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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MMDiff2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MMDiff2_1.37.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MMDiff2.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 ‘MMDiff2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff2’ version ‘1.37.0’
* 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 ‘MMDiff2’ 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  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
DBAmmd: no visible global function definition for ‘new’
getReads: no visible global function definition for ‘IRangesList’
Undefined global functions or variables:
  IRangesList new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) DBAmmd-class.Rd:20: Lost braces
    20 | \code{DBAmmd()}{returns an empty DBAmmd Object.} \cr
       |                ^
checkRd: (-1) DBAmmd-class.Rd:21-23: Lost braces
    21 | \code{DBAmmd(MetaData)}{ initializes a DBAmmd Object for a new
       |                        ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ... ERROR
Running examples in ‘MMDiff2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotPeak
> ### Title: plot Peak
> ### Aliases: plotPeak
> 
> ### ** Examples
> 
> dev.off()
null device 
          1 
> data("MMD")
> plotPeak(MMD,Peak.id='6',plot.input=FALSE)
No Samples specified, plotting all samples
No Contrast specified, plotting all samples in one plot
No normalization factors applied
> 
> # add annotation (Overlapping genes)
> data("mm9-Genes")
> GR <- list(UCSCKnownGenes = GR)
> plotPeak(MMD, Peak.id='6', plot.input = FALSE, anno=GR)
No Samples specified, plotting all samples
No Contrast specified, plotting all samples in one plot
No normalization factors applied
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: plotPeak ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
compDists        17.93  1.449  19.379
DBAmmd-Accessors  6.95  0.212   7.162
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MMDiff2.Rcheck/00check.log’
for details.