- using R Under development (unstable) (2026-02-12 r89409)
- using platform: aarch64-apple-darwin23
- R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
- running under: macOS Sequoia 15.7.1
- using session charset: UTF-8
* current time: 2026-02-13 02:02:19 UTC
- checking for file ‘hscovar/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘hscovar’ version ‘0.4.2’
- 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 whether package ‘hscovar’ can be installed ... [2s/2s] OK
See the install log for details.
- checking installed package size ... OK
- checking package 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/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [1s/1s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... 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 examples ... [2s/2s] 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
- checking PDF version of manual ... [2s/2s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '