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CHECK report for structToolbox on merida1

This page was generated on 2021-05-06 12:36:59 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the structToolbox package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1809/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.2.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/structToolbox
Branch: RELEASE_3_12
Last Commit: dea6388
Last Changed Date: 2020-10-27 11:53:02 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: structToolbox
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings structToolbox_1.2.0.tar.gz
StartedAt: 2021-05-06 06:40:53 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:48:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 460.1 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings structToolbox_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/structToolbox.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
fold_change_int           12.141  0.029  12.185
fs_line                    7.060  0.122   7.196
forward_selection_by_rank  6.535  0.078   6.628
fisher_exact               6.313  0.030   6.353
fold_change                5.575  0.065   5.647
compare_dist               5.233  0.268   5.517
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘structToolbox’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (structToolbox)

Tests output

structToolbox.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 95 ]
> 
> proc.time()
   user  system elapsed 
165.492   1.143 166.850 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.6590.0210.680
AUC1.9530.0442.000
DFA0.2530.0020.255
DatasetExperiment_boxplot1.4070.0371.448
DatasetExperiment_dist1.2150.0641.281
DatasetExperiment_factor_boxplot0.2220.0020.223
DatasetExperiment_heatmap0.2150.0090.225
HCA0.0590.0040.063
HSD1.1320.0431.178
HSDEM0.5320.0150.548
MTBLS79_DatasetExperiment0.0020.0000.002
PCA0.0030.0000.002
PLSDA0.0030.0010.004
PLSR0.0030.0010.004
SVM0.0090.0000.010
as_data_frame0.1860.0170.203
autoscale0.0830.0070.090
balanced_accuracy1.7710.0551.828
blank_filter0.5110.0110.525
blank_filter_hist0.0010.0000.002
calculate0.0070.0010.007
chart_plot0.0450.0010.046
classical_lsq0.2410.0000.241
compare_dist5.2330.2685.517
confounders_clsq2.8250.0112.839
confounders_lsq_barchart3.3340.0123.350
confounders_lsq_boxplot3.2680.0103.282
constant_sum_norm0.0030.0000.003
corr_coef0.2340.0010.236
dfa_scores_plot0.6620.0050.668
dratio_filter0.9790.0291.009
feature_boxplot0.0110.0000.011
feature_profile0.5470.0100.557
filter_by_name0.0270.0010.028
filter_na_count1.3980.0311.431
filter_smeta0.0720.0000.073
fisher_exact6.3130.0306.353
fold_change5.5750.0655.647
fold_change_int12.141 0.02912.185
fold_change_plot0.0030.0010.003
forward_selection_by_rank6.5350.0786.628
fs_line7.0600.1227.196
glog_opt_plot0.5570.0040.563
glog_transform0.3290.0010.330
grid_search_1d3.9240.0703.999
gs_line0.0010.0000.002
hca_dendrogram0.0010.0000.001
kfold_xval3.0120.0093.024
kfoldxcv_grid3.3130.0233.341
kfoldxcv_metric0.0010.0000.001
knn_impute0.0020.0000.003
kw_p_hist0.0010.0000.001
kw_rank_sum0.0810.0010.080
linear_model0.0250.0010.026
log_transform0.0030.0000.004
mean_centre0.0010.0000.001
mean_of_medians0.1640.0000.165
mixed_effect0.1950.0010.196
model_apply0.0250.0010.025
model_predict0.0580.0000.058
model_reverse0.0290.0000.029
model_train0.0640.0010.065
mv_boxplot0.3360.0020.338
mv_feature_filter0.1400.0010.141
mv_feature_filter_hist0.0010.0000.002
mv_histogram0.3070.0050.312
mv_sample_filter0.0020.0000.002
mv_sample_filter_hist0.0010.0010.001
nroot_transform0.0030.0000.003
pairs_filter0.0030.0000.003
pareto_scale0.0780.0000.079
pca_biplot0.0070.0000.007
pca_correlation_plot0.0030.0000.003
pca_dstat_plot0.0040.0010.004
pca_loadings_plot0.0050.0010.005
pca_scores_plot0.5600.0030.565
pca_scree_plot0.0000.0000.001
permutation_test0.0040.0000.004
permutation_test_plot0.0010.0000.002
permute_sample_order0.0020.0010.002
plsda_predicted_plot0.3820.0020.385
plsda_regcoeff_plot0.2520.0010.254
plsda_roc_plot0.6590.0020.662
plsda_scores_plot0.4020.0020.403
plsda_vip_plot0.2800.0020.283
plsr_cook_dist0.0010.0000.001
plsr_prediction_plot0.0000.0000.001
plsr_qq_plot0.0010.0000.001
plsr_residual_hist0.0010.0000.000
pqn_norm0.8150.0020.818
pqn_norm_hist0.0010.0000.000
prop_na0.0030.0000.003
r_squared0.0010.0010.001
rsd_filter0.0040.0000.003
rsd_filter_hist0.0010.0010.001
run0.0310.0000.031
sb_corr0.0050.0000.005
split_data0.0020.0000.002
stratified_split0.1070.0000.108
svm_plot_2d0.7170.0080.726
tSNE0.0060.0000.006
tSNE_scatter0.0020.0000.003
ttest0.0030.0000.004
vec_norm0.0000.0000.001
wilcox_p_hist0.0010.0000.000
wilcox_test0.0050.0000.005