Package: mixOmics

Version: 6.8.5

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_6.8.5.tar.gz

StartedAt: 2019-10-16 04:45:04 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:49:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 291.3 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_6.8.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/mixOmics.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘6.8.5’
* 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 11.867  4.486  16.354
tune                9.953  2.146  12.100
tune.splsda         7.888  2.255  10.144
* 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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 6.8.5
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

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 43 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  5.142   0.756   5.855 

name	user	system	elapsed
auroc	0.590	0.051	0.642
background.predict	11.867	4.486	16.354
block.pls	0.754	0.043	0.804
block.plsda	1.582	0.011	1.593
block.spls	0.862	0.024	0.886
block.splsda	0.826	0.021	0.848
cim	0.032	0.008	0.040
cimDiablo	0.267	0.008	0.275
circosPlot	0.442	0.011	0.454
colors	0.039	0.002	0.042
explained_variance	0.230	0.032	0.262
get.confusion_matrix	0.326	0.016	0.342
image.tune.rcc	3.496	0.143	3.640
imgCor	0.080	0.009	0.088
ipca	1.360	0.071	1.431
logratio.transfo	0.311	0.019	0.330
map	0.008	0.004	0.011
mat.rank	0.004	0.000	0.004
mint.block.pls	0.175	0.034	0.209
mint.block.plsda	0.152	0.019	0.172
mint.block.spls	0.149	0.024	0.173
mint.block.splsda	0.115	0.014	0.130
mint.pca	0.940	0.032	0.971
mint.pls	1.060	0.012	1.072
mint.plsda	1.204	0.014	1.224
mint.spls	0.956	0.014	0.971
mint.splsda	1.171	0.012	1.185
mixOmics	0.564	0.066	0.630
nearZeroVar	1.363	0.075	1.438
network	0.024	0.004	0.027
nipals	0.003	0.001	0.005
pca	0.428	0.037	0.464
perf	3.037	0.367	3.404
plot.perf	3.084	0.247	3.332
plot.rcc	0.019	0.004	0.023
plot.tune	0.001	0.001	0.002
plotArrow	0.145	0.011	0.155
plotDiablo	0.231	0.018	0.249
plotIndiv	0.660	0.009	0.669
plotLoadings	0.224	0.033	0.257
plotVar	1.082	0.013	1.094
pls	0.012	0.002	0.014
plsda	0.597	0.025	0.622
predict	0.264	0.024	0.289
print.methods	0.024	0.003	0.026
rcc	0.004	0.002	0.006
selectVar	0.692	0.111	0.803
sipca	0.823	0.020	0.844
spca	1.121	0.059	1.180
spls	0.334	0.022	0.355
splsda	1.166	0.047	1.212
study_split	0.039	0.008	0.047
summary	0.031	0.003	0.033
tune	9.953	2.146	12.100
tune.block.splsda	0.076	0.009	0.086
tune.mint.splsda	4.402	0.408	4.811
tune.pca	0.294	0.065	0.359
tune.rcc	3.527	0.253	3.781
tune.spls	0.082	0.014	0.096
tune.splsda	7.888	2.255	10.144
tune.splslevel	1.903	0.096	1.999
unmap	0.008	0.005	0.012
vip	0.017	0.004	0.020
withinVariation	1.934	0.044	1.979
wrapper.rgcca	0.121	0.002	0.124
wrapper.sgcca	0.265	0.022	0.288