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This page was generated on 2025-09-25 11:38 -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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings structToolbox_1.20.0.tar.gz
StartedAt: 2025-09-25 04:31:46 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 04:50:41 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 1135.5 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings structToolbox_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/structToolbox.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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           16.326  0.112  16.438
fold_change               10.929  0.084  11.013
fisher_exact               9.677  0.023   9.700
fs_line                    5.917  0.019   5.936
forward_selection_by_rank  5.666  0.060   5.727
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

structToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
188.781   1.779 190.579 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2090.0030.212
AUC1.9670.0822.050
DFA0.1850.0010.185
DatasetExperiment_boxplot1.8350.0151.851
DatasetExperiment_dist1.4750.0381.514
DatasetExperiment_factor_boxplot0.3260.0000.326
DatasetExperiment_heatmap0.5530.0020.555
HCA0.0580.0000.058
HSD0.2800.0050.288
HSDEM0.2790.0030.282
MTBLS79_DatasetExperiment0.0010.0010.002
OPLSDA0.0130.0000.012
OPLSR0.0090.0000.009
PCA0.0050.0000.005
PLSDA0.0120.0000.012
PLSR0.0090.0010.010
SVM0.0230.0000.023
as_data_frame0.1430.0000.143
autoscale0.0740.0010.075
balanced_accuracy1.7840.0061.789
blank_filter0.3170.0060.324
blank_filter_hist0.0010.0000.001
bootstrap0.0100.0000.009
calculate0.0050.0010.005
chart_plot0.0280.0010.029
classical_lsq0.3010.0010.302
compare_dist4.3390.0344.373
confounders_clsq2.8040.0312.835
confounders_lsq_barchart3.2920.0213.314
confounders_lsq_boxplot3.1500.0273.178
constant_sum_norm0.0090.0000.009
corr_coef0.2870.0030.290
dfa_scores_plot1.0140.0031.023
dratio_filter0.3510.0060.358
equal_split0.1230.0000.123
feature_boxplot0.0280.0000.028
feature_profile0.5400.0000.541
feature_profile_array0.6630.0020.665
filter_by_name0.0350.0000.035
filter_na_count0.9870.0201.007
filter_smeta0.0630.0010.064
fisher_exact9.6770.0239.700
fold_change10.929 0.08411.013
fold_change_int16.326 0.11216.438
fold_change_plot0.0060.0010.006
forward_selection_by_rank5.6660.0605.727
fs_line5.9170.0195.936
glog_opt_plot0.5360.0000.536
glog_transform0.280.000.28
grid_search_1d3.3050.0053.310
gs_line0.0000.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval3.2800.0123.292
kfoldxcv_grid3.6910.0083.699
kfoldxcv_metric0.0010.0000.001
knn_impute0.0110.0010.012
kw_p_hist0.0010.0000.001
kw_rank_sum0.0700.0010.072
linear_model0.0290.0000.029
log_transform0.0060.0000.007
mean_centre0.0030.0000.003
mean_of_medians0.1240.0010.126
mixed_effect0.1550.0000.155
model_apply0.0220.0030.025
model_predict0.0540.0000.054
model_reverse0.0250.0010.026
model_train0.0530.0010.054
mv_boxplot0.4310.0000.432
mv_feature_filter0.1030.0020.105
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.3350.0030.338
mv_sample_filter0.0090.0000.009
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0060.0010.007
ontology_cache0.0000.0000.001
pairs_filter0.0090.0000.009
pareto_scale0.0710.0000.071
pca_biplot0.0140.0010.015
pca_correlation_plot0.0060.0000.006
pca_dstat_plot0.0090.0000.009
pca_loadings_plot0.0090.0000.009
pca_scores_plot0.7210.0010.722
pca_scree_plot0.0050.0010.006
permutation_test0.0090.0010.009
permutation_test_plot0.0020.0000.003
permute_sample_order0.0070.0000.007
pls_regcoeff_plot0.4600.0000.459
pls_scores_plot0.8290.0010.830
pls_vip_plot0.5090.0010.509
plsda_feature_importance_plot0.8620.0010.863
plsda_predicted_plot0.5880.0000.589
plsda_roc_plot1.2320.0011.234
plsr_cook_dist0.0070.0000.007
plsr_prediction_plot0.0060.0010.006
plsr_qq_plot0.0060.0000.006
plsr_residual_hist0.0060.0000.006
pqn_norm0.3430.0010.344
pqn_norm_hist0.0000.0000.001
prop_na0.0090.0000.009
r_squared0.0000.0010.001
resample0.0150.0000.015
resample_chart0.0020.0010.002
rsd_filter0.0130.0000.013
rsd_filter_hist0.0000.0010.001
run0.0310.0000.031
sb_corr0.0260.0010.027
scatter_chart0.5400.0020.543
split_data0.0070.0000.007
stratified_split0.1120.0000.112
svm_plot_2d0.8210.0040.824
tSNE0.0250.0000.025
tSNE_scatter0.0070.0000.008
tic_chart0.3420.0030.346
ttest0.0210.0000.021
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0160.0000.016