| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-31 12:05 -0400 (Fri, 31 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2146/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| structToolbox 1.22.0 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the structToolbox package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/structToolbox.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: structToolbox |
| Version: 1.22.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings structToolbox_1.22.0.tar.gz |
| StartedAt: 2025-10-30 22:21:38 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 22:24:30 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 172.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: structToolbox.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings structToolbox_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/structToolbox.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.22.0’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘structToolbox’ can be installed ... OK
* 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 ... 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 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 ... OK
* checking Rd files ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
structToolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘structToolbox’ ... ** this is package ‘structToolbox’ version ‘1.22.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (structToolbox)
structToolbox.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ggplot2)
> library(structToolbox)
Loading required package: struct
>
> test_check("structToolbox")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ]
>
> proc.time()
user system elapsed
56.811 0.621 58.029
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.071 | 0.002 | 0.090 | |
| AUC | 0.648 | 0.032 | 0.734 | |
| DFA | 0.054 | 0.000 | 0.061 | |
| DatasetExperiment_boxplot | 0.357 | 0.012 | 0.393 | |
| DatasetExperiment_dist | 0.555 | 0.028 | 0.630 | |
| DatasetExperiment_factor_boxplot | 0.101 | 0.003 | 0.105 | |
| DatasetExperiment_heatmap | 0.478 | 0.012 | 0.528 | |
| HCA | 0.019 | 0.000 | 0.020 | |
| HSD | 0.092 | 0.008 | 0.112 | |
| HSDEM | 0.116 | 0.007 | 0.139 | |
| MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.000 | |
| OPLSDA | 0.003 | 0.000 | 0.003 | |
| OPLSR | 0.003 | 0.000 | 0.002 | |
| PCA | 0.001 | 0.000 | 0.002 | |
| PLSDA | 0.003 | 0.000 | 0.004 | |
| PLSR | 0.003 | 0.000 | 0.003 | |
| SVM | 0.006 | 0.001 | 0.006 | |
| as_data_frame | 0.042 | 0.000 | 0.043 | |
| autoscale | 0.022 | 0.001 | 0.022 | |
| balanced_accuracy | 0.518 | 0.005 | 0.546 | |
| blank_filter | 0.123 | 0.007 | 0.134 | |
| blank_filter_hist | 0.001 | 0.000 | 0.000 | |
| bootstrap | 0.002 | 0.000 | 0.003 | |
| calculate | 0.002 | 0.000 | 0.002 | |
| chart_plot | 0.008 | 0.001 | 0.008 | |
| classical_lsq | 0.084 | 0.000 | 0.085 | |
| compare_dist | 1.892 | 0.082 | 2.019 | |
| confounders_clsq | 0.864 | 0.005 | 0.879 | |
| confounders_lsq_barchart | 0.942 | 0.005 | 0.957 | |
| confounders_lsq_boxplot | 0.951 | 0.014 | 0.975 | |
| constant_sum_norm | 0.002 | 0.000 | 0.003 | |
| corr_coef | 0.071 | 0.001 | 0.071 | |
| dfa_scores_plot | 0.292 | 0.003 | 0.296 | |
| dratio_filter | 0.080 | 0.003 | 0.083 | |
| equal_split | 0.035 | 0.001 | 0.034 | |
| feature_boxplot | 0.016 | 0.001 | 0.017 | |
| feature_profile | 0.155 | 0.002 | 0.157 | |
