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CHECK report for structToolbox on machv2

This page was generated on 2020-10-17 11:59:44 -0400 (Sat, 17 Oct 2020).

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 1753/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.0.1
Gavin Rhys Lloyd
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/structToolbox
Branch: RELEASE_3_11
Last Commit: 8b4c746
Last Changed Date: 2020-05-26 08:44:39 -0400 (Tue, 26 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: structToolbox
Version: 1.0.1
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_1.0.1.tar.gz
StartedAt: 2020-10-17 05:43:38 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:52:30 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 531.1 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_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/structToolbox.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.0.1’
* 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 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          17.168  0.043  17.229
fisher_exact              8.841  0.023   8.870
fs_line                   8.023  0.076   8.110
forward_selection_byrank  7.359  0.089   7.457
fold_change               7.046  0.034   7.086
compare_dist              5.634  0.304   5.955
* 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 95 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
192.035   1.132 193.345 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.6570.0330.694
AUC2.0220.0822.105
DFA0.3180.0010.319
DatasetExperiment_boxplot0.8560.0360.893
DatasetExperiment_dist2.0110.1142.126
DatasetExperiment_factor_barchart0.2850.0020.287
DatasetExperiment_heatmap0.0030.0010.003
HCA0.0620.0010.062
HSD0.6310.0310.667
HSDEM0.5140.0180.532
MTBLS79_DatasetExperiment0.0020.0010.003
PCA0.0030.0000.004
PLSDA0.0020.0000.003
PLSR0.0040.0000.004
SVM0.0080.0010.009
as_data_frame0.2050.0020.209
autoscale0.1000.0010.101
balanced_accuracy1.9270.0131.940
blank_filter0.5430.0140.558
blank_filter_hist0.0000.0010.001
bootstrap1.3800.0021.382
calculate0.0070.0010.008
chart_plot0.0340.0020.035
classical_lsq0.2370.0000.238
compare_dist5.6340.3045.955
confounders_clsq3.4030.0073.412
confounders_lsq_barchart3.2080.0083.219
confounders_lsq_boxplot3.1800.0093.194
constant_sum_norm0.0020.0000.002
corr_coef0.2310.0020.232
dfa_scores_plot0.7630.0030.766
dratio_filter1.2790.0281.310
feature_boxplot0.0150.0010.015
feature_profile0.7450.0140.760
filter_by_name0.030.000.03
filter_na_count1.4140.0491.469
filter_smeta0.0790.0000.079
fisher_exact8.8410.0238.870
fold_change7.0460.0347.086
fold_change_int17.168 0.04317.229
fold_change_plot0.0020.0010.002
forward_selection_byrank7.3590.0897.457
fs_line8.0230.0768.110
glog_opt_plot0.8010.0070.810
glog_transform0.4730.0040.478
grid_search_1d4.8890.1044.997
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval3.1150.0103.132
kfoldxcv_grid3.6110.0113.629
kfoldxcv_metric0.0020.0000.002
knn_impute0.0030.0000.003
kw_p_hist0.0010.0000.001
kw_rank_sum0.0910.0000.091
linear_model0.0220.0000.022
log_transform0.0030.0000.003
mean_centre0.0010.0000.000
mean_of_medians0.1210.0010.122
mixed_effect0.2300.0000.231
model_apply0.0310.0000.031
model_predict0.0740.0010.075
model_reverse0.0300.0010.031
model_train0.0700.0010.071
mv_boxplot0.4500.0070.459
mv_feature_filter0.1800.0010.180
mv_feature_filter_hist0.0010.0010.001
mv_histogram0.3990.0020.401
mv_sample_filter0.0040.0000.004
mv_sample_filter_hist0.0010.0010.002
nroot_transform0.0030.0000.004
pairs_filter0.0040.0000.004
pareto_scale0.0870.0000.088
pca_biplot_plot0.0060.0000.006
pca_correlation_plot0.0030.0010.003
pca_dstat_plot0.0030.0000.004
pca_loadings_plot0.0030.0000.004
pca_scores_plot0.5700.0040.577
pca_scree_plot0.0010.0000.002
permutation_test0.0030.0000.003
permutation_test_plot0.0010.0000.002
permute_sample_order0.0020.0000.002
plsda_predicted_plot0.5200.0050.526
plsda_regcoeff_plot0.3380.0020.341
plsda_roc_plot0.8050.0030.808
plsda_scores_plot0.5330.0030.537
plsda_vip_plot0.3350.0020.337
plsr_cook_dist0.0010.0000.002
plsr_prediction_plot0.0010.0000.001
plsr_qq_plot0.0010.0000.001
plsr_residual_hist0.0000.0000.001
pqn_norm1.0660.0041.072
pqn_norm_hist0.0010.0010.001
prop_na0.0060.0000.006
r_squared0.0010.0000.002
rsd_filter0.0050.0000.006
rsd_filter_hist0.0010.0000.001
run0.0350.0000.035
sb_corr0.0090.0000.010
split_data0.0030.0010.003
stratified_split0.1450.0010.146
svm_plot_2d0.8600.0080.870
tSNE0.0020.0010.002
tSNE_scatter0.0010.0000.002
ttest0.0070.0000.006
vec_norm0.0010.0000.001
wilcox_p_hist0.0000.0000.001
wilcox_test0.0040.0000.005