Multiple platform build/check report for BioC 3.13 - CHECK results for structToolbox on tokay2

Package: structToolbox

Version: 1.4.3

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:structToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings structToolbox_1.4.3.tar.gz

StartedAt: 2021-10-15 06:17:19 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 06:29:31 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 732.6 seconds

RetCode: 0

Status: OK

CheckDir: structToolbox.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:structToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings structToolbox_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/structToolbox.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'structToolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'structToolbox' version '1.4.3'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
fold_change_int           15.18   0.00   15.19
fisher_exact               8.65   0.01    8.67
forward_selection_by_rank  7.68   0.13    7.81
fs_line                    6.91   0.09    7.00
fold_change                6.78   0.06    6.85
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
fold_change_int           13.41   0.00   13.41
fisher_exact               7.08   0.02    7.09
fold_change                6.28   0.01    6.30
fs_line                    5.84   0.01    5.86
forward_selection_by_rank  5.37   0.05    5.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/structToolbox_1.4.3.tar.gz && rm -rf structToolbox.buildbin-libdir && mkdir structToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=structToolbox.buildbin-libdir structToolbox_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL structToolbox_1.4.3.zip && rm structToolbox_1.4.3.tar.gz structToolbox_1.4.3.zip
###
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 17 2796k   17  490k    0     0  1294k      0  0:00:02 --:--:--  0:00:02 1294k
100 2796k  100 2796k    0     0  2305k      0  0:00:01  0:00:01 --:--:-- 2307k

install for i386

* installing *source* package 'structToolbox' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'structToolbox'
    finding HTML links ... done
    ANOVA                                   html  
    AUC                                     html  
    DFA                                     html  
    DatasetExperiment_boxplot               html  
    DatasetExperiment_dist                  html  
    DatasetExperiment_factor_boxplot        html  
    DatasetExperiment_heatmap               html  
    HCA                                     html  
    HSD                                     html  
    HSDEM                                   html  
    MTBLS79_DatasetExperiment               html  
    PCA                                     html  
    PLSDA                                   html  
    PLSR                                    html  
    SVM                                     html  
    as_data_frame                           html  
    autoscale                               html  
    balanced_accuracy                       html  
    blank_filter                            html  
    blank_filter_hist                       html  
    bootstrap                               html  
    calculate                               html  
    chart_plot                              html  
    classical_lsq                           html  
    compare_dist                            html  
    confounders_clsq                        html  
    confounders_lsq_barchart                html  
    confounders_lsq_boxplot                 html  
    constant_sum_norm                       html  
    corr_coef                               html  
    dfa_scores_plot                         html  
    dratio_filter                           html  
    feature_boxplot                         html  
    feature_profile                         html  
    feature_profile_array                   html  
    filter_by_name                          html  
    filter_na_count                         html  
    filter_smeta                            html  
    fisher_exact                            html  
    fold_change                             html  
    fold_change_int                         html  
    fold_change_plot                        html  
    forward_selection_by_rank               html  
    fs_line                                 html  
    glog_opt_plot                           html  
    glog_transform                          html  
    grid_search_1d                          html  
    gs_line                                 html  
    hca_dendrogram                          html  
    kfold_xval                              html  
    kfoldxcv_grid                           html  
    kfoldxcv_metric                         html  
    knn_impute                              html  
    kw_p_hist                               html  
    kw_rank_sum                             html  
    linear_model                            html  
    log_transform                           html  
    mean_centre                             html  
    mean_of_medians                         html  
    mixed_effect                            html  
    model_apply                             html  
    model_predict                           html  
    model_reverse                           html  
    model_train                             html  
    mv_boxplot                              html  
    mv_feature_filter                       html  
    mv_feature_filter_hist                  html  
    mv_histogram                            html  
    mv_sample_filter                        html  
    mv_sample_filter_hist                   html  
    nroot_transform                         html  
    pairs_filter                            html  
    pareto_scale                            html  
    pca_biplot                              html  
    pca_correlation_plot                    html  
    pca_dstat_plot                          html  
    pca_loadings_plot                       html  
    pca_scores_plot                         html  
    pca_scree_plot                          html  
    permutation_test                        html  
    permutation_test_plot                   html  
    permute_sample_order                    html  
    plsda_predicted_plot                    html  
    plsda_regcoeff_plot                     html  
    plsda_roc_plot                          html  
    plsda_scores_plot                       html  
    plsda_vip_plot                          html  
    plsda_vip_summary_plot                  html  
    plsr_cook_dist                          html  
    plsr_prediction_plot                    html  
    plsr_qq_plot                            html  
    plsr_residual_hist                      html  
    pqn_norm                                html  
    pqn_norm_hist                           html  
    prop_na                                 html  
    r_squared                               html  
    rsd_filter                              html  
    rsd_filter_hist                         html  
    run                                     html  
    sb_corr                                 html  
    split_data                              html  
    stratified_split                        html  
    structToolbox                           html  
    svm_plot_2d                             html  
    tSNE                                    html  
    tSNE_scatter                            html  
    tic_chart                               html  
    ttest                                   html  
    vec_norm                                html  
    wilcox_p_hist                           html  
    wilcox_test                             html  
** 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

install for x64

* installing *source* package 'structToolbox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'structToolbox' as structToolbox_1.4.3.zip
* DONE (structToolbox)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'structToolbox' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
> 
> test_check("structToolbox")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 106 ]
> 
> proc.time()
   user  system elapsed 
 154.35    1.25  155.59


