* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tidypopgen.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.3.0-5) 14.3.0
    GNU Fortran (Debian 14.3.0-5) 14.3.0
* running under: Debian GNU/Linux forky/sid
* 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 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 ‘tidypopgen’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/tidypopgen-00install.html' for details.
* used C++ compiler: ‘g++-14 (Debian 14.3.0-5) 14.3.0’
* 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/3s] 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 ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
* checking loading without being on the library search path ... [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 ... [28s/35s] OK
* checking Rd files ... [1s/2s] 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 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 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 ... [76s/114s] OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
autoplot.qc_report_loci 4.751  0.018   6.784
windows_indiv_roh       4.171  0.054   6.214
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [201s/276s] ERROR
  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [200s/275s]
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")
  Adding missing grouping variables: `population`
  [ FAIL 1 | WARN 3 | SKIP 4 | PASS 978 ]
  
  ══ 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_qc_report_indiv.R:86:3'): autoplot list ──────────────────────
  as.vector(class(plot1)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  
  [ FAIL 1 | WARN 3 | SKIP 4 | PASS 978 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [68s/104s] OK
* checking PDF version of manual ... [12s/17s] OK
* checking HTML version of manual ... [5s/8s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR