Package: mixOmics

Version: 6.10.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mixOmics_6.10.9.tar.gz

StartedAt: 2020-04-15 03:58:35 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:03:56 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 321.1 seconds

RetCode: 0

Status:  OK

CheckDir: mixOmics.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mixOmics_6.10.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/mixOmics.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mixOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mixOmics’ version ‘6.10.9’
* 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 ‘mixOmics’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
background.predict 9.130  2.390  11.653
tune.splsda        7.999  1.065   9.130
tune               7.798  1.054   8.944
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mixOmics
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘mixOmics’ ...
** using staged installation
** R
** data
** inst
** 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 (mixOmics)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(mixOmics)
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2

Loaded mixOmics 6.10.9
Thank you for using mixOmics!
Tutorials: http://mixomics.org
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at http://mixomics.org/contact-us
Cite us:  citation('mixOmics')

> 
> test_check("mixOmics")
$Comp1
           AUC   p-value
AF vs BE 0.863 2.473e-05

$Comp2
            AUC   p-value
AF vs BE 0.9981 7.124e-09


Performing repeated cross-validation...

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Performing repeated cross-validation...

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  |                                                                      |   0%══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 88 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 86.962   5.414  88.212 

name	user	system	elapsed
auroc	0.707	0.024	0.736
background.predict	9.130	2.390	11.653
block.pls	0.682	0.017	0.708
block.plsda	1.231	0.009	1.255
block.spls	0.729	0.011	0.746
block.splsda	0.751	0.011	0.770
cim	0.031	0.004	0.040
cimDiablo	0.231	0.004	0.238
circosPlot	0.468	0.007	0.491
colors	0.039	0.001	0.043
explained_variance	0.174	0.013	0.205
get.confusion_matrix	0.310	0.010	0.326
image.tune.rcc	3.218	0.040	3.306
imgCor	0.107	0.006	0.114
ipca	1.183	0.038	1.238
logratio.transfo	0.080	0.012	0.094
map	0.004	0.001	0.006
mat.rank	0.001	0.000	0.002
mint.block.pls	0.154	0.013	0.171
mint.block.plsda	0.114	0.013	0.128
mint.block.spls	0.152	0.016	0.169
mint.block.splsda	0.348	0.010	0.360
mint.pca	0.657	0.012	0.672
mint.pls	1.002	0.010	1.019
mint.plsda	1.019	0.014	1.042
mint.spls	0.831	0.010	0.852
mint.splsda	0.970	0.010	0.999
mixOmics	0.405	0.029	0.438
nearZeroVar	1.196	0.038	1.244
network	0.031	0.004	0.035
nipals	0.004	0.001	0.004
pca	0.179	0.016	0.196
perf	2.582	0.162	2.763
plot.perf	2.769	0.104	2.907
plot.rcc	0.016	0.002	0.017
plot.tune	0.001	0.001	0.001
plotArrow	0.091	0.004	0.096
plotDiablo	0.153	0.009	0.163
plotIndiv	0.492	0.007	0.505
plotLoadings	0.177	0.014	0.196
plotVar	0.800	0.005	0.816
pls	0.007	0.001	0.008
plsda	0.545	0.016	0.572
predict	0.264	0.013	0.280
print.methods	0.021	0.002	0.024
rcc	0.004	0.002	0.006
selectVar	0.550	0.026	0.583
sipca	0.659	0.013	0.678
spca	1.268	0.037	1.311
spls	0.279	0.012	0.291
splsda	0.794	0.032	0.829
study_split	0.038	0.005	0.043
summary	0.027	0.002	0.029
tune	7.798	1.054	8.944
tune.block.splsda	0.071	0.004	0.075
tune.mint.splsda	3.789	0.139	3.961
tune.pca	0.318	0.030	0.356
tune.rcc	2.952	0.037	3.030
tune.spls	0.080	0.006	0.089
tune.splsda	7.999	1.065	9.130
tune.splslevel	1.345	0.034	1.389
unmap	0.006	0.002	0.009
vip	0.015	0.001	0.017
withinVariation	1.287	0.018	1.317
wrapper.rgcca	0.104	0.002	0.106
wrapper.sgcca	0.223	0.004	0.227