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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings mixOmics_6.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mixOmics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘mixOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mixOmics’ version ‘6.24.0’
* 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  7.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.4Mb
    doc    1.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
biplot             14.948  0.156  15.104
circosPlot          7.207  0.132   7.340
background.predict  6.558  0.084   6.642
block.splsda        6.468  0.072   6.540
block.spls          5.495  0.060   5.555
* 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 ...
  ‘vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
The magick package is required to crop "Figures/Getting-Started02-pca-nutrimouse-1.png" but not available.
The magick package is required to crop "Figures/Getting-Started02-pca-nutrimouse-2.png" but not available.
The magick package is required to crop "Figures/Getting-Started02-spca-nutrimouse-1.png" but not available.
The magick package is required to crop "Figures/Getting-Started02-spca-nutrimouse-2.png" but not available.
The magick package is required to crop "Figures/PCA/03-screeplot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-pca-sample-plot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-pca-variable-plot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-pca-biplot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-pca-boxplot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-spca-tuning-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-spca-sample-plot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-spca-biplot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-spca-variable-plot-1.png" but not available.
The magick package is required to crop "Figures/PCA/03-spca-loading-plot-1.png" but not available.

Quitting from lines 684-688 [04-load-data2] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/mixOmics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL mixOmics
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘mixOmics’ ...
** using staged installation
** 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)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 6.24.0
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")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 236 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 236 ]
Warning messages:
1: In for (ijk.keepA in 1:nrow(keepA[[comp]])) { :
  closing unused connection 6 (<-localhost:11698)
2: In for (ijk.keepA in 1:nrow(keepA[[comp]])) { :
  closing unused connection 5 (<-localhost:11698)
> 
> proc.time()
   user  system elapsed 
102.395   3.420 121.447