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This page was generated on 2025-07-29 12:09 -0400 (Tue, 29 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" 4535
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" 4516
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: 2025-07-28 13:25 -0400 (Mon, 28 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: 2025-07-29 00:14:56 -0400 (Tue, 29 Jul 2025)
EndedAt: 2025-07-29 00:24:06 -0400 (Tue, 29 Jul 2025)
EllapsedTime: 550.0 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           19.678  0.114  19.915
fold_change               13.486  0.114  13.678
fisher_exact              11.602  0.067  11.728
fs_line                    6.727  0.107   6.873
forward_selection_by_rank  6.681  0.149   6.869
* 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 
212.779   2.618 216.960 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2620.0080.270
AUC3.0970.1173.235
DFA0.2370.0020.240
DatasetExperiment_boxplot0.7300.0420.776
DatasetExperiment_dist1.3450.0921.446
DatasetExperiment_factor_boxplot0.2700.0090.280
DatasetExperiment_heatmap0.4420.0110.458
HCA0.0680.0010.068
HSD0.3130.0190.339
HSDEM0.5370.0330.574
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0120.0010.012
OPLSR0.0070.0000.008
PCA0.0060.0000.007
PLSDA0.0130.0010.013
PLSR0.0080.0010.009
SVM0.0230.0010.024
as_data_frame0.1360.0010.138
autoscale0.0780.0020.080
balanced_accuracy2.6430.0452.705
blank_filter0.3520.0220.380
blank_filter_hist0.0010.0000.001
bootstrap0.0120.0000.013
calculate0.0070.0000.007
chart_plot0.0310.0010.033
classical_lsq0.3500.0120.365
compare_dist4.5060.2574.800
confounders_clsq3.4890.0283.537
confounders_lsq_barchart3.5860.0303.638
confounders_lsq_boxplot3.7430.0273.788
constant_sum_norm0.0090.0000.009
corr_coef0.3110.0030.313
dfa_scores_plot0.9090.0090.925
dratio_filter0.3490.0070.358
equal_split0.1340.0010.135
feature_boxplot0.0350.0010.036
feature_profile0.4350.0060.443
feature_profile_array0.5520.0060.562
filter_by_name0.0370.0010.038
filter_na_count1.1800.0521.242
filter_smeta0.0730.0010.077
fisher_exact11.602 0.06711.728
fold_change13.486 0.11413.678
fold_change_int19.678 0.11419.915
fold_change_plot0.0070.0000.006
forward_selection_by_rank6.6810.1496.869
fs_line6.7270.1076.873
glog_opt_plot0.5450.0050.552
glog_transform0.3710.0040.380
grid_search_1d4.4190.1664.619
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.002
kfold_xval3.5390.0293.585
kfoldxcv_grid4.4620.0444.537
kfoldxcv_metric0.0010.0000.001
knn_impute0.0160.0010.016
kw_p_hist0.0010.0000.001
kw_rank_sum0.0920.0010.094
linear_model0.0360.0010.037
log_transform0.0090.0000.009
mean_centre0.0030.0000.004
mean_of_medians0.1450.0010.147
mixed_effect0.2290.0060.236
model_apply0.0240.0010.026
model_predict0.0680.0010.069
model_reverse0.0290.0000.030
model_train0.0590.0000.060
mv_boxplot0.3270.0040.332
mv_feature_filter0.1220.0010.125
mv_feature_filter_hist0.0010.0000.002
mv_histogram0.2710.0030.275
mv_sample_filter0.0110.0010.012
mv_sample_filter_hist0.0000.0000.002
nroot_transform0.0070.0000.008
ontology_cache000
pairs_filter0.0120.0010.012
pareto_scale0.0720.0010.073
pca_biplot0.0190.0010.020
pca_correlation_plot0.0080.0010.009
pca_dstat_plot0.0120.0010.012
pca_loadings_plot0.0130.0010.013
pca_scores_plot0.5970.0100.612
pca_scree_plot0.0080.0000.009
permutation_test0.0130.0010.014
permutation_test_plot0.0040.0000.004
permute_sample_order0.0080.0000.009
pls_regcoeff_plot0.3920.0060.400
pls_scores_plot0.7730.0070.785
pls_vip_plot0.4390.0080.450
plsda_feature_importance_plot0.6740.0120.692
plsda_predicted_plot0.5700.0110.586
plsda_roc_plot1.3190.0151.343
plsr_cook_dist0.0090.0000.009
plsr_prediction_plot0.0070.0000.008
plsr_qq_plot0.0090.0000.009
plsr_residual_hist0.0080.0000.008
pqn_norm0.3930.0030.398
pqn_norm_hist0.0000.0000.001
prop_na0.0130.0000.014
r_squared0.0000.0000.001
resample0.0190.0000.020
resample_chart0.0040.0000.005
rsd_filter0.0170.0010.019
rsd_filter_hist0.0010.0000.001
run0.0320.0000.033
sb_corr0.0300.0010.032
scatter_chart0.4090.0040.416
split_data0.0090.0010.010
stratified_split0.1310.0020.133
svm_plot_2d0.7210.0180.744
tSNE0.0300.0010.031
tSNE_scatter0.0110.0010.011
tic_chart0.2340.0030.238
ttest0.0250.0010.026
vec_norm0.0010.0010.002
wilcox_p_hist0.0010.0000.001
wilcox_test0.0380.0050.044