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

This page was generated on 2025-04-22 13:19 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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: 2025-04-21 13:40 -0400 (Mon, 21 Apr 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 24.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'struct' which is not available
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'struct' which is not available
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'struct' which is not available
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'struct' which is not available
kunpeng2Linux (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: 1.20.0
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: 2025-04-21 21:58:40 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 22:01:29 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 169.0 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/structToolbox.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-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 Ventura 13.7.1
* 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 4.82  0.008   5.034
* 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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 
 55.972   0.704  57.589 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.0810.0030.092
AUC0.6040.0240.652
DFA0.0570.0000.061
DatasetExperiment_boxplot0.5860.0140.617
DatasetExperiment_dist0.4910.0240.519
DatasetExperiment_factor_boxplot0.0630.0000.064
DatasetExperiment_heatmap0.1280.0110.140
HCA0.0200.0010.022
HSD0.0890.0050.098
HSDEM0.1440.0060.155
MTBLS79_DatasetExperiment0.0010.0000.000
OPLSDA0.0030.0000.003
OPLSR0.0020.0000.002
PCA0.0020.0000.001
PLSDA0.0030.0000.004
PLSR0.0030.0000.003
SVM0.0060.0000.006
as_data_frame0.0380.0000.038
autoscale0.0210.0000.021
balanced_accuracy0.5010.0040.523
blank_filter0.1110.0060.118
blank_filter_hist000
bootstrap0.0030.0000.003
calculate0.0010.0000.002
chart_plot0.0080.0000.009
classical_lsq0.0930.0020.099
compare_dist1.5510.0931.698
confounders_clsq0.8480.0050.872
confounders_lsq_barchart0.9020.0060.916
confounders_lsq_boxplot0.8470.0040.852
constant_sum_norm0.0030.0000.003
corr_coef0.0710.0000.071
dfa_scores_plot0.2120.0020.214
dratio_filter0.0860.0030.088
equal_split0.0340.0010.034
feature_boxplot0.0080.0000.008
feature_profile0.1210.0040.124
feature_profile_array0.1380.0010.139
filter_by_name0.0110.0000.011
filter_na_count0.3730.0330.407
filter_smeta0.0170.0000.020
fisher_exact2.7890.0102.836
fold_change3.2840.0123.304
fold_change_int4.8200.0085.034
fold_change_plot0.0020.0000.002
forward_selection_by_rank1.8230.0461.960
fs_line2.1450.0622.322
glog_opt_plot0.1370.0010.141
glog_transform0.0890.0000.098
grid_search_1d1.5120.0811.692
gs_line000
hca_dendrogram0.0010.0000.000
kfold_xval1.0040.0071.042
kfoldxcv_grid1.1520.0101.244
kfoldxcv_metric000
knn_impute0.0040.0010.004
kw_p_hist0.0000.0000.001
kw_rank_sum0.0230.0000.023
linear_model0.0090.0000.009
log_transform0.0020.0000.002
mean_centre0.0010.0000.001
mean_of_medians0.0410.0000.042
mixed_effect0.0570.0010.059
model_apply0.0070.0000.007
model_predict0.0160.0010.016
model_reverse0.0080.0000.008
model_train0.0150.0000.015
mv_boxplot0.0820.0020.084
mv_feature_filter0.0330.0000.033
mv_feature_filter_hist000
mv_histogram0.0830.0030.087
mv_sample_filter0.0030.0000.003
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0020.0000.002
ontology_cache000
pairs_filter0.0030.0000.003
pareto_scale0.0190.0000.019
pca_biplot0.0040.0000.005
pca_correlation_plot0.0020.0000.002
pca_dstat_plot0.0020.0000.002
pca_loadings_plot0.0030.0010.002
pca_scores_plot0.1470.0010.149
pca_scree_plot0.0020.0000.002
permutation_test0.0030.0000.003
permutation_test_plot0.0000.0000.001
permute_sample_order0.0020.0000.002
pls_regcoeff_plot0.1020.0010.106
pls_scores_plot0.2000.0010.227
pls_vip_plot0.1060.0010.116
plsda_feature_importance_plot0.1840.0020.192
plsda_predicted_plot0.1360.0010.148
plsda_roc_plot0.3430.0040.395
plsr_cook_dist0.0020.0000.002
plsr_prediction_plot0.0020.0000.002
plsr_qq_plot0.0010.0000.002
plsr_residual_hist0.0010.0000.002
pqn_norm0.1090.0000.128
pqn_norm_hist000
prop_na0.0030.0000.003
r_squared0.0000.0000.001
resample0.0050.0000.005
resample_chart0.0010.0010.001
rsd_filter0.0040.0000.004
rsd_filter_hist000
run0.0090.0010.009
sb_corr0.0080.0000.007
scatter_chart0.1050.0010.110
split_data0.0020.0010.003
stratified_split0.0320.0000.033
svm_plot_2d0.2270.0100.280
tSNE0.0070.0010.007
tSNE_scatter0.0020.0000.005
tic_chart0.0680.0030.075
ttest0.0070.0000.007
vec_norm0.0010.0000.000
wilcox_p_hist0.0000.0000.001
wilcox_test0.0050.0010.005