Multiple platform build/check report for BioC 3.14 - CHECK results for structToolbox on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: structToolbox

Version: 1.6.1

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:structToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings structToolbox_1.6.1.tar.gz

StartedAt: 2022-04-13 03:40:14 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:53:38 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 803.4 seconds

RetCode: 0

Status: OK

CheckDir: structToolbox.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:structToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings structToolbox_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/structToolbox.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.6.1'
* 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           15.81   0.00   15.81
fold_change               10.73   0.00   10.74
fisher_exact               7.29   0.00    7.28
forward_selection_by_rank  5.47   0.05    5.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
fold_change_int           17.89   0.02   17.91
fold_change               11.25   0.00   11.25
fisher_exact               7.74   0.00    7.73
fs_line                    6.18   0.03    6.20
forward_selection_by_rank  5.99   0.09    6.08
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/structToolbox_1.6.1.tar.gz && rm -rf structToolbox.buildbin-libdir && mkdir structToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=structToolbox.buildbin-libdir structToolbox_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL structToolbox_1.6.1.zip && rm structToolbox_1.6.1.tar.gz structToolbox_1.6.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 23 2801k   23  644k    0     0   717k      0  0:00:03 --:--:--  0:00:03  716k
 78 2801k   78 2194k    0     0  1155k      0  0:00:02  0:00:01  0:00:01 1155k
100 2801k  100 2801k    0     0  1290k      0  0:00:02  0:00:02 --:--:-- 1290k

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  
    ontology_cache                          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_1.6.1.zip
* DONE (structToolbox)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'structToolbox' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 124 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 124 ]
> 
> proc.time()
   user  system elapsed 
 179.18    1.85  181.07


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 124 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 124 ]
> 
> proc.time()
   user  system elapsed 
 210.68    1.00  211.65

name	user	system	elapsed
ANOVA	0.17	0.00	0.17
AUC	1.58	0.06	1.64
DFA	0.23	0.00	0.23
DatasetExperiment_boxplot	1.10	0.05	1.14
DatasetExperiment_dist	0.86	0.11	0.97
DatasetExperiment_factor_boxplot	0.15	0.00	0.16
DatasetExperiment_heatmap	0.21	0.01	0.22
HCA	0.06	0.00	0.06
HSD	0.58	0.03	0.87
HSDEM	0.51	0.05	0.57
MTBLS79_DatasetExperiment	0	0	0
PCA	0	0	0
PLSDA	0.02	0.00	0.01
PLSR	0.00	0.02	0.02
SVM	0.00	0.01	0.01
as_data_frame	0.15	0.02	0.18
autoscale	0.11	0.01	0.12
balanced_accuracy	1.64	0.02	1.66
blank_filter	0.36	0.00	0.36
blank_filter_hist	0	0	0
bootstrap	0	0	0
calculate	0.02	0.00	0.01
chart_plot	0.03	0.00	0.03
classical_lsq	0.34	0.00	0.35
compare_dist	3.3	0.2	3.5
confounders_clsq	3.13	0.02	3.14
confounders_lsq_barchart	3.2	0.0	3.2
confounders_lsq_boxplot	3.41	0.00	3.41
constant_sum_norm	0	0	0
corr_coef	0.21	0.00	0.22
dfa_scores_plot	0.54	0.00	0.53
dratio_filter	0.62	0.01	0.64
feature_boxplot	0.02	0.00	0.01
feature_profile	0.32	0.00	0.33
feature_profile_array	0.43	0.08	0.50
filter_by_name	0.03	0.00	0.03
filter_na_count	0.89	0.06	0.96
filter_smeta	0.04	0.00	0.04
fisher_exact	7.29	0.00	7.28
fold_change	10.73	0.00	10.74
fold_change_int	15.81	0.00	15.81
fold_change_plot	0	0	0
forward_selection_by_rank	5.47	0.05	5.52
fs_line	4.88	0.12	5.00
glog_opt_plot	0.5	0.0	0.5
glog_transform	0.32	0.02	0.34
grid_search_1d	3.65	0.14	3.78
gs_line	0.01	0.00	0.02
hca_dendrogram	0	0	0
kfold_xval	3.16	0.00	3.15
kfoldxcv_grid	3.50	0.03	3.53
kfoldxcv_metric	0	0	0
knn_impute	0	0	0
kw_p_hist	0	0	0
kw_rank_sum	0.08	0.00	0.08
linear_model	0.03	0.00	0.03
log_transform	0.01	0.00	0.02
mean_centre	0	0	0
mean_of_medians	0.14	0.00	0.14
mixed_effect	0.17	0.00	0.17
model_apply	0.04	0.00	0.03
model_predict	0.06	0.00	0.07
model_reverse	0.05	0.00	0.04
model_train	0.04	0.00	0.05
mv_boxplot	0.21	0.00	0.20
mv_feature_filter	0.14	0.00	0.14
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	0	0
nroot_transform	0.01	0.00	0.02
ontology_cache	0	0	0
pairs_filter	0	0	0
pareto_scale	0.07	0.00	0.06
pca_biplot	0.01	0.00	0.01
pca_correlation_plot	0	0	0
pca_dstat_plot	0	0	0
pca_loadings_plot	0.02	0.00	0.02
pca_scores_plot	0.39	0.00	0.39
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	0.32	0.00	0.31
plsda_regcoeff_plot	0.21	0.00	0.22
plsda_roc_plot	0.52	0.01	0.53
plsda_scores_plot	0.33	0.02	0.34
plsda_vip_plot	0.25	0.00	0.25
plsda_vip_summary_plot	0.44	0.00	0.44
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	0.40	0.00	0.41
pqn_norm_hist	0	0	0
prop_na	0.02	0.00	0.01
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	0.15	0.00	0.14
svm_plot_2d	0.59	0.05	0.64
tSNE	0.01	0.00	0.02
tSNE_scatter	0	0	0
tic_chart	0.24	0.00	0.23
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	0.17	0.00	0.17
AUC	1.81	0.02	1.83
DFA	0.27	0.00	0.27
DatasetExperiment_boxplot	1.20	0.03	1.25
DatasetExperiment_dist	0.99	0.06	1.05
DatasetExperiment_factor_boxplot	0.15	0.01	0.17
DatasetExperiment_heatmap	0.75	0.02	0.76
HCA	0.08	0.00	0.08
HSD	0.39	0.05	0.44
HSDEM	0.36	0.03	0.39
MTBLS79_DatasetExperiment	0	0	0
PCA	0.02	0.00	0.01
PLSDA	0	0	0
PLSR	0	0	0
SVM	0.02	0.00	0.02
as_data_frame	0.17	0.00	0.17
autoscale	0.09	0.00	0.09
balanced_accuracy	1.67	0.00	1.67
blank_filter	0.35	0.01	0.36
blank_filter_hist	0	0	0
bootstrap	0	0	0
calculate	0	0	0
chart_plot	0.05	0.00	0.05
classical_lsq	0.31	0.00	0.31
compare_dist	3.65	0.25	3.91
confounders_clsq	3.52	0.02	3.53
confounders_lsq_barchart	3.94	0.00	3.94
confounders_lsq_boxplot	3.79	0.02	3.81
constant_sum_norm	0	0	0
corr_coef	0.22	0.00	0.22
dfa_scores_plot	0.66	0.01	0.67
dratio_filter	0.72	0.03	0.75
feature_boxplot	0.03	0.00	0.03
feature_profile	0.48	0.02	0.50
feature_profile_array	0.49	0.00	0.49
filter_by_name	0.03	0.00	0.03
filter_na_count	1.08	0.01	1.09
filter_smeta	0.04	0.00	0.05
fisher_exact	7.74	0.00	7.73
fold_change	11.25	0.00	11.25
fold_change_int	17.89	0.02	17.91
fold_change_plot	0.01	0.00	0.01
forward_selection_by_rank	5.99	0.09	6.08
fs_line	6.18	0.03	6.20
glog_opt_plot	0.67	0.00	0.67
glog_transform	0.42	0.00	0.42
grid_search_1d	4.41	0.08	4.49
gs_line	0	0	0
hca_dendrogram	0	0	0
kfold_xval	3.65	0.00	3.66
kfoldxcv_grid	3.74	0.02	3.75
kfoldxcv_metric	0	0	0
knn_impute	0.01	0.00	0.01
kw_p_hist	0	0	0
kw_rank_sum	0.08	0.00	0.08
linear_model	0.05	0.00	0.05
log_transform	0	0	0
mean_centre	0	0	0
mean_of_medians	0.15	0.00	0.15
mixed_effect	0.16	0.01	0.17
model_apply	0.03	0.00	0.04
model_predict	0.08	0.00	0.07
model_reverse	0.05	0.00	0.05
model_train	0.06	0.00	0.06
mv_boxplot	0.23	0.00	0.24
mv_feature_filter	0.16	0.02	0.17
mv_feature_filter_hist	0	0	0
mv_histogram	0.22	0.00	0.22
mv_sample_filter	0	0	0
mv_sample_filter_hist	0	0	0
nroot_transform	0.01	0.00	0.01
ontology_cache	0	0	0
pairs_filter	0	0	0
pareto_scale	0.08	0.00	0.08
pca_biplot	0.02	0.00	0.02
pca_correlation_plot	0	0	0
pca_dstat_plot	0.01	0.00	0.01
pca_loadings_plot	0	0	0
pca_scores_plot	0.49	0.00	0.49
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	0.38	0.00	0.38
plsda_regcoeff_plot	0.27	0.00	0.27
plsda_roc_plot	0.67	0.01	0.69
plsda_scores_plot	0.47	0.00	0.47
plsda_vip_plot	0.30	0.00	0.29
plsda_vip_summary_plot	0.54	0.00	0.55
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	0.52	0.00	0.51
pqn_norm_hist	0	0	0
prop_na	0	0	0
r_squared	0	0	0
rsd_filter	0.02	0.00	0.02
rsd_filter_hist	0	0	0
run	0.04	0.00	0.05
sb_corr	0.02	0.00	0.01
split_data	0	0	0
stratified_split	0.19	0.00	0.19
svm_plot_2d	0.82	0.00	0.83
tSNE	0.02	0.00	0.01
tSNE_scatter	0	0	0
tic_chart	0.23	0.00	0.24
ttest	0	0	0
vec_norm	0.02	0.00	0.01
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