- using R version 4.5.1 (2025-06-13)
- using platform: x86_64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.3.1
- using session charset: UTF-8
- checking for file ‘biometryassist/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘biometryassist’ version ‘1.3.1’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘asreml’
- 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 ... [8s/10s] OK
See the install log for details.
- 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 ... [2s/2s] 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/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 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 ... [8s/10s] OK
- checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [13s/19s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [73s/64s] ERROR
Running ‘testthat.R’ [73s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(biometryassist)
>
> test_check("biometryassist")
Starting 2 test processes
[ FAIL 1 | WARN 2 | SKIP 156 | PASS 316 ]
══ Skipped tests (156) ═════════════════════════════════════════════════════════
• .check_package_available("asreml") is not TRUE (12): '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', 'test-mct.R:111:5', 'test-mct.R:162:5',
'test-mct.R:217:5', 'test-mct.R:225:5'
• On CRAN (141): 'test-des.R:8:5', 'test-des.R:21:5', 'test-all-w2.r:4:5',
'test-all-w2.r:19:5', 'test-all-w2.r:33:5', 'test-all-w2.r:47:5',
'test-all-w2.r:61:5', 'test-all-w2.r:78:5', 'test-all-w2.r:96:5',
'test-all-w2.r:116:5', 'test-all-w2.r:143:5', 'test-all-w2.r:174:5',
'test-all-w2.r:190:5', 'test-all-w2.r:205:5', 'test-all-w2.r:219:5',
'test-all-w2.r:230:5', 'test-all-w2.r:244:5', 'test-all-w2.r:258:5',
'test-all-w2.r:274:5', 'test-all-w2.r:287:5', 'test-all-w2.r:305:5',
'test-all-w2.r:323:5', 'test-all-w2.r:345:5', 'test-all-w2.r:364:5',
'test-all-w2.r:395:5', 'test-all-w2.r:429:5', 'test-heatmap.R:26:5',
'test-heatmap.R:38:5', 'test-heatmap.R:43:5', 'test-heatmap.R:48:5',
'test-heatmap.R:53:5', 'test-heatmap.R:60:5', 'test-heatmap.R:67:5',
'test-design.R:9:5', 'test-design.R:21:5', 'test-design.R:34:5',
'test-design.R:45:5', 'test-design.R:56:5', 'test-design.R:70:5',
'test-design.R:83:5', 'test-design.R:95:5', 'test-design.R:106:5',
'test-design.R:118:5', 'test-design.R:130:5', 'test-design.R:155:5',
'test-design.R:166:5', 'test-design.R:176:5', 'test-design.R:184:5',
'test-design.R:196:5', 'test-design.R:209:5', 'test-design.R:222:5',
'test-design.R:233:5', 'test-design.R:244:5', 'test-design.R:276:5',
'test-design.R:379:5', 'test-design.R:481:5', 'test-design.R:500:5',
'test-design.R:510:5', 'test-design.R:518:5', 'test-design.R:552:5',
'test-design.R:558:5', 'test-design.R:564:5', 'test-design.R:570:5',
'test-design.R:584:5', 'test-design.R:601:5', 'test-design.R:616:5',
'test-design.R:631:5', 'test-design.R:646:5', 'test-design.R:661:5',
'test-design.R:675:5', 'test-design.R:703:5', 'test-design.R:716:5',
'test-design.R:760:5', 'test-design.R:789:5', 'test-design.R:858:5',
'test-design.R:870:5', 'test-mct.R:6:5', 'test-mct.R:49:5',
'test-mct.R:68:5', 'test-mct.R:80:5', 'test-mct.R:94:5', 'test-mct.R:101:5',
'test-mct.R:146:5', 'test-mct.R:155:5', 'test-mct.R:240:5',
'test-mct.R:252:5', 'test-mct.R:268:5', 'test-mct.R:300:5',
