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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DMRcaller_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.42.0’
* 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 ‘DMRcaller’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’ ‘S4Vectors’ ‘IRanges’ ‘betareg’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘GenomeInfoDb’ ‘Seqinfo’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.validateModif: no visible global function definition for ‘seqlengths’
extractGC: no visible global function definition for ‘seqlevels’
readONTbam: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg38’
readONTbam: no visible global function definition for ‘seqlengths’
selectCytosine: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg38’
selectCytosine : <anonymous>: no visible global function definition for
  ‘seqlengths’
selectCytosine : <anonymous>: no visible global function definition for
  ‘seqlevels<-’
selectCytosine : <anonymous>: no visible global function definition for
  ‘seqlengths<-’
selectCytosine: no visible global function definition for ‘seqlevels<-’
selectCytosine: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg38 seqlengths seqlengths<- seqlevels
  seqlevels<-
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyseReadsInsideRegionsForCondition.Rd: GRanges
  computeDMRs.Rd: GRanges
  computeMethylationDataCoverage.Rd: GRanges
  computeMethylationProfile.Rd: GRanges
  computeOverlapProfile.Rd: GRanges
  computeVMDs.Rd: GRanges
  extractGC.Rd: GRanges
  filterDMRs.Rd: GRanges
  filterVMDs.Rd: GRanges
  getWholeChromosomes.Rd: GRanges
  mergeDMRsIteratively.Rd: GRanges
  plotLocalMethylationProfile.Rd: GRanges, GRangesList
  plotMethylationDataCoverage.Rd: GRanges
  plotMethylationProfile.Rd: GRanges
  plotMethylationProfileFromData.Rd: GRanges
  plotOverlapProfile.Rd: GRanges
  poolMethylationDatasets.Rd: GRangesList, GRanges
  poolTwoMethylationDatasets.Rd: GRanges
  readBismark.Rd: GRanges
  readBismarkPool.Rd: GRanges
  saveBismark.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
computePMDs          78.725  0.358  79.209
filterVMDs           29.047  0.168  29.257
computeDMRs          10.796  0.159  10.970
mergeDMRsIteratively 10.477  0.097  10.596
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.