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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nucleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nucleR_2.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/nucleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘2.32.0’
* 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 ‘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 38.767  0.515  58.789
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/nucleR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nucleR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 Sun Oct 15 16:39:40 2023 

Goodbye at  Sun Oct 15 16:40:00 2023 
** help
*** installing help indices
** building package indices
Loading required package: usethis

Welcome at Sun Oct 15 16:40:04 2023 

Goodbye at  Sun Oct 15 16:40:04 2023 
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis

Welcome at Sun Oct 15 16:40:06 2023 

Goodbye at  Sun Oct 15 16:40:24 2023 
** testing if installed package can be loaded from final location
Loading required package: usethis

Welcome at Sun Oct 15 16:40:27 2023 

Goodbye at  Sun Oct 15 16:40:44 2023 
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
 10.793   0.523  17.167