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

This page was generated on 2025-08-30 12:06 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 2106/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.21.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 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: 2025-08-30 00:12:11 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 00:21:19 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 548.1 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           18.985  0.120  19.248
fold_change               13.614  0.116  13.826
fisher_exact              12.172  0.079  12.319
fs_line                    6.788  0.165   6.993
forward_selection_by_rank  6.609  0.105   6.761
* 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 
213.325   2.532 217.365 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2770.0090.287
AUC3.1060.1133.238
DFA0.2210.0020.223
DatasetExperiment_boxplot0.7350.0410.780
DatasetExperiment_dist1.3980.0921.500
DatasetExperiment_factor_boxplot0.2240.0070.232
DatasetExperiment_heatmap0.4160.0100.427
HCA0.0700.0010.071
HSD0.3090.0180.334
HSDEM0.3930.0300.425
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0090.0010.010
OPLSR0.0090.0010.010
PCA0.0030.0000.004
PLSDA0.0160.0010.017
PLSR0.0100.0010.010
SVM0.0230.0010.024
as_data_frame0.1460.0010.146
autoscale0.0630.0010.063
balanced_accuracy2.8390.0492.905
blank_filter0.3680.0210.391
blank_filter_hist0.0010.0000.001
bootstrap0.0140.0010.017
calculate0.0040.0000.004
chart_plot0.0280.0030.030
classical_lsq0.3080.0070.316
compare_dist4.5410.2284.791
confounders_clsq3.2080.0263.250
confounders_lsq_barchart3.4660.0263.508
confounders_lsq_boxplot3.2390.0233.273
constant_sum_norm0.0110.0000.011
corr_coef0.2810.0010.283
dfa_scores_plot0.7690.0060.778
dratio_filter0.2980.0060.305
equal_split0.1360.0010.138
feature_boxplot0.0280.0010.028
feature_profile0.4200.0040.426
feature_profile_array0.5120.0050.521
filter_by_name0.0390.0000.038
filter_na_count1.0350.0451.089
filter_smeta0.0620.0010.066
fisher_exact12.172 0.07912.319
fold_change13.614 0.11613.826
fold_change_int18.985 0.12019.248
fold_change_plot0.0090.0000.010
forward_selection_by_rank6.6090.1056.761
fs_line6.7880.1656.993
glog_opt_plot0.5110.0060.521
glog_transform0.3410.0030.347
grid_search_1d4.2300.1654.424
gs_line0.0010.0000.001
hca_dendrogram0.0010.0010.000
kfold_xval3.6590.0313.708
kfoldxcv_grid4.0420.0344.093
kfoldxcv_metric0.0010.0000.001
knn_impute0.0120.0000.014
kw_p_hist0.0010.0010.001
kw_rank_sum0.0830.0010.085
linear_model0.0350.0010.036
log_transform0.0090.0000.009
mean_centre0.0020.0010.003
mean_of_medians0.1490.0020.152
mixed_effect0.1800.0020.184
model_apply0.0220.0010.023
model_predict0.0570.0010.057
model_reverse0.0260.0000.028
model_train0.0580.0000.059
mv_boxplot0.2970.0040.302
mv_feature_filter0.1220.0020.124
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2810.0070.289
mv_sample_filter0.0080.0010.009
mv_sample_filter_hist0.0010.0000.001
nroot_transform0.0070.0000.006
ontology_cache0.0000.0010.000
pairs_filter0.0130.0000.013
pareto_scale0.0610.0000.062
pca_biplot0.0160.0000.018
pca_correlation_plot0.0080.0000.008
pca_dstat_plot0.0090.0000.010
pca_loadings_plot0.0090.0000.009
pca_scores_plot0.5590.0050.570
pca_scree_plot0.0050.0000.005
permutation_test0.0120.0010.013
permutation_test_plot0.0040.0010.004
permute_sample_order0.0070.0000.007
pls_regcoeff_plot0.4350.0050.444
pls_scores_plot0.7710.0060.781
pls_vip_plot0.4480.0050.456
plsda_feature_importance_plot0.6880.0110.705
plsda_predicted_plot0.5330.0050.542
plsda_roc_plot1.3100.0131.333
plsr_cook_dist0.0090.0000.009
plsr_prediction_plot0.0080.0010.008
plsr_qq_plot0.0070.0000.007
plsr_residual_hist0.0080.0000.009
pqn_norm0.3940.0030.400
pqn_norm_hist0.0010.0000.001
prop_na0.0110.0000.011
r_squared0.0000.0000.001
resample0.0170.0010.017
resample_chart0.0030.0000.003
rsd_filter0.0130.0010.013
rsd_filter_hist0.0010.0010.001
run0.0340.0010.035
sb_corr0.0340.0010.034
scatter_chart0.4080.0050.413
split_data0.0090.0000.009
stratified_split0.1350.0020.137
svm_plot_2d0.7440.0190.768
tSNE0.0250.0000.026
tSNE_scatter0.0090.0000.010
tic_chart0.2450.0090.255
ttest0.0210.0010.022
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0220.0010.022