Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(kmeRs)
  > 
  > test_check("kmeRs")
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-kmeRs_heatmap.R:5:3'): Generate similarity matrix and display as a heatmap ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
  Backtrace:
       ▆
    1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_heatmap.R:5:3
    2. │ ├─base::as.vector(...)
    3. │ └─base::sapply(...)
    4. │   └─base::lapply(X = X, FUN = FUN, ...)
    5. │     └─kmeRs (local) FUN(X[[i]], ...)
    6. │       ├─BiocGenerics::score(...)
    7. │       └─kmeRs:::kmeRs_twoSeqSim(...)
    8. │         ├─pwalign::pairwiseAlignment(...)
    9. │         └─pwalign::pairwiseAlignment(...)
   10. │           └─pwalign (local) .local(pattern, subject, ...)
   11. │             └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
   12. │               └─pwalign:::XStringSet.pairwiseAlignment(...)
   13. │                 ├─base::array(...)
   14. │                 └─base::unlist(substitutionMatrix, substitutionMatrix)
   15. │                   └─base::stop("'recursive' must be a length-1 vector")
   16. └─base::.handleSimpleError(...)
   17.   └─base (local) h(simpleError(msg, call))
  ── Error ('test-kmeRs_score.R:5:3'): Generate similarity matrix for given k-mers ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
  Backtrace:
       ▆
    1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_score.R:5:3
    2. │ ├─base::as.vector(...)
    3. │ └─base::sapply(...)
    4. │   └─base::lapply(X = X, FUN = FUN, ...)
    5. │     └─kmeRs (local) FUN(X[[i]], ...)
    6. │       ├─BiocGenerics::score(...)
    7. │       └─kmeRs:::kmeRs_twoSeqSim(...)
    8. │         ├─pwalign::pairwiseAlignment(...)
    9. │         └─pwalign::pairwiseAlignment(...)
   10. │           └─pwalign (local) .local(pattern, subject, ...)
   11. │             └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
   12. │               └─pwalign:::XStringSet.pairwiseAlignment(...)
   13. │                 ├─base::array(...)
   14. │                 └─base::unlist(substitutionMatrix, substitutionMatrix)
   15. │                   └─base::stop("'recursive' must be a length-1 vector")
   16. └─base::.handleSimpleError(...)
   17.   └─base (local) h(simpleError(msg, call))
  ── Error ('test-kmeRs_show_alignment.R:3:3'): multiplication works ─────────────
  Error in `unlist(substitutionMatrix, substitutionMatrix)`: 'recursive' must be a length-1 vector
  Backtrace:
      ▆
   1. └─kmeRs::kmeRs_show_alignment(...) at test-kmeRs_show_alignment.R:3:3
   2.   └─kmeRs:::kmeRs_twoSeqSim(...)
   3.     ├─pwalign::pairwiseAlignment(...)
   4.     └─pwalign::pairwiseAlignment(...)
   5.       └─pwalign (local) .local(pattern, subject, ...)
   6.         └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
   7.           └─pwalign:::XStringSet.pairwiseAlignment(...)
   8.             ├─base::array(...)
   9.             └─base::unlist(substitutionMatrix, substitutionMatrix)
  ── Error ('test-kmeRs_similarity_matrix.R:3:3'): Generate BLOSUM62 matrix ──────
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
  Backtrace:
       ▆
    1. ├─testthat::expect_true(is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))) at test-kmeRs_similarity_matrix.R:3:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))
    5. ├─kmeRs::kmeRs_similarity_matrix(submat = "BLOSUM62")
    6. │ ├─base::as.vector(...)
    7. │ └─base::sapply(...)
    8. │   └─base::lapply(X = X, FUN = FUN, ...)
    9. │     └─kmeRs (local) FUN(X[[i]], ...)
   10. │       ├─BiocGenerics::score(...)
   11. │       └─kmeRs:::kmeRs_twoSeqSim(...)
   12. │         ├─pwalign::pairwiseAlignment(...)
