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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MSstatsConvert_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.4.1’
* 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 ‘MSstatsConvert’ 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 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.findAvailable’ ‘.standardizeColnames’
* checking S3 generic/method consistency ... WARNING
as.data.frame:
  function(x, row.names, optional, ...)
as.data.frame.MSstatsValidated:
  function(x)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cleanRawPhilosopher: no visible binding for global variable
  ‘ModifiedPeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable
  ‘PeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable ‘IsUnique’
.cleanRawPhilosopher: no visible binding for global variable ‘PSM’
.cleanRawPhilosopher: no visible binding for global variable
  ‘PrecursorCharge’
.cleanRawPhilosopher: no visible binding for global variable
  ‘Intensity’
.cleanRawPhilosopher: no visible binding for global variable ‘Run’
.cleanRawPhilosopher: no visible binding for global variable
  ‘ProteinName’
.summarizeMultiplePSMs: no visible binding for global variable ‘Purity’
.summarizeMultiplePSMs: no visible binding for global variable
  ‘PeptideProphet.Probability’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘ModifiedPeptideSequence’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘PeptideSequence’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘IsUnique’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘PSM’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘PrecursorCharge’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Intensity’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Run’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘ProteinName’
Undefined global functions or variables:
  Intensity IsUnique ModifiedPeptideSequence PSM
  PeptideProphet.Probability PeptideSequence PrecursorCharge
  ProteinName Purity Run
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'getInputFile' and siglist 'MSstatsPhilosopherFiles'
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 'MSstatsClean'
  ‘channels’

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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.