Multiple platform build/check report for BioC 3.11 - CHECK report for structToolbox on tokay2

Package: structToolbox

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:structToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings structToolbox_1.0.1.tar.gz

StartedAt: 2020-10-17 08:41:29 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 08:52:25 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 656.4 seconds

RetCode: 0

Status: OK

CheckDir: structToolbox.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:structToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings structToolbox_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/structToolbox.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.0.1'
* 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          8.48   0.00    8.49
fs_line                  5.15   0.09    5.25
forward_selection_byrank 4.94   0.14    5.08
fisher_exact             5.04   0.00    5.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
fold_change_int          15.14   0.00   15.15
fs_line                   7.19   0.02    7.20
fisher_exact              6.71   0.00    6.71
forward_selection_byrank  5.66   0.00    5.65
fold_change               5.29   0.00    5.29
* 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 https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/structToolbox_1.0.1.tar.gz && rm -rf structToolbox.buildbin-libdir && mkdir structToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=structToolbox.buildbin-libdir structToolbox_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL structToolbox_1.0.1.zip && rm structToolbox_1.0.1.tar.gz structToolbox_1.0.1.zip
###
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100 2757k  100 2757k    0     0  27.2M      0 --:--:-- --:--:-- --:--:-- 28.9M

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_barchart       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  
    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_byrank                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_plot                         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  
    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  
    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_1.0.1.zip
* DONE (structToolbox)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'structToolbox' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 95 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 119.00    1.35  120.35


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 95 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 141.34    0.65  142.06

name	user	system	elapsed
ANOVA	0.49	0.02	0.50
AUC	1.21	0.09	1.31
DFA	0.18	0.00	0.17
DatasetExperiment_boxplot	0.76	0.02	0.79
DatasetExperiment_dist	1.53	0.11	1.64
DatasetExperiment_factor_barchart	0.15	0.00	0.14
DatasetExperiment_heatmap	0	0	0
HCA	0.04	0.00	0.05
HSD	0.46	0.06	0.53
HSDEM	0.46	0.02	0.48
MTBLS79_DatasetExperiment	0	0	0
PCA	0	0	0
PLSDA	0	0	0
PLSR	0.02	0.00	0.02
SVM	0	0	0
as_data_frame	0.12	0.00	0.12
autoscale	0.07	0.00	0.06
balanced_accuracy	1.09	0.01	1.11
blank_filter	0.38	0.02	0.39
blank_filter_hist	0.01	0.00	0.02
bootstrap	0.91	0.00	0.91
calculate	0	0	0
chart_plot	0.03	0.00	0.03
classical_lsq	0.17	0.00	0.17
compare_dist	3.70	0.36	4.06
confounders_clsq	1.99	0.00	1.99
confounders_lsq_barchart	1.80	0.00	1.79
confounders_lsq_boxplot	1.90	0.00	1.91
constant_sum_norm	0	0	0
corr_coef	0.16	0.00	0.16
dfa_scores_plot	0.42	0.00	0.42
dratio_filter	0.55	0.04	0.59
feature_boxplot	0.01	0.00	0.02
feature_profile	0.39	0.02	0.40
filter_by_name	0.02	0.00	0.02
filter_na_count	0.72	0.00	0.72
filter_smeta	0.04	0.00	0.04
fisher_exact	5.04	0.00	5.04
fold_change	4.28	0.08	4.35
fold_change_int	8.48	0.00	8.49
fold_change_plot	0	0	0
forward_selection_byrank	4.94	0.14	5.08
fs_line	5.15	0.09	5.25
glog_opt_plot	0.52	0.00	0.51
glog_transform	0.25	0.00	0.25
grid_search_1d	2.97	0.03	3.00
gs_line	0	0	0
hca_dendrogram	0	0	0
kfold_xval	1.83	0.00	1.83
kfoldxcv_grid	2.14	0.00	2.14
kfoldxcv_metric	0	0	0
knn_impute	0	0	0
kw_p_hist	0	0	0
kw_rank_sum	0.06	0.00	0.07
linear_model	0	0	0
log_transform	0	0	0
mean_centre	0	0	0
mean_of_medians	0.06	0.00	0.06
mixed_effect	0.13	0.00	0.13
model_apply	0.01	0.00	0.01
model_predict	0.05	0.00	0.05
model_reverse	0.02	0.00	0.02
model_train	0.03	0.00	0.03
mv_boxplot	0.2	0.0	0.2
mv_feature_filter	0.09	0.00	0.09
mv_feature_filter_hist	0	0	0
mv_histogram	0.18	0.00	0.18
mv_sample_filter	0.01	0.00	0.01
mv_sample_filter_hist	0	0	0
nroot_transform	0	0	0
pairs_filter	0	0	0
pareto_scale	0.05	0.00	0.05
pca_biplot_plot	0	0	0
pca_correlation_plot	0	0	0
pca_dstat_plot	0	0	0
pca_loadings_plot	0	0	0
pca_scores_plot	0.34	0.00	0.35
pca_scree_plot	0	0	0
permutation_test	0	0	0
permutation_test_plot	0	0	0
permute_sample_order	0	0	0
plsda_predicted_plot	0.28	0.00	0.28
plsda_regcoeff_plot	0.19	0.00	0.19
plsda_roc_plot	0.41	0.00	0.40
plsda_scores_plot	0.39	0.00	0.39
plsda_vip_plot	0.20	0.00	0.21
plsr_cook_dist	0	0	0
plsr_prediction_plot	0	0	0
plsr_qq_plot	0.02	0.00	0.01
plsr_residual_hist	0	0	0
pqn_norm	0.59	0.00	0.60
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	0.08	0.00	0.08
svm_plot_2d	0.80	0.01	0.81
tSNE	0	0	0
tSNE_scatter	0.01	0.00	0.01
ttest	0	0	0
vec_norm	0	0	0
wilcox_p_hist	0	0	0
wilcox_test	0	0	0

name	user	system	elapsed
ANOVA	0.58	0.03	0.61
AUC	1.54	0.03	1.58
DFA	0.17	0.00	0.17
DatasetExperiment_boxplot	1.58	0.03	1.61
DatasetExperiment_dist	2.16	0.10	2.25
DatasetExperiment_factor_barchart	0.26	0.00	0.27
DatasetExperiment_heatmap	0	0	0
HCA	0.08	0.00	0.08
HSD	0.56	0.07	0.64
HSDEM	0.41	0.00	0.40
MTBLS79_DatasetExperiment	0	0	0
PCA	0	0	0
PLSDA	0	0	0
PLSR	0	0	0
SVM	0.01	0.00	0.02
as_data_frame	0.11	0.00	0.11
autoscale	0.07	0.00	0.06
balanced_accuracy	1.15	0.00	1.16
blank_filter	0.39	0.00	0.39
blank_filter_hist	0	0	0
bootstrap	1.05	0.00	1.04
calculate	0.02	0.00	0.02
chart_plot	0.03	0.00	0.03
classical_lsq	0.33	0.00	0.33
compare_dist	4.56	0.38	4.94
confounders_clsq	2.54	0.00	2.54
confounders_lsq_barchart	2.22	0.00	2.22
confounders_lsq_boxplot	2.22	0.00	2.22
constant_sum_norm	0	0	0
corr_coef	0.19	0.00	0.19
dfa_scores_plot	0.5	0.0	0.5
dratio_filter	0.66	0.00	0.66
feature_boxplot	0.01	0.00	0.01
feature_profile	0.42	0.00	0.42
filter_by_name	0.02	0.00	0.02
filter_na_count	1.30	0.03	1.33
filter_smeta	0.07	0.00	0.07
fisher_exact	6.71	0.00	6.71
fold_change	5.29	0.00	5.29
fold_change_int	15.14	0.00	15.15
fold_change_plot	0	0	0
forward_selection_byrank	5.66	0.00	5.65
fs_line	7.19	0.02	7.20
glog_opt_plot	0.8	0.0	0.8
glog_transform	0.37	0.00	0.38
grid_search_1d	4.42	0.07	4.50
gs_line	0	0	0
hca_dendrogram	0	0	0
kfold_xval	3.56	0.00	3.56
kfoldxcv_grid	2.94	0.00	2.94
kfoldxcv_metric	0	0	0
knn_impute	0.01	0.00	0.02
kw_p_hist	0	0	0
kw_rank_sum	0.05	0.00	0.04
linear_model	0.02	0.00	0.02
log_transform	0	0	0
mean_centre	0	0	0
mean_of_medians	0.07	0.00	0.08
mixed_effect	0.13	0.00	0.12
model_apply	0.01	0.00	0.02
model_predict	0.03	0.00	0.04
model_reverse	0.02	0.00	0.01
model_train	0.04	0.00	0.05
mv_boxplot	0.24	0.00	0.23
mv_feature_filter	0.09	0.00	0.10
mv_feature_filter_hist	0	0	0
mv_histogram	0.24	0.02	0.25
mv_sample_filter	0	0	0
mv_sample_filter_hist	0	0	0
nroot_transform	0	0	0
pairs_filter	0	0	0
pareto_scale	0.06	0.00	0.06
pca_biplot_plot	0	0	0
pca_correlation_plot	0	0	0
pca_dstat_plot	0	0	0
pca_loadings_plot	0	0	0
pca_scores_plot	0.47	0.00	0.47
pca_scree_plot	0	0	0
permutation_test	0	0	0
permutation_test_plot	0.01	0.00	0.02
permute_sample_order	0	0	0
plsda_predicted_plot	0.47	0.00	0.47
plsda_regcoeff_plot	0.33	0.00	0.33
plsda_roc_plot	0.65	0.00	0.66
plsda_scores_plot	0.61	0.00	0.61
plsda_vip_plot	0.33	0.01	0.34
plsr_cook_dist	0.02	0.00	0.02
plsr_prediction_plot	0	0	0
plsr_qq_plot	0	0	0
plsr_residual_hist	0	0	0
pqn_norm	1.10	0.00	1.11
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	0.04	0.00	0.03
sb_corr	0	0	0
split_data	0	0	0
stratified_split	0.09	0.00	0.09
svm_plot_2d	0.59	0.00	0.59
tSNE	0.02	0.00	0.02
tSNE_scatter	0	0	0
ttest	0	0	0
vec_norm	0	0	0
wilcox_p_hist	0	0	0
wilcox_test	0.01	0.00	0.02

CHECK report for structToolbox on tokay2

Summary

Command output

Installation output

Tests output

Example timings