   13. │         └─pwalign::pairwiseAlignment(...)
   14. │           └─pwalign (local) .local(pattern, subject, ...)
   15. │             └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
   16. │               └─pwalign:::XStringSet.pairwiseAlignment(...)
   17. │                 ├─base::array(...)
   18. │                 └─base::unlist(substitutionMatrix, substitutionMatrix)
   19. │                   └─base::stop("'recursive' must be a length-1 vector")
   20. └─base::.handleSimpleError(...)
   21.   └─base (local) h(simpleError(msg, call))
  ── Error ('test-kmeRs_similarity_matrix.R:10:3'): Generate similarity matrix for given k-mer ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
  Backtrace:
       ▆
    1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_similarity_matrix.R:10:3
    2. │ ├─base::as.vector(...)
    3. │ └─base::sapply(...)
    4. │   └─base::lapply(X = X, FUN = FUN, ...)
    5. │     └─kmeRs (local) FUN(X[[i]], ...)
    6. │       ├─BiocGenerics::score(...)
    7. │       └─kmeRs:::kmeRs_twoSeqSim(...)
    8. │         ├─pwalign::pairwiseAlignment(...)
    9. │         └─pwalign::pairwiseAlignment(...)
   10. │           └─pwalign (local) .local(pattern, subject, ...)
   11. │             └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
   12. │               └─pwalign:::XStringSet.pairwiseAlignment(...)
   13. │                 ├─base::array(...)
   14. │                 └─base::unlist(substitutionMatrix, substitutionMatrix)
   15. │                   └─base::stop("'recursive' must be a length-1 vector")
   16. └─base::.handleSimpleError(...)
   17.   └─base (local) h(simpleError(msg, call))
  ── Error ('test-kmeRs_similarity_matrix.R:19:3'): Generate similarity matrix for given k-mers ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
  Backtrace:
       ▆
    1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_similarity_matrix.R:19:3
    2. │ ├─base::as.vector(...)
    3. │ └─base::sapply(...)
    4. │   └─base::lapply(X = X, FUN = FUN, ...)
    5. │     └─kmeRs (local) FUN(X[[i]], ...)
    6. │       ├─BiocGenerics::score(...)
    7. │       └─kmeRs:::kmeRs_twoSeqSim(...)
    8. │         ├─pwalign::pairwiseAlignment(...)
    9. │         └─pwalign::pairwiseAlignment(...)
   10. │           └─pwalign (local) .local(pattern, subject, ...)
   11. │             └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
   12. │               └─pwalign:::XStringSet.pairwiseAlignment(...)
   13. │                 ├─base::array(...)
   14. │                 └─base::unlist(substitutionMatrix, substitutionMatrix)
   15. │                   └─base::stop("'recursive' must be a length-1 vector")
   16. └─base::.handleSimpleError(...)
   17.   └─base (local) h(simpleError(msg, call))
  ── Error ('test-kmeRs_statistics.R:5:3'): Calculate basic statistics for the matrix ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
  Backtrace:
       ▆
    1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_statistics.R:5:3
    2. │ ├─base::as.vector(...)
    3. │ └─base::sapply(...)
    4. │   └─base::lapply(X = X, FUN = FUN, ...)
    5. │     └─kmeRs (local) FUN(X[[i]], ...)
    6. │       ├─BiocGenerics::score(...)
    7. │       └─kmeRs:::kmeRs_twoSeqSim(...)
    8. │         ├─pwalign::pairwiseAlignment(...)
    9. │         └─pwalign::pairwiseAlignment(...)
   10. │           └─pwalign (local) .local(pattern, subject, ...)
   11. │             └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
   12. │               └─pwalign:::XStringSet.pairwiseAlignment(...)
   13. │                 ├─base::array(...)
   14. │                 └─base::unlist(substitutionMatrix, substitutionMatrix)
   15. │                   └─base::stop("'recursive' must be a length-1 vector")
   16. └─base::.handleSimpleError(...)
   17.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted