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 11:53:54 -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: /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 |
##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################
* 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
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * 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)
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
mixOmics.Rcheck/mixOmics-Ex.timings
| name | user | system | elapsed | |
| auroc | 0.540 | 0.000 | 0.563 | |
| background.predict | 5.976 | 0.044 | 6.029 | |
| block.pls | 0.728 | 0.020 | 0.783 | |
| block.plsda | 0.944 | 0.000 | 0.956 | |
| block.spls | 0.788 | 0.004 | 0.794 | |
| block.splsda | 0.764 | 0.000 | 0.766 | |
| cim | 0.040 | 0.004 | 0.043 | |
| cimDiablo | 0.236 | 0.000 | 0.235 | |
| circosPlot | 0.276 | 0.000 | 0.275 | |
| colors | 0.092 | 0.004 | 0.097 | |
| explained_variance | 0.188 | 0.004 | 0.209 | |
| get.confusion_matrix | 0.280 | 0.000 | 0.283 | |
| image.tune.rcc | 2.368 | 0.000 | 2.370 | |
| imgCor | 0.076 | 0.000 | 0.078 | |
| ipca | 0.884 | 0.012 | 0.895 | |
| logratio.transfo | 0.056 | 0.012 | 0.085 | |
| map | 0.004 | 0.000 | 0.005 | |
| mat.rank | 0.000 | 0.000 | 0.002 | |
| mint.block.pls | 0.128 | 0.004 | 0.130 | |
| mint.block.plsda | 0.104 | 0.000 | 0.104 | |
| mint.block.spls | 0.136 | 0.004 | 0.139 | |
| mint.block.splsda | 0.120 | 0.000 | 0.123 | |
| mint.pca | 0.672 | 0.000 | 0.689 | |
| mint.pls | 0.568 | 0.004 | 0.572 | |
| mint.plsda | 0.740 | 0.000 | 0.742 | |
| mint.spls | 0.904 | 0.000 | 0.905 | |
| mint.splsda | 0.896 | 0.000 | 0.901 | |
| mixOmics | 0.320 | 0.000 | 0.321 | |
| nearZeroVar | 0.840 | 0.008 | 0.850 | |
| network | 0.008 | 0.004 | 0.012 | |
| nipals | 0.000 | 0.000 | 0.002 | |
| pca | 0.148 | 0.000 | 0.167 | |
| perf | 3.452 | 0.012 | 3.465 | |
| plot.perf | 3.764 | 0.008 | 3.776 | |
| plot.rcc | 0.016 | 0.000 | 0.013 | |
| plot.tune | 0 | 0 | 0 | |
| plotArrow | 0.068 | 0.008 | 0.077 | |
| plotDiablo | 0.136 | 0.000 | 0.134 | |
| plotIndiv | 0.436 | 0.000 | 0.439 | |
| plotLoadings | 0.200 | 0.004 | 0.204 | |
| plotVar | 0.944 | 0.000 | 0.945 | |
| pls | 0.008 | 0.000 | 0.027 | |
| plsda | 0.488 | 0.004 | 0.496 | |
| predict | 0.176 | 0.000 | 0.173 | |
| print.methods | 0.008 | 0.004 | 0.013 | |
| rcc | 0.004 | 0.000 | 0.003 | |
| selectVar | 0.404 | 0.000 | 0.405 | |
| sipca | 0.488 | 0.004 | 0.490 | |
| spca | 0.864 | 0.000 | 0.867 | |
| spls | 0.436 | 0.000 | 0.439 | |
| splsda | 0.404 | 0.000 | 0.401 | |
| study_split | 0.032 | 0.004 | 0.035 | |
| summary | 0.012 | 0.004 | 0.016 | |
| tune | 4.448 | 0.004 | 4.458 | |
| tune.block.splsda | 0.092 | 0.000 | 0.093 | |
| tune.mint.splsda | 3.264 | 0.008 | 3.288 | |
| tune.pca | 0.176 | 0.000 | 0.175 | |
| tune.rcc | 2.484 | 0.000 | 2.487 | |
| tune.spls | 0.084 | 0.000 | 0.082 | |
| tune.splsda | 5.188 | 0.008 | 5.204 | |
| tune.splslevel | 0.764 | 0.016 | 0.779 | |
| unmap | 0.004 | 0.000 | 0.005 | |
| vip | 0.008 | 0.000 | 0.008 | |
| withinVariation | 1.124 | 0.004 | 1.149 | |
| wrapper.rgcca | 0.112 | 0.000 | 0.113 | |
| wrapper.sgcca | 0.136 | 0.000 | 0.138 | |