Package: CopyNumberPlots

Version: 1.0.1

Command: /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_1.0.1.tar.gz

StartedAt: 2019-10-16 01:47:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:53:44 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 404.0 seconds

RetCode: 0

Status:  OK

CheckDir: CopyNumberPlots.Rcheck

Warnings: 0

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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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CopyNumberPlots.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.1’
* 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 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

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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/3.6/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)

name	user	system	elapsed
EnsemblStyle	0.473	0.041	0.513
UCSCStyle	0.274	0.014	0.287
colByCopyNumber	0.459	0.011	0.469
getBAFColumn	0.003	0.000	0.003
getChrColumn	0.003	0.000	0.003
getColumn	0.003	0.000	0.004
getCopyNumberColors	0.001	0.002	0.003
getCopyNumberColumn	0.003	0.000	0.003
getEndColumn	0.002	0.000	0.003
getIDColumn	0.003	0.000	0.003
getLOHColumn	0.002	0.000	0.003
getLRRColumn	0.002	0.000	0.002
getPosColumn	0.003	0.000	0.002
getSegmentValueColumn	0.002	0.001	0.003
getStartColumn	0.003	0.000	0.003
loadCopyNumberCalls	0.017	0.001	0.017
loadCopyNumberCallsCNVkit	0.026	0.001	0.029
loadCopyNumberCallsCnmops	0.199	0.022	0.222
loadCopyNumberCallsDECoN	0.256	0.016	0.273
loadCopyNumberCallsDNAcopy	0.997	0.020	1.016
loadCopyNumberCallsPanelcnmops	0.527	0.012	0.545
loadCopyNumberCallsSeg	0.020	0.001	0.022
loadCopyNumberCallspennCNV	0.048	0.001	0.050
loadSNPData	0.037	0.001	0.040
loadSNPDataDNAcopy	0.968	0.005	0.975
loadSNPDataFromVCF	0.001	0.000	0.002
plotBAF	0.989	0.019	1.012
plotCopyNumberCalls	0.641	0.113	0.759
plotCopyNumberCallsAsLines	1.073	0.178	1.258
plotCopyNumberSummary	1.559	0.019	1.582
plotLRR	0.334	0.004	0.340
prepareLabels	0.088	0.001	0.089
removeNAs	0.155	0.001	0.155
transformChr	0.007	0.000	0.007