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CHECK report for mixOmics on malbec1

This page was generated on 2019-04-16 11:53:54 -0400 (Tue, 16 Apr 2019).

Package 980/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.6.2
Kim-Anh Le Cao
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/mixOmics
Branch: RELEASE_3_8
Last Commit: 240e862
Last Changed Date: 2019-02-28 18:45:38 -0400 (Thu, 28 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mixOmics
Version: 6.6.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mixOmics_6.6.2.tar.gz
StartedAt: 2019-04-16 01:31:09 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:34:04 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 174.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mixOmics_6.6.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/mixOmics.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘6.6.2’
* 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 5.976  0.044   6.029
tune.splsda        5.188  0.008   5.204
* 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

mixOmics.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL mixOmics
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* installing to library ‘/home/biocbuild/bbs-3.8-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
** 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
* DONE (mixOmics)

Tests output

mixOmics.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 6.6.2

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 
  2.944   0.100   3.039 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
auroc0.5400.0000.563
background.predict5.9760.0446.029
block.pls0.7280.0200.783
block.plsda0.9440.0000.956
block.spls0.7880.0040.794
block.splsda0.7640.0000.766
cim0.0400.0040.043
cimDiablo0.2360.0000.235
circosPlot0.2760.0000.275
colors0.0920.0040.097
explained_variance0.1880.0040.209
get.confusion_matrix0.2800.0000.283
image.tune.rcc2.3680.0002.370
imgCor0.0760.0000.078
ipca0.8840.0120.895
logratio.transfo0.0560.0120.085
map0.0040.0000.005
mat.rank0.0000.0000.002
mint.block.pls0.1280.0040.130
mint.block.plsda0.1040.0000.104
mint.block.spls0.1360.0040.139
mint.block.splsda0.1200.0000.123
mint.pca0.6720.0000.689
mint.pls0.5680.0040.572
mint.plsda0.7400.0000.742
mint.spls0.9040.0000.905
mint.splsda0.8960.0000.901
mixOmics0.3200.0000.321
nearZeroVar0.8400.0080.850
network0.0080.0040.012
nipals0.0000.0000.002
pca0.1480.0000.167
perf3.4520.0123.465
plot.perf3.7640.0083.776
plot.rcc0.0160.0000.013
plot.tune000
plotArrow0.0680.0080.077
plotDiablo0.1360.0000.134
plotIndiv0.4360.0000.439
plotLoadings0.2000.0040.204
plotVar0.9440.0000.945
pls0.0080.0000.027
plsda0.4880.0040.496
predict0.1760.0000.173
print.methods0.0080.0040.013
rcc0.0040.0000.003
selectVar0.4040.0000.405
sipca0.4880.0040.490
spca0.8640.0000.867
spls0.4360.0000.439
splsda0.4040.0000.401
study_split0.0320.0040.035
summary0.0120.0040.016
tune4.4480.0044.458
tune.block.splsda0.0920.0000.093
tune.mint.splsda3.2640.0083.288
tune.pca0.1760.0000.175
tune.rcc2.4840.0002.487
tune.spls0.0840.0000.082
tune.splsda5.1880.0085.204
tune.splslevel0.7640.0160.779
unmap0.0040.0000.005
vip0.0080.0000.008
withinVariation1.1240.0041.149
wrapper.rgcca0.1120.0000.113
wrapper.sgcca0.1360.0000.138