• using R Under development (unstable) (2025-09-10 r88809)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-3) 15.2.0     GNU Fortran (Debian 15.2.0-3) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘biometryassist/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘biometryassist’ version ‘1.3.2’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 ... OK See the install log for details.
• 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/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking whether startup messages can be suppressed ... [2s/3s] 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 ... [16s/19s] 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 ... [20s/23s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [111s/69s] ERROR   Running ‘testthat.R’ [111s/69s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(biometryassist)   >   > test_check("biometryassist")   Starting 2 test processes   [ FAIL 1 | WARN 3 | SKIP 166 | PASS 335 ]      ══ Skipped tests (166) ═════════════════════════════════════════════════════════   • On CRAN (150): 'test-des.R:8:5', 'test-des.R:22:5', 'test-all-w2.r:63:5',     'test-all-w2.r:77:5', 'test-all-w2.r:90:5', 'test-all-w2.r:103:5',     'test-all-w2.r:116:5', 'test-all-w2.r:130:5', 'test-all-w2.r:145:5',     'test-all-w2.r:162:5', 'test-all-w2.r:186:5', 'test-all-w2.r:214:5',     'test-all-w2.r:229:5', 'test-all-w2.r:243:5', 'test-all-w2.r:256:5',     'test-all-w2.r:266:5', 'test-all-w2.r:279:5', 'test-all-w2.r:292:5',     'test-all-w2.r:306:5', 'test-all-w2.r:317:5', 'test-all-w2.r:331:5',     'test-all-w2.r:345:5', 'test-all-w2.r:363:5', 'test-all-w2.r:378:5',     'test-all-w2.r:404:5', 'test-all-w2.r:433:5', '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-mct.R:6:5', 'test-mct.R:58:5', 'test-mct.R:77:5', 'test-mct.R:89:5',     'test-mct.R:110:5', 'test-mct.R:155:5', 'test-mct.R:164:5',     'test-mct.R:261:5', 'test-mct.R:277:5', 'test-mct.R:311:5',     'test-mct.R:324:5', 'test-mct.R:345:5', 'test-design.R:9:5',     'test-design.R:22:5', 'test-design.R:36:5', 'test-design.R:48:5',     'test-design.R:60:5', 'test-design.R:75:5', 'test-design.R:89:5',     'test-design.R:102:5', 'test-design.R:114:5', 'test-design.R:127:5',     'test-design.R:140:5', 'test-design.R:167:5', 'test-design.R:179:5',     'test-design.R:190:5', 'test-design.R:199:5', 'test-design.R:212:5',     'test-design.R:226:5', 'test-design.R:240:5', 'test-design.R:252:5',     'test-design.R:264:5', 'test-design.R:299:5', 'test-design.R:403:5',     'test-design.R:506:5', 'test-design.R:525:5', 'test-design.R:535:5',     'test-design.R:543:5', 'test-design.R:577:5', 'test-design.R:584:5',     'test-design.R:591:5', 'test-design.R:598:5', 'test-design.R:613:5',     'test-design.R:632:5', 'test-design.R:649:5', 'test-design.R:666:5',     'test-design.R:683:5', 'test-design.R:700:5', 'test-design.R:716:5',     'test-design.R:756:5', 'test-design.R:775:5', 'test-design.R:825:5',     'test-design.R:859:5', 'test-design.R:933:5', 'test-design.R:947:5',     '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-variogram.r:21:5',     'test-variogram.r:51:5', 'test-variogram.r:69:5',     '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-zzz_install_asreml.R:709:5',     'test-zzz_install_asreml.R:734:5', 'test-zzz_install_asreml.R:760:5',     'test-zzz_install_asreml.R:784:5', 'test-zzz_install_asreml.R:817:5',     'test-zzz_install_asreml.R:850:5', 'test-zzz_install_asreml.R:883:5',     'test-zzz_install_asreml.R:907:5', 'test-zzz_install_asreml.R:931:5',     