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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsShiny.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MSstatsShiny_1.6.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MSstatsShiny.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'MSstatsShiny/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsShiny' version '1.6.2'
* 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 whether package 'MSstatsShiny' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'MSstats::SkylinetoMSstatsFormat' by 'MSstatsConvert::SkylinetoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::ProgenesistoMSstatsFormat' by 'MSstatsConvert::ProgenesistoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::SpectronauttoMSstatsFormat' by 'MSstatsConvert::SpectronauttoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::FragPipetoMSstatsFormat' by 'MSstatsConvert::FragPipetoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::DIAUmpiretoMSstatsFormat' by 'MSstatsConvert::DIAUmpiretoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::OpenMStoMSstatsFormat' by 'MSstatsConvert::OpenMStoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::MaxQtoMSstatsFormat' by 'MSstatsConvert::MaxQtoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::PDtoMSstatsFormat' by 'MSstatsConvert::PDtoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::OpenSWATHtoMSstatsFormat' by 'MSstatsConvert::OpenSWATHtoMSstatsFormat' when loading 'MSstatsShiny'
  Warning: replacing previous import 'MSstats::DIANNtoMSstatsFormat' by 'MSstatsConvert::DIANNtoMSstatsFormat' when loading 'MSstatsShiny'
See 'F:/biocbuild/bbs-3.19-bioc/meat/MSstatsShiny.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 ... NOTE
Unexported objects imported by ':::' calls:
  'shinyBS:::buildTooltipOrPopoverOptionsList' 'shinyBS:::shinyBSDep'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getAnnot: no visible binding for global variable 'annotation.pd'
getSummary1: no visible binding for global variable 'Condition'
getSummary1: no visible binding for global variable 'BioReplicate'
getSummary1: no visible binding for global variable 'Mixture'
getSummary1: no visible binding for global variable 'Run'
getSummary1: no visible binding for global variable 'TechRepMixture'
getSummary1: no visible binding for global variable 'Fraction'
getSummary1: no visible binding for global variable 'Condition_Run'
getSummary1: no visible binding for global variable 'BioReplicate_Run'
getSummary1: no visible binding for global variable 'Number of
  Fractions'
getSummary2: no visible binding for global variable 'ProteinName'
getSummary2: no visible binding for global variable 'PeptideSequence'
getSummary2: no visible binding for global variable 'Charge'
getSummary2: no visible binding for global variable 'PrecursorCharge'
getSummary2: no visible binding for global variable 'FragmentIon'
getSummary2: no visible binding for global variable 'ProductCharge'
getSummary2: no visible binding for global variable 'FEATURES'
getSummary2: no visible binding for global variable 'Intensity'
getSummary2: no visible binding for global variable 'Min_Intensity'
getSummary2: no visible binding for global variable 'Max_Intensity'
getSummary2: no visible binding for global variable 'npep'
getSummary2: no visible binding for global variable 'nfea'
getSummary2: no visible binding for global variable
  'Features_Peptides_min'
getSummary2: no visible binding for global variable
  'Features_Peptides_max'
getSummary2: no visible binding for global variable
  'Peptides_Proteins_min'
getSummary2: no visible binding for global variable
  'Peptides_Proteins_max'
loadpageServer: no visible global function definition for
  'moduleServer'
server: no visible global function definition for 'callModule'
statmodelServer: no visible global function definition for
  'updateNumericInput'
Undefined global functions or variables:
  BioReplicate BioReplicate_Run Charge Condition Condition_Run FEATURES
  Features_Peptides_max Features_Peptides_min Fraction FragmentIon
  Intensity Max_Intensity Min_Intensity Mixture Number of Fractions
  PeptideSequence Peptides_Proteins_max Peptides_Proteins_min
  PrecursorCharge ProductCharge ProteinName Run TechRepMixture
  annotation.pd callModule moduleServer nfea npep updateNumericInput
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
tmt_model              5.58   0.38    6.11
apply_adj              5.14   0.19    5.34
tmt_summarization_loop 4.96   0.19    5.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/MSstatsShiny.Rcheck/00check.log'
for details.