Last updated on 2026-03-07 04:50:46 CET.
| Package | ERROR | OK |
|---|---|---|
| hscovar | 1 | 13 |
| hsrecombi | 1 | 13 |
Current CRAN status: ERROR: 1, OK: 13
Version: 0.4.2
Check: examples
Result: ERROR
Running examples in ‘hscovar-Ex.R’ failed
The error most likely occurred in:
> ### Name: tagSNP
> ### Title: tagSNP
> ### Aliases: tagSNP
>
> ### ** Examples
>
> ### 1: INPUT DATA
> data(testdata)
> ### 2: COVARIANCE/CORRELATION MATRIX
> corrmat <- CovMat(matLD, H.sire, 100, pos.chr, corr = TRUE)
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: lapply(X = S, FUN = FUN, ...)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
6: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
7: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
8: FUN(X[[i]], ...)
9: lapply(seq_len(cores), inner.do)
10: mclapply(e1, tcrossprod)
11: CovarMatrix(expectationMat, linkMat, linkSire, Ns)
12: CovMat(matLD, H.sire, 100, pos.chr, corr = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Warning in mclapply(e1, tcrossprod) :
scheduled core 1 did not deliver a result, all values of the job will be affected
0 SNPs have non-zero variance -> output matrix has reduced dimensions.
Error in `rownames<-`(`*tmp*`, value = 1:p) :
attempt to set 'rownames' on an object with no dimensions
Calls: CovMat -> rownames<-
Execution halted
Flavor: r-devel-macos-arm64
Current CRAN status: ERROR: 1, OK: 13
Version: 1.0.1
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 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
Flavor: r-oldrel-windows-x86_64