Mac ARM64 build report for BioC 3.17 - CHECK results for structToolbox on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4347
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-mac-arm64/meat/structToolbox.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* 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           23.165  0.212  41.932
fisher_exact              13.456  0.127  24.317
fold_change               12.660  0.132  22.931
forward_selection_by_rank  7.812  0.113  14.316
fs_line                    7.407  0.108  13.475
grid_search_1d             4.854  0.088   8.495
kfoldxcv_grid              4.499  0.059   7.301
compare_dist               4.156  0.110   7.488
kfold_xval                 4.078  0.050   7.324
confounders_lsq_boxplot    3.551  0.043   6.477
confounders_lsq_barchart   3.489  0.043   6.339
confounders_clsq           3.428  0.045   6.235
* 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-arm64/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: aarch64-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, will retire 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:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
> 
> test_check("structToolbox")
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 148 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 148 ]
> 
> proc.time()
   user  system elapsed 
221.797   3.231 398.879

Example timings

name	user	system	elapsed
ANOVA	0.220	0.009	0.380
AUC	2.312	0.113	4.287
DFA	0.234	0.005	0.424
DatasetExperiment_boxplot	0.924	0.038	1.706
DatasetExperiment_dist	1.723	0.045	3.139
DatasetExperiment_factor_boxplot	0.246	0.004	0.444
DatasetExperiment_heatmap	0.341	0.014	0.635
HCA	0.076	0.002	0.139
HSD	0.504	0.048	0.990
HSDEM	0.507	0.023	0.926
MTBLS79_DatasetExperiment	0.001	0.000	0.001
PCA	0.006	0.000	0.013
PLSDA	0.023	0.000	0.038
PLSR	0.005	0.000	0.011
SVM	0.013	0.000	0.026
as_data_frame	0.155	0.002	0.262
autoscale	0.081	0.002	0.150
balanced_accuracy	2.135	0.031	3.834
blank_filter	0.450	0.034	0.840
blank_filter_hist	0.001	0.000	0.001
bootstrap	0.006	0.001	0.011
calculate	0.007	0.001	0.016
chart_plot	0.032	0.002	0.060
classical_lsq	0.317	0.005	0.562
compare_dist	4.156	0.110	7.488
confounders_clsq	3.428	0.045	6.235
confounders_lsq_barchart	3.489	0.043	6.339
confounders_lsq_boxplot	3.551	0.043	6.477
constant_sum_norm	0.019	0.000	0.036
corr_coef	0.328	0.004	0.597
dfa_scores_plot	0.790	0.012	1.435
dratio_filter	0.318	0.008	0.584
equal_split	0.158	0.003	0.288
feature_boxplot	0.021	0.000	0.035
feature_profile	0.515	0.012	0.942
feature_profile_array	0.589	0.009	1.077
filter_by_name	0.034	0.001	0.062
filter_na_count	1.771	0.046	3.251
filter_smeta	0.066	0.000	0.121
fisher_exact	13.456	0.127	24.317
fold_change	12.660	0.132	22.931
fold_change_int	23.165	0.212	41.932
fold_change_plot	0.005	0.001	0.010
forward_selection_by_rank	7.812	0.113	14.316
fs_line	7.407	0.108	13.475
glog_opt_plot	0.591	0.009	1.074
glog_transform	0.348	0.003	0.607
grid_search_1d	4.854	0.088	8.495
gs_line	0.001	0.000	0.001
hca_dendrogram	0.001	0.000	0.004
kfold_xval	4.078	0.050	7.324
kfoldxcv_grid	4.499	0.059	7.301
kfoldxcv_metric	0.001	0.001	0.001
knn_impute	0.007	0.001	0.015
kw_p_hist	0.001	0.000	0.000
kw_rank_sum	0.085	0.001	0.133
linear_model	0.028	0.000	0.045
log_transform	0.005	0.000	0.008
mean_centre	0.002	0.000	0.002
mean_of_medians	0.162	0.002	0.252
mixed_effect	0.188	0.003	0.294
model_apply	0.029	0.002	0.048
model_predict	0.072	0.002	0.113
model_reverse	0.053	0.001	0.084
model_train	0.060	0.001	0.104
mv_boxplot	0.316	0.005	0.472
mv_feature_filter	0.130	0.002	0.192
mv_feature_filter_hist	0.001	0.001	0.003
mv_histogram	0.291	0.005	0.445
mv_sample_filter	0.006	0.001	0.008
mv_sample_filter_hist	0.001	0.001	0.001
nroot_transform	0.005	0.000	0.007
ontology_cache	0.001	0.000	0.000
pairs_filter	0.007	0.001	0.011
pareto_scale	0.064	0.001	0.096
pca_biplot	0.009	0.000	0.014
pca_correlation_plot	0.004	0.000	0.005
pca_dstat_plot	0.005	0.001	0.010
pca_loadings_plot	0.006	0.000	0.010
pca_scores_plot	0.665	0.011	0.967
pca_scree_plot	0.001	0.000	0.001
permutation_test	0.007	0.001	0.012
permutation_test_plot	0.004	0.000	0.006
permute_sample_order	0.005	0.000	0.011
pls_regcoeff_plot	0.413	0.007	0.658
pls_scores_plot	0.820	0.012	1.190
pls_vip_plot	0.427	0.006	0.678
plsda_feature_importance_plot	0.713	0.014	1.249
plsda_predicted_plot	0.580	0.008	1.005
plsda_roc_plot	1.307	0.015	2.205
plsr_cook_dist	0.005	0.000	0.009
plsr_prediction_plot	0.005	0.000	0.011
plsr_qq_plot	0.005	0.001	0.009
plsr_residual_hist	0.005	0.000	0.010
pqn_norm	0.498	0.007	0.919
pqn_norm_hist	0.001	0.000	0.002
prop_na	0.006	0.000	0.011
r_squared	0.000	0.000	0.001
resample	0.012	0.001	0.021
resample_chart	0.003	0.000	0.005
rsd_filter	0.011	0.000	0.021
rsd_filter_hist	0.001	0.000	0.005
run	0.036	0.001	0.071
sb_corr	0.016	0.000	0.029
scatter_chart	0.414	0.005	0.752
split_data	0.005	0.000	0.009
stratified_split	0.139	0.002	0.244
svm_plot_2d	0.805	0.020	1.409
tSNE	0.017	0.001	0.034
tSNE_scatter	0.006	0.001	0.009
tic_chart	0.291	0.005	0.511
ttest	0.012	0.000	0.021
vec_norm	0.001	0.000	0.004
wilcox_p_hist	0.001	0.001	0.001
wilcox_test	0.012	0.001	0.025

CHECK results for structToolbox on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings