* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kmeRs.Rcheck’ * using R Under development (unstable) (2025-02-25 r87824) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-16) 14.2.0 GNU Fortran (Debian 14.2.0-16) 14.2.0 * 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-gcc/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 ... [0s/1s] OK * checking whether the package can be unloaded cleanly ... [0s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/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 ... [3s/5s] 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 ... [3s/4s] 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 ... [4s/5s] ERROR Running ‘testthat.R’ [4s/5s] 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 ] â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── 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 ... [4s/4s] 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/5s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 3 ERRORs