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This page was generated on 2025-08-18 12:05 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 2103/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.21.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-08-17 13:45 -0400 (Sun, 17 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: 2025-08-18 00:04:19 -0400 (Mon, 18 Aug 2025)
EndedAt: 2025-08-18 00:13:23 -0400 (Mon, 18 Aug 2025)
EllapsedTime: 543.9 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_1.21.0.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           17.708  0.094  17.900
fold_change               12.989  0.159  13.264
fisher_exact              12.215  0.086  12.393
fs_line                    6.739  0.112   6.888
forward_selection_by_rank  6.568  0.183   6.783
* 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 
210.638   2.485 214.697 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2480.0080.258
AUC3.0670.1113.199
DFA0.2290.0030.233
DatasetExperiment_boxplot0.6830.0360.721
DatasetExperiment_dist1.3030.0891.401
DatasetExperiment_factor_boxplot0.2220.0060.230
DatasetExperiment_heatmap0.4140.0100.425
HCA0.0640.0010.065
HSD0.3000.0200.327
HSDEM0.5130.0350.555
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0090.0000.010
OPLSR0.0080.0000.007
PCA0.0040.0010.005
PLSDA0.0100.0010.010
PLSR0.0080.0010.009
SVM0.0180.0010.018
as_data_frame0.1340.0010.136
autoscale0.0730.0010.075
balanced_accuracy2.7800.0442.839
blank_filter0.3810.0230.407
blank_filter_hist0.0010.0010.001
bootstrap0.0110.0000.011
calculate0.0060.0000.007
chart_plot0.0350.0020.038
classical_lsq0.3690.0090.380
compare_dist4.5550.2524.837
confounders_clsq3.5000.0283.544
confounders_lsq_barchart3.9170.0303.983
confounders_lsq_boxplot3.7210.0273.771
constant_sum_norm0.0070.0000.007
corr_coef0.3150.0030.321
dfa_scores_plot0.8640.0090.877
dratio_filter0.3210.0080.329
equal_split0.1500.0020.155
feature_boxplot0.0290.0010.030
feature_profile0.4230.0050.430
feature_profile_array0.5700.0060.578
filter_by_name0.0400.0010.041
filter_na_count1.1050.0521.163
filter_smeta0.0680.0010.072
fisher_exact12.215 0.08612.393
fold_change12.989 0.15913.264
fold_change_int17.708 0.09417.900
fold_change_plot0.0090.0000.010
forward_selection_by_rank6.5680.1836.783
fs_line6.7390.1126.888
glog_opt_plot0.5660.0070.578
glog_transform0.3400.0050.348
grid_search_1d4.6190.1894.839
gs_line0.0010.0000.000
hca_dendrogram0.0010.0000.001
kfold_xval4.0820.0344.139
kfoldxcv_grid4.4140.0414.480
kfoldxcv_metric0.0010.0000.001
knn_impute0.0140.0010.015
kw_p_hist0.0010.0000.001
kw_rank_sum0.0910.0000.092
linear_model0.0380.0010.040
log_transform0.0080.0010.009
mean_centre0.0030.0000.003
mean_of_medians0.1290.0010.130
mixed_effect0.2080.0050.214
model_apply0.0200.0010.021
model_predict0.0550.0010.057
model_reverse0.0290.0000.029
model_train0.0530.0000.053
mv_boxplot0.3090.0030.315
mv_feature_filter0.1350.0010.137
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2810.0040.287
mv_sample_filter0.0100.0010.012
mv_sample_filter_hist0.0010.0000.001
nroot_transform0.0090.0000.010
ontology_cache000
pairs_filter0.0110.0000.012
pareto_scale0.0700.0020.072
pca_biplot0.0170.0010.018
pca_correlation_plot0.0080.0000.009
pca_dstat_plot0.0120.0000.013
pca_loadings_plot0.0130.0000.013
pca_scores_plot0.6210.0110.635
pca_scree_plot0.0070.0000.007
permutation_test0.0090.0000.009
permutation_test_plot0.0030.0000.003
permute_sample_order0.0060.0000.006
pls_regcoeff_plot0.4180.0050.426
pls_scores_plot0.7990.0070.813
pls_vip_plot0.4430.0060.453
plsda_feature_importance_plot0.7230.0110.740
plsda_predicted_plot0.5730.0100.587
plsda_roc_plot1.3200.0131.341
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_norm0.4140.0030.421
pqn_norm_hist0.0010.0000.001
prop_na0.0130.0000.013
r_squared0.0000.0000.001
resample0.0170.0010.017
resample_chart0.0040.0000.004
rsd_filter0.0170.0000.018
rsd_filter_hist0.0010.0000.001
run0.0360.0010.038
sb_corr0.0340.0010.035
scatter_chart0.4000.0040.407
split_data0.0240.0010.024
stratified_split0.1310.0020.133
svm_plot_2d0.7830.0170.803
tSNE0.0290.0010.030
tSNE_scatter0.0100.0010.010
tic_chart0.2290.0030.235
ttest0.0250.0000.025
vec_norm0.0010.0010.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0370.0050.042