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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AneuFinder_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/AneuFinder.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.22.0’
* 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
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
simulateReads             51.240  2.956  54.263
heatmapAneuploidies       51.816  1.216  53.032
refineBreakpoints         49.126  0.380  49.507
plotHeterogeneity         32.369  0.152  32.520
heatmapGenomewideClusters 30.504  0.176  30.679
correctGC                 24.154  3.172  27.396
heatmapGenomewide         26.305  0.228  26.539
karyotypeMeasures         25.193  0.260  25.452
annotateBreakpoints       15.195  0.525  16.072
getBreakpoints            11.307  0.128  11.435
consensusSegments          9.577  0.084   9.661
getSCEcoordinates          5.925  0.196   6.315
subsetByCNVprofile         6.077  0.008   6.085
findCNVs.strandseq         5.026  0.048   5.074
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.