Last updated on 2026-03-30 06:51:22 CEST.
| Package | ERROR | OK |
|---|---|---|
| hscovar | 14 | |
| hsrecombi | 1 | 13 |
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 1.1.0
Check: re-building of vignette outputs
Result: 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 2 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 2 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
Flavor: r-devel-linux-x86_64-fedora-gcc