* using log directory ‘/srv/hornik/tmp/CRAN_pretest/biometryassist.Rcheck’
* using R Under development (unstable) (2026-02-03 r89372)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1+b1)
    Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-02-03 05:11:05Z
* checking for file ‘biometryassist/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biometryassist’ version ‘1.4.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Sam Rogers <biometrytraining@adelaide.edu.au>’

Suggests or Enhances not in mainstream repositories:
  asreml

Found the following (possibly) invalid URLs:
  URL: https://pure.au.dk/portal/en/publications/how-to-obtain-those-nasty-standard-errors-from-transformed-data-a (moved to https://pure.au.dk/portal/en/publications/how-to-obtain-those-nasty-standard-errors-from-transformed-data-a/)
    From: man/multiple_comparisons.Rd
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 ‘biometryassist’ can be installed ... [4s/4s] OK
* 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 ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] 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 ... [1s/1s] 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 ... [11s/11s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [100s/51s] ERROR
  Running ‘testthat.R’ [99s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biometryassist)
  > 
  > test_check("biometryassist")
  Starting 2 test processes.
  > test-satab.R: Source of Variation                     df
  > test-satab.R: =============================================
  > test-satab.R: trt                                     3
  > test-satab.R: Residual                                16
  > test-satab.R: =============================================
  > test-satab.R: Total                                   19
  > test-utility_functions.R:     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  > test-utility_functions.R:     |  biometryassist version 1.4.0                                     |
  > test-utility_functions.R:     |  Authors: Sharon Nielsen, Sam Rogers, Annie Conway                |
  > test-utility_functions.R:     |  Developed at the University of Adelaide with funding provided    |
  > test-utility_functions.R:     |  by the Australian Grains Research and Development Corporation.   |
  > test-utility_functions.R:     |  Package website: https://biometryhub.github.io/biometryassist    |
  > test-utility_functions.R:     |                                                                   |
  > test-utility_functions.R:     |  If you have used this package in your work, please cite it.      |
  > test-utility_functions.R:     |  Type 'citation('biometryassist')' for the citation details.      |
  > test-utility_functions.R:     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  > test-utility_functions.R: 
  > test-utility_functions.R: NULL
  > test-resplot.R: [[1]]
  > test-resplot.R: 
  Saving _problems/test-zzz_install_asreml-19.R
  > test-resplot.R: [[1]]
  > test-resplot.R: 
  > test-resplot.R: [[1]]
  > test-resplot.R: 
  [ FAIL 1 | WARN 2 | SKIP 177 | PASS 1482 ]
  
