Back to Multiple platform build/check report for BioC 3.12
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CopyNumberPlots on malbec1

This page was generated on 2021-05-06 12:27:14 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CopyNumberPlots package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 374/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumberPlots 1.6.0  (landing page)
Bernat Gel
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CopyNumberPlots
Branch: RELEASE_3_12
Last Commit: bb544ff
Last Changed Date: 2020-10-27 11:45:26 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CopyNumberPlots
Version: 1.6.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CopyNumberPlots_1.6.0.tar.gz
StartedAt: 2021-05-06 00:25:57 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:32:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 396.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CopyNumberPlots.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CopyNumberPlots_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CopyNumberPlots.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CopyNumberPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CopyNumberPlots’ version ‘1.6.0’
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CopyNumberPlots.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CopyNumberPlots
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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 version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("CopyNumberPlots")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 20.976   0.548  23.075 

Example timings

CopyNumberPlots.Rcheck/CopyNumberPlots-Ex.timings

nameusersystemelapsed
EnsemblStyle0.8400.0120.853
UCSCStyle0.5400.0560.597
Ztree2Hclust0.0080.0000.008
colByCopyNumber0.4600.0680.529
computeHclustPlotOrder0.0200.0000.023
getBAFColumn0.0040.0000.002
getChrColumn0.0040.0000.002
getColumn0.0000.0000.003
getCopyNumberColors000
getCopyNumberColumn0.0000.0000.002
getEndColumn0.0000.0000.001
getIDColumn0.0040.0000.002
getLOHColumn0.0000.0000.001
getLRRColumn0.0000.0000.002
getPosColumn0.0040.0000.002
getSegmentValueColumn0.0000.0000.002
getStartColumn0.0000.0040.002
loadCopyNumberCalls0.0200.0040.022
loadCopyNumberCallsCNVkit0.0320.0000.046
loadCopyNumberCallsCnmops0.3600.0120.377
loadCopyNumberCallsDECoN0.1400.0080.161
loadCopyNumberCallsDNAcopy0.9440.0080.956
loadCopyNumberCallsPanelcnmops0.4040.0040.433
loadCopyNumberCallsSeg0.0280.0000.028
loadCopyNumberCallspennCNV0.0560.0000.074
loadSNPData0.0840.0000.093
loadSNPDataDNAcopy0.5800.0040.583
loadSNPDataFromVCF000
plotBAF1.6400.0041.654
plotCopyNumberCalls0.7640.0000.768
plotCopyNumberCallsAsLines1.2680.0041.274
plotCopyNumberSummary2.9120.0002.916
plotLRR0.60.00.6
plotSingleCellCopyNumberCalls0.0960.0000.095
plotSingleCellCopyNumberSummary0.0600.0040.063
prepareLabels0.1480.0000.149
readHDF5Ztree000
removeNAs0.2720.0000.269
transformChr0.0040.0000.004