seqtrie

tests

Running ‘test_RadixForest.R’ [4s/5s]
  Running ‘test_RadixTree.R’ [11s/11s]
  Running ‘test_StarTree.R’ [71s/58s]
  Running ‘test_pairwise.R’ [4s/5s]
Running the tests in ‘tests/test_pairwise.R’ failed.
Complete output:
  > # This test file tests the `dist_matrix` and `dist_pairwise` functions
  > # These two functions are simple dynamic programming algorithms for computing pairwise distances and are themselves used to validate
  > # the RadixTree imeplementation (see test_radix_tree.R)
  > 
  > runtime <- Sys.time()
  > 
  > if(requireNamespace("seqtrie", quietly=TRUE) &&
  +    requireNamespace("pwalign", quietly=TRUE)
  + ) {
  + library(seqtrie)
  + library(pwalign)
  + 
  + # Use 2 threads on github actions and CRAN, 4 threads locally
  + IS_LOCAL  <- Sys.getenv("IS_LOCAL") != ""
  + NTHREADS  <- ifelse(IS_LOCAL, 4, 2)
  + NITER     <- ifelse(IS_LOCAL, 3, 1)
  + NSEQS     <- 2500
  + MAXSEQLEN <- 200
  + CHARSET   <- "ACGT"
  + 
  + test_seed <- Sys.getenv("SEQTRIE_TEST_SEED")
  +
...[truncated]...
ctor
  Loading required package: GenomeInfoDb
  
  Attaching package: 'Biostrings'
  
  The following object is masked from 'package:base':
  
      strsplit
  
  
  Attaching package: 'pwalign'
  
  The following objects are masked from 'package:Biostrings':
  
      PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned,
      alignedPattern, alignedSubject, compareStrings, deletion,
      errorSubstitutionMatrices, indel, insertion, mismatchSummary,
      mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix,
      pairwiseAlignment, pattern, pid, qualitySubstitutionMatrices,
      stringDist, unaligned, writePairwiseAlignments
  
  Test seed: 1780639412 
  [1] "Checking hamming search correctness"
  [1] "Checking levenshtein search correctness"
  Error in unlist(substitutionMatrix, substitutionMatrix) : 
    'recursive' must be a length-1 vector
  Calls: <Anonymous> ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
  Execution halted