Multiple platform build/check report for BioC 3.11 - CHECK report for CopyNumberPlots on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CopyNumberPlots_1.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CopyNumberPlots.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.3.3’
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CopyNumberPlots
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 25.734   2.116  27.807

Example timings

name	user	system	elapsed
EnsemblStyle	0.534	0.028	0.571
UCSCStyle	1.442	0.020	1.465
Ztree2Hclust	0.010	0.001	0.011
colByCopyNumber	0.848	0.039	0.888
computeHclustPlotOrder	0.007	0.002	0.012
getBAFColumn	0.003	0.000	0.003
getChrColumn	0.004	0.001	0.004
getColumn	0.005	0.000	0.007
getCopyNumberColors	0.002	0.001	0.003
getCopyNumberColumn	0.004	0.001	0.005
getEndColumn	0.004	0.001	0.005
getIDColumn	0.003	0.000	0.003
getLOHColumn	0.002	0.001	0.003
getLRRColumn	0.003	0.000	0.003
getPosColumn	0.004	0.000	0.004
getSegmentValueColumn	0.004	0.000	0.005
getStartColumn	0.004	0.000	0.005
loadCopyNumberCalls	0.048	0.009	0.057
loadCopyNumberCallsCNVkit	0.042	0.005	0.051
loadCopyNumberCallsCnmops	0.474	0.075	0.550
loadCopyNumberCallsDECoN	0.199	0.035	0.235
loadCopyNumberCallsDNAcopy	1.264	0.060	1.326
loadCopyNumberCallsPanelcnmops	0.753	0.094	0.853
loadCopyNumberCallsSeg	0.036	0.001	0.038
loadCopyNumberCallspennCNV	0.072	0.001	0.073
loadSNPData	0.092	0.002	0.094
loadSNPDataDNAcopy	1.109	0.017	1.126
loadSNPDataFromVCF	0.001	0.000	0.002
plotBAF	1.959	0.076	2.038
plotCopyNumberCalls	1.224	0.166	1.393
plotCopyNumberCallsAsLines	1.567	0.010	1.583
plotCopyNumberSummary	3.391	0.013	3.406
plotLRR	0.786	0.004	0.791
plotSingleCellCopyNumberCalls	0.075	0.001	0.077
plotSingleCellCopyNumberSummary	0.074	0.001	0.076
prepareLabels	0.178	0.001	0.179
readHDF5Ztree	0.000	0.000	0.001
removeNAs	0.315	0.002	0.317
transformChr	0.007	0.000	0.008

CHECK report for CopyNumberPlots on celaya2

Summary

Command output

Installation output

Tests output

Example timings