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This page was generated on 2025-07-16 12:06 -0400 (Wed, 16 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4786
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4523
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4563
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4509
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4509
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 2097/2311HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.21.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-07-15 13:25 -0400 (Tue, 15 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings structToolbox_1.21.0.tar.gz
StartedAt: 2025-07-16 02:58:24 -0400 (Wed, 16 Jul 2025)
EndedAt: 2025-07-16 03:16:39 -0400 (Wed, 16 Jul 2025)
EllapsedTime: 1094.2 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings structToolbox_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/structToolbox.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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           15.712  0.116  15.827
fold_change               10.502  0.056  10.558
fisher_exact               9.667  0.099   9.766
forward_selection_by_rank  6.509  0.132   6.641
fs_line                    6.051  0.003   6.055
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

structToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-pc-linux-gnu

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 
178.207   1.338 179.542 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2190.0020.221
AUC2.6520.1052.757
DFA0.1860.0000.186
DatasetExperiment_boxplot0.7690.0240.792
DatasetExperiment_dist1.2660.0351.300
DatasetExperiment_factor_boxplot0.2030.0180.220
DatasetExperiment_heatmap0.3630.0040.368
HCA0.0590.0010.061
HSD0.2660.0050.275
HSDEM0.3430.0040.347
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.010.000.01
OPLSR0.0070.0000.008
PCA0.0040.0000.004
PLSDA0.0100.0000.011
PLSR0.0090.0000.008
SVM0.020.000.02
as_data_frame0.1200.0000.121
autoscale0.0690.0000.069
balanced_accuracy2.4790.1102.590
blank_filter0.3130.0030.316
blank_filter_hist000
bootstrap0.0090.0000.009
calculate0.0040.0010.005
chart_plot0.0280.0000.028
classical_lsq0.2880.0010.289
compare_dist3.5660.0753.641
confounders_clsq2.7390.0392.778
confounders_lsq_barchart2.9820.0132.995
confounders_lsq_boxplot2.8650.0142.879
constant_sum_norm0.0060.0010.007
corr_coef0.250.000.25
dfa_scores_plot0.7400.0160.755
dratio_filter0.2600.0110.271
equal_split0.1280.0020.131
feature_boxplot0.0290.0000.030
feature_profile0.3850.0010.386
feature_profile_array0.4590.0000.459
filter_by_name0.0310.0000.031
filter_na_count0.9880.0131.002
filter_smeta0.0580.0000.058
fisher_exact9.6670.0999.766
fold_change10.502 0.05610.558
fold_change_int15.712 0.11615.827
fold_change_plot0.0060.0010.006
forward_selection_by_rank6.5090.1326.641
fs_line6.0510.0036.055
glog_opt_plot0.4550.0020.456
glog_transform0.2680.0000.268
grid_search_1d3.3250.0153.340
gs_line0.0000.0000.001
hca_dendrogram000
kfold_xval3.2320.0043.236
kfoldxcv_grid3.5650.0283.594
kfoldxcv_metric0.0010.0000.001
knn_impute0.0130.0000.012
kw_p_hist0.0010.0000.001
kw_rank_sum0.0730.0000.073
linear_model0.0280.0000.028
log_transform0.0060.0000.007
mean_centre0.0020.0000.003
mean_of_medians0.1130.0000.114
mixed_effect0.1560.0000.156
model_apply0.0210.0010.022
model_predict0.0550.0000.055
model_reverse0.0250.0000.024
model_train0.0480.0000.049
mv_boxplot0.2620.0010.264
mv_feature_filter0.1210.0010.122
mv_feature_filter_hist0.0010.0000.000
mv_histogram0.2270.0000.226
mv_sample_filter0.0080.0000.008
mv_sample_filter_hist0.0010.0000.000
nroot_transform0.0050.0010.006
ontology_cache000
pairs_filter0.0090.0000.008
pareto_scale0.0530.0000.052
pca_biplot0.0130.0000.014
pca_correlation_plot0.0060.0000.006
pca_dstat_plot0.0080.0000.008
pca_loadings_plot0.0080.0000.009
pca_scores_plot0.5120.0010.514
pca_scree_plot0.0070.0000.007
permutation_test0.0250.0000.026
permutation_test_plot0.0030.0000.002
permute_sample_order0.0070.0000.007
pls_regcoeff_plot0.3330.0020.336
pls_scores_plot0.6660.0010.668
pls_vip_plot0.3350.0030.338
plsda_feature_importance_plot0.5940.0000.595
plsda_predicted_plot0.4240.0020.425
plsda_roc_plot1.1290.0021.131
plsr_cook_dist0.0060.0000.006
plsr_prediction_plot0.0050.0000.005
plsr_qq_plot0.0060.0000.006
plsr_residual_hist0.0050.0000.006
pqn_norm0.3330.0000.333
pqn_norm_hist0.0010.0000.001
prop_na0.010.000.01
r_squared0.0000.0010.001
resample0.0150.0000.015
resample_chart0.0030.0000.003
rsd_filter0.0130.0000.013
rsd_filter_hist000
run0.0390.0000.039
sb_corr0.0270.0000.027
scatter_chart0.3240.0000.324
split_data0.0070.0000.007
stratified_split0.1150.0010.116
svm_plot_2d0.6420.0170.659
tSNE0.0230.0000.023
tSNE_scatter0.0060.0010.007
tic_chart0.1970.0040.201
ttest0.0190.0020.022
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.000
wilcox_test0.0160.0020.017