'test-zzz_install_asreml.R:948:5', 'test-zzz_install_asreml.R:967:5',     'test-resplot.R:20:5', 'test-resplot.R:25:5', 'test-resplot.R:36:5',     'test-resplot.R:40:5', 'test-resplot.R:71:5', 'test-resplot.R:90:5',     'test-resplot.R:98:5', 'test-resplot.R:108:5', 'test-resplot.R:120:5',     'test-resplot.R:151:5'   • On Linux (2): 'test-zzz_install_asreml.R:15:5', 'test-resplot.R:81:5'   • rlang::is_installed("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:120:5', 'test-mct.R:171:5',     'test-mct.R:226:5', 'test-mct.R:234:5'   • {lme4} is not installed (2): 'test-mct.R:241:5', 'test-resplot.R:62:5'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-mct.R:95:5'): Testing asreml predictions ───────────────────────   Error in `.requirePackage(package)`: unable to load required package 'Matrix'   Backtrace:        ▆     1. ├─testthat::expect_warning(...) at test-mct.R:95:5     2. │ └─testthat:::expect_condition_matching(...)     3. │ └─testthat:::quasi_capture(...)     4. │ ├─testthat (local) .capture(...)     5. │ │ └─base::withCallingHandlers(...)     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     7. └─biometryassist::multiple_comparisons(...)     8. └─biometryassist:::calculate_differences(pp, sed, ndf, sig)     9. └─1/sqrt(2) * stats::qtukey((1 - sig), nrow(pp), ndf) * sed    10. └─methods (local) `<fn>`(`<list>`, `<S4: standardGeneric>`, `<env>`)    11. └─methods:::.findInheritedMethods(classes, fdef, mtable)    12. └─methods::getClass(classes[[i]], where = where, .Force = TRUE)    13. └─methods::getClassDef(Class, where)    14. └─methods:::.requirePackage(package)      [ FAIL 1 | WARN 3 | SKIP 166 | PASS 335 ]   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   • all-w2/exercise15autoplot2.svg   • all-w2/exercise15autoplot3.svg   • all-w2/exercise1autoplot.svg   • all-w2/exercise2autoplot.svg   • all-w2/exercise3autoplot.svg   • all-w2/exercise5autoplot.svg   • all-w2/exercise6autoplot.svg   • all-w2/exercise7autoplot.svg   • all-w2/exercise9autoplot.svg   • ggplot2-new/all-w2/example1resplot.svg   • ggplot2-new/all-w2/example2resplot.svg   • ggplot2-new/all-w2/example3lmmresplot.svg   • ggplot2-new/all-w2/example3resplot.svg   • ggplot2-new/all-w2/example4lmmresplot.svg   • ggplot2-new/all-w2/example4resplot.svg   • ggplot2-new/all-w2/example5lmmresplot.svg   • ggplot2-new/all-w2/example6lmmresplot.svg   • ggplot2-new/all-w2/example6variogram.svg   • ggplot2-new/all-w2/example7lmmresplot.svg   • ggplot2-new/all-w2/example7variogram.svg   • ggplot2-new/all-w2/exercise10resplot.svg   • ggplot2-new/all-w2/exercise11resplot.svg   • ggplot2-new/all-w2/exercise12resplot.svg   • ggplot2-new/all-w2/exercise13resplot.svg   • ggplot2-new/all-w2/exercise13variogram.svg   • ggplot2-new/all-w2/exercise14resplot.svg   • ggplot2-new/all-w2/exercise14variogram.svg   • ggplot2-new/all-w2/exercise15resplot.svg   • ggplot2-new/all-w2/exercise15variogram.svg   • ggplot2-new/all-w2/exercise1resplot.svg   • ggplot2-new/all-w2/exercise2resplot.svg   • ggplot2-new/all-w2/exercise3resplot.svg   • ggplot2-new/all-w2/exercise4resplot.svg   • ggplot2-new/all-w2/exercise5resplot.svg   • ggplot2-new/all-w2/exercise6resplot.svg   • ggplot2-new/all-w2/exercise7resplot.svg   • ggplot2-new/all-w2/exercise8resplot.svg   • ggplot2-new/all-w2/exercise9resplot.svg   • ggplot2-new/des/crd-without-trt.svg   • ggplot2-new/des/rcbd-without-trt.svg   • ggplot2-new/design/3-way-factorial-with-names.svg   • ggplot2-new/design/3-way-factorial.svg   • ggplot2-new/design/3-way-rcbd-factorial-with-names.svg   • ggplot2-new/design/column-buffers-rcbd.svg   • ggplot2-new/design/column-buffers.svg   • ggplot2-new/design/crd-color-blind-option1.svg   • ggplot2-new/design/crd-color-blind-option2.svg   • ggplot2-new/design/crd-color-blind-option3.svg   • ggplot2-new/design/crd-color-blind-option4.svg   • ggplot2-new/design/crd-color-blind-option5.svg   • ggplot2-new/design/crd-colour-blind-option2.svg   • ggplot2-new/design/crd-colour-blind-option3.svg   • ggplot2-new/design/crd-colour-blind-option4.svg   • ggplot2-new/design/crd-colour-blind-option5.svg   • ggplot2-new/design/crd-colour-blind.svg   • ggplot2-new/design/crd-paired-palette.svg   • ggplot2-new/design/crd-plot-produced.svg   • ggplot2-new/design/crd-set3-palette.svg   • ggplot2-new/design/double-column-buffers-rcbd.svg   • ggplot2-new/design/double-column-buffers.svg   • ggplot2-new/design/double-row-buffers-rcbd.svg   • ggplot2-new/design/double-row-buffers.svg   • ggplot2-new/design/edge-buffers-rcbd.svg   • ggplot2-new/design/edge-buffers.svg   • ggplot2-new/design/factorial-crd-plot-no-space-sep.svg   • ggplot2-new/design/factorial-crd-with-names.svg   • ggplot2-new/design/factorial-lsd-plot-with-sep.svg   • ggplot2-new/design/factorial-rcbd-plot-produced.svg   • ggplot2-new/design/lsd-plot-produced.svg   • ggplot2-new/design/nested-lsd.svg   • ggplot2-new/design/nse-of-column-names-with-blocks.svg   • ggplot2-new/design/plot-output.svg   • ggplot2-new/design/quoted-column-names-with-blocks.svg   • ggplot2-new/design/rcbd-color-blind-option1.svg   • ggplot2-new/design/rcbd-colour-blind-cividis.svg   • ggplot2-new/design/rcbd-colour-blind-inferno.svg   • ggplot2-new/design/rcbd-colour-blind-magma.svg   • ggplot2-new/design/rcbd-colour-blind-option1.svg   • ggplot2-new/design/rcbd-colour-blind-plasma.svg   • ggplot2-new/design/rcbd-colour-blind-viridis.svg   • ggplot2-new/design/rcbd-colour-blind.svg   • ggplot2-new/design/rcbd-paired-palette.svg   • ggplot2-new/design/rcbd-plot-produced.svg   • ggplot2-new/design/rcbd-rdbu-palette.svg   • ggplot2-new/design/rcbd-set3-palette.svg   • ggplot2-new/design/split-plot-produced.svg   • ggplot2-new/design/split-plot-with-names.svg   • ggplot2-new/design/split-plot-with-vector-names.svg   • ggplot2-new/mct/3-way-interaction-internal.svg   • ggplot2-new/mct/3-way-interaction.svg   • ggplot2-new/resplot/artool-resplot-with-call.svg   • ggplot2-new/resplot/large-data-shapiro.svg   • ggplot2-new/resplot/onepage-cols-2.svg   • ggplot2-new/resplot/onepage-cols-3.svg   • ggplot2-new/resplot/onepage-off-2.svg   • ggplot2-new/resplot/onepage-off-3.svg   • ggplot2-new/resplot/onepage-on-page-1.svg   • ggplot2-new/resplot/onepage-on-page-2.svg   • ggplot2-new/resplot/onepage-on.svg   • ggplot2-new/resplot/resplot-for-asreml-pt-1.svg   • ggplot2-new/resplot/resplot-for-asreml-pt-2.svg   • ggplot2-new/resplot/resplot-for-asreml-pt-3.svg   • ggplot2-new/resplot/resplot-for-asreml-single.svg   • ggplot2-new/resplot/resplot-for-lme4.svg   • ggplot2-new/resplot/resplot-for-sommer-mmer.svg   • ggplot2-new/resplot/resplot-for-sommer-mmes.svg   • ggplot2-new/resplot/resplot-onepage-true.svg   • ggplot2-new/resplot/resplot-with-smaller-call.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/aov-aliased-output.svg   • mct/asreml-predictions.svg   • mct/axis-and-label-rotation.svg   • mct/axis-rotation-90.svg   • mct/axis-rotation.svg   • mct/interactions-work.svg   • mct/lme4-output.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   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [2s/2s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR