java.lang.NoSuchMethodError: breeze.linalg.DenseVector$.canSetD()Lbreeze/generic/UFunc$InPlaceImpl2;

GitHub | jbloom22 | 12 months ago
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    PCA throws error using Breeze 0.12 and natives (BLAS)

    GitHub | 12 months ago | jbloom22
    java.lang.NoSuchMethodError: breeze.linalg.DenseVector$.canSetD()Lbreeze/generic/UFunc$InPlaceImpl2;

    Root Cause Analysis

    1. java.lang.NoSuchMethodError

      breeze.linalg.DenseVector$.canSetD()Lbreeze/generic/UFunc$InPlaceImpl2;

      at org.apache.spark.mllib.linalg.EigenValueDecomposition$.symmetricEigs()
    2. Spark Project ML Library
      IndexedRowMatrix.computeSVD
      1. org.apache.spark.mllib.linalg.EigenValueDecomposition$.symmetricEigs(EigenValueDecomposition.scala:110)
      2. org.apache.spark.mllib.linalg.distributed.RowMatrix.computeSVD(RowMatrix.scala:269)
      3. org.apache.spark.mllib.linalg.distributed.RowMatrix.computeSVD(RowMatrix.scala:195)
      4. org.apache.spark.mllib.linalg.distributed.IndexedRowMatrix.computeSVD(IndexedRowMatrix.scala:154)
      4 frames
    3. org.broadinstitute.hail
      PipelineSuite.defaultPipeline
      1. org.broadinstitute.hail.methods.SamplePCA.apply(SamplePCA.scala:10)
      2. org.broadinstitute.hail.driver.PCA$.run(PCA.scala:23)
      3. org.broadinstitute.hail.driver.PCA$.run(PCA.scala:7)
      4. org.broadinstitute.hail.driver.Command.runCommand(Command.scala:69)
      5. org.broadinstitute.hail.driver.Command.run(Command.scala:73)
      6. org.broadinstitute.hail.PipelineSuite.defaultPipeline(PipelineSuite.scala:22)
      6 frames