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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsConvert_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.14.0’
* 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 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 whether startup messages can be suppressed ... 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
.cleanRawDIANN: no visible binding for global variable ‘PrecursorMz’
.cleanRawDIANN: no visible binding for global variable ‘FragmentInfo’
.cleanRawDIANN: no visible binding for global variable ‘FragmentIon’
.cleanRawDIANN: no visible binding for global variable ‘ProductCharge’
.cleanRawDIANN: no visible binding for global variable
  ‘PeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable ‘Run’
.summarizeMultiplePSMs: no visible binding for global variable ‘Purity’
.summarizeMultiplePSMs: no visible binding for global variable
  ‘PeptideProphet.Probability’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘DetectionQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalQValue’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘PrecursorMz’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘FragmentInfo’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘FragmentIon’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘ProductCharge’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘PeptideSequence’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Run’
Undefined global functions or variables:
  DetectionQValue FragmentInfo FragmentIon GlobalPGQValue GlobalQValue
  LibPGQValue LibQValue PeptideProphet.Probability PeptideSequence
  PrecursorMz ProductCharge Purity Run
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-filterByPattern.Rd':
  ‘pattern’

Documented arguments not in \usage in Rd file 'dot-filterFewMeasurements.Rd':
  ‘features_columns’

Documented arguments not in \usage in Rd file 'dot-getFullDesign.Rd':
  ‘`feature_column`’ ‘`measurement_col`’

Documented arguments not in \usage in Rd file 'dot-mergeAnnotation.Rd':
  ‘data.table’

Documented arguments not in \usage in Rd file 'dot-sharedParametersAmongConverters.Rd':
  ‘removeFewMeasurements’ ‘useUniquePeptide’ ‘summaryforMultipleRows’
  ‘removeProtein_with1Feature’ ‘removeProtein_with1Peptide’
  ‘removeOxidationMpeptides’ ‘removeMpeptides’ ‘use_log_file’ ‘append’
  ‘verbose’ ‘log_file_path’ ‘...’

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 ... 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-3.19-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.