Kim-Anh Le Cao
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/mixOmics |
| Branch: RELEASE_3_9 |
| Last Commit: 008e8ec |
| Last Changed Date: 2019-10-01 21:51:38 -0400 (Tue, 01 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:16:48 -0400 (Wed, 16 Oct 2019).
| Package 1023/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mixOmics 6.8.5 Kim-Anh Le Cao
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: mixOmics |
| Version: 6.8.5 |
| 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_6.8.5.tar.gz |
| StartedAt: 2019-10-16 03:16:07 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:19:25 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 198.6 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_6.8.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/mixOmics.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘6.8.5’
* 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 7.411 0.004 7.422
tune 6.559 0.003 6.564
tune.splsda 6.107 0.000 6.110
* 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-3.9-bioc/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
mixOmics.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 6.8.5
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: 43 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
3.167 0.119 3.268
mixOmics.Rcheck/mixOmics-Ex.timings
| name | user | system | elapsed | |
| auroc | 0.542 | 0.004 | 0.546 | |
| background.predict | 7.411 | 0.004 | 7.422 | |
| block.pls | 0.707 | 0.007 | 0.715 | |
| block.plsda | 1.314 | 0.000 | 1.315 | |
| block.spls | 0.578 | 0.000 | 0.579 | |
| block.splsda | 0.460 | 0.008 | 0.468 | |
| cim | 0.025 | 0.000 | 0.025 | |
| cimDiablo | 0.127 | 0.004 | 0.131 | |
| circosPlot | 0.272 | 0.008 | 0.425 | |
| colors | 0.046 | 0.000 | 0.046 | |
| explained_variance | 0.180 | 0.012 | 0.192 | |
| get.confusion_matrix | 0.263 | 0.000 | 0.263 | |
| image.tune.rcc | 3.210 | 0.009 | 3.219 | |
| imgCor | 0.129 | 0.000 | 0.129 | |
| ipca | 1.204 | 0.004 | 1.209 | |
| logratio.transfo | 0.059 | 0.000 | 0.059 | |
| map | 0.005 | 0.000 | 0.005 | |
| mat.rank | 0.002 | 0.000 | 0.001 | |
| mint.block.pls | 0.116 | 0.003 | 0.120 | |
| mint.block.plsda | 0.106 | 0.000 | 0.107 | |
| mint.block.spls | 0.130 | 0.003 | 0.135 | |
| mint.block.splsda | 0.117 | 0.008 | 0.126 | |
| mint.pca | 0.455 | 0.003 | 0.460 | |
| mint.pls | 0.513 | 0.000 | 0.513 | |
| mint.plsda | 0.618 | 0.000 | 0.617 | |
| mint.spls | 0.551 | 0.000 | 0.552 | |
| mint.splsda | 0.642 | 0.000 | 0.643 | |
| mixOmics | 0.527 | 0.007 | 0.535 | |
| nearZeroVar | 1.215 | 0.012 | 1.227 | |
| network | 0.020 | 0.000 | 0.019 | |
| nipals | 0.002 | 0.001 | 0.001 | |
| pca | 0.112 | 0.003 | 0.116 | |
| perf | 1.797 | 0.000 | 1.797 | |
| plot.perf | 1.680 | 0.000 | 1.679 | |
| plot.rcc | 0.017 | 0.005 | 0.021 | |
| plot.tune | 0.000 | 0.000 | 0.001 | |
| plotArrow | 0.1 | 0.0 | 0.1 | |
| plotDiablo | 0.186 | 0.003 | 0.191 | |
| plotIndiv | 0.485 | 0.001 | 0.486 | |
| plotLoadings | 0.195 | 0.003 | 0.199 | |
| plotVar | 0.66 | 0.00 | 0.66 | |
| pls | 0.009 | 0.000 | 0.010 | |
| plsda | 0.671 | 0.000 | 0.672 | |
| predict | 0.295 | 0.004 | 0.298 | |
| print.methods | 0.019 | 0.000 | 0.020 | |
| rcc | 0.004 | 0.000 | 0.004 | |
| selectVar | 0.614 | 0.000 | 0.615 | |
| sipca | 1.084 | 0.000 | 1.083 | |
| spca | 1.122 | 0.004 | 1.126 | |
| spls | 0.35 | 0.00 | 0.35 | |
| splsda | 0.886 | 0.000 | 0.887 | |
| study_split | 0.043 | 0.000 | 0.043 | |
| summary | 0.023 | 0.000 | 0.023 | |
| tune | 6.559 | 0.003 | 6.564 | |
| tune.block.splsda | 0.068 | 0.000 | 0.068 | |
| tune.mint.splsda | 3.028 | 0.000 | 3.029 | |
| tune.pca | 0.162 | 0.008 | 0.170 | |
| tune.rcc | 2.15 | 0.00 | 2.15 | |
| tune.spls | 0.082 | 0.000 | 0.081 | |
| tune.splsda | 6.107 | 0.000 | 6.110 | |
| tune.splslevel | 0.986 | 0.008 | 0.994 | |
| unmap | 0.007 | 0.000 | 0.008 | |
| vip | 0.013 | 0.000 | 0.012 | |
| withinVariation | 1.084 | 0.000 | 1.084 | |
| wrapper.rgcca | 0.077 | 0.004 | 0.082 | |
| wrapper.sgcca | 0.131 | 0.000 | 0.130 | |