Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-01-28 11:05:17 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
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

CHECK results for CopyNumberPlots on nebbiolo1


To the developers/maintainers of the CopyNumberPlots package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 406/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumberPlots 1.15.0  (landing page)
Bernat Gel
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/CopyNumberPlots
git_branch: master
git_last_commit: a3d45ec
git_last_commit_date: 2022-11-01 11:19:46 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CopyNumberPlots
Version: 1.15.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CopyNumberPlots_1.15.0.tar.gz
StartedAt: 2023-01-27 19:46:48 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 19:52:36 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 347.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CopyNumberPlots.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CopyNumberPlots_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CopyNumberPlots.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CopyNumberPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CopyNumberPlots’ version ‘1.15.0’
* 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 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CopyNumberPlots.Rmd’ using ‘UTF-8’... OK
 NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL CopyNumberPlots
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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 
 15.304   0.798  16.092 

Example timings

CopyNumberPlots.Rcheck/CopyNumberPlots-Ex.timings

nameusersystemelapsed
EnsemblStyle0.440.000.44
UCSCStyle0.2970.0200.317
Ztree2Hclust0.0060.0000.006
colByCopyNumber0.4380.0440.481
computeHclustPlotOrder0.0220.0000.022
getBAFColumn0.0000.0010.002
getChrColumn0.0000.0020.001
getColumn0.0000.0020.002
getCopyNumberColors0.0000.0010.001
getCopyNumberColumn0.0010.0000.002
getEndColumn0.0010.0000.002
getIDColumn0.0020.0000.002
getLOHColumn0.0020.0000.001
getLRRColumn0.0020.0000.001
getPosColumn0.0020.0000.001
getSegmentValueColumn0.0020.0000.001
getStartColumn0.0010.0000.002
loadCopyNumberCalls0.0160.0040.020
loadCopyNumberCallsCNVkit0.0500.0030.054
loadCopyNumberCallsCnmops0.1490.0210.169
loadCopyNumberCallsDECoN0.0610.0110.073
loadCopyNumberCallsDNAcopy0.5520.0010.553
loadCopyNumberCallsPanelcnmops0.2610.0040.267
loadCopyNumberCallsSeg0.0170.0000.017
loadCopyNumberCallspennCNV0.0320.0000.032
loadSNPData0.0430.0000.043
loadSNPDataDNAcopy0.4890.0040.493
loadSNPDataFromVCF0.0010.0000.001
plotBAF0.9530.0040.956
plotCopyNumberCalls0.1540.0040.158
plotCopyNumberCallsAsLines0.1350.0040.139
plotCopyNumberSummary0.1670.0000.167
plotLRR0.3790.0000.379
plotSingleCellCopyNumberCalls0.0550.0000.054
plotSingleCellCopyNumberSummary0.0320.0000.032
prepareLabels0.0650.0000.065
readHDF5Ztree000
removeNAs0.1420.0000.142
transformChr0.0030.0000.004