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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/flagme.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.52.0’
* 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 ‘flagme’ 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘MSnbase’
Missing or unexported object: ‘xcms::rectUnique’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addXCMSPeaks: no visible global function definition for ‘bpparam’
addXCMSPeaks : <anonymous> : <anonymous>: no visible global function
  definition for ‘setNames’
importSpec : <anonymous>: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  bpparam setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotAlignment-peaksAlignment-method.Rd':
  ‘plotAlignment’

Missing link or links in documentation object 'plotClustAlignment-clusterAlignment-method.Rd':
  ‘plotAlignment’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                              user system elapsed
plotAlignedFrags                           127.051 21.268  76.641
addXCMSPeaks                                69.673 10.208  57.598
peaksAlignment-class                        68.567 10.621  56.159
progressiveAlignment-class                  68.438 10.628  56.145
plotFrags                                   68.410 10.287  56.082
dynRT                                       67.982 10.676  55.819
corPrt                                      67.878 10.292  55.382
retFatMatrix                                67.467 10.596  55.814
ndpRT                                       67.111 10.317  54.739
plotAlignment-peaksAlignment-method         66.856 10.433  54.385
imputePeaks                                 14.523  0.280  14.841
plotChrom-peaksDataset-method               12.516  0.490  13.031
calcTimeDiffs                               10.827  0.552  11.454
rmaFitUnit                                  10.618  0.382  11.020
gatherInfo                                  10.470  0.393  10.887
multipleAlignment-class                      9.510  0.136   9.668
clusterAlignment                             9.162  0.147   9.329
dp                                           8.917  0.349   9.304
normDotProduct                               8.790  0.385   9.202
plotClustAlignment-clusterAlignment-method   8.821  0.161   8.999
peaksDataset                                 8.084  0.348   8.450
addAMDISPeaks                                7.140  0.214   7.384
plotImage                                    5.366  0.291   5.668
addChromaTOFPeaks                            5.389  0.173   5.673
parseChromaTOF                               5.375  0.032   5.420
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/flagme.Rcheck/00check.log’
for details.