* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/pedprobr.Rcheck’
* using R Under development (unstable) (2025-05-04 r88189)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (GCC) 15.1.0
    GNU Fortran (GCC) 15.1.0
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘pedprobr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pedprobr’ version ‘1.0.0’
* 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 ‘pedprobr’ can be installed ... [14s/29s] 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 ... 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 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 ... [24s/34s] 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 examples ... ERROR
Running examples in ‘pedprobr-Ex.R’ failed
The error most likely occurred in:

> ### Name: lumpAlleles
> ### Title: Allele lumping
> ### Aliases: lumpAlleles
> 
> ### ** Examples
> 
> x = nuclearPed() |> addMarker(geno = c(NA, NA, "1/1"), alleles = 1:5)
> 
> # Before lumping
> afreq(x, 1)
  1   2   3   4   5 
0.2 0.2 0.2 0.2 0.2 
> 
> # Lump
> y = lumpAlleles(x, verbose = TRUE)
Marker NA: 1 of 5 alleles, no model. Regular lumping: 5 -> 2
> afreq(y, 1)
   1 lump 
 0.2  0.8 
> 
> # With lumpable mutation model
> x2 = setMutmod(x, model = "equal", rate = 0.1)
> mutmod(x2, 1)
Unisex mutation matrix:
      1     2     3     4     5
1 0.900 0.025 0.025 0.025 0.025
2 0.025 0.900 0.025 0.025 0.025
3 0.025 0.025 0.900 0.025 0.025
4 0.025 0.025 0.025 0.900 0.025
5 0.025 0.025 0.025 0.025 0.900

Model: Equal 
Rate: 0.1 
Frequencies: 0.2, 0.2, 0.2, 0.2, 0.2 

Bounded: Yes 
Stationary: Yes 
Reversible: Yes 
Lumpable: Always 
Overall rate: 0.1 
> 
> y2 = lumpAlleles(x2, verbose = TRUE)
Marker NA: 1 of 5 alleles, equal model. Regular lumping: 5 -> 2
> mutmod(y2, 1)
Unisex mutation matrix:
         1  lump
1    0.900 0.100
lump 0.025 0.975

Model: Equal 
Rate: 0.1 
Frequencies: 0.2, 0.8 

Bounded: Yes 
Stationary: Yes 
Reversible: Yes 
Lumpable: Always 
Overall rate: 0.04 
> 
> # Mutation model requiring special lumping
> x3 = setMutmod(x, model = "random", rate = 0.1, seed = 1)
> mutmod(x3, 1)
Unisex mutation matrix:
            1           2           3           4           5
1 0.867523435 0.054497816 0.038121075 0.036293256 0.003564417
2 0.016300348 0.884960904 0.013972290 0.054369386 0.030397073
3 0.021258422 0.013743480 0.917791239 0.019816337 0.027390522
4 0.004512246 0.009230788 0.011097972 0.972640177 0.002518817
5 0.065103325 0.012543169 0.026695802 0.038573459 0.857084245

Model: Random 
Rate: 0.1 
Frequencies: 0.2, 0.2, 0.2, 0.2, 0.2 

Bounded: Yes 
Stationary: No 
Reversible: No 
Lumpable: Not always 
Overall rate: 0.1 
> 
> # Lump
> y3 = lumpAlleles(x3, verbose = TRUE)
Marker NA: 1 of 5 alleles, random model. Special lumping: 5 -> 2
> mutmod(y3, 1)
Unisex mutation matrix:
              1       lump
1    0.86752343 0.13247657
lump 0.02679359 0.97320641

Model: Random, lumped 
Rate: NA 
Frequencies: 0.2, 0.8 

Bounded: Yes 
Stationary: No 
Reversible: No 
Lumpable: Always 
Overall rate: 0.04793 
> 
> stopifnot(likelihood(x) == likelihood(y),
+           likelihood(x2) == likelihood(y2),
+           likelihood(x3) == likelihood(y3))
Error: likelihood(x3) == likelihood(y3) is not TRUE
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... 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
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/pedprobr.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:51.86, 101.59 + 10.30