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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings AneuFinder_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/AneuFinder.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.26.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
simulateReads             49.582  3.235  52.850
refineBreakpoints         47.005  0.500  47.506
heatmapAneuploidies       40.266  0.763  41.030
plotHeterogeneity         28.623  0.088  28.711
correctGC                 24.629  3.208  27.907
heatmapGenomewideClusters 25.498  0.292  25.791
karyotypeMeasures         21.330  0.128  21.458
heatmapGenomewide         19.562  0.201  19.773
annotateBreakpoints       15.324  0.352  16.078
getBreakpoints            10.681  0.164  10.845
consensusSegments          7.469  0.036   7.505
subsetByCNVprofile         5.245  0.012   5.257
* 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 ...
  ‘AneuFinder.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.