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### Running command:
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###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:stageR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings stageR_1.24.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/stageR.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'stageR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'stageR' version '1.24.0'
* 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 'stageR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  'methods' '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
.stageWiseTest : <anonymous>: warning in gsub(x = paste(namesList[ii],
  namesListElements[[ii]]), pattern = " ", replace = ":"): partial
  argument match of 'replace' to 'replacement'
.stageWiseTest: no visible global function definition for 'p.adjust'
stageR: no visible global function definition for 'new'
stageRTx: no visible global function definition for 'new'
Undefined global functions or variables:
  new p.adjust
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "p.adjust")
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 ... WARNING
Missing link or links in documentation object 'getAdjustedPValues.Rd':
  'stageWiseAdjustment,stageR,character,numeric-method'

Missing link or links in documentation object 'stageRClass.Rd':
  'getAdjustedPValues,stageR,logical,logical-method'
  'getResults,stageR-method'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  'stageRTx' 'stageR'
Undocumented S4 methods:
  generic 'adjustedAlphaLevel' and siglist 'stageR'
  generic 'getAdjustedPValues' and siglist 'stageR,logical,logical'
  generic 'getAlpha' and siglist 'stageR'
  generic 'getMethod' and siglist 'stageR'
  generic 'getPConfirmation' and siglist 'stageR'
  generic 'getPScreen' and siglist 'stageR'
  generic 'getResults' and siglist 'stageR'
  generic 'getSignificantGenes' and siglist 'stageRTx'
  generic 'getSignificantTx' and siglist 'stageRTx'
  generic 'getTx2gene' and siglist 'stageRTx'
  generic 'isAdjusted' and siglist 'stageR'
  generic 'isPScreenAdjusted' and siglist 'stageR'
  generic 'stageWiseAdjustment' and siglist 'stageR,character,numeric'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'adjustedAlphaLevel'
  '...'
Objects in \usage without \alias in documentation object 'adjustedAlphaLevel':
  '\S4method{adjustedAlphaLevel}{stageR}'

Objects in \usage without \alias in documentation object 'getAdjustedPValues':
  '\S4method{getAdjustedPValues}{stageR,logical,logical}'

Objects in \usage without \alias in documentation object 'getAlpha':
  '\S4method{getAlpha}{stageR}'

Objects in \usage without \alias in documentation object 'getMethod':
  '\S4method{getMethod}{stageR}'

Undocumented arguments in documentation object 'getPConfirmation'
  '...'
Objects in \usage without \alias in documentation object 'getPConfirmation':
  '\S4method{getPConfirmation}{stageR}'

Objects in \usage without \alias in documentation object 'getPScreen':
  '\S4method{getPScreen}{stageR}'

Undocumented arguments in documentation object 'getResults'
  '...'
Objects in \usage without \alias in documentation object 'getResults':
  '\S4method{getResults}{stageR}'

Undocumented arguments in documentation object 'getSignificantGenes'
  '...'
Objects in \usage without \alias in documentation object 'getSignificantGenes':
  '\S4method{getSignificantGenes}{stageRTx}'

Undocumented arguments in documentation object 'getSignificantTx'
  '...'
Objects in \usage without \alias in documentation object 'getSignificantTx':
  '\S4method{getSignificantTx}{stageRTx}'

Objects in \usage without \alias in documentation object 'getTx2gene':
  '\S4method{getTx2gene}{stageRTx}'

Objects in \usage without \alias in documentation object 'isAdjusted':
  '\S4method{isAdjusted}{stageR}'

Objects in \usage without \alias in documentation object 'isPScreenAdjusted':
  '\S4method{isPScreenAdjusted}{stageR}'

Documented arguments not in \usage in documentation object 'stageR':
  '...'

Documented arguments not in \usage in documentation object 'stageRTx':
  '...'

Objects in \usage without \alias in documentation object 'stageWiseAdjustment':
  '\S4method{stageWiseAdjustment}{stageR,character,numeric}'

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 LazyData ... 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 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: 3 WARNINGs, 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/stageR.Rcheck/00check.log'
for details.