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This page was generated on 2025-07-28 12:10 -0400 (Mon, 28 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4512
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 2099/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.21.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-07-27 13:25 -0400 (Sun, 27 Jul 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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: 2025-07-28 00:07:08 -0400 (Mon, 28 Jul 2025)
EndedAt: 2025-07-28 00:16:28 -0400 (Mon, 28 Jul 2025)
EllapsedTime: 559.9 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_1.21.0.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           18.799  0.100  19.002
fold_change               13.067  0.121  13.284
fisher_exact              11.433  0.082  11.579
fs_line                    7.248  0.132   7.416
forward_selection_by_rank  7.167  0.158   7.361
compare_dist               4.829  0.244   5.101
* 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 
215.655   2.517 219.726 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2690.0090.278
AUC3.3830.1263.539
DFA0.2510.0030.255
DatasetExperiment_boxplot0.7460.0390.791
DatasetExperiment_dist1.4500.1191.577
DatasetExperiment_factor_boxplot0.2690.0070.279
DatasetExperiment_heatmap0.4820.0110.496
HCA0.0800.0010.086
HSD0.3460.0210.380
HSDEM0.5970.0350.637
MTBLS79_DatasetExperiment0.0020.0000.002
OPLSDA0.0130.0000.014
OPLSR0.0100.0000.011
PCA0.0060.0000.006
PLSDA0.0150.0010.016
PLSR0.0080.0010.009
SVM0.0240.0010.025
as_data_frame0.1660.0010.167
autoscale0.0870.0010.089
balanced_accuracy3.0970.0503.160
blank_filter0.4340.0230.460
blank_filter_hist0.0010.0000.001
bootstrap0.0120.0000.013
calculate0.0050.0000.005
chart_plot0.0330.0020.035
classical_lsq0.3710.0090.381
compare_dist4.8290.2445.101
confounders_clsq3.5190.0243.553
confounders_lsq_barchart3.7260.0253.763
confounders_lsq_boxplot3.6320.0253.673
constant_sum_norm0.0090.0010.010
corr_coef0.3050.0030.311
dfa_scores_plot0.7950.0080.808
dratio_filter0.3180.0080.329
equal_split0.1340.0010.136
feature_boxplot0.0350.0010.037
feature_profile0.4120.0050.420
feature_profile_array0.5440.0070.554
filter_by_name0.0360.0000.036
filter_na_count1.0450.0511.104
filter_smeta0.0570.0000.058
fisher_exact11.433 0.08211.579
fold_change13.067 0.12113.284
fold_change_int18.799 0.10019.002
fold_change_plot0.0090.0000.010
forward_selection_by_rank7.1670.1587.361
fs_line7.2480.1327.416
glog_opt_plot0.4980.0040.504
glog_transform0.3620.0030.366
grid_search_1d4.7100.1734.911
gs_line0.0010.0000.001
hca_dendrogram0.0000.0000.001
kfold_xval4.1400.0334.195
kfoldxcv_grid4.6910.0414.763
kfoldxcv_metric0.0010.0000.001
knn_impute0.0140.0010.015
kw_p_hist0.0010.0000.000
kw_rank_sum0.0940.0010.096
linear_model0.0370.0010.038
log_transform0.0080.0000.008
mean_centre0.0030.0000.004
mean_of_medians0.1560.0010.159
mixed_effect0.2060.0070.213
model_apply0.0290.0010.030
model_predict0.0670.0010.068
model_reverse0.0260.0000.027
model_train0.0520.0010.052
mv_boxplot0.3260.0030.331
mv_feature_filter0.1350.0010.137
mv_feature_filter_hist0.0000.0000.001
mv_histogram0.2890.0030.295
mv_sample_filter0.010.000.01
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0070.0000.007
ontology_cache0.0010.0000.001
pairs_filter0.010.000.01
pareto_scale0.0650.0010.067
pca_biplot0.0190.0000.019
pca_correlation_plot0.0080.0010.008
pca_dstat_plot0.0130.0000.013
pca_loadings_plot0.0100.0000.011
pca_scores_plot0.6160.0110.630
pca_scree_plot0.0070.0000.008
permutation_test0.0110.0000.011
permutation_test_plot0.0020.0010.003
permute_sample_order0.0100.0000.009
pls_regcoeff_plot0.4330.0070.445
pls_scores_plot0.7980.0070.812
pls_vip_plot0.4480.0060.456
plsda_feature_importance_plot0.7020.0120.718
plsda_predicted_plot0.5690.0070.580
plsda_roc_plot1.3720.0121.390
plsr_cook_dist0.0080.0000.008
plsr_prediction_plot0.0070.0010.008
plsr_qq_plot0.0080.0000.008
plsr_residual_hist0.0080.0000.008
pqn_norm0.4320.0020.437
pqn_norm_hist0.0010.0010.001
prop_na0.0130.0000.013
r_squared0.0000.0000.001
resample0.0190.0010.019
resample_chart0.0040.0000.004
rsd_filter0.0160.0000.018
rsd_filter_hist0.0010.0000.000
run0.0270.0010.027
sb_corr0.0250.0010.026
scatter_chart0.4390.0030.442
split_data0.0080.0010.008
stratified_split0.1360.0010.138
svm_plot_2d0.7780.0150.799
tSNE0.0290.0010.030
tSNE_scatter0.0070.0010.007
tic_chart0.2490.0040.255
ttest0.0270.0000.027
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0370.0040.042