##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSstatsConvert_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.12.1’
* 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 loading without being on the library search path ... OK
* checking 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
  ‘FragmentQuantCorrected’
.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’
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
  ‘FragmentQuantCorrected’
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:
  FragmentInfo FragmentIon FragmentQuantCorrected
  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 ... 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 ‘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 ...
  ‘msstats_data_format.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.