* using log directory 'd:/Rcompile/CRANpkg/local/4.5/pedbuildr.Rcheck'
* using R version 4.5.3 (2026-03-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'pedbuildr/DESCRIPTION' ... OK
* this is package 'pedbuildr' version '0.4.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'pedbuildr' can be installed ... OK
* 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 ... [3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s] OK
* checking loading without being on the library search path ... [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 ... [12s] NOTE
listPOsets: no visible global function definition for '%notin%'
Undefined global functions or variables:
  %notin%
* checking Rd files ... [1s] 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] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... [4s] ERROR
Running examples in 'pedbuildr-Ex.R' failed
The error most likely occurred in:

> ### Name: buildPeds
> ### Title: Build a list of pedigrees
> ### Aliases: buildPeds
> 
> ### ** Examples
> 
> # Two individuals + 1 extra
> plist = buildPeds(1:2, extra = 1, age = "1>2")
Pedigree parameters:
  ID labels: 1, 2
  Sex: 1, 1
  Extra: 1
  Age info: 1>2
  Known PO: -
  Known non-PO: -
  No children: -
  Connected only: TRUE
  Symmetry filter: TRUE
  Max inbreeding: 0.0625
  Linear inbreeding: FALSE

Building pedigree list:
  All 2 + 0 extra: 1 solutions | 2 candidates (0.000973 secs)
  All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00422 secs)
  Total solutions: 3 
  Converting to ped
  Excessive inbreeding: 0 
  Time used: 0.0113 secs 
> plot(plist)
> 
> # Allow disconnected
> plist2 = buildPeds(1:2, extra = 1, age = "1>2", connected = FALSE)
Pedigree parameters:
  ID labels: 1, 2
  Sex: 1, 1
  Extra: 1
  Age info: 1>2
  Known PO: -
  Known non-PO: -
  No children: -
  Connected only: FALSE
  Symmetry filter: TRUE
  Max inbreeding: 0.0625
  Linear inbreeding: FALSE

Building pedigree list:
  All 2 + 0 extra: 2 solutions | 2 candidates (0.000869 secs)
  All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00365 secs)
  Total solutions: 4 
  Converting to ped
  Excessive inbreeding: 0 
  Time used: 0.00903 secs 
> plot(plist2, frames = TRUE)
> 
> # Note that full sibs require 2 extras
> plist3 = buildPeds(1:2, extra = 2, age = "1>2")
Pedigree parameters:
  ID labels: 1, 2
  Sex: 1, 1
  Extra: 2
  Age info: 1>2
  Known PO: -
  Known non-PO: -
  No children: -
  Connected only: TRUE
  Symmetry filter: TRUE
  Max inbreeding: 0.0625
  Linear inbreeding: FALSE

Building pedigree list:
  All 2 + 0 extra: 1 solutions | 2 candidates (0.000922 secs)
  All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00625 secs)
  All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0296 secs)
  Total solutions: 9 
  Converting to ped
  Excessive inbreeding: 2 
  Time used: 0.0413 secs 
> plot(plist3)
> 
> # With 2 extras, allowing any inbreeding
> plist4 = buildPeds(1:2, extra = 2, age = "1>2", maxInbreeding = 1)
Pedigree parameters:
  ID labels: 1, 2
  Sex: 1, 1
  Extra: 2
  Age info: 1>2
  Known PO: -
  Known non-PO: -
  No children: -
  Connected only: TRUE
  Symmetry filter: TRUE
  Max inbreeding: 1
  Linear inbreeding: FALSE

Building pedigree list:
  All 2 + 0 extra: 1 solutions | 2 candidates (0.00096 secs)
  All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00652 secs)
  All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0299 secs)
  Total solutions: 9 
  Converting to ped
  Time used: 0.032 secs 
> plot(plist4)
> 
> # Full sibs are also included when `extra = "parents"`
> plist5 = buildPeds(1:2, extra = "parents", age = "1>2")
Pedigree parameters:
  ID labels: 1, 2
  Sex: 1, 1
  Extra: parents
  Age info: 1>2
  Known PO: -
  Known non-PO: -
  No children: -
  Connected only: TRUE
  Symmetry filter: TRUE
  Max inbreeding: 0.0625
  Linear inbreeding: FALSE

Building pedigree list:
Error in allPOchar %notin% c(knownPOchar, notPOchar) : 
  could not find function "%notin%"
Calls: buildPeds -> buildPedsParents -> listPOsets
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [4s] ERROR
  Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pedbuildr)
  Loading required package: pedtools
  > 
  > test_check("pedbuildr")
  Saving _problems/test-buildPeds-9.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-buildPeds.R:8:3'): buildPeds cathces errors ──────────────────
  `bp(1:3, sex = 1:3, verb = F)` threw an error with unexpected message.
  Expected match: "Illegal elements found in `sex`"
  Actual message: "could not find function \"%notin%\""
  Backtrace:
      ▆
   1. ├─testthat::expect_error(bp(1:3, sex = 1:3, verb = F), "Illegal elements found in `sex`") at test-buildPeds.R:8:3
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─pedbuildr (local) bp(1:3, sex = 1:3, verb = F)
   7.   └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
   8.     └─pedbuildr:::buildPedsParents(...)
   9.       └─pedbuildr:::listPOsets(...)
  ── Error ('test-buildPeds.R:17:3'): buildPeds() parses age correctly ───────────
  Error in `allPOchar %notin% c(knownPOchar, notPOchar)`: could not find function "%notin%"
  Backtrace:
       ▆
    1. ├─testthat::expect_output(bp(1:3, age = c(1, 1, 1)), "Age info: -") at test-buildPeds.R:17:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─testthat::capture_output_lines(code, print, width = width)
    5. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
    6. │   │     ├─withr::with_output_sink(path, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. └─pedbuildr (local) bp(1:3, age = c(1, 1, 1))
   11.   └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
   12.     └─pedbuildr:::buildPedsParents(...)
   13.       └─pedbuildr:::listPOsets(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [16s] OK
* checking HTML version of manual ... [1s] OK
* DONE
Status: 2 ERRORs, 1 NOTE