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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
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: 2025-07-31 13:40 -0400 (Thu, 31 Jul 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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: 2025-08-01 10:55:10 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 11:13:44 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 1114.0 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.20.0.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           39.485  0.149  43.705
fold_change               27.660  0.149  28.737
fisher_exact              23.415  0.086  23.856
forward_selection_by_rank 15.126  0.212  17.710
fs_line                   14.659  0.267  16.790
kfoldxcv_grid              9.054  0.060  10.236
kfold_xval                 8.293  0.052   9.598
grid_search_1d             7.883  0.158   9.315
confounders_lsq_barchart   7.587  0.047   8.791
compare_dist               7.284  0.248   8.603
confounders_lsq_boxplot    7.471  0.045   8.162
confounders_clsq           7.448  0.051   8.235
AUC                        4.885  0.246   5.180
balanced_accuracy          4.423  0.033   5.216
* 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 
441.710   3.664 462.133 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.5040.0140.524
AUC4.8850.2465.180
DFA0.4810.0030.509
DatasetExperiment_boxplot2.1780.0612.502
DatasetExperiment_dist2.5480.1072.979
DatasetExperiment_factor_boxplot0.5080.0050.578
DatasetExperiment_heatmap0.9810.0401.139
HCA0.1480.0120.176
HSD0.6820.0270.789
HSDEM0.9030.0311.104
MTBLS79_DatasetExperiment0.0020.0000.005
OPLSDA0.0290.0000.033
OPLSR0.0210.0010.028
PCA0.0120.0000.023
PLSDA0.0310.0010.038
PLSR0.0240.0010.031
SVM0.0600.0020.076
as_data_frame0.3140.0020.365
autoscale0.1800.0030.205
balanced_accuracy4.4230.0335.216
blank_filter0.8230.0300.948
blank_filter_hist0.0010.0000.003
bootstrap0.0280.0010.033
calculate0.0130.0010.013
chart_plot0.0790.0040.100
classical_lsq0.7770.0070.879
compare_dist7.2840.2488.603
confounders_clsq7.4480.0518.235
confounders_lsq_barchart7.5870.0478.791
confounders_lsq_boxplot7.4710.0458.162
constant_sum_norm0.0170.0010.019
corr_coef0.6390.0060.697
dfa_scores_plot1.7920.0191.955
dratio_filter0.7220.0190.769
equal_split0.2920.0030.304
feature_boxplot0.0700.0010.074
feature_profile0.9600.0151.017
feature_profile_array1.0930.0081.136
filter_by_name0.0820.0010.090
filter_na_count2.8020.0903.092
filter_smeta0.1610.0020.163
fisher_exact23.415 0.08623.856
fold_change27.660 0.14928.737
fold_change_int39.485 0.14943.705
fold_change_plot0.0170.0000.019
forward_selection_by_rank15.126 0.21217.710
fs_line14.659 0.26716.790
glog_opt_plot1.1520.0141.382
glog_transform0.7450.0110.861
grid_search_1d7.8830.1589.315
gs_line0.0010.0000.002
hca_dendrogram0.0020.0000.004
kfold_xval8.2930.0529.598
kfoldxcv_grid 9.054 0.06010.236
kfoldxcv_metric0.0010.0000.002
knn_impute0.0290.0010.031
kw_p_hist0.0020.0000.002
kw_rank_sum0.1830.0020.207
linear_model0.0730.0010.077
log_transform0.0170.0010.020
mean_centre0.0080.0000.008
mean_of_medians0.2890.0020.333
mixed_effect0.3990.0080.504
model_apply0.0550.0020.071
model_predict0.1340.0020.164
model_reverse0.0630.0000.075
model_train0.1270.0030.157
mv_boxplot0.6500.0050.738
mv_feature_filter0.2620.0020.301
mv_feature_filter_hist0.0020.0000.002
mv_histogram0.6150.0080.701
mv_sample_filter0.0190.0010.021
mv_sample_filter_hist0.0010.0000.002
nroot_transform0.0170.0000.019
ontology_cache0.0000.0010.001
pairs_filter0.0240.0010.026
pareto_scale0.1360.0010.153
pca_biplot0.0390.0000.042
pca_correlation_plot0.0150.0010.018
pca_dstat_plot0.0230.0000.026
pca_loadings_plot0.0230.0010.024
pca_scores_plot1.2630.0091.439
pca_scree_plot0.0160.0010.016
permutation_test0.0240.0010.028
permutation_test_plot0.0070.0000.010
permute_sample_order0.0170.0010.019
pls_regcoeff_plot0.8120.0090.927
pls_scores_plot1.6700.0091.892
pls_vip_plot0.8830.0070.995
plsda_feature_importance_plot1.4080.0141.607
plsda_predicted_plot1.0760.0101.238
plsda_roc_plot3.0060.0283.568
plsr_cook_dist0.0180.0000.019
plsr_prediction_plot0.0150.0010.016
plsr_qq_plot0.0160.0010.020
plsr_residual_hist0.0160.0000.017
pqn_norm0.8860.0061.016
pqn_norm_hist0.0010.0000.003
prop_na0.0260.0010.036
r_squared0.0010.0010.002
resample0.0410.0010.045
resample_chart0.0060.0000.008
rsd_filter0.0330.0020.039
rsd_filter_hist0.0020.0000.002
run0.0720.0020.083
sb_corr0.0690.0020.078
scatter_chart0.8590.0070.977
split_data0.0160.0010.019
stratified_split0.2710.0020.316
svm_plot_2d1.4920.0221.723
tSNE0.0610.0020.073
tSNE_scatter0.0160.0010.018
tic_chart0.5000.0090.577
ttest0.0560.0010.062
vec_norm0.0020.0010.003
wilcox_p_hist0.0010.0000.001
wilcox_test0.0460.0010.054