* using log directory ‘/srv/hornik/tmp/CRAN/optiSel.Rcheck’
* using R Under development (unstable) (2024-05-27 r86634)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.4 (1)
    Debian flang-new version 18.1.4 (1)
* running under: Debian GNU/Linux trixie/sid
* 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 ... [3s/4s] NOTE
Maintainer: ‘Robin Wellmann <r.wellmann@uni-hohenheim.de>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  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 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 ... [63s/63s] OK
* used C++ compiler: ‘Debian clang version 18.1.5 (2)’
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [2s/2s] 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 ... [16s/16s] OK
* checking Rd files ... [0s/0s] 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 ... [0s/0s] 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 ... [3s/3s] 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)

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: rcpp_makeA_lowMem(as.integer(Pedig$numSire), as.integer(Pedig$numDam),     AFounder, as.integer(numFounder - 1), as.character(indKeep),     as.integer(numKeep - 1), as.integer(Pedig$Indiv %in% indKeep),     as.integer(Pedig$nOff))
 2: makeA(Pedig, keep.only = keep.only, keep = keep, AFounder = AFounder)
 3: pedIBD(Pedig, keep.only = Population)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s/22s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ocs-vignette.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: rcpp_makeA_lowMem(as.integer(Pedig$numSire), as.integer(Pedig$numDam),     AFounder, as.integer(numFounder - 1), as.character(indKeep),     as.integer(numKeep - 1), as.integer(Pedig$Indiv %in% indKeep),     as.integer(Pedig$nOff))
 2: makeA(Pedig, keep.only = keep.only, keep = keep, AFounder = AFounder)
 3: pedIBD(Pedig, keep.only = phen$Indiv)
 4: eval(expr, envir, enclos)
 5: eval(expr, envir, enclos)
 6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
 9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
12: evaluate::evaluate(...)
13: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
14: in_dir(input_dir(), expr)
15: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
16: eng_r(options)
17: block_exec(params)
18: call_block(x)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(e, loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
22: process_file(text, output)
23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
25: vweave_rmarkdown(...)
26: engine$weave(file, quiet = quiet, encoding = enc)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
31: tools:::.buildOneVignette("ocs-vignette.Rmd", "/srv/hornik/tmp/CRAN/optiSel.Rcheck/vign_test/optiSel",     TRUE, FALSE, "ocs-vignette", "UTF-8", "/tmp/RtmpTinVwU/working_dir/RtmpdkVz9l/file33a5656da2a22c.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
--- re-building ‘ped-vignette.Rmd’ using rmarkdown
** Processing: /srv/hornik/tmp/CRAN/optiSel.Rcheck/vign_test/optiSel/vignettes/ped-vignette_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4897 bytes
Input file size = 5743 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4258
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4258

Output IDAT size = 4258 bytes (639 bytes decrease)
Output file size = 4336 bytes (1407 bytes = 24.50% decrease)

** Processing: /srv/hornik/tmp/CRAN/optiSel.Rcheck/vign_test/optiSel/vignettes/ped-vignette_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15408 bytes
Input file size = 15498 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12253
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12253

Output IDAT size = 12253 bytes (3155 bytes decrease)
Output file size = 12331 bytes (3167 bytes = 20.43% decrease)


 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: rcpp_makeA_lowMem(as.integer(Pedig$numSire), as.integer(Pedig$numDam),     AFounder, as.integer(numFounder - 1), as.character(indKeep),     as.integer(numKeep - 1), as.integer(Pedig$Indiv %in% indKeep),     as.integer(Pedig$nOff))
 2: makeA(Pedig, keep.only = keep.only, keep = keep, AFounder = AFounder)
 3: pedIBD(Pedig, keep.only = Phen$Indiv)
 4: eval(expr, envir, enclos)
 5: eval(expr, envir, enclos)
 6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
 9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
12: evaluate::evaluate(...)
13: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
14: in_dir(input_dir(), expr)
15: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
16: eng_r(options)
17: block_exec(params)
18: call_block(x)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(e, loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
22: process_file(text, output)
23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
25: vweave_rmarkdown(...)
26: engine$weave(file, quiet = quiet, encoding = enc)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
31: tools:::.buildOneVignette("ped-vignette.Rmd", "/srv/hornik/tmp/CRAN/optiSel.Rcheck/vign_test/optiSel",     TRUE, FALSE, "ped-vignette", "UTF-8", "/tmp/RtmpTinVwU/working_dir/RtmpdkVz9l/file33a56573287bb6.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
--- re-building ‘seg-vignette.Rmd’ using rmarkdown
** Processing: /srv/hornik/tmp/CRAN/optiSel.Rcheck/vign_test/optiSel/vignettes/seg-vignette_files/figure-html/unnamed-chunk-11-1.png
288x288 pixels, 8 bits/pixel, 253 colors in palette
Input IDAT size = 4226 bytes
Input file size = 5075 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3879
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3844
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3844

Output IDAT size = 3844 bytes (382 bytes decrease)
Output file size = 4693 bytes (382 bytes = 7.53% decrease)

** Processing: /srv/hornik/tmp/CRAN/optiSel.Rcheck/vign_test/optiSel/vignettes/seg-vignette_files/figure-html/unnamed-chunk-12-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18710 bytes
Input file size = 18812 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15069
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15069

Output IDAT size = 15069 bytes (3641 bytes decrease)
Output file size = 15147 bytes (3665 bytes = 19.48% decrease)

** Processing: /srv/hornik/tmp/CRAN/optiSel.Rcheck/vign_test/optiSel/vignettes/seg-vignette_files/figure-html/unnamed-chunk-13-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21720 bytes
Input file size = 21822 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17345
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17345

Output IDAT size = 17345 bytes (4375 bytes decrease)
Output file size = 17423 bytes (4399 bytes = 20.16% decrease)

--- finished re-building ‘seg-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘ocs-vignette.Rmd’ ‘ped-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE