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This page was generated on 2025-10-06 11:39 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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: 2025-10-02 13:40 -0400 (Thu, 02 Oct 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    OK  


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: 2025-10-03 11:06:24 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 11:25:41 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 1156.8 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           39.530  0.149  43.840
fold_change               27.487  0.113  28.405
fisher_exact              23.036  0.092  23.980
forward_selection_by_rank 15.082  0.168  17.014
fs_line                   14.958  0.151  17.355
compare_dist               9.275  0.257  10.798
kfoldxcv_grid              9.466  0.056  10.796
grid_search_1d             8.631  0.161   9.991
kfold_xval                 8.332  0.050   9.453
confounders_lsq_barchart   8.021  0.049   9.120
confounders_lsq_boxplot    7.681  0.046   8.724
confounders_clsq           7.334  0.044   8.363
AUC                        4.822  0.191   5.154
* 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 
457.672   3.840 479.883 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.4540.0110.467
AUC4.8220.1915.154
DFA0.4720.0040.477
DatasetExperiment_boxplot2.8660.0712.990
DatasetExperiment_dist2.1940.0992.308
DatasetExperiment_factor_boxplot0.8520.0210.890
DatasetExperiment_heatmap1.4410.0451.649
HCA0.1400.0020.156
HSD0.6880.0210.807
HSDEM0.7440.0310.889
MTBLS79_DatasetExperiment0.0020.0000.003
OPLSDA0.0280.0010.032
OPLSR0.0220.0000.024
PCA0.0100.0000.012
PLSDA0.0330.0010.038
PLSR0.0250.0010.032
SVM0.0580.0020.071
as_data_frame0.3040.0030.341
autoscale0.1740.0020.192
balanced_accuracy4.4010.0544.978
blank_filter0.7990.0280.951
blank_filter_hist0.0020.0010.002
bootstrap0.0240.0010.027
calculate0.0120.0010.015
chart_plot0.0680.0030.078
classical_lsq0.7640.0070.855
compare_dist 9.275 0.25710.798
confounders_clsq7.3340.0448.363
confounders_lsq_barchart8.0210.0499.120
confounders_lsq_boxplot7.6810.0468.724
constant_sum_norm0.0170.0010.018
corr_coef0.6280.0040.651
dfa_scores_plot2.4180.0292.576
dratio_filter0.7140.0190.769
equal_split0.2900.0020.303
feature_boxplot0.0670.0020.070
feature_profile1.3070.0321.402
feature_profile_array1.5920.0111.674
filter_by_name0.0820.0020.086
filter_na_count2.8170.1003.181
filter_smeta0.1600.0010.168
fisher_exact23.036 0.09223.980
fold_change27.487 0.11328.405
fold_change_int39.530 0.14943.840
fold_change_plot0.0170.0010.020
forward_selection_by_rank15.082 0.16817.014
fs_line14.958 0.15117.355
glog_opt_plot1.4040.0111.581
glog_transform0.7400.0050.827
grid_search_1d8.6310.1619.991
gs_line0.0020.0000.002
hca_dendrogram0.0010.0010.002
kfold_xval8.3320.0509.453
kfoldxcv_grid 9.466 0.05610.796
kfoldxcv_metric0.0010.0000.001
knn_impute0.0300.0010.035
kw_p_hist0.0010.0000.003
kw_rank_sum0.1780.0020.201
linear_model0.0710.0020.080
log_transform0.0170.0010.018
mean_centre0.0070.0000.009
mean_of_medians0.2910.0020.331
mixed_effect0.3860.0060.445
model_apply0.0550.0030.063
model_predict0.1300.0020.150
model_reverse0.0610.0010.070
model_train0.1220.0010.138
mv_boxplot1.0520.0091.184
mv_feature_filter0.2810.0040.324
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.8680.0060.982
mv_sample_filter0.0190.0010.021
mv_sample_filter_hist0.0010.0000.002
nroot_transform0.0170.0010.021
ontology_cache000
pairs_filter0.0240.0010.029
pareto_scale0.1390.0010.154
pca_biplot0.0380.0010.045
pca_correlation_plot0.0150.0000.017
pca_dstat_plot0.0230.0010.027
pca_loadings_plot0.0230.0010.024
pca_scores_plot1.7820.0142.023
pca_scree_plot0.0150.0010.017
permutation_test0.0240.0010.027
permutation_test_plot0.0060.0010.010
permute_sample_order0.0180.0000.023
pls_regcoeff_plot1.1530.0101.405
pls_scores_plot2.1890.0132.482
pls_vip_plot1.2420.0111.420
plsda_feature_importance_plot2.1800.0172.453
plsda_predicted_plot1.5030.0121.698
plsda_roc_plot3.2610.0253.699
plsr_cook_dist0.0150.0000.019
plsr_prediction_plot0.0160.0010.020
plsr_qq_plot0.0140.0010.017
plsr_residual_hist0.0150.0010.018
pqn_norm0.8700.0040.980
pqn_norm_hist0.0020.0000.002
prop_na0.0240.0010.027
r_squared0.0020.0000.001
resample0.0400.0010.047
resample_chart0.0060.0010.007
rsd_filter0.0340.0010.040
rsd_filter_hist0.0010.0010.003
run0.0730.0020.085
sb_corr0.0690.0010.081
scatter_chart1.3550.0091.537
split_data0.0170.0010.021
stratified_split0.2710.0030.313
svm_plot_2d1.9700.0322.775
tSNE0.0670.0050.127
tSNE_scatter0.0170.0010.024
tic_chart0.8780.0111.203
ttest0.0590.0010.068
vec_norm0.0020.0010.002
wilcox_p_hist0.0020.0010.002
wilcox_test0.0460.0020.056