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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:barbieQ.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings barbieQ_1.1.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/barbieQ.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'barbieQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'barbieQ' version '1.1.2'
* 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 'barbieQ' can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      2.6Mb
    extdata   2.9Mb
* 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createBarbieQ: no visible global function definition for 'is'
extractBarcodePairs: no visible global function definition for 'is'
extractSampleMetadataAndPrimaryFactor: no visible global function
  definition for 'is'
plotBarcodeMA: no visible binding for global variable 'Amean'
plotBarcodeMA: no visible binding for global variable 'meanDiff'
plotBarcodeMA: no visible binding for global variable 'tendencyTo'
plotBarcodeMA: no visible binding for global variable 'meanOcc'
plotBarcodeMA: no visible binding for global variable 'logOR'
plotBarcodePValue: no visible binding for global variable 'adj.P.Val'
plotBarcodePValue: no visible binding for global variable 'tendencyTo'
plotBarcodePairCorrelation: no visible binding for global variable
  'coefficient'
plotBarcodePairCorrelation: no visible binding for global variable
  'count'
plotBarcodePairCorrelation: no visible binding for global variable
  '..y..'
plotBarcodePareto: no visible binding for global variable 'group'
plotBarcodePareto: no visible binding for global variable 'value'
plotBarcodePareto: no visible binding for global variable 'id'
plotBarcodeSankey: no visible binding for global variable 'category'
plotBarcodeSankey: no visible binding for global variable 'value'
plotBarcodeSankey: no visible binding for global variable 'variable'
plotSamplePairCorrelation: no visible binding for global variable
  'rowNumber'
plotSignifBarcodeProportion: no visible binding for global variable
  'tendencyTo'
plotSignifBarcodeProportion: no visible global function definition for
  'everything'
plotSignifBarcodeProportion: no visible binding for global variable
  'sampleGroup'
plotSignifBarcodeProportion: no visible binding for global variable
  'id'
plotSignifBarcodeProportion: no visible binding for global variable
  'mid_point'
Undefined global functions or variables:
  ..y.. Amean adj.P.Val category coefficient count everything group id
  is logOR meanDiff meanOcc mid_point rowNumber sampleGroup tendencyTo
  value variable
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 data for ASCII and uncompressed saves ... 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 ... 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
  'F:/biocbuild/bbs-3.22-bioc/meat/barbieQ.Rcheck/00check.log'
for details.