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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AneuFinder_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/AneuFinder.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.32.0’
* 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 ‘AneuFinder’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Aneufinder: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* 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 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
refineBreakpoints         132.212  1.438 143.671
simulateReads             110.107  4.586 126.600
heatmapAneuploidies       111.029  0.688 124.655
plotHeterogeneity          70.888  0.901  78.298
heatmapGenomewideClusters  62.121  0.621  67.013
karyotypeMeasures          54.869  0.594  59.105
correctGC                  52.128  2.685  60.506
heatmapGenomewide          52.731  0.590  56.740
annotateBreakpoints        32.716  0.903  37.534
getBreakpoints             26.325  0.748  29.331
consensusSegments          20.493  0.158  22.883
subsetByCNVprofile         13.880  0.139  15.746
getSCEcoordinates          12.267  0.849  14.734
findCNVs.strandseq          9.886  0.650  10.937
variableWidthBins           9.654  0.201  11.128
findCNVs                    8.668  0.785  10.215
loadFromFiles               8.075  0.103   8.905
clusterByQuality            5.955  0.145   7.634
collapseBins                4.183  0.191   5.274
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.