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This page was generated on 2022-01-24 13:07:58 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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: 2022-01-23 01:55:04 -0500 (Sun, 23 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: 2022-01-23 15:20:05 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 15:26:50 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 405.7 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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             17.096  0.080  17.195
background.predict 10.698  1.416  12.126
circosPlot         10.686  0.082  10.781
block.splsda        9.120  0.062   9.195
block.spls          8.022  0.070   8.101
pca                 6.545  0.048   6.600
tune                6.239  0.317   6.563
tune.splsda         5.621  0.373   5.996
plotArrow           5.648  0.062   5.724
spca                4.948  0.120   5.073
* 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...

  |                                                                            
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  |=======================                                               |  33%
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  |===============================================                       |  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 
 69.734   2.599  70.388 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0290.0050.035
auroc1.1530.0511.217
background.predict10.698 1.41612.126
biplot17.096 0.08017.195
block.pls0.7180.0090.728
block.plsda1.1920.0131.207
block.spls8.0220.0708.101
block.splsda9.1200.0629.195
cim0.0540.0090.064
cimDiablo0.4990.0100.513
circosPlot10.686 0.08210.781
colors0.0460.0020.048
explained_variance0.4420.0060.448
get.confusion_matrix0.3150.0040.318
image.tune.rcc3.0200.0743.122
imgCor0.1240.0150.139
impute.nipals0.0200.0040.024
ipca1.2390.0231.266
logratio-transformations0.1050.0060.110
map0.0050.0050.010
mat.rank0.0040.0010.004
mint.block.pls0.1640.0050.170
mint.block.plsda0.1580.0070.166
mint.block.spls0.1790.0070.188
mint.block.splsda0.1350.0050.142
mint.pca0.5890.0080.601
mint.pls0.7570.0160.819
mint.plsda0.8860.0060.894
mint.spls0.8040.0070.813
mint.splsda0.8790.0060.887
mixOmics0.5030.0270.529
nearZeroVar1.4460.0251.472
network0.0160.0050.021
pca6.5450.0486.600
perf4.8800.1054.987
plot.rcc0.0180.0060.025
plot.tune0.0010.0010.002
plotArrow5.6480.0625.724
plotDiablo0.2060.0090.216
plotIndiv0.3690.0080.379
plotLoadings0.1590.0070.167
plotMarkers000
plotVar0.7830.0100.794
pls0.0120.0030.014
plsda0.4740.0070.482
predict0.3400.0110.351
rcc0.0050.0020.007
selectVar0.6450.0370.682
sipca0.9860.0211.008
spca4.9480.1205.073
spls0.2070.0130.219
splsda0.5680.0040.573
study_split0.0080.0020.010
summary0.0240.0040.028
tune6.2390.3176.563
tune.block.splsda0.0010.0010.001
tune.mint.splsda4.2190.1004.323
tune.pca0.3080.0050.313
tune.rcc2.8610.0872.950
tune.spca1.0820.0221.105
tune.spls0.0000.0010.001
tune.splsda5.6210.3735.996
tune.splslevel1.6060.0431.650
unmap0.0060.0050.011
vip0.0180.0030.020
withinVariation1.2310.0071.241
wrapper.rgcca0.0920.0040.095
wrapper.sgcca0.3000.0150.316