Package: mixOmics

Version: 6.7.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings mixOmics_6.7.1.tar.gz

StartedAt: 2019-03-29 03:19:38 -0400 (Fri, 29 Mar 2019)

EndedAt: 2019-03-29 03:23:46 -0400 (Fri, 29 Mar 2019)

EllapsedTime: 248.0 seconds

RetCode: 0

Status:  OK

CheckDir: mixOmics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings mixOmics_6.7.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/mixOmics.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘6.7.1’
* 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 8.135  0.068   9.647
tune               6.498  0.016   7.396
tune.splsda        6.425  0.008   7.710
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL mixOmics
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘mixOmics’ ...
files ‘R/MCVfold.R’, ‘R/multilevel.R’, ‘R/plotContrib.R’, ‘R/scatterutil.R’, ‘R/tune.multilevel.R’, ‘man/multilevel.Rd’, ‘man/plotContrib.Rd’, ‘man/scatterutil.Rd’, ‘man/tune.multilevel.Rd’ are missing
files ‘DESCRIPTION’, ‘NAMESPACE’, ‘NEWS’, ‘R/LOGOCV.R’, ‘R/bin.color.R’, ‘R/block.pls.R’, ‘R/block.plsda.R’, ‘R/block.spls.R’, ‘R/block.splsda.R’, ‘R/check_entry.R’, ‘R/cim.R’, ‘R/cimDiablo.R’, ‘R/circosPlot.R’, ‘R/color.GreenRed.R’, ‘R/color.jet.R’, ‘R/color.mixo.R’, ‘R/color.spectral.R’, ‘R/explained_variance.R’, ‘R/ica.def.par.R’, ‘R/image.tune.rcc.R’, ‘R/imageMap.R’, ‘R/imgCor.R’, ‘R/internal_graphicModule.R’, ‘R/internal_mint.block.R’, ‘R/internal_mint.block_helpers.R’, ‘R/internal_predict.DA.R’, ‘R/internal_wrapper.mint.R’, ‘R/internal_wrapper.mint.block.R’, ‘R/mat.rank.R’, ‘R/mint.block.pls.R’, ‘R/mint.block.plsda.R’, ‘R/mint.block.spls.R’, ‘R/mint.block.splsda.R’, ‘R/mint.pls.R’, ‘R/mint.plsda.R’, ‘R/mint.spls.R’, ‘R/mint.splsda.R’, ‘R/mixOmics.R’, ‘R/network.R’, ‘R/nipals.R’, ‘R/pca.R’, ‘R/pcasvd.R’, ‘R/perf.R’, ‘R/perf.diablo.R’, ‘R/perf.mint.splsda.R’, ‘R/plot.pca.R’, ‘R/plot.perf.R’, ‘R/plotArrow.R’, ‘R/plotDiablo.R’, ‘R/plotIndiv.R’, ‘R/plotIndiv.mint.R’, ‘R/plotIndiv.pca.R’, ‘R/plotIndiv.pls.R’, ‘R/plotIndiv.sgcca.R’, ‘R/plotLoadings.R’, ‘R/plotLoadings.mint.spls.R’, ‘R/plotLoadings.mint.splsda.R’, ‘R/plotLoadings.spls.R’, ‘R/plotLoadings.splsda.R’, ‘R/plotVar.R’, ‘R/pls.R’, ‘R/plsda.R’, ‘R/predict.mint.block.pls.R’, ‘R/print.methods.R’, ‘R/selectVar.R’, ‘R/sipca.R’, ‘R/spca.R’, ‘R/spls.R’, ‘R/splsda.R’, ‘R/summary.R’, ‘R/tune.R’, ‘R/tune.mint.splsda.R’, ‘R/tune.rcc.R’, ‘R/tune.splsda.R’, ‘R/tune.splslevel.R’, ‘R/vip.R’, ‘R/wrapper.ilr.R’, ‘R/wrapper.rgcca.R’, ‘R/wrapper.sgcca.R’, ‘R/zzz.R’, ‘data/Koren.16S.rda’, ‘data/datalist’, ‘data/diverse.16S.rda’, ‘data/vac18.simulated.rda’, ‘man/Koren.16S.Rd’, ‘man/block.pls.Rd’, ‘man/block.plsda.Rd’, ‘man/block.spls.Rd’, ‘man/block.splsda.Rd’, ‘man/breast.TCGA.Rd’, ‘man/breast.tumors.Rd’, ‘man/cim.Rd’, ‘man/cimDiablo.Rd’, ‘man/circosPlot.Rd’, ‘man/colors.Rd’, ‘man/diverse.16S.Rd’, ‘man/estim.regul.Rd’, ‘man/explained_variance.Rd’, ‘man/image.estim.regul.Rd’, ‘man/image.tune.rcc.Rd’, ‘man/imgCor.Rd’, ‘man/ipca.Rd’, ‘man/linnerud.Rd’, ‘man/liver.toxicity.Rd’, ‘man/logratio.transfo.Rd’, ‘man/map.Rd’, ‘man/mat.rank.Rd’, ‘man/mint.block.pls.Rd’, ‘man/mint.block.plsda.Rd’, ‘man/mint.block.spls.Rd’, ‘man/mint.block.splsda.Rd’, ‘man/mint.pls.Rd’, ‘man/mint.plsda.Rd’, ‘man/mint.spls.Rd’, ‘man/mint.splsda.Rd’, ‘man/mixOmics.Rd’, ‘man/multidrug.Rd’, ‘man/nearZeroVar.Rd’, ‘man/network.Rd’, ‘man/nipals.Rd’, ‘man/nutrimouse.Rd’, ‘man/pca.Rd’, ‘man/pcatune.Rd’, ‘man/perf.Rd’, ‘man/plot.perf.Rd’, ‘man/plot.rcc.Rd’, ‘man/plotArrow.Rd’, ‘man/plotDiablo.Rd’, ‘man/plotIndiv.Rd’, ‘man/plotLoadings.Rd’, ‘man/plotVar.Rd’, ‘man/pls.Rd’, ‘man/plsda.Rd’, ‘man/predict.Rd’, ‘man/print.methods.Rd’, ‘man/rcc.Rd’, ‘man/selectVar.Rd’, ‘man/sipca.Rd’, ‘man/spca.Rd’, ‘man/spls.Rd’, ‘man/splsda.Rd’, ‘man/srbct.Rd’, ‘man/stemcells.Rd’, ‘man/study_split.Rd’, ‘man/summary.Rd’, ‘man/tune.Rd’, ‘man/tune.mint.splsda.Rd’, ‘man/tune.pca.Rd’, ‘man/tune.rcc.Rd’, ‘man/tune.splsda.Rd’, ‘man/unmap.Rd’, ‘man/vac18.Rd’, ‘man/vac18.simulated.Rd’, ‘man/vip.Rd’, ‘man/withinVariation.Rd’, ‘man/wrapper.rgcca.Rd’, ‘man/wrapper.sgcca.Rd’, ‘man/yeast.Rd’ have the wrong MD5 checksums
** 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 6.7.1

