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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings mixOmics_6.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/mixOmics.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘mixOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mixOmics’ version ‘6.25.0’
* 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  8.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.3Mb
    doc    1.9Mb
* 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             18.221  0.179  18.401
image.tune.rcc     14.743  0.023  14.768
tune.rcc           14.710  0.016  14.726
background.predict 11.196  0.108  11.304
circosPlot         10.143  0.120  10.264
block.splsda        8.983  0.075   9.060
block.spls          7.438  0.053   7.491
tune                6.906  0.057   6.962
perf                6.443  0.020   6.464
pca                 6.238  0.036   6.274
tune.splsda         6.154  0.008   6.160
plotArrow           5.907  0.032   5.940
spca                5.243  0.007   5.251
* 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-3.18-bioc/meat/mixOmics.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL mixOmics
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 6.25.0
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 (i in seq_len(n)) { :
  closing unused connection 6 (<-localhost:11339)
2: In for (i in seq_len(n)) { :
  closing unused connection 5 (<-localhost:11339)
> 
> proc.time()
   user  system elapsed 
355.483   3.784 383.045