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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dupRadar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dupRadar_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/dupRadar.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dupRadar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dupRadar’ version ‘1.28.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dupRadar’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
analyzeDuprates: no visible global function definition for
  ‘capture.output’
cumulativeDuprateBarplot: no visible global function definition for
  ‘barplot’
duprateExpBoxplot: no visible global function definition for ‘par’
duprateExpBoxplot: no visible global function definition for ‘boxplot’
duprateExpBoxplot: no visible global function definition for ‘axis’
duprateExpBoxplot: no visible global function definition for ‘title’
duprateExpDensPlot: no visible global function definition for
  ‘colorRampPalette’
duprateExpDensPlot: no visible global function definition for
  ‘densCols’
duprateExpDensPlot: no visible global function definition for ‘Axis’
duprateExpDensPlot: no visible global function definition for ‘lines’
duprateExpDensPlot: no visible global function definition for ‘predict’
duprateExpDensPlot: no visible global function definition for ‘legend’
duprateExpDensPlot: no visible global function definition for ‘abline’
duprateExpFit: no visible global function definition for ‘glm’
duprateExpFit: no visible global function definition for ‘binomial’
duprateExpFit: no visible global function definition for ‘coef’
duprateExpIdentify: no visible global function definition for
  ‘identify’
duprateExpPlot: no visible global function definition for
  ‘smoothScatter’
duprateExpPlot: no visible global function definition for ‘axis’
duprateExpPlot: no visible global function definition for ‘abline’
duprateExpPlot: no visible global function definition for ‘legend’
expressionHist: no visible global function definition for ‘hist’
expressionHist: no visible global function definition for ‘axis’
expressionHist: no visible global function definition for ‘abline’
getDupMatBin: no visible global function definition for ‘quantile’
getDynamicRange : medianrpkm: no visible global function definition for
  ‘quantile’
getDynamicRange : medianrpkm: no visible global function definition for
  ‘median’
getRpkBinReadCountFraction: no visible global function definition for
  ‘quantile’
getRpkCumulativeReadCountFraction: no visible global function
  definition for ‘quantile’
readcountExpBoxplot: no visible global function definition for
  ‘barplot’
readcountExpBoxplot: no visible global function definition for ‘title’
Undefined global functions or variables:
  Axis abline axis barplot binomial boxplot capture.output coef
  colorRampPalette densCols glm hist identify legend lines median par
  predict quantile smoothScatter title
Consider adding
  importFrom("grDevices", "colorRampPalette", "densCols")
  importFrom("graphics", "Axis", "abline", "axis", "barplot", "boxplot",
             "hist", "identify", "legend", "lines", "par",
             "smoothScatter", "title")
  importFrom("stats", "binomial", "coef", "glm", "median", "predict",
             "quantile")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) dupRadar.Rd:0-7: Must have a \description
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/dupRadar.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dupRadar
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘dupRadar’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (dupRadar)