Kim-Anh Le Cao
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/mixOmics |
| Branch: RELEASE_3_10 |
| Last Commit: b399f33 |
| Last Changed Date: 2020-03-29 18:28:20 -0400 (Sun, 29 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:14:56 -0400 (Wed, 15 Apr 2020).
| Package 1066/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mixOmics 6.10.9 Kim-Anh Le Cao
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: mixOmics |
| Version: 6.10.9 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings mixOmics_6.10.9.tar.gz |
| StartedAt: 2020-04-15 06:07:47 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:12:26 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 279.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mixOmics.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings mixOmics_6.10.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/mixOmics.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘6.10.9’
* 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 6.624 0.040 6.684
tune.splsda 5.996 0.056 6.114
tune 5.800 0.100 5.923
* 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-3.10-bioc/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 6.10.9
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
Performing repeated cross-validation...
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Performing repeated cross-validation...
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| | 0%══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 88 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
82.848 2.372 85.437
mixOmics.Rcheck/mixOmics-Ex.timings
| name | user | system | elapsed | |
| auroc | 0.572 | 0.020 | 0.593 | |
| background.predict | 6.624 | 0.040 | 6.684 | |
| block.pls | 0.664 | 0.000 | 0.666 | |
| block.plsda | 1.168 | 0.000 | 1.168 | |
| block.spls | 0.728 | 0.004 | 0.730 | |
| block.splsda | 0.596 | 0.004 | 0.599 | |
| cim | 0.028 | 0.000 | 0.030 | |
| cimDiablo | 0.152 | 0.000 | 0.153 | |
| circosPlot | 0.448 | 0.000 | 0.449 | |
| colors | 0.036 | 0.000 | 0.038 | |
| explained_variance | 0.184 | 0.004 | 0.185 | |
| get.confusion_matrix | 0.472 | 0.004 | 0.478 | |
| image.tune.rcc | 2.896 | 0.004 | 2.939 | |
| imgCor | 0.128 | 0.000 | 0.128 | |
| ipca | 1.296 | 0.000 | 1.297 | |
| logratio.transfo | 0.096 | 0.004 | 0.099 | |
| map | 0.000 | 0.004 | 0.006 | |
| mat.rank | 0.000 | 0.000 | 0.003 | |
| mint.block.pls | 0.168 | 0.004 | 0.171 | |
| mint.block.plsda | 0.144 | 0.000 | 0.145 | |
| mint.block.spls | 0.188 | 0.004 | 0.195 | |
| mint.block.splsda | 0.156 | 0.004 | 0.159 | |
| mint.pca | 0.688 | 0.004 | 0.692 | |
| mint.pls | 0.928 | 0.004 | 0.934 | |
| mint.plsda | 1.088 | 0.000 | 1.089 | |
| mint.spls | 0.900 | 0.000 | 0.905 | |
| mint.splsda | 1.100 | 0.000 | 1.112 | |
| mixOmics | 0.464 | 0.004 | 0.469 | |
| nearZeroVar | 1.284 | 0.004 | 1.289 | |
| network | 0.020 | 0.000 | 0.019 | |
| nipals | 0.004 | 0.000 | 0.003 | |
| pca | 0.452 | 0.000 | 0.452 | |
| perf | 1.924 | 0.020 | 1.945 | |
| plot.perf | 1.636 | 0.012 | 1.651 | |
| plot.rcc | 0.02 | 0.00 | 0.02 | |
| plot.tune | 0.000 | 0.000 | 0.001 | |
| plotArrow | 0.084 | 0.008 | 0.096 | |
| plotDiablo | 0.192 | 0.000 | 0.193 | |
| plotIndiv | 0.460 | 0.004 | 0.463 | |
| plotLoadings | 0.164 | 0.004 | 0.170 | |
| plotVar | 0.520 | 0.004 | 0.528 | |
| pls | 0.008 | 0.000 | 0.009 | |
| plsda | 0.592 | 0.000 | 0.594 | |
| predict | 0.284 | 0.000 | 0.288 | |
| print.methods | 0.020 | 0.000 | 0.019 | |
| rcc | 0.000 | 0.004 | 0.004 | |
| selectVar | 0.616 | 0.008 | 0.625 | |
| sipca | 0.488 | 0.000 | 0.487 | |
| spca | 1.056 | 0.000 | 1.060 | |
| spls | 0.576 | 0.000 | 0.590 | |
| splsda | 0.592 | 0.000 | 0.596 | |
| study_split | 0.044 | 0.004 | 0.045 | |
| summary | 0.024 | 0.000 | 0.023 | |
| tune | 5.800 | 0.100 | 5.923 | |
| tune.block.splsda | 0.088 | 0.000 | 0.089 | |
| tune.mint.splsda | 3.308 | 0.004 | 3.325 | |
| tune.pca | 0.264 | 0.004 | 0.267 | |
| tune.rcc | 2.152 | 0.000 | 2.153 | |
| tune.spls | 0.044 | 0.004 | 0.048 | |
| tune.splsda | 5.996 | 0.056 | 6.114 | |
| tune.splslevel | 1.216 | 0.020 | 1.239 | |
| unmap | 0.004 | 0.000 | 0.005 | |
| vip | 0.008 | 0.000 | 0.008 | |
| withinVariation | 1.368 | 0.000 | 1.369 | |
| wrapper.rgcca | 0.108 | 0.004 | 0.111 | |
| wrapper.sgcca | 0.200 | 0.008 | 0.206 | |