* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/agriutilities.Rcheck’ * using R Under development (unstable) (2025-09-23 r88869) * 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 * checking for file ‘agriutilities/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘agriutilities’ 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 ‘agriutilities’ can be installed ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... 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 ... OK * checking loading without being on the library search path ... 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/16s] 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 ... OK * checking examples with --run-donttest ... [11s/11s] ERROR Running examples in ‘agriutilities-Ex.R’ failed The error most likely occurred in: > ### Name: plot.smaAgri > ### Title: Plot an object of class 'smaAgri' > ### Aliases: plot.smaAgri > > ### ** Examples > > ## No test: > library(agridat) > library(agriutilities) > data(besag.met) > dat <- besag.met > results <- check_design_met( + data = dat, + genotype = "gen", + trial = "county", + traits = c("yield"), + rep = "rep", + block = "block", + col = "col", + row = "row" + ) > out <- single_trial_analysis(results, progress = FALSE) > print(out) --------------------------------------------------------------------- Summary Fitted Models: --------------------------------------------------------------------- trait trial heritability CV VarGen VarErr design 1: yield C1 0.70 6.370054 85.28086 92.70982 row_col 2: yield C2 0.39 16.987235 26.87283 105.50494 row_col 3: yield C3 0.64 12.366843 82.84379 118.86865 row_col 4: yield C4 0.41 8.179794 35.75059 136.21686 row_col 5: yield C5 0.80 7.042116 104.44077 66.96454 row_col 6: yield C6 0.49 16.583972 72.16813 206.54020 row_col --------------------------------------------------------------------- Outliers Removed: --------------------------------------------------------------------- Null data.table (0 rows and 0 cols) --------------------------------------------------------------------- First Predicted Values and Standard Errors (BLUEs/BLUPs): --------------------------------------------------------------------- trait genotype trial BLUEs seBLUEs BLUPs seBLUPs wt 1: yield G01 C1 142.9316 6.380244 144.5151 5.421481 0.02456549 2: yield G02 C1 156.7765 6.277083 155.0523 5.367425 0.02537957 3: yield G03 C1 126.5654 6.402526 133.1766 5.444349 0.02439480 4: yield G04 C1 155.7790 6.391590 154.2435 5.440070 0.02447836 5: yield G05 C1 163.9856 6.443261 160.7620 5.444314 0.02408732 6: yield G06 C1 129.5092 6.400364 134.7404 5.421543 0.02441129 > plot(out, type = "summary", horizontal = TRUE) Error: ! The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 and is now defunct. ℹ Please use the `rows` argument instead. Backtrace: ▆ 1. ├─base::plot(out, type = "summary", horizontal = TRUE) 2. └─agriutilities:::plot.smaAgri(out, type = "summary", horizontal = TRUE) 3. └─ggplot2::facet_grid(...) 4. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [16s/16s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/agriutilities.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:12.01, 123.56 + 67.35