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This page was generated on 2025-09-01 12:05 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 2106/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.21.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 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 24.04.3 LTS) / x86_64  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 13.7.7 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: 2025-09-01 00:07:39 -0400 (Mon, 01 Sep 2025)
EndedAt: 2025-09-01 00:16:42 -0400 (Mon, 01 Sep 2025)
EllapsedTime: 543.1 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           19.315  0.122  19.576
fold_change               13.327  0.110  13.516
fisher_exact              12.263  0.067  12.398
fs_line                    6.714  0.147   6.915
forward_selection_by_rank  6.637  0.115   6.794
* 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 
211.482   2.528 215.498 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2550.0090.266
AUC2.9500.1083.075
DFA0.2320.0020.236
DatasetExperiment_boxplot0.7150.0380.758
DatasetExperiment_dist1.3380.0981.450
DatasetExperiment_factor_boxplot0.2570.0070.265
DatasetExperiment_heatmap0.4030.0110.416
HCA0.0700.0010.072
HSD0.2900.0220.319
HSDEM0.4030.0300.437
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0120.0000.013
OPLSR0.0080.0000.008
PCA0.0040.0000.005
PLSDA0.0130.0000.013
PLSR0.0090.0000.010
SVM0.0200.0000.021
as_data_frame0.1430.0010.146
autoscale0.0760.0020.081
balanced_accuracy2.7910.0422.844
blank_filter0.4070.0230.432
blank_filter_hist0.0010.0000.001
bootstrap0.010.000.01
calculate0.0050.0000.006
chart_plot0.0290.0010.031
classical_lsq0.3330.0080.342
compare_dist4.4920.2424.760
confounders_clsq3.3210.0263.362
confounders_lsq_barchart3.5490.0273.597
confounders_lsq_boxplot3.2780.0223.313
constant_sum_norm0.0080.0010.008
corr_coef0.3020.0030.306
dfa_scores_plot0.8500.0110.866
dratio_filter0.3440.0110.355
equal_split0.1600.0020.162
feature_boxplot0.0260.0010.026
feature_profile0.4120.0040.417
feature_profile_array0.5360.0080.547
filter_by_name0.0350.0010.035
filter_na_count1.1620.0551.224
filter_smeta0.0750.0010.075
fisher_exact12.263 0.06712.398
fold_change13.327 0.11013.516
fold_change_int19.315 0.12219.576
fold_change_plot0.0070.0000.006
forward_selection_by_rank6.6370.1156.794
fs_line6.7140.1476.915
glog_opt_plot0.5280.0050.536
glog_transform0.2960.0020.300
grid_search_1d4.3120.1974.546
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval3.6020.0343.656
kfoldxcv_grid4.0620.0364.122
kfoldxcv_metric0.0000.0000.001
knn_impute0.0150.0010.017
kw_p_hist0.0000.0000.001
kw_rank_sum0.0950.0010.097
linear_model0.0380.0010.039
log_transform0.0090.0010.010
mean_centre0.0030.0000.003
mean_of_medians0.1540.0030.157
mixed_effect0.1990.0030.203
model_apply0.0250.0010.027
model_predict0.0590.0010.061
model_reverse0.0280.0000.029
model_train0.0560.0000.057
mv_boxplot0.3180.0070.332
mv_feature_filter0.1330.0010.136
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2780.0080.288
mv_sample_filter0.0090.0000.010
mv_sample_filter_hist0.0010.0000.002
nroot_transform0.0090.0000.009
ontology_cache0.0000.0000.001
pairs_filter0.010.000.01
pareto_scale0.0630.0000.065
pca_biplot0.0160.0000.016
pca_correlation_plot0.0080.0000.008
pca_dstat_plot0.0100.0010.010
pca_loadings_plot0.0120.0000.012
pca_scores_plot0.5900.0060.598
pca_scree_plot0.0080.0000.008
permutation_test0.0110.0000.012
permutation_test_plot0.0040.0000.004
permute_sample_order0.010.000.01
pls_regcoeff_plot0.4130.0060.422
pls_scores_plot0.7720.0080.786
pls_vip_plot0.4410.0070.451
plsda_feature_importance_plot0.7180.0100.735
plsda_predicted_plot0.5440.0060.554
plsda_roc_plot1.3380.0131.357
plsr_cook_dist0.0070.0010.007
plsr_prediction_plot0.0060.0000.007
plsr_qq_plot0.0080.0000.008
plsr_residual_hist0.0080.0000.008
pqn_norm0.4230.0040.428
pqn_norm_hist0.0010.0000.001
prop_na0.0140.0000.015
r_squared0.0010.0000.001
resample0.0180.0000.018
resample_chart0.0040.0000.004
rsd_filter0.0170.0000.017
rsd_filter_hist0.0010.0000.001
run0.0400.0010.041
sb_corr0.0360.0010.037
scatter_chart0.4120.0050.419
split_data0.0080.0000.008
stratified_split0.1240.0010.126
svm_plot_2d0.7400.0150.758
tSNE0.0270.0010.027
tSNE_scatter0.0080.0000.008
tic_chart0.2380.0090.247
ttest0.0250.0010.024
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0240.0010.025