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
> 
> test_check("structToolbox")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 106 ]
> 
> proc.time()
   user  system elapsed 
 174.89    0.50  175.39

name	user	system	elapsed
ANOVA	0.55	0.03	0.58
AUC	1.64	0.25	1.89
DFA	0.23	0.00	0.24
DatasetExperiment_boxplot	1.10	0.04	1.14
DatasetExperiment_dist	1.92	0.08	2.00
DatasetExperiment_factor_boxplot	0.26	0.00	0.26
DatasetExperiment_heatmap	0.25	0.02	0.27
HCA	0.10	0.00	0.09
HSD	0.70	0.01	0.75
HSDEM	0.47	0.03	0.50
MTBLS79_DatasetExperiment	0.01	0.00	0.02
PCA	0	0	0
PLSDA	0	0	0
PLSR	0	0	0
SVM	0.02	0.00	0.01
as_data_frame	0.16	0.00	0.16
autoscale	0.09	0.00	0.09
balanced_accuracy	1.59	0.02	1.61
blank_filter	0.35	0.02	0.36
blank_filter_hist	0	0	0
calculate	0.01	0.00	0.02
chart_plot	0.03	0.00	0.03
classical_lsq	0.27	0.00	0.27
compare_dist	3.61	0.18	3.79
confounders_clsq	2.62	0.00	2.63
confounders_lsq_barchart	2.94	0.00	2.94
confounders_lsq_boxplot	2.88	0.00	2.87
constant_sum_norm	0	0	0
corr_coef	0.2	0.0	0.2
dfa_scores_plot	0.56	0.00	0.57
dratio_filter	0.63	0.07	0.68
feature_boxplot	0.01	0.00	0.02
feature_profile	0.41	0.01	0.42
feature_profile_array	0.47	0.10	0.56
filter_by_name	0.03	0.00	0.03
filter_na_count	1	0	1
filter_smeta	0.08	0.00	0.08
fisher_exact	8.65	0.01	8.67
fold_change	6.78	0.06	6.85
fold_change_int	15.18	0.00	15.19
fold_change_plot	0	0	0
forward_selection_by_rank	7.68	0.13	7.81
fs_line	6.91	0.09	7.00
glog_opt_plot	0.58	0.00	0.58
glog_transform	0.36	0.00	0.36
grid_search_1d	3.61	0.09	3.70
gs_line	0	0	0
hca_dendrogram	0	0	0
kfold_xval	3.25	0.02	3.27
kfoldxcv_grid	3.33	0.00	3.33
kfoldxcv_metric	0	0	0
knn_impute	0	0	0
kw_p_hist	0	0	0
kw_rank_sum	0.07	0.00	0.08
linear_model	0.03	0.00	0.03
log_transform	0	0	0
mean_centre	0	0	0
mean_of_medians	0.15	0.00	0.14
mixed_effect	0.15	0.00	0.15
model_apply	0.03	0.00	0.04
model_predict	0.07	0.00	0.06
model_reverse	0.03	0.00	0.03
model_train	0.06	0.00	0.06
mv_boxplot	0.25	0.00	0.25
mv_feature_filter	0.17	0.00	0.17
mv_feature_filter_hist	0	0	0
mv_histogram	0.31	0.00	0.32
mv_sample_filter	0	0	0
mv_sample_filter_hist	0.00	0.01	0.01
nroot_transform	0	0	0
pairs_filter	0	0	0
pareto_scale	0.11	0.00	0.11
pca_biplot	0	0	0
pca_correlation_plot	0.02	0.00	0.02
pca_dstat_plot	0	0	0
pca_loadings_plot	0	0	0
pca_scores_plot	0.56	0.00	0.56
pca_scree_plot	0	0	0
permutation_test	0	0	0
permutation_test_plot	0	0	0
permute_sample_order	0.02	0.00	0.02
plsda_predicted_plot	0.36	0.00	0.35
plsda_regcoeff_plot	0.26	0.00	0.27
plsda_roc_plot	0.5	0.0	0.5
plsda_scores_plot	0.35	0.02	0.36
plsda_vip_plot	0.25	0.00	0.25
plsda_vip_summary_plot	0.45	0.00	0.45
plsr_cook_dist	0	0	0
plsr_prediction_plot	0	0	0
plsr_qq_plot	0	0	0
plsr_residual_hist	0	0	0
pqn_norm	0.43	0.00	0.42
pqn_norm_hist	0	0	0
prop_na	0	0	0
r_squared	0	0	0
rsd_filter	0	0	0
rsd_filter_hist	0	0	0
run	0.03	0.00	0.03
sb_corr	0.01	0.00	0.02
split_data	0	0	0
stratified_split	0.13	0.00	0.12
svm_plot_2d	0.69	0.00	0.69
tSNE	0	0	0
tSNE_scatter	0	0	0
tic_chart	0.2	0.0	0.2
ttest	0	0	0
vec_norm	0	0	0
wilcox_p_hist	0	0	0
wilcox_test	0.02	0.00	0.01

