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This page was generated on 2025-09-01 11:41 -0400 (Mon, 01 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: 2025-08-28 13:40 -0400 (Thu, 28 Aug 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: 2025-08-29 10:58:12 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 11:16:44 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 1111.8 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           39.410  0.145  42.102
fold_change               27.853  0.166  28.925
fisher_exact              23.360  0.095  24.460
forward_selection_by_rank 15.207  0.185  17.466
fs_line                   14.714  0.140  16.928
kfoldxcv_grid              9.074  0.053  10.370
kfold_xval                 8.287  0.055   9.384
grid_search_1d             7.958  0.163   8.930
confounders_lsq_barchart   7.717  0.056   8.907
confounders_lsq_boxplot    7.552  0.053   8.742
confounders_clsq           7.452  0.048   8.634
compare_dist               7.237  0.260   8.357
AUC                        4.851  0.253   5.139
* 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 
439.662   3.670 461.491 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.5110.0150.528
AUC4.8510.2535.139
DFA0.4730.0030.483
DatasetExperiment_boxplot2.2000.0732.333
DatasetExperiment_dist2.4290.1012.568
DatasetExperiment_factor_boxplot0.4860.0030.497
DatasetExperiment_heatmap0.9480.0320.983
HCA0.1420.0080.150
HSD0.6700.0220.701
HSDEM0.7460.0280.778
MTBLS79_DatasetExperiment0.0020.0010.002
OPLSDA0.0280.0010.028
OPLSR0.0200.0000.021
PCA0.010.000.01
PLSDA0.0310.0010.032
PLSR0.0240.0010.025
SVM0.0560.0010.057
as_data_frame0.3050.0030.310
autoscale0.1670.0020.169
balanced_accuracy4.2660.0244.516
blank_filter0.7920.0310.898
blank_filter_hist0.0010.0010.002
bootstrap0.0260.0000.029
calculate0.0110.0010.014
chart_plot0.0700.0030.080
classical_lsq0.7740.0070.859
compare_dist7.2370.2608.357
confounders_clsq7.4520.0488.634
confounders_lsq_barchart7.7170.0568.907
confounders_lsq_boxplot7.5520.0538.742
constant_sum_norm0.0170.0010.020
corr_coef0.6100.0040.700
dfa_scores_plot1.7220.0111.942
dratio_filter0.7150.0180.795
equal_split0.2810.0020.313
feature_boxplot0.0670.0020.078
feature_profile0.9430.0131.047
feature_profile_array1.0750.0091.180
filter_by_name0.0740.0010.084
filter_na_count2.7910.0963.153
filter_smeta0.1610.0010.177
fisher_exact23.360 0.09524.460
fold_change27.853 0.16628.925
fold_change_int39.410 0.14542.102
fold_change_plot0.0180.0010.022
forward_selection_by_rank15.207 0.18517.466
fs_line14.714 0.14016.928
glog_opt_plot1.1660.0091.355
glog_transform0.7510.0070.973
grid_search_1d7.9580.1638.930
gs_line0.0010.0000.004
hca_dendrogram0.0020.0000.001
kfold_xval8.2870.0559.384
kfoldxcv_grid 9.074 0.05310.370
kfoldxcv_metric0.0020.0010.002
knn_impute0.0320.0010.040
kw_p_hist0.0010.0000.004
kw_rank_sum0.1810.0020.213
linear_model0.0740.0010.088
log_transform0.0170.0000.020
mean_centre0.0080.0010.009
mean_of_medians0.2910.0020.326
mixed_effect0.3900.0060.450
model_apply0.0550.0020.069
model_predict0.1350.0020.156
model_reverse0.0640.0010.077
model_train0.1280.0020.144
mv_boxplot0.6570.0080.759
mv_feature_filter0.2680.0030.307
mv_feature_filter_hist0.0020.0000.002
mv_histogram0.6220.0120.723
mv_sample_filter0.0190.0010.025
mv_sample_filter_hist0.0020.0010.004
nroot_transform0.0170.0010.019
ontology_cache000
pairs_filter0.0240.0010.027
pareto_scale0.1390.0020.156
pca_biplot0.0380.0010.041
pca_correlation_plot0.0160.0010.018
pca_dstat_plot0.0230.0000.030
pca_loadings_plot0.0240.0010.026
pca_scores_plot1.2510.0081.436
pca_scree_plot0.0160.0010.021
permutation_test0.0240.0010.028
permutation_test_plot0.0060.0000.006
permute_sample_order0.0180.0010.022
pls_regcoeff_plot0.8180.0090.962
pls_scores_plot1.6680.0101.875
pls_vip_plot0.8850.0060.999
plsda_feature_importance_plot1.3930.0121.586
plsda_predicted_plot1.0820.0081.215
plsda_roc_plot2.9720.0203.371
plsr_cook_dist0.0170.0010.019
plsr_prediction_plot0.0170.0000.018
plsr_qq_plot0.0160.0010.017
plsr_residual_hist0.0170.0000.019
pqn_norm0.8990.0071.019
pqn_norm_hist0.0010.0000.002
prop_na0.0250.0010.031
r_squared0.0010.0010.002
resample0.0420.0020.052
resample_chart0.0060.0000.038
rsd_filter0.0330.0010.046
rsd_filter_hist0.0020.0010.002
run0.0720.0010.084
sb_corr0.0680.0020.076
scatter_chart0.8600.0110.980
split_data0.0170.0010.019
stratified_split0.2740.0030.312
svm_plot_2d1.5200.0221.815
tSNE0.0610.0010.071
tSNE_scatter0.0170.0020.021
tic_chart0.5050.0080.586
ttest0.0600.0010.070
vec_norm0.0020.0010.003
wilcox_p_hist0.0010.0010.003
wilcox_test0.0480.0020.052