##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CNVMetrics_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CNVMetrics.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.14.0’
* 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 ‘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 ... NOTE
checkRd: (-1) CNVMetrics-package.Rd:23-24: Lost braces
    23 |     \item \code{\link{calculateOverlapMetric}} {for calculating metric
       |                                                ^
checkRd: (-1) CNVMetrics-package.Rd:25-26: Lost braces
    25 |     \item \code{\link{calculateLog2ratioMetric}} {for calculating metric
       |                                                  ^
checkRd: (-1) CNVMetrics-package.Rd:27: Lost braces; missing escapes or markup?
    27 |     \item \code{\link{processSim}} {for generating simulations}
       |                                    ^
checkRd: (-1) CNVMetrics-package.Rd:28: Lost braces; missing escapes or markup?
    28 |     \item \code{\link{plotMetric}} {for plotting metrics}
       |                                    ^
checkRd: (-1) calculateLog2ratioMetric.Rd:42-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateLog2ratioMetric.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateLog2ratioMetric.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOneLog2valueMetricT.Rd:37: Lost braces
    37 | that have to be excluded for the metric calculation or code{NULL}.}
       |                                                            ^
checkRd: (-1) calculateOneLog2valueMetricT.Rd:42-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOneOverlapMetricT.Rd:33-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:39-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:26: Lost braces
    26 | a code{list} containing one entry per simulation. Each entry is
       |       ^
checkRd: (-1) simChr.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:31-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CNVMetrics.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CNVMetrics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘CNVMetrics’ ...
** this is package ‘CNVMetrics’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNVMetrics)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CNVMetrics)
> 
> ## Run all unit tests
> test_check("CNVMetrics")
CNV Metrics
Metric:
sorensen

AMPLIFICATION:
           sample01 sample02 sample03
sample01         NA       NA       NA
sample02 0.04647582       NA       NA
sample03 0.05465532        0       NA


DELETION:
          sample01 sample02 sample03
sample01        NA       NA       NA
sample02 0.0541291       NA       NA
sample03 0.0000000        0       NA

CNV Metrics
Metric:
sorensen

AMPLIFICATION:
           sample01  sample02  sample03 sample04 sample05
sample01         NA        NA        NA       NA       NA
sample02 0.04647582        NA        NA       NA       NA
sample03 0.05465532 0.0000000        NA       NA       NA
sample04 0.05820635 0.0000000 0.9676239       NA       NA
sample05 0.14207052 0.3293641 0.0000000        0       NA
[ -- omitted 1 row/column ]

DELETION:
          sample01 sample02  sample03  sample04 sample05
sample01        NA       NA        NA        NA       NA
sample02 0.0541291       NA        NA        NA       NA
sample03 0.0000000        0        NA        NA       NA
sample04 0.0000000        0 0.9791909        NA       NA
sample05 0.0000000        0 0.9363260 0.9570782       NA
[ -- omitted 1 row/column ]
CNV Metrics
Metric:
szymkiewicz

AMPLIFICATION:
           sample01  sample02 sample03 sample04 sample05
sample01         NA        NA       NA       NA       NA
sample02 0.07796751        NA       NA       NA       NA
sample03 1.00000000 0.0000000       NA       NA       NA
sample04 1.00000000 0.0000000        1       NA       NA
sample05 0.64222246 0.7269269        0        0       NA
[ -- omitted 2 rows/columns ]

