Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-01-17 13:08:00 -0500 (Mon, 17 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 machv2


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: 2022-01-16 01:55:05 -0500 (Sun, 16 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.18.1.tar.gz
StartedAt: 2022-01-16 15:19:42 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 15:26:28 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 406.0 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/mixOmics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    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             16.397  0.071  16.495
background.predict 10.645  1.581  12.237
circosPlot         10.802  0.083  10.896
block.splsda        9.264  0.071   9.348
block.spls          8.568  0.064   8.646
pca                 6.559  0.048   6.616
tune                6.156  0.278   6.440
tune.splsda         5.764  0.381   6.149
plotArrow           5.463  0.062   5.534
spca                5.152  0.108   5.265
perf                4.967  0.103   5.072
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/mixOmics.Rcheck/00check.log’
for details.



Installation output

mixOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%
Performing repeated cross-validation with nrepeat = 3...

  |                                                                            
  |                                                                      |   0%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 68.316   2.511  69.406 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0190.0040.023
auroc1.2240.0601.285
background.predict10.645 1.58112.237
biplot16.397 0.07116.495
block.pls0.6990.0110.711
block.plsda1.1280.0141.143
block.spls8.5680.0648.646
block.splsda9.2640.0719.348
cim0.0510.0070.057
cimDiablo0.5610.0090.572
circosPlot10.802 0.08310.896
colors0.0430.0020.045
explained_variance0.4580.0060.463
get.confusion_matrix0.3010.0030.304
image.tune.rcc2.9470.0683.017
imgCor0.1070.0160.123
impute.nipals0.0190.0050.023
ipca1.2180.0211.241
logratio-transformations0.1180.0060.123
map0.0060.0040.010
mat.rank0.0030.0000.004
mint.block.pls0.1800.0070.187
mint.block.plsda0.1700.0130.184
mint.block.spls0.1810.0050.186
mint.block.splsda0.1570.0050.162
mint.pca0.6200.0050.625
mint.pls0.7680.0070.776
mint.plsda0.8440.0090.857
mint.spls0.8280.0080.837
mint.splsda0.8820.0060.889
mixOmics0.5240.0170.542
nearZeroVar1.4540.0241.481
network0.0180.0060.024
pca6.5590.0486.616
perf4.9670.1035.072
plot.rcc0.0210.0040.025
plot.tune0.0010.0030.004
plotArrow5.4630.0625.534
plotDiablo0.2400.0080.250
plotIndiv0.4450.0120.459
plotLoadings0.1580.0100.169
plotMarkers0.0010.0010.001
plotVar0.8240.0140.840
pls0.0110.0020.014
plsda0.5650.0070.572
predict0.3160.0120.328
rcc0.0030.0020.005
selectVar0.6230.0450.669
sipca0.9230.0200.943
spca5.1520.1085.265
spls0.2980.0140.312
splsda0.5560.0060.563
study_split0.0060.0010.007
summary0.0260.0040.030
tune6.1560.2786.440
tune.block.splsda0.0000.0010.001
tune.mint.splsda4.3220.1074.432
tune.pca0.2810.0030.284
tune.rcc2.8430.0592.906
tune.spca1.0560.0251.082
tune.spls0.0000.0000.001
tune.splsda5.7640.3816.149
tune.splslevel1.5170.0201.539
unmap0.0070.0080.014
vip0.0150.0030.018
withinVariation1.3460.0361.385
wrapper.rgcca0.1130.0050.117
wrapper.sgcca0.2860.0110.296