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This page was generated on 2025-07-26 12:10 -0400 (Sat, 26 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4795
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4534
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4577
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4518
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4512
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 2099/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.21.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-07-25 13:25 -0400 (Fri, 25 Jul 2025)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: devel
git_last_commit: 36d5ff1
git_last_commit_date: 2025-04-15 11:54:06 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for structToolbox on lconway

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: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2025-07-25 23:59:23 -0400 (Fri, 25 Jul 2025)
EndedAt: 2025-07-26 00:08:33 -0400 (Sat, 26 Jul 2025)
EllapsedTime: 550.1 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/structToolbox.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.21.0’
* 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           18.499  0.100  18.703
fold_change               12.718  0.109  12.903
fisher_exact              11.412  0.080  11.557
fs_line                    6.920  0.141   7.089
forward_selection_by_rank  6.927  0.111   7.079
compare_dist               5.054  0.254   5.335
* 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 ‘1.21.0’
** 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 (2025-06-13) -- "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 
212.050   2.562 216.122 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2530.0090.265
AUC3.0110.1203.152
DFA0.2130.0020.215
DatasetExperiment_boxplot0.6900.0380.734
DatasetExperiment_dist1.3350.1101.454
DatasetExperiment_factor_boxplot0.2430.0080.252
DatasetExperiment_heatmap0.4480.0120.462
HCA0.0700.0010.071
HSD0.3360.0230.369
HSDEM0.5570.0320.592
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0110.0000.011
OPLSR0.0100.0010.011
PCA0.0040.0000.004
PLSDA0.0160.0010.017
PLSR0.0110.0010.012
SVM0.0270.0010.029
as_data_frame0.1500.0010.152
autoscale0.0830.0010.085
balanced_accuracy3.0490.0553.123
blank_filter0.4420.0210.465
blank_filter_hist0.0020.0000.001
bootstrap0.0130.0000.013
calculate0.0070.0000.008
chart_plot0.0340.0010.035
classical_lsq0.3840.0080.394
compare_dist5.0540.2545.335
confounders_clsq3.7780.0273.829
confounders_lsq_barchart3.7470.0273.793
confounders_lsq_boxplot3.7740.0303.827
constant_sum_norm0.0080.0000.009
corr_coef0.3170.0020.320
dfa_scores_plot0.8260.0070.840
dratio_filter0.3250.0080.335
equal_split0.1280.0010.130
feature_boxplot0.0260.0010.028
feature_profile0.4040.0050.412
feature_profile_array0.5240.0070.535
filter_by_name0.0340.0010.034
filter_na_count1.1740.0561.241
filter_smeta0.0780.0000.080
fisher_exact11.412 0.08011.557
fold_change12.718 0.10912.903
fold_change_int18.499 0.10018.703
fold_change_plot0.0100.0010.010
forward_selection_by_rank6.9270.1117.079
fs_line6.9200.1417.089
glog_opt_plot0.5550.0050.562
glog_transform0.3520.0030.357
grid_search_1d4.8120.1564.995
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval4.1660.0394.232
kfoldxcv_grid4.4910.0434.568
kfoldxcv_metric0.0000.0000.002
knn_impute0.0140.0000.015
kw_p_hist000
kw_rank_sum0.0920.0010.094
linear_model0.0330.0010.033
log_transform0.0090.0000.010
mean_centre0.0030.0000.003
mean_of_medians0.1410.0010.142
mixed_effect0.2020.0030.206
model_apply0.0300.0020.032
model_predict0.0690.0010.070
model_reverse0.0240.0010.024
model_train0.0620.0010.063
mv_boxplot0.3400.0040.348
mv_feature_filter0.1390.0020.143
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.3150.0100.328
mv_sample_filter0.0110.0010.012
mv_sample_filter_hist0.0010.0000.001
nroot_transform0.0090.0000.009
ontology_cache0.0000.0010.001
pairs_filter0.0120.0000.013
pareto_scale0.0770.0000.077
pca_biplot0.0160.0000.015
pca_correlation_plot0.0070.0000.008
pca_dstat_plot0.0130.0000.013
pca_loadings_plot0.0130.0010.013
pca_scores_plot0.6470.0060.656
pca_scree_plot0.0080.0010.009
permutation_test0.0120.0000.012
permutation_test_plot0.0030.0000.002
permute_sample_order0.010.000.01
pls_regcoeff_plot0.4470.0050.455
pls_scores_plot0.7810.0070.794
pls_vip_plot0.4480.0050.458
plsda_feature_importance_plot0.6760.0120.692
plsda_predicted_plot0.5470.0060.558
plsda_roc_plot1.3350.0141.359
plsr_cook_dist0.0070.0000.008
plsr_prediction_plot0.0070.0000.008
plsr_qq_plot0.0070.0000.008
plsr_residual_hist0.0060.0000.006
pqn_norm0.4240.0040.432
pqn_norm_hist0.0010.0000.001
prop_na0.0120.0010.012
r_squared0.0010.0010.001
resample0.0240.0010.025
resample_chart0.0040.0000.004
rsd_filter0.0190.0010.019
rsd_filter_hist0.0010.0000.001
run0.0410.0010.042
sb_corr0.0320.0010.033
scatter_chart0.4430.0050.450
split_data0.0080.0000.009
stratified_split0.1410.0010.143
svm_plot_2d0.8000.0170.824
tSNE0.0280.0010.029
tSNE_scatter0.0110.0010.012
tic_chart0.2610.0090.272
ttest0.0220.0010.024
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0230.0010.024