##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SCnorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SCnorm_1.31.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SCnorm.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SCnorm/DESCRIPTION’ ... OK
* this is package ‘SCnorm’ version ‘1.31.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SCnorm’ 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 code 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 ... NOTE
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetTD: no visible global function definition for ‘poly’
GetTD: no visible binding for global variable ‘na.exclude’
GetTD: no visible global function definition for ‘predict’
SCnorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
SCnormFit: no visible global function definition for ‘density’
SCnormFit: no visible global function definition for ‘poly’
SCnormFit: no visible binding for global variable ‘na.exclude’
SCnormFit: no visible global function definition for ‘predict’
SCnormFit: no visible global function definition for ‘quantile’
correctWithin: no visible global function definition for ‘quantile’
correctWithin: no visible global function definition for ‘loess’
correctWithin: no visible global function definition for ‘predict’
correctWithin: no visible global function definition for ‘median’
evaluateK : <anonymous>: no visible global function definition for
  ‘median’
generateEvalPlot: no visible binding for global variable ‘median’
getDens: no visible global function definition for ‘density’
getDens: no visible global function definition for ‘na.omit’
plotCountDepth : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
plotWithinFactor : <anonymous>: no visible global function definition
  for ‘median’
plotWithinFactor : <anonymous> : <anonymous>: no visible global
  function definition for ‘median’
scaleNormMultCont : <anonymous>: no visible global function definition
  for ‘median’
scaleNormMultCont: no visible global function definition for ‘median’
Undefined global functions or variables:
  density loess median na.exclude na.omit poly predict quantile
Consider adding
  importFrom("stats", "density", "loess", "median", "na.exclude",
             "na.omit", "poly", "predict", "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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SCnorm.Rcheck/00check.log’
for details.