Multiple platform build/check report for BioC 3.17 - CHECK results for structToolbox on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.2 LTS)	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4626
palomino3	Windows Server 2022 Datacenter	x64	4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"	4379
merida1	macOS 12.6.4 Monterey	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4395
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*

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### Running command:
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###   /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_1.12.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/structToolbox.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.12.3’
* 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 R 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           43.610  0.202  54.930
fold_change               26.673  0.115  32.927
fisher_exact              23.003  0.120  29.535
fs_line                   14.422  0.175  18.500
forward_selection_by_rank 14.237  0.165  18.641
kfoldxcv_grid              8.464  0.051  10.774
kfold_xval                 7.645  0.051   9.925
grid_search_1d             7.475  0.172   9.773
compare_dist               7.139  0.263  10.668
confounders_lsq_barchart   6.791  0.036   8.706
confounders_lsq_boxplot    6.708  0.033   8.510
confounders_clsq           6.539  0.043   8.564
AUC                        4.440  0.296   5.947
balanced_accuracy          4.031  0.064   5.314
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL structToolbox
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘structToolbox’ ...
** 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


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
> 
> test_check("structToolbox")
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 148 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 148 ]
> 
> proc.time()
   user  system elapsed 
415.413   4.826 550.322

Example timings

name	user	system	elapsed
ANOVA	0.386	0.012	0.520
AUC	4.440	0.296	5.947
DFA	0.434	0.003	0.545
DatasetExperiment_boxplot	1.519	0.054	1.998
DatasetExperiment_dist	2.552	0.124	3.475
DatasetExperiment_factor_boxplot	0.458	0.004	0.583
DatasetExperiment_heatmap	0.612	0.018	0.814
HCA	0.126	0.008	0.172
HSD	0.906	0.064	1.248
HSDEM	0.791	0.028	1.045
MTBLS79_DatasetExperiment	0.002	0.000	0.003
PCA	0.010	0.000	0.012
PLSDA	0.043	0.001	0.058
PLSR	0.011	0.000	0.016
SVM	0.028	0.001	0.034
as_data_frame	0.280	0.003	0.356
autoscale	0.154	0.003	0.200
balanced_accuracy	4.031	0.064	5.314
blank_filter	0.735	0.041	0.996
blank_filter_hist	0.001	0.000	0.002
bootstrap	0.014	0.000	0.016
calculate	0.010	0.001	0.014
chart_plot	0.059	0.003	0.078
classical_lsq	0.622	0.004	0.790
compare_dist	7.139	0.263	10.668
confounders_clsq	6.539	0.043	8.564
confounders_lsq_barchart	6.791	0.036	8.706
confounders_lsq_boxplot	6.708	0.033	8.510
constant_sum_norm	0.010	0.001	0.014
corr_coef	0.591	0.004	0.738
dfa_scores_plot	1.477	0.011	1.865
dratio_filter	0.704	0.017	0.915
equal_split	0.250	0.002	0.313
feature_boxplot	0.038	0.001	0.051
feature_profile	0.937	0.015	1.189
feature_profile_array	1.088	0.010	1.373
filter_by_name	0.062	0.000	0.084
filter_na_count	2.673	0.095	3.527
filter_smeta	0.144	0.001	0.190
fisher_exact	23.003	0.120	29.535
fold_change	26.673	0.115	32.927
fold_change_int	43.610	0.202	54.930
fold_change_plot	0.009	0.000	0.013
forward_selection_by_rank	14.237	0.165	18.641
fs_line	14.422	0.175	18.500
glog_opt_plot	1.091	0.008	1.351
glog_transform	0.651	0.004	0.805
grid_search_1d	7.475	0.172	9.773
gs_line	0.002	0.001	0.002
hca_dendrogram	0.001	0.001	0.006
kfold_xval	7.645	0.051	9.925
kfoldxcv_grid	8.464	0.051	10.774
kfoldxcv_metric	0.001	0.000	0.002
knn_impute	0.014	0.001	0.023
kw_p_hist	0.001	0.000	0.001
kw_rank_sum	0.153	0.002	0.197
linear_model	0.054	0.001	0.075
log_transform	0.009	0.000	0.012
mean_centre	0.003	0.000	0.003
mean_of_medians	0.283	0.001	0.369
mixed_effect	0.314	0.003	0.419
model_apply	0.049	0.002	0.071
model_predict	0.118	0.002	0.176
model_reverse	0.090	0.001	0.138
model_train	0.111	0.001	0.149
mv_boxplot	0.601	0.006	0.799
mv_feature_filter	0.229	0.001	0.292
mv_feature_filter_hist	0.002	0.000	0.002
mv_histogram	0.572	0.009	0.759
mv_sample_filter	0.010	0.000	0.013
mv_sample_filter_hist	0.001	0.001	0.001
nroot_transform	0.010	0.001	0.013
ontology_cache	0.000	0.001	0.001
pairs_filter	0.012	0.000	0.015
pareto_scale	0.121	0.001	0.153
pca_biplot	0.018	0.000	0.021
pca_correlation_plot	0.008	0.001	0.008
pca_dstat_plot	0.011	0.001	0.014
pca_loadings_plot	0.011	0.001	0.015
pca_scores_plot	1.194	0.008	1.538
pca_scree_plot	0.002	0.000	0.001
permutation_test	0.013	0.000	0.014
permutation_test_plot	0.006	0.000	0.006
permute_sample_order	0.010	0.000	0.013
pls_regcoeff_plot	0.754	0.006	0.975
pls_scores_plot	1.532	0.008	1.925
pls_vip_plot	0.798	0.006	1.010
plsda_feature_importance_plot	1.327	0.014	1.791
plsda_predicted_plot	1.084	0.012	1.443
plsda_roc_plot	2.783	0.029	3.692
plsr_cook_dist	0.009	0.001	0.011
plsr_prediction_plot	0.009	0.001	0.012
plsr_qq_plot	0.009	0.000	0.011
plsr_residual_hist	0.009	0.001	0.011
pqn_norm	0.892	0.019	1.175
pqn_norm_hist	0.001	0.000	0.002
prop_na	0.014	0.001	0.021
r_squared	0.002	0.000	0.002
resample	0.019	0.001	0.024
resample_chart	0.006	0.001	0.006
rsd_filter	0.016	0.001	0.021
rsd_filter_hist	0.001	0.000	0.002
run	0.064	0.001	0.081
sb_corr	0.032	0.001	0.038
scatter_chart	0.776	0.007	1.003
split_data	0.008	0.001	0.010
stratified_split	0.241	0.002	0.317
svm_plot_2d	1.431	0.025	1.858
tSNE	0.028	0.001	0.047
tSNE_scatter	0.009	0.000	0.010
tic_chart	0.528	0.004	0.689
ttest	0.023	0.001	0.036
vec_norm	0.001	0.000	0.002
wilcox_p_hist	0.001	0.000	0.005
wilcox_test	0.023	0.001	0.030

CHECK results for structToolbox on merida1

Summary

Command output

Installation output

Tests output

Example timings