Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-14 11:47 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
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: 2025-08-11 13:40 -0400 (Mon, 11 Aug 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
palomino7Windows Server 2022 Datacenter / x64  OK    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    OK  


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: 2025-08-13 12:53:15 -0400 (Wed, 13 Aug 2025)
EndedAt: 2025-08-13 13:02:21 -0400 (Wed, 13 Aug 2025)
EllapsedTime: 545.7 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           15.871  0.068  16.271
fold_change               10.797  0.082  11.136
fisher_exact              10.309  0.059  10.629
forward_selection_by_rank  6.379  0.144   6.667
fs_line                    6.285  0.126   6.538
* 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 
194.719   2.553 201.305 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2660.0150.291
AUC2.0950.1162.243
DFA0.2050.0030.213
DatasetExperiment_boxplot1.8350.0411.912
DatasetExperiment_dist2.3350.0722.442
DatasetExperiment_factor_boxplot0.2180.0020.224
DatasetExperiment_heatmap0.4340.0220.466
HCA0.0650.0020.066
HSD0.2970.0180.355
HSDEM0.5040.0260.553
MTBLS79_DatasetExperiment0.0020.0000.001
OPLSDA0.0120.0010.014
OPLSR0.0080.0010.008
PCA0.0040.0000.005
PLSDA0.0110.0010.012
PLSR0.0110.0020.015
SVM0.0250.0020.027
as_data_frame0.1340.0030.140
autoscale0.0730.0030.079
balanced_accuracy1.8430.0191.892
blank_filter0.3930.0190.421
blank_filter_hist0.0000.0000.001
bootstrap0.0080.0000.009
calculate0.0050.0000.006
chart_plot0.0300.0020.032
classical_lsq0.3170.0040.327
compare_dist3.9240.2444.280
confounders_clsq3.0320.1043.226
confounders_lsq_barchart3.1640.0353.361
confounders_lsq_boxplot3.1240.0303.401
constant_sum_norm0.0080.0010.008
corr_coef0.2640.0030.272
dfa_scores_plot0.7360.0110.762
dratio_filter0.2780.0070.290
equal_split0.1250.0020.129
feature_boxplot0.0240.0010.024
feature_profile0.3910.0100.403
feature_profile_array0.4840.0070.516
filter_by_name0.0340.0000.036
filter_na_count1.0970.0451.289
filter_smeta0.0610.0000.062
fisher_exact10.309 0.05910.629
fold_change10.797 0.08211.136
fold_change_int15.871 0.06816.271
fold_change_plot0.0070.0010.007
forward_selection_by_rank6.3790.1446.667
fs_line6.2850.1266.538
glog_opt_plot0.4880.0060.506
glog_transform0.3080.0030.315
grid_search_1d3.8540.1444.066
gs_line0.0010.0010.001
hca_dendrogram0.0010.0000.001
kfold_xval3.5770.0393.689
kfoldxcv_grid3.8270.0373.914
kfoldxcv_metric0.0010.0000.001
knn_impute0.0130.0010.014
kw_p_hist0.0000.0000.001
kw_rank_sum0.0840.0010.086
linear_model0.0300.0010.032
log_transform0.0070.0010.007
mean_centre0.0030.0000.003
mean_of_medians0.1380.0040.143
mixed_effect0.1670.0020.170
model_apply0.0230.0010.024
model_predict0.0560.0010.060
model_reverse0.0270.0010.029
model_train0.0540.0010.057
mv_boxplot0.2870.0050.298
mv_feature_filter0.1100.0020.111
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2710.0050.282
mv_sample_filter0.0100.0010.012
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0060.0000.007
ontology_cache0.0000.0000.001
pairs_filter0.0090.0000.009
pareto_scale0.0610.0010.062
pca_biplot0.0140.0000.013
pca_correlation_plot0.0060.0000.006
pca_dstat_plot0.0080.0000.008
pca_loadings_plot0.0110.0000.013
pca_scores_plot0.5470.0080.560
pca_scree_plot0.0090.0000.014
permutation_test0.0100.0000.013
permutation_test_plot0.0020.0000.002
permute_sample_order0.0090.0010.011
pls_regcoeff_plot0.3640.0090.381
pls_scores_plot0.6860.0060.706
pls_vip_plot0.3690.0090.381
plsda_feature_importance_plot0.6050.0080.627
plsda_predicted_plot0.4720.0070.487
plsda_roc_plot1.1950.0131.234
plsr_cook_dist0.0070.0000.008
plsr_prediction_plot0.0070.0000.007
plsr_qq_plot0.0060.0000.006
plsr_residual_hist0.0210.0010.022
pqn_norm0.3610.0030.368
pqn_norm_hist0.0020.0010.001
prop_na0.010.000.01
r_squared0.0010.0000.001
resample0.0130.0010.014
resample_chart0.0030.0000.003
rsd_filter0.0160.0010.018
rsd_filter_hist0.0010.0000.001
run0.0310.0000.031
sb_corr0.0240.0010.024
scatter_chart0.3690.0060.383
split_data0.0070.0000.007
stratified_split0.1080.0010.111
svm_plot_2d0.7060.0240.742
tSNE0.0260.0010.028
tSNE_scatter0.0060.0000.007
tic_chart0.2110.0030.219
ttest0.0200.0000.021
vec_norm0.0020.0000.002
wilcox_p_hist0.0010.0000.001
wilcox_test0.0180.0010.019