java.lang.NoSuchMethodError: org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/P artitioner;)Lorg/apache/spark/rdd/RDD;

Google Groups | Sungwook Yoon | 2 years ago
  1. 0

    error in avocado

    Google Groups | 2 years ago | Sungwook Yoon
    java.lang.NoSuchMethodError: org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/P artitioner;)Lorg/apache/spark/rdd/RDD;
  2. 0

    avocado-submit not working? - Failure at step "groupby at BiallelicGenotyper.Scala"

    Google Groups | 2 years ago | Unknown author
    java.lang.NoSuchMethodError: org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/Partitioner;)Lorg/apache/spark/rdd/RDD;
  3. 0

    GitHub comment 78#224771763

    GitHub | 6 months ago | javadba
    java.lang.NoSuchMethodError: org.apache.spark.sql.SQLContext.createDataFrame(Lorg/apache/spark/rdd/RDD;Lorg/apache/spark/sql/types/StructType;)Lorg/apache/spark/sql/DataFrame;
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  5. 0

    GitHub comment 40#104960431

    GitHub | 2 years ago | nkconnor
    java.lang.NoSuchMethodError: org.apache.spark.sql.SQLContext.jsonRDD(Lorg/apache/spark/rdd/RDD;)Lorg/apache/spark/sql/DataFrame;
  6. 0

    Apache Spark User List - SchemaRDD.count error

    nabble.com | 5 months ago
    java.lang.NoSuchMethodError: org.apache.spark.rdd.ShuffledRDD.<init>(Lorg/apache/spark/rdd/RDD;Lorg/apache/spark/Partitioner;)V

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    Root Cause Analysis

    1. java.lang.NoSuchMethodError

      org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/P artitioner;)Lorg/apache/spark/rdd/RDD;

      at org.bdgenomics.avocado.genotyping.BiallelicGenotyper.genotype()
    2. org.bdgenomics.avocado
      CallGenotypes$$anonfun$apply$1.apply
      1. org.bdgenomics.avocado.genotyping.BiallelicGenotyper.genotype(BiallelicGenotyper.scala:369)
      2. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1.apply(CallGenotypes.scala:43)
      3. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1.apply(CallGenotypes.scala:43)
      3 frames
    3. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    4. org.bdgenomics.avocado
      Avocado$$anonfun$callVariants$1.apply
      1. org.bdgenomics.avocado.genotyping.CallGenotypes$.apply(CallGenotypes.scala:36)
      2. org.bdgenomics.avocado.cli.Avocado$$anonfun$callVariants$1.apply(Avocado.scala:154)
      3. org.bdgenomics.avocado.cli.Avocado$$anonfun$callVariants$1.apply(Avocado.scala:148)
      3 frames
    5. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    6. org.bdgenomics.avocado
      Avocado.run
      1. org.bdgenomics.avocado.cli.Avocado.callVariants(Avocado.scala:148)
      2. org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:213)
      2 frames
    7. org.bdgenomics.adam
      ADAMSparkCommand$class.run
      1. org.bdgenomics.adam.cli.ADAMSparkCommand$class.run(ADAMCommand.scala:57)
      1 frame
    8. org.bdgenomics.avocado
      Avocado.run
      1. org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:81)
      1 frame
    9. org.bdgenomics.adam
      ADAMCommandCompanion$class.main
      1. org.bdgenomics.adam.cli.ADAMCommandCompanion$class.main(ADAMCommand.scala:35)
      1 frame
    10. org.bdgenomics.avocado
      Avocado.main
      1. org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:51)
      2. org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
      2 frames
    11. 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
    12. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:328)
      2. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75)
      3. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      3 frames