DELETION:
          sample01 sample02 sample03 sample04 sample05
sample01        NA       NA       NA       NA       NA
sample02 0.6477475       NA       NA       NA       NA
sample03 0.0000000        0       NA       NA       NA
sample04 0.0000000        0        1       NA       NA
sample05 0.0000000        0        1        1       NA
[ -- omitted 2 rows/columns ]
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 69 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-CNVMetricInternalMethods.R:27:5'): createDisjoinSegmentsForTwoSamples() must return expected results ──
Error in `S4Vectors:::load_package_gracefully("XVector", "by the range() method ", 
    "for CompressedIRangesList objects")`: Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Backtrace:
     ▆
  1. └─CNVMetrics:::createDisjoinSegmentsForTwoSamples(...) at test-CNVMetricInternalMethods.R:27:5
  2.   ├─IRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  3.   └─GenomicRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  4.     └─GenomicRanges (local) .local(x, ...)
  5.       ├─methods::callGeneric(rgl, with.revmap = with.revmap)
  6.       │ └─base::eval(call, parent.frame())
  7.       │   └─base::eval(call, parent.frame())
  8.       ├─IRanges::disjoin(rgl, with.revmap = with.revmap)
  9.       └─IRanges::disjoin(rgl, with.revmap = with.revmap)
 10.         └─IRanges (local) .local(x, ...)
 11.           ├─methods (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 12.           └─IRanges (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 13.             └─IRanges (local) .local(x, ..., na.rm = na.rm)
 14.               └─IRanges:::.range_CompressedIRangesList(x, with.revmap = with.revmap)
 15.                 └─S4Vectors:::load_package_gracefully(...)
── Error ('test-CNVMetricInternalMethods.R:59:5'): createDisjoinSegmentsForTwoSamples() must return expected results when exclusion file used ──
Error in `S4Vectors:::load_package_gracefully("XVector", "by the range() method ", 
    "for CompressedIRangesList objects")`: Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Backtrace:
     ▆
  1. └─CNVMetrics:::createDisjoinSegmentsForTwoSamples(...) at test-CNVMetricInternalMethods.R:59:5
  2.   ├─IRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  3.   └─GenomicRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  4.     └─GenomicRanges (local) .local(x, ...)
  5.       ├─methods::callGeneric(rgl, with.revmap = with.revmap)
  6.       │ └─base::eval(call, parent.frame())
  7.       │   └─base::eval(call, parent.frame())
  8.       ├─IRanges::disjoin(rgl, with.revmap = with.revmap)
  9.       └─IRanges::disjoin(rgl, with.revmap = with.revmap)
 10.         └─IRanges (local) .local(x, ...)
 11.           ├─methods (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 12.           └─IRanges (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 13.             └─IRanges (local) .local(x, ..., na.rm = na.rm)
 14.               └─IRanges:::.range_CompressedIRangesList(x, with.revmap = with.revmap)
 15.                 └─S4Vectors:::load_package_gracefully(...)
── Error ('test-CNVMetricMethods.R:214:5'): plotMetric() must return a gtable when graph for log2ratio metric ──
Error in `calculateLog2ratioMetric(demo, method = "weightedEuclideanDistance")`: At least one parallel task has failed.
Backtrace:
    ▆
 1. └─CNVMetrics::calculateLog2ratioMetric(demo, method = "weightedEuclideanDistance") at test-CNVMetricMethods.R:214:5
── Error ('test-CNVMetricsLog2ratioInternalMethods.R:137:5'): createDisjoinSegmentsForTwoSamples() must return expected result when bedExclusion=NULL ──
Error in `S4Vectors:::load_package_gracefully("XVector", "by the range() method ", 
    "for CompressedIRangesList objects")`: Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Backtrace:
     ▆
  1. └─CNVMetrics:::createDisjoinSegmentsForTwoSamples(...) at test-CNVMetricsLog2ratioInternalMethods.R:137:5
  2.   ├─IRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  3.   └─GenomicRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  4.     └─GenomicRanges (local) .local(x, ...)
  5.       ├─methods::callGeneric(rgl, with.revmap = with.revmap)
  6.       │ └─base::eval(call, parent.frame())
  7.       │   └─base::eval(call, parent.frame())
  8.       ├─IRanges::disjoin(rgl, with.revmap = with.revmap)
  9.       └─IRanges::disjoin(rgl, with.revmap = with.revmap)
 10.         └─IRanges (local) .local(x, ...)
 11.           ├─methods (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 12.           └─IRanges (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 13.             └─IRanges (local) .local(x, ..., na.rm = na.rm)
 14.               └─IRanges:::.range_CompressedIRangesList(x, with.revmap = with.revmap)
 15.                 └─S4Vectors:::load_package_gracefully(...)
── Error ('test-CNVMetricsLog2ratioInternalMethods.R:176:5'): createDisjoinSegmentsForTwoSamples() must return expected result for specific bedExclusion data ──
Error in `S4Vectors:::load_package_gracefully("XVector", "by the range() method ", 
    "for CompressedIRangesList objects")`: Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Backtrace:
     ▆
  1. └─CNVMetrics:::createDisjoinSegmentsForTwoSamples(...) at test-CNVMetricsLog2ratioInternalMethods.R:176:5
  2.   ├─IRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  3.   └─GenomicRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  4.     └─GenomicRanges (local) .local(x, ...)
  5.       ├─methods::callGeneric(rgl, with.revmap = with.revmap)
  6.       │ └─base::eval(call, parent.frame())
  7.       │   └─base::eval(call, parent.frame())
  8.       ├─IRanges::disjoin(rgl, with.revmap = with.revmap)
  9.       └─IRanges::disjoin(rgl, with.revmap = with.revmap)
 10.         └─IRanges (local) .local(x, ...)
 11.           ├─methods (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 12.           └─IRanges (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
 13.             └─IRanges (local) .local(x, ..., na.rm = na.rm)
 14.               └─IRanges:::.range_CompressedIRangesList(x, with.revmap = with.revmap)
 15.                 └─S4Vectors:::load_package_gracefully(...)
── Error ('test-CNVMetricsLog2ratioInternalMethods.R:221:5'): calculateOneLog2valueMetricT() must return expected result when bedExclusion=NULL ──
Error in `S4Vectors:::load_package_gracefully("XVector", "by the range() method ", 
    "for CompressedIRangesList objects")`: Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Backtrace:
     ▆
  1. └─CNVMetrics:::calculateOneLog2valueMetricT(...) at test-CNVMetricsLog2ratioInternalMethods.R:221:5
  2.   └─CNVMetrics:::createDisjoinSegmentsForTwoSamples(...)
  3.     ├─IRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  4.     └─GenomicRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  5.       └─GenomicRanges (local) .local(x, ...)
  6.         ├─methods::callGeneric(rgl, with.revmap = with.revmap)
  7.         │ └─base::eval(call, parent.frame())
  8.         │   └─base::eval(call, parent.frame())
  9.         ├─IRanges::disjoin(rgl, with.revmap = with.revmap)
 10.         └─IRanges::disjoin(rgl, with.revmap = with.revmap)
 11.           └─IRanges (local) .local(x, ...)
 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-CNVMetricsLog2ratioInternalMethods.R:252:5'): calculateOneLog2valueMetricT() must return expected result when no overlap between samples ──
Error in `S4Vectors:::load_package_gracefully("XVector", "by the range() method ", 
    "for CompressedIRangesList objects")`: Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Backtrace:
     ▆
  1. └─CNVMetrics:::calculateOneLog2valueMetricT(...) at test-CNVMetricsLog2ratioInternalMethods.R:252:5
  2.   └─CNVMetrics:::createDisjoinSegmentsForTwoSamples(...)
  3.     ├─IRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  4.     └─GenomicRanges::disjoin(c(segmentDataSample1, segmentDataSample2))
  5.       └─GenomicRanges (local) .local(x, ...)
  6.         ├─methods::callGeneric(rgl, with.revmap = with.revmap)
  7.         │ └─base::eval(call, parent.frame())
  8.         │   └─base::eval(call, parent.frame())
  9.         ├─IRanges::disjoin(rgl, with.revmap = with.revmap)
 10.         └─IRanges::disjoin(rgl, with.revmap = with.revmap)
 11.           └─IRanges (local) .local(x, ...)
 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