Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-23 12:07 -0400 (Sat, 23 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 2105/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.21.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 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 kjohnson3

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: 2025-08-22 21:51:40 -0400 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 21:54:25 -0400 (Fri, 22 Aug 2025)
EllapsedTime: 164.9 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 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 13.7.7
* 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
* 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 ‘1.21.0’
** 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 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 
 56.063   0.625  56.929 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.0660.0020.068
AUC0.8570.0220.880
DFA0.0550.0010.056
DatasetExperiment_boxplot0.2840.0110.296
DatasetExperiment_dist0.4860.0240.510
DatasetExperiment_factor_boxplot0.0640.0010.065
DatasetExperiment_heatmap0.1200.0030.123
HCA0.0180.0010.019
HSD0.0850.0070.095
HSDEM0.1510.0090.161
MTBLS79_DatasetExperiment000
OPLSDA0.0030.0000.003
OPLSR0.0020.0000.002
PCA0.0010.0000.001
PLSDA0.0030.0000.004
PLSR0.0020.0010.003
SVM0.0060.0000.006
as_data_frame0.0360.0000.043
autoscale0.0190.0000.020
balanced_accuracy0.8280.0180.846
blank_filter0.1170.0070.123
blank_filter_hist000
bootstrap0.0030.0010.004
calculate0.0020.0000.002
chart_plot0.0090.0010.010
classical_lsq0.0950.0110.107
compare_dist1.5370.0781.617
confounders_clsq0.8390.0050.843
confounders_lsq_barchart0.8840.0050.890
confounders_lsq_boxplot0.8430.0030.848
constant_sum_norm0.0020.0000.002
corr_coef0.0710.0000.071
dfa_scores_plot0.2080.0020.212
dratio_filter0.0890.0030.091
equal_split0.0330.0010.034
feature_boxplot0.0080.0000.008
feature_profile0.1090.0010.111
feature_profile_array0.1480.0020.150
filter_by_name0.010.000.01
filter_na_count0.3260.0210.347
filter_smeta0.0180.0000.018
fisher_exact2.7740.0112.790
fold_change3.3020.0283.426
fold_change_int4.7850.0094.997
fold_change_plot0.0020.0000.003
forward_selection_by_rank1.8280.0601.944
fs_line1.8340.0411.902
glog_opt_plot0.1420.0010.143
glog_transform0.0830.0000.083
grid_search_1d1.4930.0891.604
gs_line0.0010.0000.000
hca_dendrogram000
kfold_xval0.9950.0061.063
kfoldxcv_grid1.0850.0101.159
kfoldxcv_metric0.0010.0010.001
knn_impute0.0030.0000.004
kw_p_hist000
kw_rank_sum0.0270.0000.028
linear_model0.0080.0010.011
log_transform0.0020.0000.003
mean_centre0.0010.0000.001
mean_of_medians0.0330.0000.037
mixed_effect0.0500.0000.052
model_apply0.0070.0000.007
model_predict0.0160.0000.017
model_reverse0.0080.0010.008
model_train0.0150.0000.015
mv_boxplot0.0830.0020.086
mv_feature_filter0.0340.0000.036
mv_feature_filter_hist0.0000.0000.001
mv_histogram0.0820.0060.089
mv_sample_filter0.0030.0000.004
mv_sample_filter_hist0.0010.0000.000
nroot_transform0.0020.0000.002
ontology_cache000
pairs_filter0.0030.0000.003
pareto_scale0.0160.0000.022
pca_biplot0.0040.0000.004
pca_correlation_plot0.0020.0000.001
pca_dstat_plot0.0020.0000.002
pca_loadings_plot0.0030.0000.003
pca_scores_plot0.1490.0010.156
pca_scree_plot0.0030.0000.002
permutation_test0.0030.0000.003
permutation_test_plot0.0010.0000.001
permute_sample_order0.0020.0000.002
pls_regcoeff_plot0.1140.0010.125
pls_scores_plot0.1980.0030.207
pls_vip_plot0.1080.0020.112
plsda_feature_importance_plot0.1870.0020.202
plsda_predicted_plot0.1350.0010.151
plsda_roc_plot0.3460.0080.355
plsr_cook_dist0.0030.0000.003
plsr_prediction_plot0.0020.0000.002
plsr_qq_plot0.0020.0010.002
plsr_residual_hist0.0020.0000.002
pqn_norm0.0990.0000.099
pqn_norm_hist0.0010.0000.000
prop_na0.0030.0000.003
r_squared0.0000.0000.001
resample0.0050.0000.004
resample_chart0.0010.0000.001
rsd_filter0.0040.0010.004
rsd_filter_hist0.0010.0000.000
run0.0110.0000.011
sb_corr0.0080.0010.008
scatter_chart0.1130.0010.114
split_data0.0020.0000.002
stratified_split0.0310.0010.033
svm_plot_2d0.2080.0070.220
tSNE0.0080.0010.007
tSNE_scatter0.0020.0000.002
tic_chart0.0610.0010.063
ttest0.0060.0000.006
vec_norm000
wilcox_p_hist0.0010.0000.000
wilcox_test0.0050.0000.005