• using R Under development (unstable) (2026-03-08 r89578)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (3+b1)     Debian flang version 21.1.8 (3+b1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-03-10 02:13:25 UTC
• checking for file ‘hsrecombi/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘hsrecombi’ version ‘1.0.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• 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 whether package ‘hsrecombi’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
• 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 ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/4s] 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 ... [15s/19s] OK
• checking Rd files ... [0s/1s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [13s/16s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [29s/34s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘hsrecombi_workflow.Rmd’ using rmarkdown Quitting from hsrecombi_workflow.Rmd:136-166 [recombination-rate] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `{     map <- read.table(file.path(path.dat, paste0("map_chr", chr, ".map")),     col.names = c("Chr", "SNP", "locus_Mb", "locus_bp"))     genomatrix <- data.table::fread(file.path(path.dat, paste0(       "hsphase_input_chr", chr, ".raw")))     X <- as.matrix(genomatrix[, -c(1:6)])     X[is.na(X)] <- 9     daughterSire <- genomatrix$PAT     hap <- makehappm(unique(daughterSire), daughterSire, X)     save("hap", file = file.path(path.res, paste0("hsphase_output_chr", chr,       ".Rdata")))     io <- sapply(1:nrow(map), function(z) {       grepl(x = colnames(X)[z], pattern = map$SNP[z])     })     if (sum(io) != nrow(map)) stop("ERROR in dimension")     res <- hsrecombi(hap, X)     final <- editraw(res, map)     save(list = c("final", "map"), file = file.path(path.res, paste0(       "Results_chr", chr, ".Rdata")))     ifelse(nrow(final) > 0, "OK", "no result")   }`: ! task 1 failed - "argument is of length zero" --- Backtrace:     ▆  1. └─foreach(chr = 1:nchr, .packages = "hsrecombi") %dopar% ...  2. └─e$fun(obj, substitute(ex), parent.frame(), e$data) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'hsrecombi_workflow.Rmd' failed with diagnostics: task 1 failed - "argument is of length zero" --- failed re-building ‘hsrecombi_workflow.Rmd’ SUMMARY: processing the following file failed:   ‘hsrecombi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR