Package: CopyNumberPlots

Version: 1.0.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CopyNumberPlots_1.0.1.tar.gz

StartedAt: 2019-10-16 00:48:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:52:59 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 294.7 seconds

RetCode: 0

Status:  OK

CheckDir: CopyNumberPlots.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CopyNumberPlots_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CopyNumberPlots.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.1’
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CopyNumberPlots
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* installing to library ‘/home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
EnsemblStyle	0.400	0.012	0.412
UCSCStyle	0.203	0.004	0.207
colByCopyNumber	0.444	0.000	0.445
getBAFColumn	0.004	0.000	0.003
getChrColumn	0.000	0.003	0.003
getColumn	0.004	0.000	0.004
getCopyNumberColors	0.001	0.000	0.001
getCopyNumberColumn	0.003	0.000	0.002
getEndColumn	0.003	0.000	0.003
getIDColumn	0.002	0.000	0.003
getLOHColumn	0.003	0.000	0.002
getLRRColumn	0.003	0.000	0.003
getPosColumn	0.003	0.000	0.003
getSegmentValueColumn	0.003	0.000	0.003
getStartColumn	0.002	0.001	0.003
loadCopyNumberCalls	0.014	0.002	0.016
loadCopyNumberCallsCNVkit	0.023	0.000	0.038
loadCopyNumberCallsCnmops	0.166	0.008	0.176
loadCopyNumberCallsDECoN	0.177	0.008	0.184
loadCopyNumberCallsDNAcopy	0.889	0.000	0.889
loadCopyNumberCallsPanelcnmops	0.459	0.000	0.881
loadCopyNumberCallsSeg	0.016	0.000	0.017
loadCopyNumberCallspennCNV	0.943	0.000	0.943
loadSNPData	0.035	0.000	0.051
loadSNPDataDNAcopy	0.716	0.000	0.716
loadSNPDataFromVCF	0.000	0.000	0.001
plotBAF	0.557	0.000	0.556
plotCopyNumberCalls	0.337	0.040	0.376
plotCopyNumberCallsAsLines	0.457	0.032	0.488
plotCopyNumberSummary	1.208	0.005	1.223
plotLRR	0.311	0.000	0.310
prepareLabels	0.081	0.000	0.082
removeNAs	0.151	0.000	0.150
transformChr	0.005	0.000	0.006