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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:14:00 -0400 (Tue, 16 Apr 2019).
| Package 980/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mixOmics 6.6.2 Kim-Anh Le Cao
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: mixOmics |
| Version: 6.6.2 |
| 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_6.6.2.tar.gz |
| StartedAt: 2019-04-16 01:21:48 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:25:18 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 209.5 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_6.6.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/mixOmics.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘6.6.2’
* 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 8.540 2.330 11.005
tune.splsda 5.563 1.051 6.682
tune 5.451 1.064 6.571
* 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
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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)
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-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 6.6.2
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
3.200 0.254 3.450
mixOmics.Rcheck/mixOmics-Ex.timings
| name | user | system | elapsed | |
| auroc | 0.387 | 0.022 | 0.413 | |
| background.predict | 8.540 | 2.330 | 11.005 | |
| block.pls | 0.653 | 0.014 | 0.676 | |
| block.plsda | 1.141 | 0.005 | 1.165 | |
| block.spls | 0.797 | 0.015 | 0.817 | |
| block.splsda | 0.701 | 0.010 | 0.719 | |
| cim | 0.035 | 0.004 | 0.039 | |
| cimDiablo | 0.209 | 0.004 | 0.215 | |
| circosPlot | 0.256 | 0.005 | 0.264 | |
| colors | 0.073 | 0.001 | 0.075 | |
| explained_variance | 0.158 | 0.011 | 0.171 | |
| get.confusion_matrix | 0.238 | 0.009 | 0.249 | |
| image.tune.rcc | 2.922 | 0.043 | 2.995 | |
| imgCor | 0.086 | 0.005 | 0.093 | |
| ipca | 1.254 | 0.025 | 1.286 | |
| logratio.transfo | 0.080 | 0.013 | 0.093 | |
| map | 0.004 | 0.002 | 0.006 | |
| mat.rank | 0.004 | 0.000 | 0.004 | |
| mint.block.pls | 0.143 | 0.017 | 0.161 | |
| mint.block.plsda | 0.131 | 0.009 | 0.141 | |
| mint.block.spls | 0.147 | 0.014 | 0.163 | |
| mint.block.splsda | 0.124 | 0.007 | 0.131 | |
| mint.pca | 0.623 | 0.010 | 0.641 | |
| mint.pls | 0.963 | 0.010 | 0.982 | |
| mint.plsda | 0.822 | 0.006 | 0.833 | |
| mint.spls | 0.709 | 0.006 | 0.724 | |
| mint.splsda | 0.911 | 0.007 | 0.930 | |
| mixOmics | 0.401 | 0.019 | 0.424 | |
| nearZeroVar | 1.036 | 0.025 | 1.075 | |
| network | 0.022 | 0.001 | 0.024 | |
| nipals | 0.004 | 0.000 | 0.005 | |
| pca | 0.181 | 0.012 | 0.194 | |
| perf | 3.566 | 0.190 | 3.789 | |
| plot.perf | 3.868 | 0.110 | 4.009 | |
| plot.rcc | 0.023 | 0.002 | 0.025 | |
| plot.tune | 0.000 | 0.001 | 0.001 | |
| plotArrow | 0.120 | 0.004 | 0.131 | |
| plotDiablo | 0.148 | 0.008 | 0.158 | |
| plotIndiv | 0.427 | 0.007 | 0.439 | |
| plotLoadings | 0.155 | 0.013 | 0.170 | |
| plotVar | 0.776 | 0.004 | 0.786 | |
| pls | 0.010 | 0.001 | 0.011 | |
| plsda | 0.506 | 0.015 | 0.529 | |
| predict | 0.229 | 0.010 | 0.241 | |
| print.methods | 0.015 | 0.001 | 0.016 | |
| rcc | 0.005 | 0.001 | 0.006 | |
| selectVar | 0.521 | 0.035 | 0.556 | |
| sipca | 0.704 | 0.014 | 0.721 | |
| spca | 1.008 | 0.033 | 1.053 | |
| spls | 0.533 | 0.015 | 0.557 | |
| splsda | 0.607 | 0.022 | 0.632 | |
| study_split | 0.037 | 0.005 | 0.042 | |
| summary | 0.022 | 0.001 | 0.023 | |
| tune | 5.451 | 1.064 | 6.571 | |
| tune.block.splsda | 0.061 | 0.003 | 0.064 | |
| tune.mint.splsda | 3.457 | 0.156 | 3.652 | |
| tune.pca | 0.262 | 0.029 | 0.291 | |
| tune.rcc | 2.811 | 0.045 | 2.906 | |
| tune.spls | 0.072 | 0.008 | 0.081 | |
| tune.splsda | 5.563 | 1.051 | 6.682 | |
| tune.splslevel | 1.321 | 0.037 | 1.375 | |
| unmap | 0.007 | 0.003 | 0.010 | |
| vip | 0.015 | 0.001 | 0.017 | |
| withinVariation | 1.346 | 0.016 | 1.388 | |
| wrapper.rgcca | 0.121 | 0.002 | 0.126 | |
| wrapper.sgcca | 0.233 | 0.003 | 0.238 | |