Multiple platform build/check report for BioC 3.11 - CHECK report for mixOmics on celaya2

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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_6.11.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/mixOmics.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘6.11.6’
* 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 (user + system) or elapsed time > 5s
                     user system elapsed
background.predict 11.926  4.701  16.693
tune.splsda         8.077  2.050  10.133
tune                7.927  2.059   9.989
tune.mint.splsda    4.882  0.376   5.274
* 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

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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/4.0/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)

Tests output


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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 6.11.6
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: 87 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
115.709  11.769 120.004

Example timings

name	user	system	elapsed
auroc	0.733	0.056	0.789
background.predict	11.926	4.701	16.693
block.pls	0.835	0.042	0.876
block.plsda	1.581	0.013	1.607
block.spls	0.796	0.022	0.820
block.splsda	0.951	0.025	0.978
cim	0.042	0.007	0.049
cimDiablo	0.238	0.009	0.247
circosPlot	0.391	0.009	0.402
colors	0.046	0.003	0.050
explained_variance	0.219	0.030	0.248
get.confusion_matrix	0.413	0.025	0.438
image.tune.rcc	3.364	0.224	3.591
imgCor	0.103	0.011	0.116
ipca	1.609	0.073	1.686
logratio.transfo	0.106	0.027	0.134
map	0.008	0.004	0.011
mat.rank	0.003	0.001	0.004
mint.block.pls	0.195	0.032	0.228
mint.block.plsda	0.425	0.035	0.482
mint.block.spls	0.208	0.025	0.233
mint.block.splsda	0.180	0.020	0.199
mint.pca	0.985	0.032	1.032
mint.pls	1.074	0.024	1.113
mint.plsda	1.270	0.025	1.302
mint.spls	1.082	0.023	1.158
mint.splsda	1.358	0.025	1.457
mixOmics	0.568	0.067	0.636
nearZeroVar	1.317	0.116	1.435
network	0.023	0.003	0.029
nipals	0.005	0.002	0.008
pca	0.217	0.026	0.272
perf	3.576	0.392	4.020
plot.perf	2.790	0.234	3.028
plot.rcc	0.019	0.004	0.023
plot.tune	0.001	0.001	0.001
plotArrow	0.126	0.008	0.135
plotDiablo	0.212	0.021	0.233
plotIndiv	0.666	0.024	0.692
plotLoadings	0.233	0.032	0.266
plotVar	1.158	0.015	1.178
pls	0.014	0.002	0.017
plsda	0.648	0.026	0.675
predict	0.342	0.029	0.373
print.methods	0.024	0.004	0.028
rcc	0.006	0.002	0.010
selectVar	0.845	0.116	0.959
sipca	0.980	0.061	1.042
spca	1.308	0.114	1.422
spls	0.391	0.021	0.412
splsda	0.823	0.034	0.858
study_split	0.040	0.009	0.053
summary	0.028	0.003	0.032
tune	7.927	2.059	9.989
tune.block.splsda	0.068	0.009	0.077
tune.mint.splsda	4.882	0.376	5.274
tune.pca	0.379	0.056	0.435
tune.rcc	3.382	0.223	3.607
tune.spls	0.085	0.012	0.097
tune.splsda	8.077	2.050	10.133
tune.splslevel	1.493	0.098	1.592
unmap	0.009	0.005	0.014
vip	0.019	0.003	0.022
withinVariation	1.706	0.026	1.735
wrapper.rgcca	0.145	0.003	0.148
wrapper.sgcca	0.332	0.013	0.345

CHECK report for mixOmics on celaya2

Summary

Command output

Installation output

Tests output

Example timings