* using log directory 'd:/RCompile/CRANincoming/R-devel/optiSel.Rcheck'
* using R Under development (unstable) (2024-05-27 r86634 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'optiSel/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'optiSel' version '2.0.8'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Robin Wellmann <r.wellmann@uni-hohenheim.de>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  genotype (9:331)
  haplotype (9:394)
  introgressed (9:521)
  kinships (9:365, 9:375)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-12-06 as requires archived package
    'nadiv'.
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'optiSel' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 13.2.0'
* checking installed package size ... OK
* 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 ... 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 ... [31s] 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 ... ERROR
Running examples in 'optiSel-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: candes
> ### Title: Candidate Description
> ### Aliases: candes
> 
> ### ** Examples
> 
> data(PedigWithErrors)
> 
> Pedig      <- prePed(PedigWithErrors, thisBreed="Hinterwaelder", lastNative=1970, 
+                    keep=PedigWithErrors$Born%in%1992)
Pedigree loops were detected. We recommend to correct them manually before
using prePed(). The parents of the following individuals are set to unknown
to remove the loops.
                           Sire             Dam
276000802875148 276000803622423 276000890878480
276000811476506 276000810087663 276000811476506

The sex of the following animals was not compatible with the pedigree, so
it was modified:
                           Sire             Dam
276000810087663 276000802940621 276000802925028

> use        <- Pedig$Born %in% (1980:1990) & Pedig$Breed=="Hinterwaelder"
> Population <- Pedig$Indiv[use]
> 
> Pedig$NC   <- pedBreedComp(Pedig, thisBreed="Hinterwaelder")$native
> pKin       <- pedIBD(Pedig, keep.only=Population)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [19s] ERROR
Error(s) in re-building vignettes:
--- re-building 'ocs-vignette.Rmd' using rmarkdown

* checking PDF version of manual ... [29s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE