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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings CNVMetrics_1.15.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/CNVMetrics.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CNVMetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVMetrics’ version ‘1.15.1’
* 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 ‘CNVMetrics’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CNVMetrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateLog2ratioMetric
> ### Title: Calculate metric using overlapping amplified/deleted regions
> ### Aliases: calculateLog2ratioMetric
> 
> ### ** Examples
> 
> 
> ## Load required package to generate the samples
> require(GenomicRanges)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

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
> 
> ## Create a GRangesList object with 3 samples
> ## The stand of the regions doesn't affect the calculation of the metric
> demo <- GRangesList()
> demo[["sample01"]] <- GRanges(seqnames="chr1",
+     ranges=IRanges(start=c(1905048, 4554832, 31686841),
+     end=c(2004603, 4577608, 31695808)), strand="*",
+     log2ratio=c(2.5555, 1.9932, -0.9999))
> 
> demo[["sample02"]] <- GRanges(seqnames="chr1",
+     ranges=IRanges(start=c(1995066, 31611222, 31690000),
+     end=c(2204505, 31689898, 31895666)), strand=c("-", "+", "+"),
+     log2ratio=c(0.3422, 0.5454, -1.4444))
> 
> ## The amplified region in sample03 is a subset of the amplified regions
> ## in sample01
> demo[["sample03"]] <- GRanges(seqnames="chr1",
+     ranges=IRanges(start=c(1906069, 4558838),
+     end=c(1909505, 4570601)), strand="*",
+     log2ratio=c(3.2222, -1.3232))
> 
> ## Calculating Sorensen metric
> calculateLog2ratioMetric(demo, method="weightedEuclideanDistance", nJobs=1)
Error in calculateLog2ratioMetric(demo, method = "weightedEuclideanDistance",  : 
  At least one parallel task has failed.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   12.             ├─methods (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
   13.             └─IRanges (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
   14.               └─IRanges (local) .local(x, ..., na.rm = na.rm)
   15.                 └─IRanges:::.range_CompressedIRangesList(x, with.revmap = with.revmap)
   16.                   └─S4Vectors:::load_package_gracefully(...)
  ── Error ('test-genericCNVMetric.R:149:5'): print() for CNVMetric object must return expected result with weighted Euclidean Distance-based metric ──
  Error in `calculateLog2ratioMetric(demo, method = "weightedEuclideanDistance", minThreshold = 0.2, excludedRegions = NULL)`: At least one parallel task has failed.
  Backtrace:
      ▆
   1. └─CNVMetrics::calculateLog2ratioMetric(...) at test-genericCNVMetric.R:149:5
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 69 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘CNVMetrics.Rmd’ using rmarkdown

Quitting from CNVMetrics.Rmd:487-492 [demoCalculateMetricLog]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `calculateLog2ratioMetric()`:
! At least one parallel task has failed.
---
Backtrace:
    ▆
 1. └─CNVMetrics::calculateLog2ratioMetric(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CNVMetrics.Rmd' failed with diagnostics:
At least one parallel task has failed.
--- failed re-building ‘CNVMetrics.Rmd’

SUMMARY: processing the following file failed:
  ‘CNVMetrics.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/CNVMetrics.Rcheck/00check.log’
for details.