| feature_profile_array | 0.202 | 0.002 | 0.206 | |
| filter_by_name | 0.017 | 0.000 | 0.016 | |
| filter_na_count | 0.340 | 0.018 | 0.366 | |
| filter_smeta | 0.018 | 0.000 | 0.018 | |
| fisher_exact | 2.803 | 0.008 | 2.816 | |
| fold_change | 3.417 | 0.018 | 3.440 | |
| fold_change_int | 4.883 | 0.003 | 4.897 | |
| fold_change_plot | 0.002 | 0.000 | 0.002 | |
| forward_selection_by_rank | 1.832 | 0.041 | 1.917 | |
| fs_line | 2.224 | 0.067 | 2.380 | |
| glog_opt_plot | 0.182 | 0.003 | 0.196 | |
| glog_transform | 0.094 | 0.001 | 0.105 | |
| grid_search_1d | 1.180 | 0.066 | 1.312 | |
| gs_line | 0.000 | 0.000 | 0.001 | |
| hca_dendrogram | 0.001 | 0.000 | 0.000 | |
| kfold_xval | 1.025 | 0.007 | 1.032 | |
| kfoldxcv_grid | 1.168 | 0.013 | 1.180 | |
| kfoldxcv_metric | 0.000 | 0.000 | 0.001 | |
| knn_impute | 0.003 | 0.000 | 0.004 | |
| kw_p_hist | 0 | 0 | 0 | |
| kw_rank_sum | 0.029 | 0.000 | 0.030 | |
| linear_model | 0.009 | 0.000 | 0.009 | |
| log_transform | 0.002 | 0.000 | 0.003 | |
| mean_centre | 0.001 | 0.000 | 0.001 | |
| mean_of_medians | 0.033 | 0.000 | 0.032 | |
| mixed_effect | 0.049 | 0.000 | 0.049 | |
| model_apply | 0.007 | 0.001 | 0.007 | |
| model_predict | 0.016 | 0.000 | 0.017 | |
| model_reverse | 0.008 | 0.000 | 0.008 | |
| model_train | 0.015 | 0.000 | 0.015 | |
| mv_boxplot | 0.137 | 0.002 | 0.139 | |
| mv_feature_filter | 0.034 | 0.000 | 0.034 | |
| mv_feature_filter_hist | 0 | 0 | 0 | |
| mv_histogram | 0.115 | 0.002 | 0.116 | |
| mv_sample_filter | 0.003 | 0.000 | 0.002 | |
| mv_sample_filter_hist | 0 | 0 | 0 | |
| nroot_transform | 0.002 | 0.000 | 0.002 | |
| ontology_cache | 0.000 | 0.000 | 0.001 | |
| pairs_filter | 0.003 | 0.000 | 0.003 | |
| pareto_scale | 0.017 | 0.000 | 0.016 | |
| pca_biplot | 0.004 | 0.000 | 0.004 | |
| pca_correlation_plot | 0.002 | 0.000 | 0.002 | |
| pca_dstat_plot | 0.002 | 0.000 | 0.003 | |
| pca_loadings_plot | 0.003 | 0.000 | 0.003 | |
| pca_scores_plot | 0.213 | 0.001 | 0.214 | |
| pca_scree_plot | 0.002 | 0.000 | 0.002 | |
| permutation_test | 0.003 | 0.000 | 0.003 | |
| permutation_test_plot | 0.001 | 0.000 | 0.000 | |
| permute_sample_order | 0.002 | 0.000 | 0.002 | |
| pls_regcoeff_plot | 0.144 | 0.001 | 0.145 | |
| pls_scores_plot | 0.262 | 0.001 | 0.264 | |
| pls_vip_plot | 0.150 | 0.001 | 0.151 | |
| plsda_feature_importance_plot | 0.263 | 0.001 | 0.265 | |
| plsda_predicted_plot | 0.181 | 0.001 | 0.183 | |
| plsda_roc_plot | 0.381 | 0.003 | 0.383 | |
| plsr_cook_dist | 0.002 | 0.000 | 0.002 | |
| plsr_prediction_plot | 0.002 | 0.000 | 0.002 | |
| plsr_qq_plot | 0.002 | 0.000 | 0.002 | |
| plsr_residual_hist | 0.001 | 0.000 | 0.002 | |
| pqn_norm | 0.096 | 0.000 | 0.097 | |
| pqn_norm_hist | 0.000 | 0.001 | 0.000 | |
| prop_na | 0.003 | 0.000 | 0.003 | |
| r_squared | 0 | 0 | 0 | |
| resample | 0.005 | 0.000 | 0.005 | |
| resample_chart | 0.001 | 0.000 | 0.001 | |
| rsd_filter | 0.003 | 0.001 | 0.004 | |
| rsd_filter_hist | 0 | 0 | 0 | |
| run | 0.013 | 0.000 | 0.014 | |
| sb_corr | 0.007 | 0.001 | 0.007 | |
| scatter_chart | 0.165 | 0.002 | 0.167 | |
| split_data | 0.002 | 0.000 | 0.003 | |
| stratified_split | 0.032 | 0.001 | 0.032 | |
| svm_plot_2d | 0.248 | 0.005 | 0.253 | |
| tSNE | 0.007 | 0.000 | 0.007 | |
| tSNE_scatter | 0.002 | 0.000 | 0.002 | |
| tic_chart | 0.105 | 0.002 | 0.106 | |
| ttest | 0.006 | 0.000 | 0.007 | |
| vec_norm | 0 | 0 | 0 | |
| wilcox_p_hist | 0.001 | 0.000 | 0.000 | |
| wilcox_test | 0.005 | 0.001 | 0.005 | |