name	user	system	elapsed
ANOVA	0.42	0.03	0.45
AUC	1.56	0.05	1.61
DFA	0.2	0.0	0.2
DatasetExperiment_boxplot	1.11	0.01	1.12
DatasetExperiment_dist	1.00	0.08	1.08
DatasetExperiment_factor_boxplot	0.17	0.00	0.17
DatasetExperiment_heatmap	0.72	0.00	0.72
HCA	0.05	0.00	0.05
HSD	0.42	0.00	0.42
HSDEM	0.38	0.00	0.38
MTBLS79_DatasetExperiment	0.01	0.00	0.01
PCA	0	0	0
PLSDA	0	0	0
PLSR	0	0	0
SVM	0	0	0
as_data_frame	0.14	0.00	0.14
autoscale	0.11	0.00	0.11
balanced_accuracy	1.52	0.01	1.53
blank_filter	0.37	0.00	0.37
blank_filter_hist	0	0	0
calculate	0.02	0.00	0.02
chart_plot	0.03	0.00	0.03
classical_lsq	0.3	0.0	0.3
compare_dist	4.42	0.30	4.72
confounders_clsq	2.89	0.00	2.89
confounders_lsq_barchart	3.14	0.00	3.14
confounders_lsq_boxplot	2.85	0.00	2.85
constant_sum_norm	0	0	0
corr_coef	0.2	0.0	0.2
dfa_scores_plot	0.52	0.00	0.52
dratio_filter	0.58	0.03	0.61
feature_boxplot	0.01	0.00	0.01
feature_profile	0.33	0.00	0.33
feature_profile_array	0.44	0.00	0.44
filter_by_name	0.03	0.00	0.03
filter_na_count	0.86	0.00	0.86
filter_smeta	0.06	0.00	0.06
fisher_exact	7.08	0.02	7.09
fold_change	6.28	0.01	6.30
fold_change_int	13.41	0.00	13.41
fold_change_plot	0	0	0
forward_selection_by_rank	5.37	0.05	5.42
fs_line	5.84	0.01	5.86
glog_opt_plot	0.54	0.00	0.53
glog_transform	0.35	0.00	0.36
grid_search_1d	3.80	0.08	3.87
gs_line	0	0	0
hca_dendrogram	0	0	0
kfold_xval	2.64	0.00	2.64
kfoldxcv_grid	2.77	0.00	2.77
kfoldxcv_metric	0	0	0
knn_impute	0	0	0
kw_p_hist	0	0	0
kw_rank_sum	0.06	0.00	0.06
linear_model	0.03	0.00	0.03
log_transform	0	0	0
mean_centre	0	0	0
mean_of_medians	0.11	0.00	0.11
mixed_effect	0.13	0.00	0.13
model_apply	0.03	0.00	0.03
model_predict	0.04	0.00	0.05
model_reverse	0.04	0.00	0.03
model_train	0.04	0.00	0.04
mv_boxplot	0.21	0.00	0.21
mv_feature_filter	0.12	0.00	0.12
mv_feature_filter_hist	0	0	0
mv_histogram	0.17	0.00	0.17
mv_sample_filter	0	0	0
mv_sample_filter_hist	0.02	0.00	0.02
nroot_transform	0	0	0
pairs_filter	0	0	0
pareto_scale	0.06	0.00	0.06
pca_biplot	0	0	0
pca_correlation_plot	0	0	0
pca_dstat_plot	0	0	0
pca_loadings_plot	0	0	0
pca_scores_plot	0.36	0.00	0.36
pca_scree_plot	0	0	0
permutation_test	0.02	0.00	0.02
permutation_test_plot	0	0	0
permute_sample_order	0	0	0
plsda_predicted_plot	0.29	0.00	0.29
plsda_regcoeff_plot	0.19	0.00	0.19
plsda_roc_plot	0.46	0.00	0.47
plsda_scores_plot	0.35	0.00	0.34
plsda_vip_plot	0.23	0.00	0.23
plsda_vip_summary_plot	0.46	0.00	0.46
plsr_cook_dist	0	0	0
plsr_prediction_plot	0	0	0
plsr_qq_plot	0	0	0
plsr_residual_hist	0	0	0
pqn_norm	0.39	0.00	0.39
pqn_norm_hist	0	0	0
prop_na	0	0	0
r_squared	0	0	0
rsd_filter	0	0	0
rsd_filter_hist	0	0	0
run	0.03	0.00	0.03
sb_corr	0	0	0
split_data	0	0	0
stratified_split	0.13	0.00	0.13
svm_plot_2d	0.58	0.00	0.58
tSNE	0	0	0
tSNE_scatter	0	0	0
tic_chart	0.15	0.00	0.15
ttest	0	0	0
vec_norm	0	0	0
wilcox_p_hist	0	0	0
wilcox_test	0	0	0

CHECK results for structToolbox on tokay2

Summary

Command output

Installation output

Tests output

Example timings