* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/kmeRs.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘kmeRs/DESCRIPTION’ ... OK
* this is package ‘kmeRs’ version ‘2.1.0’
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘kmeRs’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/kmeRs-00install.html' for details.
* 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 ... [0s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
* checking loading without being on the library search path ... [0s/1s] 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 ... [4s/6s] OK
* checking Rd files ... [0s/0s] 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 ... [5s/6s] 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 ... [6s/9s] ERROR
  Running ‘testthat.R’ [6s/8s]
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:
       â–†
    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:
       â–†
    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:
      â–†
   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:
       â–†
    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:
       â–†
    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:
       â–†
    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:
       â–†
    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 ... [6s/8s] 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 ... [4s/6s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 3 ERRORs