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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:Repitools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Repitools_1.56.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Repitools.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.56.0’
* 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 ‘Repitools’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 whether 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 ... OK
* checking Rd files ... WARNING
checkRd: (5) AdjustedCopyEstimate-class.Rd:16-34: \item in \describe must have non-empty label
checkRd: (5) BayMethList-class.Rd:58-88: \item in \describe must have non-empty label
checkRd: (-1) ChromaResults-class.Rd:25: Lost braces
    25 |     \code{blocks:}{\code{GRanges} of the blocks used across the genome, with their calculated RPKM}
       |                   ^
checkRd: (-1) ChromaResults-class.Rd:26: Lost braces
    26 |     \code{regions:}{\code{IRangesList} of regions determined to be enriched}
       |                    ^
checkRd: (-1) ChromaResults-class.Rd:27: Lost braces
    27 |     \code{FDRTable:}{\code{data.frame} showing the FDR at each cutoff tested}
       |                     ^
checkRd: (-1) ChromaResults-class.Rd:28: Lost braces
    28 |     \code{cutoff:}{The cutoff used to determine enrichment}
       |                   ^
checkRd: (5) ClusteredScoresList-class.Rd:29-50: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:57-60: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:61-64: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:75-78: \item in \describe must have non-empty label
checkRd: (5) CopyEstimate-class.Rd:14-23: \item in \describe must have non-empty label
checkRd: (5) GCAdjustParams-class.Rd:14-37: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:24-27: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:28-31: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:32-35: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:42-45: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:46-49: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AdjustedCopyEstimate-class.Rd: GRanges-class, GRangesList-class
  BayMethList-class.Rd: GRanges-class
  ClusteredScoresList-class.Rd: GRanges-class
  CopyEstimate-class.Rd: GRanges-class, GRangesList-class
  GCAdjustParams-class.Rd: BSgenome-class
  MappabilitySource-class.Rd: BSgenome-class
  annoDF2GR.Rd: GRanges-class
  featureBlocks.Rd: GRanges-class
  featureScores.Rd: BSgenome-class
  mergeReplicates.Rd: GRangesList-class
  relativeCN.Rd: segment
  samplesList.Rd: GRangesList-class
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Repitools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: empBayes
> ### Title: Function to calculate prior parameters using empirical Bayes.
> ### Aliases: empBayes
> ### Keywords: programming
> 
> ### ** Examples
> 
>     if(require(BSgenome.Hsapiens.UCSC.hg18)){
+         windows <- genomeBlocks(Hsapiens, chrs="chr21", width=100, spacing=100)
+         cpgdens <- cpgDensityCalc(windows, organism=Hsapiens, 
+             w.function="linear", window=700)  
+         co <- matrix(rnbinom(length(windows), mu=10, size=2), ncol=1)
+         sI <- matrix(rnbinom(2*length(windows), mu=5, size=2), ncol=2)
+         bm <- BayMethList(windows=windows, control=co, 
+             sampleInterest=sI, cpgDens=cpgdens)
+         bm <- determineOffset(bm)
+  
+         # mask out unannotated high copy number regions
+         # see Pickrell et al. (2011), Bioinformatics 27: 2144-2146.
+ 
+         # should take about 3 minutes for both sample of interests with 2 CPUs.
+         bm <- empBayes(bm, ngroups=20) 
+    }
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: GenomicRanges
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:Repitools’:

    blocks

CpG density calculated for a sample.


	You provided 1 SssI samples and 2 samples of interest

Offset is determined for sample of interest: 1

Offset is determined for sample of interest: 2


	Information: The program will take advantage of 10 CPUs from total 32
	If you would like to change this please cancel and set explicitly the argument 'ncpus'


Error in .check_ncores(cores) : 10 simultaneous processes spawned
Calls: empBayes -> mclapply -> .check_ncores
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
cpgDensityCalc    9.042  0.472  12.409
BayMethList-class 7.921  0.185   8.966
determineOffset   5.583  0.040   6.235
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.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: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Repitools.Rcheck/00check.log’
for details.