Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-09-22 11:41 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 442/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumberPlots 1.24.0  (landing page)
Bernat Gel
Snapshot Date: 2025-09-18 13:40 -0400 (Thu, 18 Sep 2025)
git_url: https://git.bioconductor.org/packages/CopyNumberPlots
git_branch: RELEASE_3_21
git_last_commit: be5b59c
git_last_commit_date: 2025-04-15 11:43:55 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CopyNumberPlots on kunpeng2

To the developers/maintainers of the CopyNumberPlots package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CopyNumberPlots.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CopyNumberPlots
Version: 1.24.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CopyNumberPlots_1.24.0.tar.gz
StartedAt: 2025-09-19 08:30:16 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 08:37:27 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 430.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CopyNumberPlots.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CopyNumberPlots_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CopyNumberPlots.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CopyNumberPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CopyNumberPlots’ version ‘1.24.0’
* 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 ‘CopyNumberPlots’ 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotBAF.Rd: plotKaryotype
  plotLRR.Rd: plotKaryotype
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CopyNumberPlots.Rcheck/00check.log’
for details.


Installation output

CopyNumberPlots.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CopyNumberPlots
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘CopyNumberPlots’ ...
** this is package ‘CopyNumberPlots’ version ‘1.24.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (CopyNumberPlots)

Tests output

CopyNumberPlots.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
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Type 'q()' to quit R.

> library(testthat)
> library(CopyNumberPlots)
Loading required package: karyoploteR
Loading required package: regioneR
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: GenomeInfoDb
> 
> test_check("CopyNumberPlots")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 18.945   0.700  19.680 

Example timings

CopyNumberPlots.Rcheck/CopyNumberPlots-Ex.timings

nameusersystemelapsed
EnsemblStyle0.5570.0280.587
UCSCStyle0.4080.0520.462
Ztree2Hclust0.0070.0000.007
colByCopyNumber0.8400.0160.858
computeHclustPlotOrder0.0240.0000.024
getBAFColumn0.0020.0000.002
getChrColumn0.0020.0000.002
getColumn0.0020.0000.003
getCopyNumberColors000
getCopyNumberColumn0.0000.0020.002
getEndColumn0.0000.0010.002
getIDColumn0.0020.0000.001
getLOHColumn0.0020.0000.002
getLRRColumn0.0010.0000.002
getPosColumn0.0020.0000.002
getSegmentValueColumn0.0020.0000.002
getStartColumn0.0020.0000.002
loadCopyNumberCalls0.0260.0000.026
loadCopyNumberCallsCNVkit0.0690.0000.070
loadCopyNumberCallsCnmops0.1700.0000.172
loadCopyNumberCallsDECoN0.0850.0000.085
loadCopyNumberCallsDNAcopy0.8130.0230.838
loadCopyNumberCallsPanelcnmops0.3570.0040.369
loadCopyNumberCallsSeg0.0240.0000.026
loadCopyNumberCallspennCNV0.0930.0080.102
loadSNPData0.0600.0000.061
loadSNPDataDNAcopy1.9230.1352.064
loadSNPDataFromVCF0.0010.0000.001
plotBAF1.2760.0601.340
plotCopyNumberCalls0.2240.0240.250
plotCopyNumberCallsAsLines0.2270.0320.259
plotCopyNumberSummary0.2510.0120.264
plotLRR0.5340.0440.580
plotSingleCellCopyNumberCalls0.0650.0040.069
plotSingleCellCopyNumberSummary0.0480.0000.048
prepareLabels0.0980.0000.098
readHDF5Ztree0.0010.0000.000
removeNAs0.2120.0080.220
transformChr0.0050.0000.004