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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings AneuFinder_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/AneuFinder.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.30.0’
* 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
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ... 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 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 ... ERROR
Running examples in ‘AneuFinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: correctGC
> ### Title: GC correction
> ### Aliases: correctGC
> 
> ### ** Examples
> 
> ## Get a BED file, bin it and run GC correction
> bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
> binned <- binReads(bedfile, assembly='mm10', binsize=1e6,
+                   chromosomes=c(1:19,'X','Y'))
Reading file KK150311_VI_07.bam.bed.gz ... 1.15s
Fetching chromosome lengths from UCSC ... 0.01s
Subsetting chromosomes ... 0.03s
Filtering reads ... 0.14s
Subsetting specified chromosomes ... 0.02s
Calculating complexity ... 0.3s
Removing duplicate reads ... 0.19s
Calculating coverage ... 0.66s
Making fixed-width bins for bin size 1e+06 ... 0.03s
Splitting into strands ... 0.02s
Counting overlaps for binsize_1e+06 ... 0.23s
> plot(binned[[1]], type=1)
> if (require(BSgenome.Mmusculus.UCSC.mm10)) {
+  binned.GC <- correctGC(list(binned[[1]]), GC.BSgenome=BSgenome.Mmusculus.UCSC.mm10)
+  plot(binned.GC[[1]], type=1)
+ }
Loading required package: BSgenome.Mmusculus.UCSC.mm10
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

The following object is masked from ‘package:BiocIO’:

    FileForFormat

Calculating GC content per bin and stepsize ...
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.