* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/optiSel.Rcheck’
* using R Under development (unstable) (2026-08-25 r90448)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-26 18:44:14 UTC
* checking for file ‘optiSel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘optiSel’ 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 whether package ‘optiSel’ can be installed ... [103s/191s] OK
* used C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [23s/52s] OK
* checking Rd files ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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 ... [29s/68s] OK
* checking examples with --run-donttest ... [9s/31s] ERROR
Running examples in ‘optiSel-Ex.R’ failed
The error most likely occurred in:

> ### Name: haplofreq
> ### Title: Evaluates the Occurrence of Haplotype Segments in Particular
> ###   Breeds
> ### Aliases: haplofreq
> 
> ### ** Examples
> 
> data(map)
> data(Cattle)
> dir   <- system.file("extdata", package="optiSel")
> files <- file.path(dir, paste("Chr", 1:2, ".phased", sep=""))
> 
> Freq <- freqlist(
+  haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Rotbunt",   minL=2.0),
+  haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Holstein",  minL=2.0),
+  haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Fleckvieh", minL=2.0)
+   )
Using  skip = 2 
Using cskip = 2 
Reading chromosome  1 ...  M=400, Reference breeds: Rotbunt
Reading chromosome  2 ...  M=400, Reference breeds: Rotbunt
Using  skip = 2 
Using cskip = 2 
Reading chromosome  1 ...  M=400, Reference breeds: Holstein
Reading chromosome  2 ...  M=400, Reference breeds: Holstein
Using  skip = 2 
Using cskip = 2 
Reading chromosome  1 ...  M=400, Reference breeds: Fleckvieh
Reading chromosome  2 ...  M=400, Reference breeds: Fleckvieh
> 
> plot(Freq, ID=1, hap=2, refBreed="Rotbunt")
> plot(Freq, ID=1, hap=2, refBreed="Holstein", Chr=1)
> 
> ## No test: 
> ## Test for using multiple cores:
> 
> Freq1 <- haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Rotbunt", 
+                    minL=2.0, cores=NA)$freq
Using  skip = 2 
Using cskip = 2 
Using 2 cores... finished.
> range(Freq[[1]]-Freq1)
[1] 0 0
> #[1] 0 0
> ## End(No test)
> 
> ## Creating output files with allele frequencies and allele origins:
> ## No test: 
> rdir  <- system.file("extdata", package = "optiSel")
> wdir  <- file.path(tempdir(), "HaplotypeEval")
> chr   <- unique(map$Chr)
> files <- file.path(rdir, paste("Chr", chr, ".phased", sep=""))
> wfile <- haplofreq(files, Cattle, map, thisBreed="Angler", minL=2.0, w.dir=wdir)
Using  skip = 2 
Using cskip = 2 
Reading chromosome  1 ...  M=400, Reference breeds: Holstein Fleckvieh Rotbunt
Reading chromosome  2 ...  M=400, Reference breeds: Holstein Fleckvieh Rotbunt
> 
> View(read.table(wfile$match[1],skip=1))
Warning in check_screen_device("View()") : View() should not be used in examples etc

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: View(read.table(wfile$match[1], skip = 1))
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [62s/147s] OK
* checking PDF version of manual ... [6s/15s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-donttest/optiSel.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 11:05.97, 275.50 + 24.67