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### Running command:
###
###   /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_1.41.2.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 ‘1.41.2’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’ ‘S4Vectors’ ‘IRanges’
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’ ‘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’
findUnmodCoverageCpp: no visible binding for global variable
  ‘_DMRcaller_findUnmodCoverageCpp’
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 _DMRcaller_findUnmodCoverageCpp
  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:
  DMRcaller.Rd: GRanges
  DMRsNoiseFilterCG.Rd: GRanges
  PMDsBinsCG.Rd: GRanges
  PMDsNoiseFilterCG.Rd: GRanges
  analyseReadsInsideRegionsForCondition.Rd: GRanges
  analyseReadsInsideRegionsForConditionPMD.Rd: GRanges
  computeDMRs.Rd: GRanges
  computeDMRsReplicates.Rd: GRanges
  computeMethylationDataCoverage.Rd: GRanges
  computeMethylationDataSpatialCorrelation.Rd: GRanges
  computeMethylationProfile.Rd: GRanges
  computeOverlapProfile.Rd: GRanges
  computePMDs.Rd: GRanges
  computeVMDs.Rd: GRanges
  extractGC.Rd: GRanges
  filterDMRs.Rd: GRanges
  filterPMDs.Rd: GRanges
  filterVMDs.Rd: GRanges
  getWholeChromosomes.Rd: GRanges
  joinReplicates.Rd: GRanges
  mergeDMRsIteratively.Rd: GRanges
  mergePMDsIteratively.Rd: GRanges
  plotLocalMethylationProfile.Rd: GRanges, GRangesList
  plotMethylationDataCoverage.Rd: GRanges
  plotMethylationDataSpatialCorrelation.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
  scanBamChr1Random5.Rd: scanBam, Rsamtools
  syntheticDataReplicates.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 ... WARNING
Undocumented data sets:
  ‘ont_gr_GM18870_chr1_PMD_bins_1k’
  ‘ont_gr_GM18870_chr1_sorted_bins_1k’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘DMRcaller.Rmd’ ‘DMRcaller.bib’ ‘apa.csl’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/DMRcaller.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system  elapsed
filterVMRsONT        2946.791 25.599 1746.827
filterVMDs             32.180  0.194   32.513
mergeDMRsIteratively   12.451  0.723   13.352
computeDMRs            12.131  0.163   12.355
readBismarkPool         5.042  0.293    5.400
mergePMDsIteratively    5.103  0.065    5.227
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  
  
  Attaching package: 'S4Vectors'
  
  The following object is masked from 'package:utils':
  
      findMatches
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Error in BiocGenerics:::testPackage("DMRcaller") : 
    unable to find unit tests, no subdir 'unitTests'
  Execution halted
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DMRcaller
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DMRcaller’ ...
** this is package ‘DMRcaller’ version ‘1.41.2’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
make: Nothing to be done for `all'.
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-DMRcaller/00new/DMRcaller/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DMRcaller)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("DMRcaller")

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Error in BiocGenerics:::testPackage("DMRcaller") : 
  unable to find unit tests, no subdir 'unitTests'
Execution halted