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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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 427/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumberPlots 1.21.0  (landing page)
Bernat Gel
Snapshot Date: 2024-06-14 14:00 -0400 (Fri, 14 Jun 2024)
git_url: https://git.bioconductor.org/packages/CopyNumberPlots
git_branch: devel
git_last_commit: f3b8d6f
git_last_commit_date: 2024-04-30 11:14:18 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CopyNumberPlots on nebbiolo2

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.

raw results


Summary

Package: CopyNumberPlots
Version: 1.21.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CopyNumberPlots_1.21.0.tar.gz
StartedAt: 2024-06-14 21:51:48 -0400 (Fri, 14 Jun 2024)
EndedAt: 2024-06-14 21:57:48 -0400 (Fri, 14 Jun 2024)
EllapsedTime: 360.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CopyNumberPlots.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CopyNumberPlots_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CopyNumberPlots.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CopyNumberPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CopyNumberPlots’ version ‘1.21.0’
* 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 ... 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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CopyNumberPlots.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CopyNumberPlots
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘CopyNumberPlots’ ...
** 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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 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(CopyNumberPlots)
Loading required package: karyoploteR
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 
 13.597   0.707  14.291 

Example timings

CopyNumberPlots.Rcheck/CopyNumberPlots-Ex.timings

nameusersystemelapsed
EnsemblStyle0.3480.0240.372
UCSCStyle0.2550.0390.295
Ztree2Hclust0.0060.0000.006
colByCopyNumber0.6680.0280.696
computeHclustPlotOrder0.0210.0000.021
getBAFColumn0.0020.0000.002
getChrColumn0.0020.0000.002
getColumn0.0020.0000.002
getCopyNumberColors0.0010.0000.001
getCopyNumberColumn0.0010.0000.001
getEndColumn0.0010.0000.001
getIDColumn0.0020.0000.002
getLOHColumn0.0010.0000.001
getLRRColumn0.0010.0000.001
getPosColumn0.0010.0000.001
getSegmentValueColumn0.0010.0000.001
getStartColumn0.0010.0000.001
loadCopyNumberCalls0.0160.0000.016
loadCopyNumberCallsCNVkit0.0450.0000.045
loadCopyNumberCallsCnmops0.1070.0000.106
loadCopyNumberCallsDECoN0.0550.0000.054
loadCopyNumberCallsDNAcopy0.5210.0000.521
loadCopyNumberCallsPanelcnmops0.2590.0030.265
loadCopyNumberCallsSeg0.0180.0010.017
loadCopyNumberCallspennCNV0.060.000.06
loadSNPData0.0400.0000.039
loadSNPDataDNAcopy0.5530.0080.561
loadSNPDataFromVCF0.0010.0000.001
plotBAF0.8810.0230.905
plotCopyNumberCalls0.1640.0120.176
plotCopyNumberCallsAsLines0.1440.0160.160
plotCopyNumberSummary0.1340.0360.170
plotLRR1.2990.0681.367
plotSingleCellCopyNumberCalls0.0490.0000.049
plotSingleCellCopyNumberSummary0.030.000.03
prepareLabels0.0610.0000.061
readHDF5Ztree000
removeNAs0.1290.0010.129
transformChr0.0030.0000.003