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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).

CHECK results for mixOmics on nebbiolo1

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 1161/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.16.3  (landing page)
Al J Abadi
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/mixOmics
git_branch: RELEASE_3_13
git_last_commit: 759d581
git_last_commit_date: 2021-07-27 22:15:58 -0400 (Tue, 27 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 6.16.3
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings mixOmics_6.16.3.tar.gz
StartedAt: 2021-10-14 10:38:59 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:42:29 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 210.1 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings mixOmics_6.16.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/mixOmics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘6.16.3’
* 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  5.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.4Mb
* checking package directory ... OK
* checking ‘build’ 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             13.195  0.268  13.465
background.predict  5.855  0.067   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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/mixOmics.Rcheck/00check.log’
for details.



Installation output

mixOmics.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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 6.16.3
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 with nrepeat = 3...

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

  |                                                                            
  |                                                                      |   0%[ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ]
> 
> proc.time()
   user  system elapsed 
 42.684   2.349  42.882 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0170.0010.017
auroc0.5250.0000.526
background.predict5.8550.0675.923
biplot13.195 0.26813.465
block.pls0.4080.0360.444
block.plsda0.6110.0080.619
block.spls0.4060.0080.415
block.splsda0.7550.0760.831
cim0.0230.0040.027
cimDiablo0.1030.0040.107
circosPlot0.8080.0040.812
colors0.020.000.02
explained_variance0.0820.0160.097
get.confusion_matrix0.1340.0000.133
image.tune.rcc1.6000.0161.616
imgCor0.0690.0030.072
impute.nipals0.0130.0000.014
ipca0.6400.0040.644
logratio-transformations0.0490.0040.053
map0.0050.0000.004
mat.rank0.0020.0000.002
mint.block.pls0.1210.0000.121
mint.block.plsda0.1000.0020.100
mint.block.spls0.1380.0020.141
mint.block.splsda0.1160.0000.116
mint.pca0.3080.0000.308
mint.pls0.3980.0000.398
mint.plsda0.4810.0000.480
mint.spls0.4030.0000.402
mint.splsda0.7370.0040.741
mixOmics0.2440.0080.252
nearZeroVar0.8750.0000.875
network0.0080.0040.011
pca3.6840.0043.689
perf2.5930.0042.598
plot.rcc0.0130.0000.013
plot.tune0.0000.0020.001
plotArrow2.5440.0092.554
plotDiablo0.1580.0040.162
plotIndiv0.2430.0040.246
plotLoadings0.1020.0040.106
plotVar0.4660.0000.466
pls0.0070.0000.007
plsda0.2830.0080.291
predict0.1510.0020.153
rcc0.0010.0010.003
selectVar0.3570.0030.361
sipca0.4730.0000.474
spca2.7840.0122.796
spls0.4290.0080.437
splsda0.2700.0040.275
study_split0.0060.0000.005
summary0.0130.0000.014
tune3.7340.0213.753
tune.block.splsda0.0010.0000.001
tune.mint.splsda2.7100.0012.710
tune.pca0.1580.0000.158
tune.rcc1.6410.0001.642
tune.spca0.4890.0080.497
tune.spls000
tune.splsda3.9330.0133.964
tune.splslevel0.6910.0170.707
unmap0.0060.0000.006
vip0.0050.0040.009
withinVariation0.650.000.65
wrapper.rgcca0.0580.0000.058
wrapper.sgcca0.1080.0020.110