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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_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/AneuFinder.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 ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.24.0’
* 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 ... WARNING
Missing link or links in documentation object 'Aneufinder.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'bed2GRanges.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'binReads.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'blacklist.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'fixedWidthBins.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'mergeStrandseqFiles.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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         108.789  0.740 110.200
simulateReads             100.807  3.340 104.518
heatmapAneuploidies        92.923  0.304  93.436
plotHeterogeneity          58.993  0.313  59.435
heatmapGenomewideClusters  53.732  0.194  54.000
correctGC                  50.273  2.248  52.743
karyotypeMeasures          46.600  0.267  46.937
heatmapGenomewide          45.080  0.178  45.339
annotateBreakpoints        29.299  0.758  30.424
getBreakpoints             23.336  0.531  23.902
consensusSegments          17.201  0.076  17.313
subsetByCNVprofile         11.017  0.042  11.074
getSCEcoordinates          10.142  0.388  10.891
loadFromFiles               9.969  0.061  10.072
findCNVs.strandseq          9.006  0.241   9.264
variableWidthBins           7.956  0.116   8.084
findCNVs                    7.346  0.350   7.713
clusterByQuality            5.470  0.107   5.604
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.