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This page was generated on 2022-01-19 13:05:40 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for mixOmics on nebbiolo2


To the developers/maintainers of the mixOmics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mixOmics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1178/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.18.1  (landing page)
Al J Abadi
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/mixOmics
git_branch: RELEASE_3_14
git_last_commit: 5ef4960
git_last_commit_date: 2021-11-17 07:39:17 -0500 (Wed, 17 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mixOmics
Version: 6.18.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mixOmics_6.18.1.tar.gz
StartedAt: 2022-01-18 08:23:19 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 08:26:56 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 216.9 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mixOmics_6.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/mixOmics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘6.18.1’
* package encoding: UTF-8
* 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 ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
 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 (user + system) or elapsed time > 5s
                     user system elapsed
biplot             12.997  0.104  13.101
background.predict  6.709  0.340   7.048
circosPlot          5.484  0.008   5.492
block.splsda        5.025  0.008   5.034
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/mixOmics.Rcheck/00check.log’
for details.



Installation output

mixOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘mixOmics’ ...
** using staged installation
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
** 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)

Tests output

mixOmics.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 6.18.1
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


adding block name to feature names in the output similarity matrix as there are similar feature names across blocks.

Performing repeated cross-validation with nrepeat = 3...

  |                                                                            
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  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
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  |======================================================================| 100%
Performing repeated cross-validation with nrepeat = 3...

  |                                                                            
  |                                                                      |   0%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 35.357   1.450  36.509 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0160.0000.016
auroc0.9390.0310.971
background.predict6.7090.3407.048
biplot12.997 0.10413.101
block.pls0.3850.0080.393
block.plsda0.5610.0000.561
block.spls4.3800.0284.408
block.splsda5.0250.0085.034
cim0.0370.0000.037
cimDiablo0.2610.0000.261
circosPlot5.4840.0085.492
colors0.0270.0000.026
explained_variance0.0940.0080.103
get.confusion_matrix0.1570.0000.158
image.tune.rcc1.7640.0001.765
imgCor0.0720.0000.073
impute.nipals0.0110.0000.011
ipca0.6080.0160.624
logratio-transformations0.0480.0040.053
map0.0040.0000.004
mat.rank0.0000.0010.002
mint.block.pls0.1150.0060.120
mint.block.plsda0.0960.0040.100
mint.block.spls0.1340.0000.134
mint.block.splsda0.1180.0000.118
mint.pca0.2980.0000.298
mint.pls0.3930.0000.393
mint.plsda0.4200.0040.423
mint.spls0.3830.0080.390
mint.splsda0.4500.0030.454
mixOmics0.3150.0090.323
nearZeroVar0.6520.0040.657
network0.0100.0000.011
pca3.7220.0043.726
perf2.5500.0282.577
plot.rcc0.0110.0000.012
plot.tune0.0000.0000.001
plotArrow2.8580.0042.863
plotDiablo0.1550.0000.156
plotIndiv0.2300.0000.231
plotLoadings0.0940.0000.095
plotMarkers000
plotVar0.4820.0000.481
pls0.0060.0000.006
plsda0.2870.0000.287
predict0.150.000.15
rcc0.0030.0000.002
selectVar0.3280.0000.328
sipca0.3850.0000.386
spca2.5520.0082.561
spls0.4490.0040.453
splsda0.2860.0000.286
study_split0.0050.0000.005
summary0.0130.0000.013
tune4.0270.0304.071
tune.block.splsda000
tune.mint.splsda2.0080.0042.011
tune.pca0.1670.0080.175
tune.rcc1.7900.0081.798
tune.spca0.5120.0200.532
tune.spls000
tune.splsda3.7050.0223.742
tune.splslevel0.9810.0040.985
unmap0.0040.0000.004
vip0.0080.0000.008
withinVariation0.6760.0000.675
wrapper.rgcca0.0570.0000.057
wrapper.sgcca0.1230.0000.123