Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-01-24 13:07:05 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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? here 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 1.6.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_14
git_last_commit: 46cf01a
git_last_commit_date: 2021-10-26 12:57:03 -0500 (Tue, 26 Oct 2021)
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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2022-01-24 03:10:18 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 03:23:47 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 809.5 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/structToolbox.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.6.0'
* 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           18.73   0.02   18.75
fold_change               12.41   0.00   12.41
fisher_exact               7.81   0.00    7.81
fs_line                    6.60   0.07    6.67
forward_selection_by_rank  5.83   0.04    5.87
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
fold_change_int           17.89   0.00   17.89
fold_change               11.14   0.03   11.17
fisher_exact               8.69   0.00    8.69
forward_selection_by_rank  7.12   0.03    7.16
fs_line                    6.41   0.05    6.53
* 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_1.6.0.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_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL structToolbox_1.6.0.zip && rm structToolbox_1.6.0.tar.gz structToolbox_1.6.0.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
 59 2800k   59 1678k    0     0  2295k      0  0:00:01 --:--:--  0:00:01 2295k
100 2800k  100 2800k    0     0  2648k      0  0:00:01  0:00:01 --:--:-- 2649k

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_1.6.0.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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 121 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 121 ]
> 
> proc.time()
   user  system elapsed 
 180.37    1.64  182.04 

structToolbox.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 121 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 121 ]
> 
> proc.time()
   user  system elapsed 
 206.21    0.98  207.20 

Example timings

structToolbox.Rcheck/examples_i386/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.190.000.19
AUC1.800.161.95
DFA0.290.000.28
DatasetExperiment_boxplot1.290.051.34
DatasetExperiment_dist1.530.061.59
DatasetExperiment_factor_boxplot0.170.000.17
DatasetExperiment_heatmap0.240.020.25
HCA0.060.000.07
HSD0.530.060.86
HSDEM0.500.080.57
MTBLS79_DatasetExperiment000
PCA0.010.000.02
PLSDA0.000.010.02
PLSR000
SVM0.020.000.01
as_data_frame0.170.030.20
autoscale0.10.00.1
balanced_accuracy1.860.001.86
blank_filter0.390.000.39
blank_filter_hist000
bootstrap000
calculate0.010.000.01
chart_plot0.030.000.03
classical_lsq0.350.000.35
compare_dist3.860.354.23
confounders_clsq3.980.014.00
confounders_lsq_barchart3.940.003.94
confounders_lsq_boxplot4.040.024.06
constant_sum_norm0.020.000.02
corr_coef0.30.00.3
dfa_scores_plot0.640.000.64
dratio_filter0.640.040.68
feature_boxplot0.010.000.02
feature_profile0.380.020.39
feature_profile_array0.470.070.54
filter_by_name0.030.000.03
filter_na_count1.050.051.10
filter_smeta0.060.000.06
fisher_exact7.810.007.81
fold_change12.41 0.0012.41
fold_change_int18.73 0.0218.75
fold_change_plot000
forward_selection_by_rank5.830.045.87
fs_line6.600.076.67
glog_opt_plot0.580.010.59
glog_transform0.360.000.36
grid_search_1d3.640.113.75
gs_line0.020.000.02
hca_dendrogram000
kfold_xval3.50.03.5
kfoldxcv_grid3.550.003.55
kfoldxcv_metric000
knn_impute000
kw_p_hist000
kw_rank_sum0.070.000.07
linear_model0.030.000.04
log_transform0.020.000.01
mean_centre000
mean_of_medians0.140.000.14
mixed_effect0.160.000.16
model_apply0.030.000.03
model_predict0.080.000.08
model_reverse0.040.000.04
model_train0.070.000.07
mv_boxplot0.210.000.22
mv_feature_filter0.150.000.14
mv_feature_filter_hist000
mv_histogram0.20.00.2
mv_sample_filter000
mv_sample_filter_hist000
nroot_transform0.010.000.02
ontology_cache000
pairs_filter000
pareto_scale0.080.000.07
pca_biplot000
pca_correlation_plot0.020.000.02
pca_dstat_plot000
pca_loadings_plot000
pca_scores_plot0.480.000.48
pca_scree_plot000
permutation_test0.020.000.02
permutation_test_plot000
permute_sample_order000
plsda_predicted_plot0.310.030.34
plsda_regcoeff_plot0.250.000.25
plsda_roc_plot0.630.000.63
plsda_scores_plot0.390.000.39
plsda_vip_plot0.250.000.25
plsda_vip_summary_plot0.480.000.48
plsr_cook_dist000
plsr_prediction_plot000
plsr_qq_plot000
plsr_residual_hist000
pqn_norm0.470.000.47
pqn_norm_hist000
prop_na000
r_squared000
rsd_filter0.010.000.02
rsd_filter_hist000
run0.040.000.03
sb_corr0.010.000.01
split_data000
stratified_split0.140.000.14
svm_plot_2d0.690.020.71
tSNE0.020.000.01
tSNE_scatter000
tic_chart0.20.00.2
ttest0.020.000.02
vec_norm000
wilcox_p_hist000
wilcox_test000

structToolbox.Rcheck/examples_x64/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.340.010.36
AUC2.100.022.11
DFA0.30.00.3
DatasetExperiment_boxplot1.340.031.38
DatasetExperiment_dist1.080.081.15
DatasetExperiment_factor_boxplot0.190.000.19
DatasetExperiment_heatmap0.230.000.23
HCA0.070.000.07
HSD0.510.050.56
HSDEM0.530.070.61
MTBLS79_DatasetExperiment000
PCA000
PLSDA0.020.000.01
PLSR0.020.000.02
SVM0.010.000.01
as_data_frame0.160.000.16
autoscale0.110.000.11
balanced_accuracy1.790.001.80
blank_filter0.360.020.37
blank_filter_hist000
bootstrap000
calculate000
chart_plot0.050.000.05
classical_lsq0.420.000.42
compare_dist3.670.203.88
confounders_clsq3.550.003.54
confounders_lsq_barchart3.560.023.58
confounders_lsq_boxplot3.520.013.53
constant_sum_norm000
corr_coef0.250.000.25
dfa_scores_plot0.610.000.61
dratio_filter0.640.040.67
feature_boxplot0.010.000.02
feature_profile0.470.000.47
feature_profile_array0.460.000.45
filter_by_name0.040.000.05
filter_na_count1.080.001.08
filter_smeta0.060.000.06
fisher_exact8.690.008.69
fold_change11.14 0.0311.17
fold_change_int17.89 0.0017.89
fold_change_plot0.020.000.01
forward_selection_by_rank7.120.037.16
fs_line6.410.056.53
glog_opt_plot0.610.000.61
glog_transform0.420.000.42
grid_search_1d4.190.034.22
gs_line000
hca_dendrogram000
kfold_xval3.390.013.41
kfoldxcv_grid3.670.003.67
kfoldxcv_metric000
knn_impute000
kw_p_hist000
kw_rank_sum0.080.000.08
linear_model0.050.000.04
log_transform000
mean_centre000
mean_of_medians0.150.000.16
mixed_effect0.170.000.17
model_apply0.030.000.03
model_predict0.080.000.08
model_reverse0.070.000.06
model_train0.060.000.07
mv_boxplot0.230.000.23
mv_feature_filter0.140.000.14
mv_feature_filter_hist000
mv_histogram0.210.000.21
mv_sample_filter000
mv_sample_filter_hist000
nroot_transform0.010.000.01
ontology_cache000
pairs_filter000
pareto_scale0.080.000.08
pca_biplot000
pca_correlation_plot0.020.000.01
pca_dstat_plot000
pca_loadings_plot000
pca_scores_plot0.460.000.47
pca_scree_plot000
permutation_test000
permutation_test_plot000
permute_sample_order0.020.000.02
plsda_predicted_plot0.370.000.37
plsda_regcoeff_plot0.270.000.27
plsda_roc_plot0.690.000.69
plsda_scores_plot0.420.000.42
plsda_vip_plot0.310.000.31
plsda_vip_summary_plot0.520.020.53
plsr_cook_dist000
plsr_prediction_plot000
plsr_qq_plot0.010.000.02
plsr_residual_hist000
pqn_norm0.550.000.55
pqn_norm_hist000
prop_na0.020.000.01
r_squared000
rsd_filter000
rsd_filter_hist000
run0.040.000.04
sb_corr0.020.000.02
split_data000
stratified_split0.150.000.16
svm_plot_2d0.790.000.78
tSNE0.030.000.03
tSNE_scatter000
tic_chart0.360.000.36
ttest0.010.000.02
vec_norm000
wilcox_p_hist000
wilcox_test0.020.000.01