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This page was generated on 2025-09-04 11:40 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2122/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.20.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-09-01 13:40 -0400 (Mon, 01 Sep 2025)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_21
git_last_commit: 1668438
git_last_commit_date: 2025-04-15 11:54:06 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for structToolbox on merida1

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.

raw results


Summary

Package: structToolbox
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2025-09-02 11:20:47 -0400 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 11:46:44 -0400 (Tue, 02 Sep 2025)
EllapsedTime: 1557.6 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/structToolbox.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.20.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
fold_change_int           38.654  0.147  40.270
fold_change               27.326  0.173  28.803
fisher_exact              22.851  0.093  24.193
forward_selection_by_rank 13.319  0.147  13.679
fs_line                   12.691  0.137  13.205
kfoldxcv_grid              8.566  0.044   8.941
kfold_xval                 7.642  0.060   7.790
compare_dist               7.071  0.291   7.884
confounders_lsq_barchart   7.193  0.032   7.306
confounders_lsq_boxplot    7.127  0.044   7.266
confounders_clsq           7.039  0.033   7.202
grid_search_1d             6.735  0.154   6.930
AUC                        4.929  0.261   5.492
* 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


Installation output

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-x86_64/Resources/library’
* installing *source* package ‘structToolbox’ ...
** this is package ‘structToolbox’ version ‘1.20.0’
** 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)

Tests output

structToolbox.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
438.169   3.579 461.620 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.5290.0170.726
AUC4.9290.2615.492
DFA0.4920.0030.522
DatasetExperiment_boxplot2.1210.0582.827
DatasetExperiment_dist2.3400.1072.550
DatasetExperiment_factor_boxplot0.4830.0030.661
DatasetExperiment_heatmap0.9510.0391.041
HCA0.1440.0120.159
HSD0.6690.0271.034
HSDEM0.7320.0371.894
MTBLS79_DatasetExperiment0.0030.0010.003
OPLSDA0.0280.0000.029
OPLSR0.0210.0010.023
PCA0.010.000.01
PLSDA0.0280.0020.030
PLSR0.0180.0010.020
SVM0.0490.0010.050
as_data_frame0.2180.0030.221
autoscale0.1530.0050.160
balanced_accuracy3.4590.0403.517
blank_filter0.7540.0391.813
blank_filter_hist0.0020.0000.002
bootstrap0.0250.0010.026
calculate0.0110.0010.013
chart_plot0.0670.0030.071
classical_lsq0.7270.0070.743
compare_dist7.0710.2917.884
confounders_clsq7.0390.0337.202
confounders_lsq_barchart7.1930.0327.306
confounders_lsq_boxplot7.1270.0447.266
constant_sum_norm0.0170.0000.018
corr_coef0.6200.0040.633
dfa_scores_plot1.7380.0091.821
dratio_filter0.6860.0160.709
equal_split0.2810.0020.285
feature_boxplot0.0630.0010.065
feature_profile0.9080.0150.983
feature_profile_array1.0320.0091.185
filter_by_name0.0730.0010.074
filter_na_count2.6420.1002.772
filter_smeta0.1570.0010.168
fisher_exact22.851 0.09324.193
fold_change27.326 0.17328.803
fold_change_int38.654 0.14740.270
fold_change_plot0.0160.0010.017
forward_selection_by_rank13.319 0.14713.679
fs_line12.691 0.13713.205
glog_opt_plot1.0030.0081.237
glog_transform0.6980.0050.708
grid_search_1d6.7350.1546.930
gs_line0.0010.0000.002
hca_dendrogram0.0010.0000.002
kfold_xval7.6420.0607.790
kfoldxcv_grid8.5660.0448.941
kfoldxcv_metric0.0010.0010.002
knn_impute0.0310.0000.033
kw_p_hist0.0020.0010.002
kw_rank_sum0.1650.0010.166
linear_model0.0570.0010.058
log_transform0.0170.0010.019
mean_centre0.0070.0000.008
mean_of_medians0.2790.0020.284
mixed_effect0.3840.0050.404
model_apply0.0520.0010.053
model_predict0.1170.0020.119
model_reverse0.0540.0010.055
model_train0.1210.0030.139
mv_boxplot0.6230.0070.633
mv_feature_filter0.2560.0030.259
mv_feature_filter_hist0.0010.0010.002
mv_histogram0.5770.0130.592
mv_sample_filter0.0180.0010.019
mv_sample_filter_hist0.0010.0000.002
nroot_transform0.0160.0010.016
ontology_cache0.0000.0000.001
pairs_filter0.0230.0010.024
pareto_scale0.1330.0010.134
pca_biplot0.0370.0010.038
pca_correlation_plot0.0130.0010.014
pca_dstat_plot0.0210.0010.021
pca_loadings_plot0.0230.0010.023
pca_scores_plot1.0790.0071.243
pca_scree_plot0.0140.0010.015
permutation_test0.0200.0010.019
permutation_test_plot0.0060.0000.006
permute_sample_order0.0130.0000.014
pls_regcoeff_plot0.7420.0070.918
pls_scores_plot1.4210.0101.515
pls_vip_plot0.8750.0080.953
plsda_feature_importance_plot1.1200.0161.481
plsda_predicted_plot0.9430.0090.969
plsda_roc_plot2.8240.0262.929
plsr_cook_dist0.0150.0000.016
plsr_prediction_plot0.0140.0010.015
plsr_qq_plot0.0150.0010.016
plsr_residual_hist0.0160.0000.017
pqn_norm0.8160.0050.822
pqn_norm_hist0.0020.0000.002
prop_na0.0210.0000.020
r_squared0.0020.0000.001
resample0.0320.0010.033
resample_chart0.0050.0000.005
rsd_filter0.0300.0010.031
rsd_filter_hist0.0010.0010.001
run0.0680.0010.069
sb_corr0.0630.0020.064
scatter_chart0.7570.0080.892
split_data0.0170.0000.017
stratified_split0.2560.0020.259
svm_plot_2d1.4270.0181.781
tSNE0.0590.0010.065
tSNE_scatter0.0160.0010.020
tic_chart0.4890.0070.513
ttest0.0570.0010.062
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.002
wilcox_test0.0460.0010.051