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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MQmetrics_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MQmetrics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MQmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MQmetrics’ version ‘1.8.0’
* 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 ‘MQmetrics’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
* 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 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
PlotAndromedaScore: no visible binding for global variable
  ‘median(Score)’
Undefined global functions or variables:
  median(Score)
* 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
PlotPTM                 10.442  0.608  13.789
PlotAcquisitionCycle     9.874  0.855  13.152
PlotProteaseSpecificity  6.704  0.572   8.751
PlotProteinCoverage      6.618  0.570   8.516
PlotAndromedaScore       6.336  0.599   8.458
PlotAllDynamicRange      5.496  0.635   7.263
PlotiRT                  5.043  0.565   6.604
PlotiRTScore             4.957  0.555   6.866
PlotHydrophobicity       4.840  0.575   6.290
PlotCharge               4.616  0.567   6.093
PlotIntensity            4.527  0.583   6.078
PlotTotalIonCurrent      4.319  0.582   6.076
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/meat/MQmetrics.Rcheck/00check.log’
for details.