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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:MSstatsConvert.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MSstatsConvert_1.17.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MSstatsConvert.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 'MSstatsConvert/DESCRIPTION' ... OK
* this is package 'MSstatsConvert' version '1.17.0'
* 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 whether package 'MSstatsConvert' can be installed ... WARNING
Found the following significant warnings:
  Warning: MSstatsConvert.Rd:3: docType '_PACKAGE' is unrecognized
See 'E:/biocbuild/bbs-3.21-bioc/meat/MSstatsConvert.Rcheck/00install.out' for details.
* 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'
SkylinetoMSstatsFormat: no visible binding for global variable
  'Intensity'
SpectronauttoMSstatsFormat: no visible binding for global variable
  'Intensity'
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
  Intensity LibPGQValue LibQValue PeptideProphet.Probability
  PeptideSequence PrecursorMz ProductCharge Purity Run
* checking Rd files ... WARNING
prepare_Rd: MSstatsConvert.Rd:3: docType '_PACKAGE' is unrecognized
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: MSstatsConvert.Rd:3: docType '_PACKAGE' is unrecognized
 OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'dot-cleanRawPDMSstats.Rd':
.cleanRawPDMSstats
  Code: function(msstats_object, quantification_column,
                 protein_id_column, sequence_column, remove_shared,
                 run_column = "SpectrumFile")
  Docs: function(msstats_object, quantification_column,
                 protein_id_column, sequence_column, remove_shared)
  Argument names in code not in docs:
    run_column

Codoc mismatches from Rd file 'dot-cleanRawPDTMT.Rd':
.cleanRawPDTMT
  Code: function(msstats_object, remove_shared = TRUE,
                 remove_protein_groups = TRUE, protein_id_column =
                 "ProteinAccessions", intensity_columns_regexp =
                 "Abundance", run_column = "SpectrumFile")
  Docs: function(msstats_object, remove_shared = TRUE,
                 remove_protein_groups = TRUE, protein_id_column =
                 "ProteinAccessions", intensity_columns_regexp =
                 "Abundance")
  Argument names in code not in docs:
    run_column

Codoc mismatches from Rd file 'dot-validatePDTMTInputColumns.Rd':
.validatePDTMTInputColumns
  Code: function(pd_input, protein_id_column, num_proteins_column,
                 run_column, channels)
  Docs: function(pd_input, protein_id_column, num_proteins_column,
                 channels)
  Argument names in code not in docs:
    run_column
  Mismatches in argument names:
    Position: 4 Code: run_column Docs: channels

* 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: 3 WARNINGs, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/MSstatsConvert.Rcheck/00check.log'
for details.