  ══ Skipped tests (177) ═════════════════════════════════════════════════════════
  • On CRAN (161): 'test-all-w2.r:5:5', 'test-all-w2.r:19:5',
    'test-all-w2.r:32:5', 'test-all-w2.r:45:5', 'test-all-w2.r:58:5',
    'test-all-w2.r:72:5', 'test-all-w2.r:87:5', 'test-all-w2.r:132:5',
    'test-all-w2.r:157:5', 'test-all-w2.r:186:5', 'test-all-w2.r:202:5',
    'test-all-w2.r:216:5', 'test-all-w2.r:230:5', 'test-all-w2.r:240:5',
    'test-all-w2.r:253:5', 'test-all-w2.r:266:5', 'test-all-w2.r:280:5',
    'test-all-w2.r:291:5', 'test-all-w2.r:305:5', 'test-all-w2.r:319:5',
    'test-all-w2.r:337:5', 'test-all-w2.r:352:5', 'test-all-w2.r:378:5',
    'test-all-w2.r:408:5', 'test-heatmap.R:25:1', 'test-heatmap.R:37:1',
    'test-heatmap.R:42:1', 'test-heatmap.R:47:1', 'test-heatmap.R:54:1',
    'test-heatmap.R:61:1', 'test-mct.R:319:1', 'test-mct.R:381:1',
    'test-mct.R:394:1', 'test-mct.R:407:1', 'test-mct.R:429:1',
    'test-mct.R:442:1', 'test-mct.R:645:1', 'test-mct.R:655:1',
    'test-mct.R:667:1', 'test-mct.R:682:1', 'test-mct.R:708:1',
    'test-mct.R:730:1', 'test-mct.R:824:1', 'test-mct.R:840:1',
    'test-mct.R:875:1', 'test-mct.R:906:1', 'test-mct.R:947:1',
    'test-mct.R:963:1', 'test-design.R:1:1', 'test-design.R:16:1',
    'test-design.R:32:1', 'test-design.R:47:1', 'test-design.R:59:1',
    'test-design.R:74:1', 'test-design.R:119:1', 'test-design.R:137:1',
    'test-design.R:151:1', 'test-design.R:165:1', 'test-design.R:179:1',
    'test-design.R:212:1', 'test-design.R:227:1', 'test-design.R:241:1',
    'test-design.R:254:1', 'test-design.R:265:1', 'test-design.R:280:1',
    'test-design.R:295:1', 'test-design.R:310:1', 'test-design.R:324:1',
    'test-design.R:352:1', 'test-design.R:470:1', 'test-design.R:619:1',
    'test-design.R:652:1', 'test-design.R:662:1', 'test-design.R:669:1',
    'test-design.R:676:1', 'test-design.R:683:1', 'test-design.R:690:1',
    'test-design.R:709:1', 'test-design.R:726:1', 'test-design.R:743:1',
    'test-design.R:760:1', 'test-design.R:777:1', 'test-design.R:794:1',
    'test-design.R:833:1', 'test-design.R:858:1', 'test-design.R:892:1',
    'test-design.R:925:1', 'test-design.R:972:1', 'test-design.R:986:1',
    'test-summary_graph.R:7:1', 'test-summary_graph.R:13:1',
    'test-summary_graph.R:19:1', 'test-use_template.R:9:3',
    'test-use_template.R:18:3', 'test-use_template.R:27:3',
    'test-use_template.R:38:3', 'test-use_template.R:49:3',
    'test-use_template.R:59:3', 'test-use_template.R:75:3',
    'test-use_template.R:97:3', 'test-use_template.R:116:3',
    'test-utility_functions.R:6:1', 'test-variogram.r:74:5',
    'test-variogram.r:139:5', 'test-variogram.r:190:5',
    'test-zzz_install_asreml.R:234:5', 'test-zzz_install_asreml.R:260:5',
    'test-zzz_install_asreml.R:277:5', 'test-zzz_install_asreml.R:396:5',
    'test-zzz_install_asreml.R:411:5', 'test-zzz_install_asreml.R:566:5',
    'test-zzz_install_asreml.R:575:5', 'test-zzz_install_asreml.R:587:5',
    'test-zzz_install_asreml.R:599:5', 'test-zzz_install_asreml.R:627:5',
    'test-zzz_install_asreml.R:641:5', 'test-zzz_install_asreml.R:651:5',
    'test-zzz_install_asreml.R:680:5', 'test-zzz_install_asreml.R:694:5',
    'test-zzz_install_asreml.R:708:5', 'test-zzz_install_asreml.R:719:5',
    'test-zzz_install_asreml.R:737:5', 'test-zzz_install_asreml.R:761:5',
    'test-zzz_install_asreml.R:782:5', 'test-zzz_install_asreml.R:803:5',
    'test-zzz_install_asreml.R:818:5', 'test-zzz_install_asreml.R:833:5',
    'test-zzz_install_asreml.R:843:5', 'test-zzz_install_asreml.R:853:5',
    'test-zzz_install_asreml.R:862:5', 'test-zzz_install_asreml.R:875:5',
    'test-zzz_install_asreml.R:884:5', 'test-zzz_install_asreml.R:900:5',
    'test-zzz_install_asreml.R:916:5', 'test-zzz_install_asreml.R:937:5',
    'test-zzz_install_asreml.R:956:5', 'test-zzz_install_asreml.R:984:5',
    'test-zzz_install_asreml.R:1015:5', 'test-zzz_install_asreml.R:1083:5',
    'test-zzz_install_asreml.R:1106:5', 'test-zzz_install_asreml.R:1132:5',
    'test-zzz_install_asreml.R:1154:5', 'test-zzz_install_asreml.R:1179:5',
    'test-zzz_install_asreml.R:1205:5', 'test-zzz_install_asreml.R:1229:5',
    'test-zzz_install_asreml.R:1262:5', 'test-zzz_install_asreml.R:1295:5',
    'test-zzz_install_asreml.R:1328:5', 'test-zzz_install_asreml.R:1350:5',
    'test-zzz_install_asreml.R:1374:5', 'test-zzz_install_asreml.R:1391:5',
    'test-zzz_install_asreml.R:1410:5', 'test-resplot.R:17:1',
    'test-resplot.R:23:1', 'test-resplot.R:33:1', 'test-resplot.R:63:5',
    'test-resplot.R:93:1', 'test-resplot.R:111:1', 'test-resplot.R:119:1',
    'test-resplot.R:138:1', 'test-resplot.R:149:1'
  • On Linux (2): 'test-resplot.R:106:5', 'test-resplot.R:134:5'
  • rlang::is_installed("asreml") is not TRUE (8): 'test-logltest.R:4:5',
    'test-logltest.R:26:5', 'test-logltest.R:34:5', 'test-logltest.R:47:5',
    'test-logltest.R:59:5', 'test-logltest.R:75:5', 'test-logltest.R:92:5',
    'test-logltest.R:98:5'
  • {asreml} is not installed (4): 'test-mct.R:692:5', 'test-mct.R:743:5',
    'test-mct.R:798:5', 'test-mct.R:806:5'
  • {lme4} is not installed (2): 'test-mct.R:813:5', 'test-resplot.R:87:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-zzz_install_asreml.R:19:9'): get_r_os returns correct structure and values ──
  Expected `result$os_ver` to match regexp "^[-a-z0-9]+-[0-9]+-[0-9]{2}(-arm)?$".
  Actual text:
  x | debian-NA-46
  
  [ FAIL 1 | WARN 2 | SKIP 177 | PASS 1482 ]
  Deleting unused snapshots: 'all-w2/example1autoplot.svg',
  'all-w2/example2autoplot.svg', 'all-w2/example3autoplot.svg',
  'all-w2/example3lmmautoplot.svg', 'all-w2/example4autoplot.svg',
  'all-w2/example4lmmautoplot.svg', 'all-w2/example5lmmautoplot1.svg',
  'all-w2/example5lmmautoplot2.svg', 'all-w2/example6lmmautoplot2.svg',
  'all-w2/example7lmmautoplot.svg', 'all-w2/exercise10autoplot.svg',
  'all-w2/exercise11autoplot1.svg', 'all-w2/exercise11autoplot2.svg',
  'all-w2/exercise12autoplot.svg', 'all-w2/exercise13autoplot1.svg',
  'all-w2/exercise13autoplot2.svg', 'all-w2/exercise14autoplot.svg',
  'all-w2/exercise15autoplot1.svg', …,
  'variogram/variogram-palette-colourblind.svg', and
  'variogram/variogram-produced.svg'
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [5s/5s] OK
* 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: 1 ERROR, 1 NOTE