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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:NADfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings NADfinder_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/NADfinder.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 ‘NADfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NADfinder’ version ‘1.26.0’
* 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 ‘NADfinder’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   5.0Mb
* 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 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘NADfinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: callPeaks
> ### Title: Call peaks using transformed, background corrected, and smoothed
> ###   ratios with biological replicates
> ### Aliases: callPeaks
> 
> ### ** Examples
> 
> 
> data(triplicate.count)
> se <- triplicate.count
> se <- log2se(se, transformation = "log2CPMRatio",
+              nucleolusCols = c("N18.subsampled.srt-2.bam",
+              "N18.subsampled.srt-3.bam",
+              "N18.subsampled.srt.bam"),
+              genomeCols = c("G18.subsampled.srt-2.bam",
+              "G18.subsampled.srt-3.bam",
+              "G18.subsampled.srt.bam"))
> se<- smoothRatiosByChromosome(se, chr="chr18")
> #add some variability to the data since the triplicate.count data was created using one sample only
> assays(se[[1]])$bcRatio[,2] <- assays(se[[1]])$bcRatio[,2] + 0.3
> assays(se[[1]])$bcRatio[,3] <- assays(se[[1]])$bcRatio[,3] - 0.3
> peaks <- callPeaks(se[[1]],
+                 cutoffAdjPvalue=0.001, countFilter=10)
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  1.1341e-16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.935
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 8.065
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 25
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 11.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 11.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 11.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.935
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 8.065
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 25
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 12.055
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 7.055
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 12.055
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 7.055
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/NADfinder.Rcheck/00check.log’
for details.