* using log directory 'd:/RCompile/CRANincoming/R-devel/kmeRs.Rcheck'
* using R Under development (unstable) (2025-03-11 r87944 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'kmeRs/DESCRIPTION' ... OK
* this is package 'kmeRs' version '2.1.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Rafal Urniaz <rafal.urniaz@cantab.net>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  BLOSUM (9:180, 9:284)
  BLOcks (9:152)
  HeatMap (2:43, 9:42)
  Mers (2:10)
  SUbstitution (9:159)
  mers (9:79)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2025-03-09 as issues were not corrected
    in time.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'kmeRs' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'kmeRs-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmeRs_heatmap
> ### Title: K-mer similarity score heatmap
> ### Aliases: kmeRs_heatmap
> 
> ### ** Examples
> 
> # Use RColorBrewer to generate a figure similar to publication
> library(RColorBrewer)
> h.palette <- rev(brewer.pal(9, "YlGnBu"))
> q0 <- c("GATTACA", "ACAGATT", "GAATTAC", "GAAATCT", "CTATAGA", "GTACATA", "AACGATT")
> example <- kmeRs_similarity_matrix(q0, submat = "BLOSUM62")
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
Calls: kmeRs_similarity_matrix ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
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)
  > 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_kmeRs_package.Rmd' using rmarkdown

Quitting from lines 40-44 [unnamed-chunk-2] (Introduction_to_kmeRs_package.Rmd)
Error: processing vignette 'Introduction_to_kmeRs_package.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
--- failed re-building 'Introduction_to_kmeRs_package.Rmd'

SUMMARY: processing the following file failed:
  'Introduction_to_kmeRs_package.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... OK
* DONE
Status: 3 ERRORs, 1 NOTE