* using log directory 'd:/Rcompile/CRANpkg/local/4.5/tidypopgen.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'tidypopgen/DESCRIPTION' ... OK
* this is package 'tidypopgen' version '0.3.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: 'admixtools'
* 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 'tidypopgen' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* 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 ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [1s] 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 ... [15s] OK
* checking Rd files ... [2s] 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 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 pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [96s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [139s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [139s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tidypopgen)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: tibble
  > 
  > test_check("tidypopgen")
  Creating directory "D:/temp/2025_09_02_09_03_13_2588/RtmpgHP" which didn't exist..
  Adding missing grouping variables: `population`
  /usr/bin/which: no admixture in (/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/d/RCompile/recent/R-4.5.1/bin/x64:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:.:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/c/Program Files/MiKTeX/miktex/bin/x64:/c/Program Files/gs/gs/bin:/d/compiler/qpdf/bin:/d/RCompile/CRANpkg/extralibs/localsolver_4_0/bin:/d/RCompile/CRANpkg/extralibs/MARK:/c/Program Files/7-Zip:/d/Compiler/gretl:/c/Program Files/Quarto/bin:/d/compiler/Ruby/bin:/c/Program Files/Microsoft MPI/Bin:/c/Program Files/Python/Scripts:/c/Program Files/Python:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0:/c/Windows/System32/OpenSSH:/c/Program Files/PuTTY:/c/Program Files (x86)/WinSCP:/c/Program Files/Pandoc:/c/Program Files/MiKTeX/miktex/bin/x64:/c/Program Files (x86)/Windows Kits/10/Windows Performance Toolkit:/c/Program Files/gs/gs/bin:/c/Program Files/jdk-11.0.18.10-hotspot/bin:/d/compiler/perl/c/bin:/d/compiler/perl/perl/site/bin:/d/compiler/perl/perl/bin:/c/Users/CRAN/.cargo/bin:/c/Users/CRAN/AppData/Local/Microsoft/WindowsApps:/usr/bin:/c/Program Files/Julia/bin:/c/Users/CRAN/.cargo/bin:/d/compiler/LDC/bin:/d/RCompile/recent/R-4.5.1/bin/x64/)
  /usr/bin/which: no admixture in (/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/d/RCompile/recent/R-4.5.1/bin/x64:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:.:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/c/Program Files/MiKTeX/miktex/bin/x64:/c/Program Files/gs/gs/bin:/d/compiler/qpdf/bin:/d/RCompile/CRANpkg/extralibs/localsolver_4_0/bin:/d/RCompile/CRANpkg/extralibs/MARK:/c/Program Files/7-Zip:/d/Compiler/gretl:/c/Program Files/Quarto/bin:/d/compiler/Ruby/bin:/c/Program Files/Microsoft MPI/Bin:/c/Program Files/Python/Scripts:/c/Program Files/Python:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0:/c/Windows/System32/OpenSSH:/c/Program Files/PuTTY:/c/Program Files (x86)/WinSCP:/c/Program Files/Pandoc:/c/Program Files/MiKTeX/miktex/bin/x64:/c/Program Files (x86)/Windows Kits/10/Windows Performance Toolkit:/c/Program Files/gs/gs/bin:/c/Program Files/jdk-11.0.18.10-hotspot/bin:/d/compiler/perl/c/bin:/d/compiler/perl/perl/site/bin:/d/compiler/perl/perl/bin:/c/Users/CRAN/.cargo/bin:/c/Users/CRAN/AppData/Local/Microsoft/WindowsApps:/usr/bin:/c/Program Files/Julia/bin:/c/Users/CRAN/.cargo/bin:/d/compiler/LDC/bin:/d/RCompile/recent/R-4.5.1/bin/x64/)
  [ FAIL 5 | WARN 1 | SKIP 4 | PASS 974 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • (system2("which", args = "admixture", stdout = NULL) != 0) && (2):
    'test_gt_admix_methods.R:2:1', 'test_gt_admixture.R:2:1'
  • On CRAN (1): 'test_gt_pca.R:348:1'
  • {admixtools} is not installed (1): 'test_gt_extract_f2.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_gen_tibble_versioning.R:39:3'): versioning updates correctly through gt_order_loci ──
  dir.exists(tempfile_dir) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test_gen_tibble_versioning.R:59:3'): versioning updates correctly through gt_order_loci ──
  gt_get_file_names(test_gt)[1] (`actual`) not equal to paste0(file, "_v3.rds") (`expected`).
  
  actual vs expected
  - "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39016e2da5_v2.rds"
  + "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39016e2da5_v3.rds"
  ── Failure ('test_gen_tibble_versioning.R:60:3'): versioning updates correctly through gt_order_loci ──
  gt_get_file_names(test_gt)[2] (`actual`) not equal to paste0(file, "_v3.bk") (`expected`).
  
  actual vs expected
  - "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39016e2da5_v2.bk"
  + "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39016e2da5_v3.bk"
  ── Failure ('test_gen_tibble_versioning.R:120:3'): versioning if .bk already exists ──
  new_files[2] (`actual`) not equal to paste0(file, "_v2.bk") (`expected`).
  
  actual vs expected
  - "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39077606bb7.bk"
  + "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39077606bb7_v2.bk"
  ── Failure ('test_gen_tibble_versioning.R:137:3'): versioning if .bk already exists ──
  new_version_files[2] (`actual`) not equal to paste0(file, "_v3.bk") (`expected`).
  
  actual vs expected
  - "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39077606bb7_v2.bk"
  + "D:\\temp\\2025_09_02_09_03_13_2588\\RtmpgHP\\file2e39077606bb7_v3.bk"
  
  [ FAIL 5 | WARN 1 | SKIP 4 | PASS 974 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [51s] OK
* checking PDF version of manual ... [24s] OK
* checking HTML version of manual ... [20s] OK
* DONE
Status: 1 ERROR