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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ABSSeq.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ABSSeq_1.61.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ABSSeq.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ABSSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ABSSeq' version '1.61.0'
* 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 'ABSSeq' 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
'library' or 'require' call to 'edgeR' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ABSDataSet: no visible global function definition for 'new'
ABSSeqlm: no visible global function definition for 'pnorm'
ABSSeqlm: no visible global function definition for 'p.adjust'
ReplaceOutliersByMAD: no visible global function definition for 'is'
ReplaceOutliersByMAD: no visible global function definition for
  'model.matrix'
ReplaceOutliersByMAD: no visible global function definition for
  'predict'
aFoldcomplexDesign: no visible binding for global variable 'sd'
aFoldcomplexDesign: no visible binding for global variable 'var'
aFoldcomplexDesign: no visible global function definition for 'sd'
callDEs: no visible global function definition for 'is'
callDEs: no visible binding for global variable 'p.adjust.methods'
callDEs: no visible global function definition for 'pnorm'
callDEs: no visible global function definition for 'pnbinom'
callDEs: no visible global function definition for 'p.adjust'
callParameter: no visible global function definition for 'is'
callParameter: no visible binding for global variable 'var'
callParameter: no visible global function definition for 'quantile'
callParameter: no visible global function definition for 'predict'
callParameter: no visible global function definition for 'model.matrix'
callParameterwithoutReplicates: no visible global function definition
  for 'is'
callParameterwithoutReplicates: no visible binding for global variable
  'sd'
callParameterwithoutReplicates: no visible global function definition
  for 'predict'
callParameterwithoutReplicates: no visible binding for global variable
  'var'
callParameterwithoutReplicates: no visible global function definition
  for 'quantile'
callParameterwithoutReplicates: no visible global function definition
  for 'model.matrix'
callPergroup: no visible binding for global variable 'var'
estimateSizeFactorsForMatrix: no visible binding for global variable
  'median'
genAFold: no visible binding for global variable 'var'
genAFold: no visible binding for global variable 'sd'
genAFold: no visible global function definition for 'sd'
normalFactors: no visible global function definition for 'is'
normalFactors: no visible global function definition for 'validObject'
normalFactors : rowQuar: no visible global function definition for
  'quantile'
normalFactors: no visible global function definition for
  'calcNormFactors'
plotDifftoBase: no visible global function definition for 'is'
preAFold: no visible global function definition for 'quantile'
preAFold: no visible global function definition for 'var'
preAFold: no visible global function definition for 'predict'
preAFoldComplex: no visible global function definition for 'quantile'
preAFoldComplex: no visible global function definition for 'var'
preAFoldComplex: no visible global function definition for 'predict'
qtotalNormalized : rowQuar: no visible global function definition for
  'quantile'
qtotalNormalized : rowQuar: no visible global function definition for
  'sd'
qtotalNormalized : rowQuar: no visible global function definition for
  'median'
qtotalNormalized : rowQuar : <anonymous>: no visible global function
  definition for 'median'
replaceByrow: no visible global function definition for 'median'
replaceByrow: no visible global function definition for 'mad'
LevelstoNormFC<-,ABSDataSet-numeric: no visible global function
  definition for 'validObject'
[[<-,SumInfo-character-missing: no visible global function definition
  for 'as'
counts<-,ABSDataSet-matrix: no visible global function definition for
  'validObject'
excounts<-,ABSDataSet-matrix: no visible global function definition for
  'validObject'
groups<-,ABSDataSet-factor: no visible global function definition for
  'validObject'
maxRates<-,ABSDataSet-numeric: no visible global function definition
  for 'validObject'
minRates<-,ABSDataSet-numeric: no visible global function definition
  for 'validObject'
minimalDispersion<-,ABSDataSet-numeric: no visible global function
  definition for 'validObject'
normMethod<-,ABSDataSet-character: no visible global function
  definition for 'validObject'
paired<-,ABSDataSet-logical: no visible global function definition for
  'validObject'
sFactors<-,ABSDataSet-numeric: no visible global function definition
  for 'validObject'
Undefined global functions or variables:
  as calcNormFactors is mad median model.matrix new p.adjust
  p.adjust.methods pnbinom pnorm predict quantile sd validObject var
Consider adding
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "mad", "median", "model.matrix", "p.adjust",
             "p.adjust.methods", "pnbinom", "pnorm", "predict",
             "quantile", "sd", "var")
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotDifftoBase       11.57   1.24   12.82
ABSSeq               11.11   1.35   12.45
callDEs              11.25   1.15   12.43
results              10.88   1.36   12.25
callParameter        10.90   1.16   12.08
ReplaceOutliersByMAD  8.83   1.18   10.00
excounts              8.17   1.03    9.20
ABSSeqlm              7.37   0.87    8.28
aFoldcomplexDesign    4.81   0.41    5.23
genAFold              4.57   0.50    5.07
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/ABSSeq.Rcheck/00check.log'
for details.