- 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 the install log 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:
▆
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 ... [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