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This page was generated on 2025-09-04 11:42 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
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: 2025-09-01 13:40 -0400 (Mon, 01 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 kjohnson1

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: 2025-09-03 13:09:06 -0400 (Wed, 03 Sep 2025)
EndedAt: 2025-09-03 13:17:36 -0400 (Wed, 03 Sep 2025)
EllapsedTime: 510.2 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 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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           15.682  0.042  15.739
fold_change               10.176  0.057  10.234
fisher_exact               9.628  0.035   9.666
forward_selection_by_rank  6.376  0.196   6.623
fs_line                    5.461  0.101   5.589
* 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-arm64/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
185.927   2.105 188.746 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2540.0160.276
AUC2.0180.0932.173
DFA0.1970.0020.199
DatasetExperiment_boxplot1.7740.0411.814
DatasetExperiment_dist2.2230.0632.286
DatasetExperiment_factor_boxplot0.2130.0030.217
DatasetExperiment_heatmap0.4150.0220.437
HCA0.0630.0030.067
HSD0.2820.0170.303
HSDEM0.3640.0220.404
MTBLS79_DatasetExperiment0.0010.0010.001
OPLSDA0.010.000.01
OPLSR0.0070.0000.007
PCA0.0040.0000.005
PLSDA0.0110.0010.011
PLSR0.0080.0010.009
SVM0.0190.0010.020
as_data_frame0.1280.0020.129
autoscale0.0720.0010.074
balanced_accuracy1.7920.0161.811
blank_filter0.3790.0200.400
blank_filter_hist0.0010.0000.001
bootstrap0.0090.0000.009
calculate0.0050.0010.005
chart_plot0.0290.0010.030
classical_lsq0.3060.0030.309
compare_dist3.9100.2044.117
confounders_clsq2.8940.0192.919
confounders_lsq_barchart3.0380.0223.115
confounders_lsq_boxplot2.8920.0212.917
constant_sum_norm0.0070.0000.007
corr_coef0.2500.0020.252
dfa_scores_plot0.7160.0050.741
dratio_filter0.2580.0060.269
equal_split0.1130.0010.136
feature_boxplot0.0220.0010.024
feature_profile0.3130.0050.324
feature_profile_array0.2590.0040.279
filter_by_name0.0160.0000.017
filter_na_count1.0840.0581.146
filter_smeta0.060.000.06
fisher_exact9.6280.0359.666
fold_change10.176 0.05710.234
fold_change_int15.682 0.04215.739
fold_change_plot0.0060.0010.007
forward_selection_by_rank6.3760.1966.623
fs_line5.4610.1015.589
glog_opt_plot0.4660.0050.471
glog_transform0.2870.0020.289
grid_search_1d3.8330.2784.143
gs_line0.0010.0000.000
hca_dendrogram0.0010.0000.001
kfold_xval3.3940.0273.426
kfoldxcv_grid3.7130.0333.750
kfoldxcv_metric0.0010.0000.001
knn_impute0.0110.0010.013
kw_p_hist0.0010.0010.001
kw_rank_sum0.0720.0010.072
linear_model0.0280.0010.028
log_transform0.0070.0000.007
mean_centre0.0030.0000.003
mean_of_medians0.1150.0010.115
mixed_effect0.1820.0020.184
model_apply0.0240.0010.024
model_predict0.0560.0010.057
model_reverse0.0250.0000.025
model_train0.0510.0000.052
mv_boxplot0.2860.0080.295
mv_feature_filter0.1130.0010.113
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2590.0140.272
mv_sample_filter0.0090.0000.008
mv_sample_filter_hist0.0010.0010.001
nroot_transform0.0060.0000.006
ontology_cache0.0000.0010.000
pairs_filter0.0090.0000.009
pareto_scale0.0540.0010.054
pca_biplot0.0130.0000.013
pca_correlation_plot0.0050.0000.006
pca_dstat_plot0.0090.0000.010
pca_loadings_plot0.0090.0000.010
pca_scores_plot0.5110.0050.516
pca_scree_plot0.0060.0010.007
permutation_test0.0090.0000.009
permutation_test_plot0.0030.0000.004
permute_sample_order0.0070.0010.007
pls_regcoeff_plot0.3300.0060.337
pls_scores_plot0.6590.0050.665
pls_vip_plot0.3690.0060.374
plsda_feature_importance_plot0.5510.0080.559
plsda_predicted_plot0.5000.0150.515
plsda_roc_plot1.1000.0191.120
plsr_cook_dist0.0070.0000.007
plsr_prediction_plot0.0060.0000.006
plsr_qq_plot0.0060.0010.006
plsr_residual_hist0.0060.0000.006
pqn_norm0.3490.0020.351
pqn_norm_hist0.0020.0000.002
prop_na0.0100.0000.009
r_squared0.0010.0000.001
resample0.0150.0010.015
resample_chart0.0030.0000.003
rsd_filter0.0120.0000.013
rsd_filter_hist0.0010.0010.001
run0.0300.0010.030
sb_corr0.0240.0010.025
scatter_chart0.3810.0060.388
split_data0.0080.0000.007
stratified_split0.1130.0010.117
svm_plot_2d0.6700.0190.705
tSNE0.0220.0010.023
tSNE_scatter0.0070.0010.008
tic_chart0.2240.0040.228
ttest0.0200.0000.021
vec_norm0.0010.0000.001
wilcox_p_hist0.0000.0010.000
wilcox_test0.0150.0000.016