Thank you for using mixOmics! Learn how to apply our methods with our tutorials on www.mixOmics.org, vignette and bookdown on  https://github.com/mixOmicsTeam/mixOmics
Questions: email us at mixomics[at]math.univ-toulouse.fr  
Bugs, Issues? https://github.com/mixOmicsTeam/mixOmics/issues
Cite us:  citation('mixOmics')
> 
> test_check("mixOmics")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 41 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  2.981   0.129   4.214 

name	user	system	elapsed
auroc	0.482	0.004	0.526
background.predict	8.135	0.068	9.647
block.pls	0.663	0.015	0.975
block.plsda	1.199	0.000	1.711
block.spls	0.873	0.007	0.966
block.splsda	0.704	0.000	0.704
cim	0.036	0.000	0.035
cimDiablo	0.220	0.000	0.228
circosPlot	0.284	0.008	0.296
colors	0.030	0.000	0.031
explained_variance	0.173	0.008	0.180
get.confusion_matrix	0.264	0.008	0.299
image.tune.rcc	3.050	0.016	3.300
imgCor	0.111	0.008	0.119
ipca	1.126	0.000	1.315
logratio.transfo	0.089	0.000	0.090
map	0.006	0.000	0.006
mat.rank	0.002	0.000	0.002
mint.block.pls	0.157	0.001	0.159
mint.block.plsda	0.131	0.006	0.136
mint.block.spls	0.174	0.011	0.187
mint.block.splsda	0.159	0.000	0.159
mint.pca	0.672	0.000	0.684
mint.pls	0.731	0.008	0.753
mint.plsda	0.940	0.000	0.941
mint.spls	0.844	0.008	0.932
mint.splsda	0.941	0.003	1.149
mixOmics	0.678	0.008	0.774
nearZeroVar	1.145	0.001	1.333
network	0.012	0.004	0.016
nipals	0.002	0.000	0.002
pca	0.157	0.007	0.166
perf	2.507	0.005	2.790
plot.perf	2.421	0.004	2.729
plot.rcc	0.020	0.000	0.021
plot.tune	0	0	0
plotArrow	0.101	0.000	0.154
plotDiablo	0.157	0.004	0.217
plotIndiv	0.417	0.007	0.567
plotLoadings	0.170	0.004	0.286
plotVar	0.780	0.008	0.999
pls	0.008	0.000	0.008
plsda	0.483	0.000	0.510
predict	0.262	0.004	0.306
print.methods	0.019	0.000	0.020
rcc	0.005	0.000	0.004
selectVar	0.528	0.004	0.538
sipca	0.641	0.008	0.695
spca	0.995	0.004	1.014
spls	0.278	0.004	0.281
splsda	0.803	0.004	0.861
study_split	0.043	0.000	0.044
summary	0.023	0.000	0.023
tune	6.498	0.016	7.396
tune.block.splsda	0.081	0.004	0.085
tune.mint.splsda	3.306	0.004	3.903
tune.pca	0.262	0.000	0.364
tune.rcc	2.941	0.020	3.400
tune.spls	0.074	0.000	0.075
tune.splsda	6.425	0.008	7.710
tune.splslevel	1.117	0.008	1.407
unmap	0.007	0.000	0.008
vip	0.012	0.000	0.014
withinVariation	1.289	0.004	1.412
wrapper.rgcca	0.11	0.00	0.11
wrapper.sgcca	0.156	0.000	0.161