* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/biometryassist.Rcheck’
* using R Under development (unstable) (2025-02-15 r87726)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘biometryassist/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biometryassist’ version ‘1.2.1’
* 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 ... [13s/35s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/biometryassist-00install.html' for details.
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘install_asreml.R’
* 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 ... [5s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/12s] OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... [5s/14s] OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... [5s/13s] 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 ... [33s/86s] OK
* checking Rd files ... 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 ... [31s/84s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [126s/164s] ERROR
Running ‘testthat.R’ [126s/162s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(biometryassist)
>
> test_check("biometryassist")
Starting 2 test processes
Superclass process has cloneable=FALSE, but subclass r_session has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for r_session.
Superclass process has cloneable=FALSE, but subclass r_session has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for r_session.
[ FAIL 1 | WARN 9 | SKIP 118 | PASS 172 ]
â•â• Skipped tests (118) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
• On CRAN (111): 'test-des.R:8:5', 'test-des.R:21:5', 'test-all-w2.r:10:5',
'test-all-w2.r:25:5', 'test-all-w2.r:39:5', 'test-all-w2.r:53:5',
'test-all-w2.r:67:5', 'test-all-w2.r:84:5', 'test-all-w2.r:102:5',
'test-all-w2.r:121:5', 'test-all-w2.r:148:5', 'test-all-w2.r:179:5',
'test-all-w2.r:195:5', 'test-all-w2.r:210:5', 'test-all-w2.r:224:5',
'test-all-w2.r:235:5', 'test-all-w2.r:249:5', 'test-all-w2.r:263:5',
'test-all-w2.r:279:5', 'test-all-w2.r:292:5', 'test-all-w2.r:310:5',
'test-all-w2.r:328:5', 'test-all-w2.r:350:5', 'test-all-w2.r:369:5',
'test-all-w2.r:399:5', 'test-all-w2.r:432:5', 'test-heatmap.R:18:5',
'test-heatmap.R:30:5', 'test-heatmap.R:35:5', 'test-heatmap.R:40:5',
'test-heatmap.R:45:5', 'test-heatmap.R:52:5', 'test-heatmap.R:59:5',
'test-design.R:9:5', 'test-design.R:21:5', 'test-design.R:30:5',
'test-design.R:38:5', 'test-design.R:49:5', 'test-design.R:63:5',
'test-design.R:76:5', 'test-design.R:88:5', 'test-design.R:99:5',
'test-design.R:111:5', 'test-design.R:123:5', 'test-design.R:148:5',
'test-design.R:159:5', 'test-design.R:169:5', 'test-design.R:177:5',
'test-design.R:189:5', 'test-design.R:202:5', 'test-design.R:215:5',
'test-design.R:226:5', 'test-design.R:237:5', 'test-design.R:269:5',
'test-design.R:389:5', 'test-design.R:490:5', 'test-design.R:507:5',
'test-design.R:516:5', 'test-design.R:548:5', 'test-design.R:554:5',
'test-design.R:560:5', 'test-design.R:566:5', 'test-design.R:580:5',
'test-design.R:597:5', 'test-design.R:612:5', 'test-design.R:627:5',
'test-design.R:642:5', 'test-design.R:657:5', 'test-design.R:671:5',
'test-design.R:699:5', 'test-design.R:724:5', 'test-design.R:744:5',
'test-design.R:815:5', 'test-design.R:827:5', 'test-mct.R:33:5',
'test-mct.R:77:5', 'test-mct.R:96:5', 'test-mct.R:109:5', 'test-mct.R:117:5',
'test-mct.R:165:5', 'test-mct.R:174:5', 'test-mct.R:261:5',
'test-mct.R:273:5', 'test-mct.R:289:5', 'test-mct.R:313:5',
'test-summary_graph.R:8:5', 'test-summary_graph.R:14:5',
'test-summary_graph.R:20:5', 'test-summary_graph.R:26:5',
'test-resplot.R:6:5', 'test-resplot.R:13:5', 'test-resplot.R:24:5',
'test-resplot.R:55:5', 'test-resplot.R:70:5', 'test-resplot.R:85:5',
'test-resplot.R:94:5', 'test-resplot.R:106:5',
'test-utility_functions.R:7:5', 'test-zzz_install_asreml.R:4:5',
'test-zzz_install_asreml.R:13:5', 'test-zzz_install_asreml.R:21:5',
'test-zzz_install_asreml.R:30:5', 'test-zzz_install_asreml.R:38:5',
'test-zzz_install_asreml.R:47:5', 'test-zzz_install_asreml.R:57:5',
'test-zzz_install_asreml.R:67:5', 'test-zzz_install_asreml.R:80:5',
'test-zzz_install_asreml.R:92:5', 'test-zzz_install_asreml.R:101:5',
'test-variogram.r:22:5', 'test-variogram.r:52:5'
• requireNamespace("asreml", quietly = TRUE) is not TRUE (7):
'test-logltest.R:4:5', 'test-logltest.R:26:5', 'test-mct.R:127:5',
'test-mct.R:181:5', 'test-mct.R:235:5', 'test-mct.R:245:3',
'test-resplot.R:28:5'
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── Failure ('test-mct.R:256:5'): lme4 model works ──────────────────────────────
output$std.error (`actual`) not equal to rep(7.39, 4) (`expected`).
`actual`: 6.0 6.0 6.0 6.0
`expected`: 7.4 7.4 7.4 7.4
[ FAIL 1 | WARN 9 | SKIP 118 | PASS 172 ]
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/exercise14autoplot.svg
• all-w2/exercise14resplot.svg
• all-w2/exercise15autoplot1.svg
• all-w2/exercise15autoplot2.svg
• all-w2/exercise15autoplot3.svg
• all-w2/exercise15resplot.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-palatte.svg
• design/crd-plot-produced.svg
• design/crd-rdbu-palatte.svg
• design/crd-set3-palatte.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/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-palatte.svg
• design/rcbd-plot-produced.svg
• design/rcbd-rdbu-palatte.svg
• design/rcbd-set3-palatte.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-geom-tile.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/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/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-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 ... [18s/49s] OK
* checking PDF version of manual ... [8s/21s] OK
* checking HTML version of manual ... 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