'test-mct.R:313:5', 'test-mct.R:334:5', 'test-summary_graph.R:8:5',
'test-summary_graph.R:14:5', 'test-summary_graph.R:20:5',
'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:8:5',
'test-zzz_install_asreml.R:20:5', 'test-zzz_install_asreml.R:46:5',
'test-zzz_install_asreml.R:63:5', 'test-zzz_install_asreml.R:128:5',
'test-zzz_install_asreml.R:143:5', 'test-zzz_install_asreml.R:224:5',
'test-zzz_install_asreml.R:233:5', 'test-zzz_install_asreml.R:245:5',
'test-zzz_install_asreml.R:257:5', 'test-zzz_install_asreml.R:285:5',
'test-zzz_install_asreml.R:299:5', 'test-zzz_install_asreml.R:309:5',
'test-zzz_install_asreml.R:338:5', 'test-zzz_install_asreml.R:347:5',
'test-zzz_install_asreml.R:360:5', 'test-zzz_install_asreml.R:369:5',
'test-zzz_install_asreml.R:394:5', 'test-zzz_install_asreml.R:414:5',
'test-zzz_install_asreml.R:442:5', 'test-zzz_install_asreml.R:468:5',
'test-zzz_install_asreml.R:506:5', 'test-zzz_install_asreml.R:545:5',
'test-zzz_install_asreml.R:622:5', 'test-zzz_install_asreml.R:656:5',
'test-zzz_install_asreml.R:682:5', 'test-resplot.R:6:5',
'test-resplot.R:13:5', 'test-resplot.R:25:5', 'test-resplot.R:29:5',
'test-resplot.R:56:5', 'test-resplot.R:70:5', 'test-resplot.R:83:5',
'test-resplot.R:92:5', 'test-resplot.R:103:5', 'test-resplot.R:117:5',
'test-resplot.R:131:5', 'test-resplot.R:156:5', 'test-resplot.R:173:5'
• On Mac (3): 'test-variogram.r:20:5', 'test-variogram.r:50:5',
'test-variogram.r:68:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-zzz_install_asreml.R:16:5'): get_r_os returns correct structure and values ──
result$arm is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 2 | SKIP 156 | PASS 316 ]
Deleting unused snapshots:
• all-w2/example1autoplot.svg
• all-w2/example1resplot.svg
• all-w2/example2autoplot.svg
• all-w2/example2resplot.svg
• all-w2/example3autoplot.svg
• all-w2/example3lmmautoplot.svg
• all-w2/example3lmmresplot.svg
• all-w2/example3resplot.svg
• all-w2/example4autoplot.svg
• all-w2/example4lmmautoplot.svg
• all-w2/example4lmmresplot.svg
• all-w2/example4resplot.svg
• all-w2/example5lmmautoplot1.svg
• all-w2/example5lmmautoplot2.svg
• all-w2/example5lmmresplot.svg
• all-w2/example6lmmautoplot2.svg
• all-w2/example6lmmresplot.svg
• all-w2/example6variogram.svg
• all-w2/example7lmmautoplot.svg
• all-w2/example7lmmresplot.svg
• all-w2/example7variogram.svg
• all-w2/exercise10autoplot.svg
• all-w2/exercise10resplot.svg
• all-w2/exercise11autoplot1.svg
• all-w2/exercise11autoplot2.svg
• all-w2/exercise11resplot.svg
• all-w2/exercise12autoplot.svg
• all-w2/exercise12resplot.svg
• all-w2/exercise13autoplot1.svg
• all-w2/exercise13autoplot2.svg
• all-w2/exercise13resplot.svg
• all-w2/exercise13variogram.svg
• all-w2/exercise14autoplot.svg
• all-w2/exercise14resplot.svg
• all-w2/exercise14variogram.svg
• all-w2/exercise15autoplot1.svg
• all-w2/exercise15autoplot2.svg
• all-w2/exercise15autoplot3.svg
• all-w2/exercise15resplot.svg
• all-w2/exercise15variogram.svg
• all-w2/exercise1autoplot.svg
• all-w2/exercise1resplot.svg
• all-w2/exercise2autoplot.svg
• all-w2/exercise2resplot.svg
• all-w2/exercise3autoplot.svg
• all-w2/exercise3resplot.svg
• all-w2/exercise4resplot.svg
• all-w2/exercise5autoplot.svg
• all-w2/exercise5resplot.svg
• all-w2/exercise6autoplot.svg
• all-w2/exercise6resplot.svg
• all-w2/exercise7autoplot.svg
• all-w2/exercise7resplot.svg
• all-w2/exercise8resplot.svg
• all-w2/exercise9autoplot.svg
• all-w2/exercise9resplot.svg
• des/crd-without-trt.svg
• des/rcbd-without-trt.svg
• design/3-way-factorial-with-names.svg
• design/3-way-factorial.svg
• design/3-way-rcbd-factorial-with-names.svg
• design/column-buffers-rcbd.svg
• design/column-buffers.svg
• design/crd-color-blind-option1.svg
• design/crd-color-blind-option2.svg
• design/crd-color-blind-option3.svg
• design/crd-color-blind-option4.svg
• design/crd-color-blind-option5.svg
• design/crd-colour-blind-option2.svg
• design/crd-colour-blind-option3.svg
• design/crd-colour-blind-option4.svg
• design/crd-colour-blind-option5.svg
• design/crd-colour-blind.svg
• design/crd-paired-palette.svg
• design/crd-plot-produced.svg
• design/crd-set3-palette.svg
• design/double-column-buffers-rcbd.svg
• design/double-column-buffers.svg
• design/double-row-buffers-rcbd.svg
• design/double-row-buffers.svg
• design/edge-buffers-rcbd.svg
• design/edge-buffers.svg
• design/factorial-crd-plot-no-space-sep.svg
• design/factorial-crd-with-names.svg
• design/factorial-lsd-plot-with-sep.svg
• design/factorial-rcbd-plot-produced.svg
• design/lsd-plot-produced.svg
• design/nested-lsd.svg
• design/nse-of-column-names-with-blocks.svg
• design/plot-output.svg
• design/quoted-column-names-with-blocks.svg
• design/rcbd-color-blind-option1.svg
• design/rcbd-colour-blind-cividis.svg
• design/rcbd-colour-blind-inferno.svg
• design/rcbd-colour-blind-magma.svg
• design/rcbd-colour-blind-option1.svg
• design/rcbd-colour-blind-plasma.svg
• design/rcbd-colour-blind-viridis.svg
• design/rcbd-colour-blind.svg
• design/rcbd-paired-palette.svg
• design/rcbd-plot-produced.svg
• design/rcbd-rdbu-palette.svg
• design/rcbd-set3-palette.svg
• design/split-plot-produced.svg
• design/split-plot-with-names.svg
• design/split-plot-with-vector-names.svg
• heatmap/heatmap-of-interpolated-grouped-data.svg
• heatmap/heatmap-with-free-y.svg
• heatmap/heatmap-with-one-row.svg
• heatmap/heatmap-with-red-green-palette.svg
• mct/3-way-interaction-internal.svg
• mct/3-way-interaction.svg
• mct/aov-aliased-output.svg
• mct/asreml-predictions.svg
• mct/axis-and-label-rotation.svg
• mct/axis-rotation.svg
• mct/interactions-work.svg
• mct/mct-descending-output.svg
• mct/mct-inverse-output.svg
• mct/mct-logit-output.svg
• mct/mct-output-2se.svg
• mct/mct-power-output.svg
• mct/mct-sqrt-output.svg
• mct/rotation-and-axis-rotation.svg
• mct/rotation-and-label-rotation.svg
• mct/rotation-with-hjust-and-vjust.svg
• resplot/artool-resplot-with-call.svg
• resplot/large-data-shapiro.svg
• resplot/onepage-cols-2.svg
• resplot/onepage-off-2.svg
• resplot/onepage-off-3.svg
• resplot/onepage-on-page-1.svg
• resplot/onepage-on-page-2.svg
• resplot/onepage-on.svg
• resplot/resplot-for-asreml-pt-1.svg
• resplot/resplot-for-asreml-pt-2.svg
• resplot/resplot-for-asreml-pt-3.svg
• resplot/resplot-for-asreml-single.svg
• resplot/resplot-for-sommer-mmes.svg
• resplot/resplot-onepage-true.svg
• resplot/resplot-with-smaller-call.svg
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [15s/28s] OK
- checking PDF version of manual ... [7s/13s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '