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This page was generated on 2022-04-13 12:07:26 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for structToolbox on tokay2


To the developers/maintainers of the structToolbox package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/structToolbox.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1896/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.6.1  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_14
git_last_commit: 29455a0
git_last_commit_date: 2022-02-04 04:54:45 -0400 (Fri, 04 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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


Installation output

structToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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

Tests output

structToolbox.Rcheck/tests_i386/testthat.Rout


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 

structToolbox.Rcheck/tests_x64/testthat.Rout


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 

Example timings

structToolbox.Rcheck/examples_i386/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.170.000.17
AUC1.580.061.64
DFA0.230.000.23
DatasetExperiment_boxplot1.100.051.14
DatasetExperiment_dist0.860.110.97
DatasetExperiment_factor_boxplot0.150.000.16
DatasetExperiment_heatmap0.210.010.22
HCA0.060.000.06
HSD0.580.030.87
HSDEM0.510.050.57
MTBLS79_DatasetExperiment000
PCA000
PLSDA0.020.000.01
PLSR0.000.020.02
SVM0.000.010.01
as_data_frame0.150.020.18
autoscale0.110.010.12
balanced_accuracy1.640.021.66
blank_filter0.360.000.36
blank_filter_hist000
bootstrap000
calculate0.020.000.01
chart_plot0.030.000.03
classical_lsq0.340.000.35
compare_dist3.30.23.5
confounders_clsq3.130.023.14
confounders_lsq_barchart3.20.03.2
confounders_lsq_boxplot3.410.003.41
constant_sum_norm000
corr_coef0.210.000.22
dfa_scores_plot0.540.000.53
dratio_filter0.620.010.64
feature_boxplot0.020.000.01
feature_profile0.320.000.33
feature_profile_array0.430.080.50
filter_by_name0.030.000.03
filter_na_count0.890.060.96
filter_smeta0.040.000.04
fisher_exact7.290.007.28
fold_change10.73 0.0010.74
fold_change_int15.81 0.0015.81
fold_change_plot000
forward_selection_by_rank5.470.055.52
fs_line4.880.125.00
glog_opt_plot0.50.00.5
glog_transform0.320.020.34
grid_search_1d3.650.143.78
gs_line0.010.000.02
hca_dendrogram000
kfold_xval3.160.003.15
kfoldxcv_grid3.500.033.53
kfoldxcv_metric000
knn_impute000
kw_p_hist000
kw_rank_sum0.080.000.08
linear_model0.030.000.03
log_transform0.010.000.02
mean_centre000
mean_of_medians0.140.000.14
mixed_effect0.170.000.17
model_apply0.040.000.03
model_predict0.060.000.07
model_reverse0.050.000.04
model_train0.040.000.05
mv_boxplot0.210.000.20
mv_feature_filter0.140.000.14
mv_feature_filter_hist000
mv_histogram0.170.000.17
mv_sample_filter000
mv_sample_filter_hist000
nroot_transform0.010.000.02
ontology_cache000
pairs_filter000
pareto_scale0.070.000.06
pca_biplot0.010.000.01
pca_correlation_plot000
pca_dstat_plot000
pca_loadings_plot0.020.000.02
pca_scores_plot0.390.000.39
pca_scree_plot000
permutation_test000
permutation_test_plot000
permute_sample_order000
plsda_predicted_plot0.320.000.31
plsda_regcoeff_plot0.210.000.22
plsda_roc_plot0.520.010.53
plsda_scores_plot0.330.020.34
plsda_vip_plot0.250.000.25
plsda_vip_summary_plot0.440.000.44
plsr_cook_dist000
plsr_prediction_plot000
plsr_qq_plot000
plsr_residual_hist000
pqn_norm0.400.000.41
pqn_norm_hist000
prop_na0.020.000.01
r_squared000
rsd_filter000
rsd_filter_hist000
run0.030.000.03
sb_corr0.010.000.02
split_data000
stratified_split0.150.000.14
svm_plot_2d0.590.050.64
tSNE0.010.000.02
tSNE_scatter000
tic_chart0.240.000.23
ttest000
vec_norm000
wilcox_p_hist000
wilcox_test0.020.000.01

structToolbox.Rcheck/examples_x64/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.170.000.17
AUC1.810.021.83
DFA0.270.000.27
DatasetExperiment_boxplot1.200.031.25
DatasetExperiment_dist0.990.061.05
DatasetExperiment_factor_boxplot0.150.010.17
DatasetExperiment_heatmap0.750.020.76
HCA0.080.000.08
HSD0.390.050.44
HSDEM0.360.030.39
MTBLS79_DatasetExperiment000
PCA0.020.000.01
PLSDA000
PLSR000
SVM0.020.000.02
as_data_frame0.170.000.17
autoscale0.090.000.09
balanced_accuracy1.670.001.67
blank_filter0.350.010.36
blank_filter_hist000
bootstrap000
calculate000
chart_plot0.050.000.05
classical_lsq0.310.000.31
compare_dist3.650.253.91
confounders_clsq3.520.023.53
confounders_lsq_barchart3.940.003.94
confounders_lsq_boxplot3.790.023.81
constant_sum_norm000
corr_coef0.220.000.22
dfa_scores_plot0.660.010.67
dratio_filter0.720.030.75
feature_boxplot0.030.000.03
feature_profile0.480.020.50
feature_profile_array0.490.000.49
filter_by_name0.030.000.03
filter_na_count1.080.011.09
filter_smeta0.040.000.05
fisher_exact7.740.007.73
fold_change11.25 0.0011.25
fold_change_int17.89 0.0217.91
fold_change_plot0.010.000.01
forward_selection_by_rank5.990.096.08
fs_line6.180.036.20
glog_opt_plot0.670.000.67
glog_transform0.420.000.42
grid_search_1d4.410.084.49
gs_line000
hca_dendrogram000
kfold_xval3.650.003.66
kfoldxcv_grid3.740.023.75
kfoldxcv_metric000
knn_impute0.010.000.01
kw_p_hist000
kw_rank_sum0.080.000.08
linear_model0.050.000.05
log_transform000
mean_centre000
mean_of_medians0.150.000.15
mixed_effect0.160.010.17
model_apply0.030.000.04
model_predict0.080.000.07
model_reverse0.050.000.05
model_train0.060.000.06
mv_boxplot0.230.000.24
mv_feature_filter0.160.020.17
mv_feature_filter_hist000
mv_histogram0.220.000.22
mv_sample_filter000
mv_sample_filter_hist000
nroot_transform0.010.000.01
ontology_cache000
pairs_filter000
pareto_scale0.080.000.08
pca_biplot0.020.000.02
pca_correlation_plot000
pca_dstat_plot0.010.000.01
pca_loadings_plot000
pca_scores_plot0.490.000.49
pca_scree_plot000
permutation_test000
permutation_test_plot000
permute_sample_order000
plsda_predicted_plot0.380.000.38
plsda_regcoeff_plot0.270.000.27
plsda_roc_plot0.670.010.69
plsda_scores_plot0.470.000.47
plsda_vip_plot0.300.000.29
plsda_vip_summary_plot0.540.000.55
plsr_cook_dist000
plsr_prediction_plot000
plsr_qq_plot000
plsr_residual_hist000
pqn_norm0.520.000.51
pqn_norm_hist000
prop_na000
r_squared000
rsd_filter0.020.000.02
rsd_filter_hist000
run0.040.000.05
sb_corr0.020.000.01
split_data000
stratified_split0.190.000.19
svm_plot_2d0.820.000.83
tSNE0.020.000.01
tSNE_scatter000
tic_chart0.230.000.24
ttest000
vec_norm0.020.000.01
wilcox_p_hist000
wilcox_test000