R Under development (unstable) (2025-03-11 r87944 ucrt) -- "Unsuffered Consequences"
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> # 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)
> library(pwalign)
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: Biostrings
Loading required package: XVector
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_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