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This page was generated on 2021-12-06 13:05:04 -0500 (Mon, 06 Dec 2021).

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: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
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 20.04.3 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: 2021-12-05 08:44:36 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 08:48:15 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 219.1 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             13.246  0.041  13.287
background.predict  6.170  0.068   6.238
circosPlot          5.632  0.031   5.664
* 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

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##############################################################################
###
### 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%
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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 
 34.405   1.352  35.350 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0160.0000.015
auroc0.8460.0230.869
background.predict6.1700.0686.238
biplot13.246 0.04113.287
block.pls0.3870.0070.395
block.plsda0.5930.0010.592
block.spls4.6020.0274.630
block.splsda4.8660.0284.894
cim0.0360.0040.040
cimDiablo0.2490.0010.249
circosPlot5.6320.0315.664
colors0.0280.0000.029
explained_variance0.0960.0040.099
get.confusion_matrix0.1710.0000.172
image.tune.rcc2.0290.0112.041
imgCor0.0760.0000.076
impute.nipals0.0110.0010.010
ipca0.6800.0000.682
logratio-transformations0.0620.0000.063
map0.0050.0000.004
mat.rank0.0020.0000.002
mint.block.pls0.1160.0070.124
mint.block.plsda0.1170.0000.117
mint.block.spls0.1440.0000.145
mint.block.splsda0.1310.0000.131
mint.pca0.6670.0000.667
mint.pls0.4270.0040.432
mint.plsda0.4570.0000.457
mint.spls0.4010.0040.408
mint.splsda0.4770.0000.477
mixOmics0.2680.0040.271
nearZeroVar0.6670.0040.671
network0.0100.0000.011
pca3.8790.0203.900
perf2.4060.0082.413
plot.rcc0.0120.0000.012
plot.tune0.0010.0000.001
plotArrow3.2200.0243.244
plotDiablo0.1540.0080.163
plotIndiv0.2180.0040.222
plotLoadings0.0910.0000.091
plotMarkers000
plotVar0.4530.0000.454
pls0.0060.0000.006
plsda0.2790.0040.283
predict0.1340.0040.138
rcc0.0020.0000.002
selectVar0.3270.0080.335
sipca0.3650.0000.365
spca2.4800.0162.497
spls0.4290.0040.433
splsda0.2690.0000.270
study_split0.0050.0000.005
summary0.0120.0000.012
tune4.0070.0214.043
tune.block.splsda000
tune.mint.splsda2.0610.0042.066
tune.pca0.1820.0080.190
tune.rcc1.5450.0081.553
tune.spca0.5190.0000.519
tune.spls000
tune.splsda3.8570.0273.903
tune.splslevel0.6890.0080.697
unmap0.0040.0000.004
vip0.0080.0000.008
withinVariation0.6850.0000.686
wrapper.rgcca0.0570.0000.057
wrapper.sgcca0.1160.0000.117