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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSstatsBig.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSstatsBig_1.9.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MSstatsBig.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsBig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsBig’ version ‘1.9.2’
* 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 ‘MSstatsBig’ 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 loading without being on the library search path ... 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
MSstatsPreprocessBig: no visible binding for global variable ‘input’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘PeptideSequence’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘PrecursorCharge’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘FragmentIon’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘ProductCharge’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘ProteinName’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘Feature’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘Intensity’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘MeanAbundance’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘feature_rank’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘NumProteins’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘%>%’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘group_by’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘across’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘all_of’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘summarise’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘inner_join’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘filter’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘max_intensity’
MSstatsPreprocessBigArrow: no visible global function definition for
  ‘select’
MSstatsPreprocessBigArrow: no visible binding for global variable
  ‘NumObs’
MSstatsPreprocessBigSparklyr: no visible global function definition for
  ‘%>%’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘Condition’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘BioReplicate’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘PeptideSequence’
MSstatsPreprocessBigSparklyr: no visible global function definition for
  ‘n_distinct’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘ProteinName’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘NumProteins’
MSstatsPreprocessBigSparklyr: no visible global function definition for
  ‘tbl’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘PrecursorCharge’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘FragmentIon’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘ProductCharge’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘IsotopeLabelType’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘Run’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘Intensity’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘NumObs’
MSstatsPreprocessBigSparklyr: no visible global function definition for
  ‘min_rank’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
  ‘Rank’
cleanDIANNChunk: no visible global function definition for
  ‘MSstatsMakeAnnotation’
cleanSpectronautChunk: no visible global function definition for
  ‘all_of’
cleanSpectronautChunk: no visible binding for global variable
  ‘Intensity’
cleanSpectronautChunk: no visible binding for global variable
  ‘Excluded’
cleanSpectronautChunk: no visible binding for global variable
  ‘Identified’
cleanSpectronautChunk: no visible binding for global variable
  ‘EGQvalue’
cleanSpectronautChunk: no visible binding for global variable
  ‘PGQvalue’
cleanSpectronautChunk: no visible binding for global variable
  ‘FFrgLossType’
cleanSpectronautChunk: no visible binding for global variable
  ‘LabeledSequence’
cleanSpectronautChunk: no visible global function definition for ‘:=’
cleanSpectronautChunk: no visible binding for global variable
  ‘IsotopeLabelType’
cleanSpectronautChunk: no visible binding for global variable
  ‘IsLabeled’
Undefined global functions or variables:
  %>% := BioReplicate Condition EGQvalue Excluded FFrgLossType Feature
  FragmentIon Identified Intensity IsLabeled IsotopeLabelType
  LabeledSequence MSstatsMakeAnnotation MeanAbundance NumObs
  NumProteins PGQvalue PeptideSequence PrecursorCharge ProductCharge
  ProteinName Rank Run across all_of feature_rank filter group_by
  inner_join input max_intensity min_rank n_distinct select summarise
  tbl
Consider adding
  importFrom("stats", "filter")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'bigDIANNtoMSstatsFormat.Rd':
bigDIANNtoMSstatsFormat
  Code: function(input_file, annotation = NULL, output_file_name,
                 backend, MBR = TRUE, quantificationColumn =
                 "FragmentQuantCorrected", global_qvalue_cutoff = 0.01,
                 qvalue_cutoff = 0.01, pg_qvalue_cutoff = 0.01,
                 max_feature_count = 100, filter_unique_peptides =
                 FALSE, aggregate_psms = FALSE, filter_few_obs = FALSE,
                 remove_annotation = FALSE, calculateAnomalyScores =
                 FALSE, anomalyModelFeatures = c(), connection = NULL)
  Docs: function(input_file, output_file_name, backend, MBR = TRUE,
                 quantificationColumn = "FragmentQuantCorrected",
                 global_qvalue_cutoff = 0.01, qvalue_cutoff = 0.01,
                 pg_qvalue_cutoff = 0.01, max_feature_count = 100,
                 filter_unique_peptides = FALSE, aggregate_psms =
                 FALSE, filter_few_obs = FALSE, remove_annotation =
                 FALSE, calculateAnomalyScores = FALSE,
                 anomalyModelFeatures = c(), connection = NULL)
  Argument names in code not in docs:
    annotation
  Mismatches in argument names (first 3):
    Position: 2 Code: annotation Docs: output_file_name
    Position: 3 Code: output_file_name Docs: backend
    Position: 4 Code: backend Docs: MBR

Codoc mismatches from Rd file 'cleanDIANNChunk.Rd':
cleanDIANNChunk
  Code: function(input, output_path, MBR, quantificationColumn, pos,
                 global_qvalue_cutoff = 0.01, qvalue_cutoff = 0.01,
                 pg_qvalue_cutoff = 0.01, annotation = NULL)
  Docs: function(input, output_path, MBR, quantificationColumn, pos,
                 global_qvalue_cutoff = 0.01, qvalue_cutoff = 0.01,
                 pg_qvalue_cutoff = 0.01)
  Argument names in code not in docs:
    annotation

Codoc mismatches from Rd file 'reduceBigDIANN.Rd':
reduceBigDIANN
  Code: function(input_file, output_path, MBR = TRUE,
                 quantificationColumn = "FragmentQuantCorrected",
                 global_qvalue_cutoff = 0.01, qvalue_cutoff = 0.01,
                 pg_qvalue_cutoff = 0.01, annotation = NULL)
  Docs: function(input_file, output_path, MBR = TRUE,
                 quantificationColumn = "FragmentQuantCorrected",
                 global_qvalue_cutoff = 0.01, qvalue_cutoff = 0.01,
                 pg_qvalue_cutoff = 0.01)
  Argument names in code not in docs:
    annotation

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/MSstatsBig.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MSstatsBig
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘MSstatsBig’ ...
** this is package ‘MSstatsBig’ version ‘1.9.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsBig)