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This page was generated on 2025-09-25 11:40 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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: 2025-09-22 13:40 -0400 (Mon, 22 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: 2025-09-23 11:27:50 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 11:47:50 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 1199.4 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           39.585  0.178  42.709
fold_change               28.315  0.171  32.238
fisher_exact              23.781  0.121  27.052
forward_selection_by_rank 14.821  0.187  15.408
fs_line                   14.732  0.148  15.486
kfoldxcv_grid              9.479  0.043   9.750
compare_dist               9.219  0.220  10.971
kfold_xval                 8.321  0.049   8.995
confounders_lsq_barchart   8.101  0.051   9.546
grid_search_1d             7.952  0.175   8.788
confounders_lsq_boxplot    7.873  0.044   9.145
confounders_clsq           7.344  0.056   8.771
AUC                        5.077  0.209   6.230
balanced_accuracy          4.388  0.041   5.017
* 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 
396.398   3.971 411.403 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.4850.0110.513
AUC5.0770.2096.230
DFA0.4930.0030.547
DatasetExperiment_boxplot2.8860.0633.264
DatasetExperiment_dist2.1830.0932.407
DatasetExperiment_factor_boxplot0.8550.0110.998
DatasetExperiment_heatmap1.4830.0421.796
HCA0.1450.0020.157
HSD0.7020.0232.461
HSDEM0.7430.0321.766
MTBLS79_DatasetExperiment0.0030.0000.002
OPLSDA0.0280.0010.030
OPLSR0.0210.0000.023
PCA0.0110.0000.011
PLSDA0.0280.0010.030
PLSR0.0240.0010.025
SVM0.0550.0010.057
as_data_frame0.3070.0030.383
autoscale0.1730.0010.175
balanced_accuracy4.3880.0415.017
blank_filter0.7770.0291.611
blank_filter_hist0.0010.0000.002
bootstrap0.0270.0010.033
calculate0.0120.0010.012
chart_plot0.0650.0030.069
classical_lsq0.7540.0080.848
compare_dist 9.219 0.22010.971
confounders_clsq7.3440.0568.771
confounders_lsq_barchart8.1010.0519.546
confounders_lsq_boxplot7.8730.0449.145
constant_sum_norm0.0170.0010.024
corr_coef0.6110.0040.714
dfa_scores_plot2.4610.0252.877
dratio_filter0.7290.0200.863
equal_split0.2860.0030.360
feature_boxplot0.0690.0020.091
feature_profile1.3380.0181.635
feature_profile_array1.6030.0101.891
filter_by_name0.0750.0010.087
filter_na_count2.8420.0963.274
filter_smeta0.1670.0010.192
fisher_exact23.781 0.12127.052
fold_change28.315 0.17132.238
fold_change_int39.585 0.17842.709
fold_change_plot0.0150.0010.016
forward_selection_by_rank14.821 0.18715.408
fs_line14.732 0.14815.486
glog_opt_plot1.4080.0121.498
glog_transform0.7220.0060.734
grid_search_1d7.9520.1758.788
gs_line0.0010.0000.002
hca_dendrogram0.0020.0000.002
kfold_xval8.3210.0498.995
kfoldxcv_grid9.4790.0439.750
kfoldxcv_metric0.0010.0000.001
knn_impute0.0300.0010.033
kw_p_hist0.0020.0010.001
kw_rank_sum0.1790.0020.182
linear_model0.0870.0050.094
log_transform0.0170.0000.017
mean_centre0.0080.0000.008
mean_of_medians0.2790.0010.282
mixed_effect0.3740.0040.406
model_apply0.0550.0020.057
model_predict0.1330.0010.136
model_reverse0.0620.0010.063
model_train0.1280.0010.135
mv_boxplot1.0720.0131.138
mv_feature_filter0.2670.0040.275
mv_feature_filter_hist0.0010.0010.002
mv_histogram0.9050.0080.932
mv_sample_filter0.0190.0010.020
mv_sample_filter_hist0.0020.0010.002
nroot_transform0.0160.0000.017
ontology_cache000
pairs_filter0.0220.0000.022
pareto_scale0.1340.0010.135
pca_biplot0.0360.0000.037
pca_correlation_plot0.0160.0000.016
pca_dstat_plot0.0220.0010.023
pca_loadings_plot0.0220.0000.023
pca_scores_plot1.7360.0091.767
pca_scree_plot0.0140.0010.015
permutation_test0.0230.0000.024
permutation_test_plot0.0070.0010.007
permute_sample_order0.0160.0010.016
pls_regcoeff_plot1.1580.0081.218
pls_scores_plot2.1370.0092.188
pls_vip_plot1.2470.0111.377
plsda_feature_importance_plot2.2580.0202.562
plsda_predicted_plot1.5050.0111.665
plsda_roc_plot3.3060.0203.555
plsr_cook_dist0.0160.0000.016
plsr_prediction_plot0.0160.0010.017
plsr_qq_plot0.0160.0010.016
plsr_residual_hist0.0150.0000.016
pqn_norm0.8650.0040.933
pqn_norm_hist0.0020.0000.002
prop_na0.0260.0010.029
r_squared0.0010.0010.002
resample0.0410.0010.045
resample_chart0.0070.0010.007
rsd_filter0.0330.0010.035
rsd_filter_hist0.0020.0010.002
run0.0740.0010.078
sb_corr0.0730.0020.081
scatter_chart1.3610.0081.438
split_data0.0160.0010.016
stratified_split0.2970.0020.307
svm_plot_2d1.9750.0252.211
tSNE0.0580.0020.059
tSNE_scatter0.0180.0010.019
tic_chart0.8210.0050.992
ttest0.0600.0020.061
vec_norm0.0010.0000.002
wilcox_p_hist0.0010.0010.003
wilcox_test0.0480.0010.052