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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:nucleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings nucleR_2.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/nucleR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘2.41.0’
* 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 ‘nucleR’ 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 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 loading without being on the library search path ... 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
.loadPairedBam: no visible global function definition for
  ‘sortSeqlevels’
peakDetection,list: no visible global function definition for
  ‘seqlevels<-’
peakScoring,IRangesList: no visible global function definition for
  ‘seqlevels<-’
Undefined global functions or variables:
  seqlevels<- sortSeqlevels
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘Starr’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'dot-fftRegion.Rd'
  ‘data2’ ‘pcKeepComp’

Undocumented arguments in Rd file 'dot-loadFiles.Rd'
  ‘singleLoad’ ‘pairedLoad’

Undocumented arguments in Rd file 'dot-loadPairedBam.Rd'
  ‘file’

Undocumented arguments in Rd file 'dot-loadSingleBam.Rd'
  ‘exp’

Undocumented arguments in Rd file 'dot-mid.Rd'
  ‘x’

Undocumented arguments in Rd file 'dot-unlist_as_integer.Rd'
  ‘x’

Undocumented arguments in Rd file 'dot-xlapply.Rd'
  ‘X’ ‘FUN’ ‘...’ ‘mc.cores’

Documented arguments not in \usage in Rd file 'pcKeepCompDetect.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... ERROR
Running examples in ‘nucleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mergeCalls
> ### Title: Automatic merging of overlapped nucleosome calls
> ### Aliases: mergeCalls mergeCalls,GRanges-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> # Generate a synthetic coverage map (assuming reads of 40bp and fragments
> # of 130)
> map <- syntheticNucMap(
+     wp.num=20, fuz.num=20,  nuc.len=40, lin.len=130, rnd.seed=1
+ )
> cover <- filterFFT(coverage.rpm(map$syn.reads))
> 
> # Find peaks over FFT filtered coverage
> calls <- peakDetection(filterFFT(
+     cover, pcKeepComp=0.02), width=130, score=TRUE
+ )
> 
> # Merge overlapped calls
> merged_calls <- mergeCalls(calls)
* Starting space: *
 - Finding overlapped reads
 - Done (6 non-overlapped | 17 merged calls)
> 
> plotPeaks(merged_calls, cover)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'runLength': could not find function "seqnames"
Calls: plotPeaks -> plotPeaks -> runLength -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/nucleR.Rcheck/00check.log’
for details.