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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:savR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings savR_1.33.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/savR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'savR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'savR' version '1.33.0'
* 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 whether package 'savR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 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 ... NOTE
buildReports,savProject-character: no visible global function
  definition for 'dev.off'
qualityHeatmap,savProject-integer-integer-logical: no visible global
  function definition for 'quantile'
Undefined global functions or variables:
  dev.off quantile
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "quantile")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/savR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL savR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'savR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'savR'
    finding HTML links ... done
    buildReports                            html  
    clusterQualityGtN                       html  
    clusters                                html  
    correctedIntensities                    html  
    cycles                                  html  
    directions                              html  
    errorMetrics                            html  
    extractionMetrics                       html  
    flowcellLayout                          html  
    illuminaFlowCellLayout-class            html  
    illuminaRead-class                      html  
    location                                html  
    pfBoxplot                               html  
    pfClusters                              html  
    plotFWHM                                html  
    plotIntensity                           html  
    plotQGT30                               html  
    qualityHeatmap                          html  
    qualityMetrics                          html  
    reads                                   html  
    run                                     html  
    savCorrectedIntensityFormat-class       html  
    savData-class                           html  
    savErrorFormat-class                    html  
    savExtractionFormat-class               html  
    savFormat-class                         html  
    savProject-class                        html  
    savQualityFormat-class                  html  
    savQualityFormatV5-class                html  
    savR-package                            html  
    savR                                    html  
    savTileFormat-class                     html  
    tileMetrics                             html  
** 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 (savR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'hopach' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(savR)
Loading required package: ggplot2
> 
> test_check("savR")
[ FAIL 0 | WARN 0 | SKIP 7 | PASS 8 ]

== Skipped tests ===============================================================
* On CRAN (6)
* Test data folder not available (1)

[ FAIL 0 | WARN 0 | SKIP 7 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
   3.98    0.12    4.09