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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nucleR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings nucleR_2.27.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/nucleR.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 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '2.27.1'
* 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 whether package 'nucleR' 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package 'Starr' in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object '.fftRegion'
  'data2' 'pcKeepComp'

Undocumented arguments in documentation object '.loadFiles'
  'singleLoad' 'pairedLoad'

Undocumented arguments in documentation object '.loadPairedBam'
  'file'

Undocumented arguments in documentation object '.loadSingleBam'
  'exp'

Undocumented arguments in documentation object '.mid'
  'x'

Undocumented arguments in documentation object '.unlist_as_integer'
  'x'

Undocumented arguments in documentation object '.xlapply'
  'X' 'FUN' '...' 'mc.cores'

Documented arguments not in \usage in documentation object 'pcKeepCompDetect':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
syntheticNucMap 21.48   0.08   21.56
* 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 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/nucleR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL nucleR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'nucleR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Loading required package: usethis

Welcome at Thu Mar 17 15:51:59 2022 

Goodbye at  Thu Mar 17 15:52:10 2022 
** help
*** installing help indices
  converting help for package 'nucleR'
    finding HTML links ... done
    controlCorrection                       html  
    coverage.rpm                            html  
    dot-fftRegion                           html  
    dot-getThreshold                        html  
    dot-loadFiles                           html  
    dot-loadPairedBam                       html  
    dot-loadSingleBam                       html  
    dot-mid                                 html  
    dot-processStrand                       html  
    dot-unlist_as_integer                   html  
    dot-vectorizedAll                       html  
    dot-xlapply                             html  
    export.bed                              html  
    export.wig                              html  
    filterFFT                               html  
    fragmentLenDetect                       html  
    mergeCalls                              html  
    nucleR-package                          html  
    nucleosome_htseq                        html  
    nucleosome_tiling                       html  
    pcKeepCompDetect                        html  
    peakDetection                           html  
    peakScoring                             html  
    plotPeaks                               html  
    processReads                            html  
    processTilingArray                      html  
    readBAM                                 html  
    readBowtie                              html  
    syntheticNucMap                         html  
** building package indices
Loading required package: usethis

Welcome at Thu Mar 17 15:52:13 2022 

Goodbye at  Thu Mar 17 15:52:13 2022 
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis

Welcome at Thu Mar 17 15:52:14 2022 

Goodbye at  Thu Mar 17 15:52:19 2022 
** testing if installed package can be loaded from final location
Loading required package: usethis

Welcome at Thu Mar 17 15:52:20 2022 

Goodbye at  Thu Mar 17 15:52:26 2022 
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)
Making 'packages.html' ... 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(nucleR)
> 
> test_check("nucleR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
   7.46    0.48    7.92