt.compiler.AggressiveCompile$$anonfun$3$$anonfun$compileScala$1$1.apply(AggressiveCompile.scala:99)
      6. sbt.compiler.AggressiveCompile$$anonfun$3$$anonfun$compileScala$1$1.apply(AggressiveCompile.scala:99)
      7. sbt.compiler.AggressiveCompile.sbt$compiler$AggressiveCompile$$timed(AggressiveCompile.scala:166)
      8. sbt.compiler.AggressiveCompile$$anonfun$3.compileScala$1(AggressiveCompile.scala:98)
      9. sbt.compiler.AggressiveCompile$$anonfun$3.apply(AggressiveCompile.scala:143)
      10. sbt.compiler.AggressiveCompile$$anonfun$3.apply(AggressiveCompile.scala:87)
      11. sbt.inc.IncrementalCompile$$anonfun$doCompile$1.apply(Compile.scala:39)
      12. sbt.inc.IncrementalCompile$$anonfun$doCompile$1.apply(Compile.scala:37)
      13. sbt.inc.IncrementalCommon.cycle(Incremental.scala:99)
      14. sbt.inc.Incremental$$anonfun$1.apply(Incremental.scala:38)
      15. sbt.inc.Incremental$$anonfun$1.apply(Incremental.scala:37)
      16. sbt.inc.Incremental$.manageClassfiles(Incremental.scala:65)
      17. sbt.inc.Incremental$.compile(Incremental.scala:37)
      18. sbt.inc.IncrementalCompile$.apply(Compile.scala:27)
      19. sbt.compiler.AggressiveCompile.compile2(AggressiveCompile.scala:157)
      20. sbt.compiler.AggressiveCompile.compile1(AggressiveCompile.scala:71)
      20 frames
    7. com.typesafe.zinc
      Nailgun.nailMain
      1. com.typesafe.zinc.Compiler.compile(Compiler.scala:193)
      2. com.typesafe.zinc.Compiler.compile(Compiler.scala:174)
      3. com.typesafe.zinc.Main$.run(Main.scala:98)
      4. com.typesafe.zinc.Nailgun$.zinc(Nailgun.scala:93)
      5. com.typesafe.zinc.Nailgun$.nailMain(Nailgun.scala:82)
      6. com.typesafe.zinc.Nailgun.nailMain(Nailgun.scala)
      6 frames
    8. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
      2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      3. java.lang.reflect.Method.invoke(Method.java:606)
      3 frames
    9. JRuby Main Maven Artifact
      NGSession.run
      1. com.martiansoftware.nailgun.NGSession.run(NGSession.java:280)[INFO]
      1 frame