Package: copynumber

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:copynumber.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings copynumber_1.22.0.tar.gz

StartedAt: 2019-04-15 23:13:44 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:16:19 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 154.0 seconds

RetCode: 0

Status:  OK

CheckDir: copynumber.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:copynumber.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings copynumber_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/copynumber.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.22.0’
* 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 ‘copynumber’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package in Depends field not imported from: ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addArmlines: no visible global function definition for ‘modifyList’
addArmlines: no visible global function definition for ‘abline’
addChromlines: no visible global function definition for ‘modifyList’
addChromlines: no visible global function definition for ‘abline’
addChromlines: no visible global function definition for ‘mtext’
addToFreqPlot: no visible global function definition for ‘abline’
addToFreqPlot: no visible global function definition for ‘axis’
addToFreqPlot: no visible global function definition for ‘title’
addToPlot: no visible global function definition for ‘axis’
addToPlot: no visible global function definition for ‘mtext’
addToPlot: no visible global function definition for ‘title’
addToPlot: no visible global function definition for ‘abline’
aspcf: no visible global function definition for ‘read.table’
aspcf: no visible global function definition for ‘write.table’
c.lines: no visible global function definition for ‘lines’
chromPattern: no visible global function definition for ‘rect’
chromPattern: no visible global function definition for ‘par’
chromosomeAberration: no visible global function definition for
  ‘dev.cur’
chromosomeAberration: no visible global function definition for
  ‘dev.new’
chromosomeAberration: no visible global function definition for ‘par’
chromosomeAberration: no visible global function definition for ‘plot’
chromosomeAberration: no visible global function definition for ‘rect’
chromosomeAberration: no visible global function definition for ‘title’
chromosomeAberration: no visible global function definition for ‘axis’
chromosomeAberration: no visible global function definition for
  ‘abline’
chromosomeAberration: no visible global function definition for
  ‘devAskNewPage’
chromosomeFreq: no visible global function definition for ‘dev.cur’
chromosomeFreq: no visible global function definition for ‘dev.new’
chromosomeFreq: no visible global function definition for ‘par’
chromosomeFreq: no visible global function definition for ‘plot’
chromosomeFreq: no visible global function definition for ‘rect’
chromosomeFreq: no visible global function definition for ‘abline’
chromosomeFreq: no visible global function definition for ‘title’
chromosomeFreq: no visible global function definition for
  ‘devAskNewPage’
chromosomeHeat: no visible global function definition for ‘dev.cur’
chromosomeHeat: no visible global function definition for ‘dev.new’
chromosomeHeat: no visible global function definition for ‘par’
chromosomeHeat: no visible global function definition for ‘plot’
chromosomeHeat: no visible global function definition for ‘rect’
chromosomeHeat: no visible global function definition for ‘title’
chromosomeHeat: no visible global function definition for ‘axis’
chromosomeHeat: no visible global function definition for ‘abline’
chromosomeHeat: no visible global function definition for
  ‘devAskNewPage’
colorSetup: no visible global function definition for
  ‘colorRampPalette’
connectSeg: no visible global function definition for ‘segments’
draw.roundEdge: no visible global function definition for ‘polygon’
drawStalk: no visible global function definition for ‘polygon’
filterMarkS4: no visible global function definition for ‘quantile’
genomeAberration: no visible global function definition for ‘dev.cur’
genomeAberration: no visible global function definition for ‘dev.new’
genomeAberration: no visible global function definition for ‘par’
genomeAberration: no visible global function definition for ‘plot’
genomeAberration: no visible global function definition for ‘rect’
genomeAberration: no visible global function definition for ‘title’
genomeAberration: no visible global function definition for ‘axis’
genomeAberration: no visible global function definition for ‘abline’
genomeAberration: no visible global function definition for
  ‘devAskNewPage’
genomeFreq: no visible global function definition for ‘dev.cur’
genomeFreq: no visible global function definition for ‘dev.new’
genomeFreq: no visible global function definition for ‘par’
genomeFreq: no visible global function definition for ‘plot’
genomeFreq: no visible global function definition for ‘title’
genomeFreq: no visible global function definition for ‘rect’
genomeFreq: no visible global function definition for ‘abline’
genomeFreq: no visible global function definition for ‘devAskNewPage’
genomeHeat: no visible global function definition for ‘dev.cur’
genomeHeat: no visible global function definition for ‘dev.new’
genomeHeat: no visible global function definition for ‘par’
genomeHeat: no visible global function definition for ‘plot’
genomeHeat: no visible global function definition for ‘rect’
genomeHeat: no visible global function definition for ‘title’
genomeHeat: no visible global function definition for ‘axis’
genomeHeat: no visible global function definition for ‘abline’
genomeHeat: no visible global function definition for ‘devAskNewPage’
getFreqPlotParameters: no visible global function definition for
  ‘modifyList’
getHeatParameters: no visible global function definition for
  ‘modifyList’
getMad: no visible global function definition for ‘mad’
getPlotParameters: no visible global function definition for ‘rainbow’
getPlotParameters: no visible global function definition for
  ‘modifyList’
madWins: no visible global function definition for ‘mad’
medianFilter: no visible global function definition for ‘runmed’
multipcf: no visible global function definition for ‘read.table’
multipcf: no visible global function definition for ‘write.table’
pcf: no visible global function definition for ‘read.table’
pcf: no visible global function definition for ‘write.table’
pcfWins: no visible global function definition for ‘mad’
plotAllele: no visible global function definition for ‘modifyList’
plotAllele: no visible global function definition for ‘pdf’
plotAllele: no visible global function definition for ‘dev.cur’
plotAllele: no visible global function definition for ‘dev.new’
plotAllele: no visible global function definition for ‘devAskNewPage’
plotAllele: no visible global function definition for ‘quantile’
plotAllele: no visible global function definition for ‘par’
plotAllele: no visible global function definition for ‘legend’
plotAllele: no visible global function definition for ‘title’
plotAllele: no visible global function definition for ‘graphics.off’
plotChrom: no visible global function definition for ‘pdf’
plotChrom: no visible global function definition for ‘dev.cur’
plotChrom: no visible global function definition for ‘dev.new’
plotChrom: no visible global function definition for ‘devAskNewPage’
plotChrom: no visible global function definition for ‘quantile’
plotChrom: no visible global function definition for ‘par’
plotChrom: no visible global function definition for ‘legend’
plotChrom: no visible global function definition for ‘title’
plotChrom: no visible global function definition for ‘graphics.off’
plotCircle: no visible global function definition for ‘par’
plotCircle: no visible global function definition for ‘plot’
plotCircle: no visible global function definition for ‘text’
plotCircle: no visible global function definition for ‘xspline’
plotCircle: no visible global function definition for ‘lines’
plotGamma: no visible global function definition for ‘quantile’
plotGamma: no visible global function definition for ‘col2rgb’
plotGamma: no visible global function definition for ‘rgb’
plotGamma: no visible global function definition for ‘dev.cur’
plotGamma: no visible global function definition for ‘dev.new’
plotGamma: no visible global function definition for ‘par’
plotGamma: no visible global function definition for ‘plot’
plotGamma: no visible global function definition for ‘axis’
plotGamma: no visible global function definition for ‘box’
plotGamma: no visible global function definition for ‘legend’
plotGamma: no visible global function definition for ‘barplot’
plotGamma: no visible global function definition for ‘abline’
plotGamma: no visible global function definition for ‘mtext’
plotGamma: no visible global function definition for ‘points’
plotGenome: no visible global function definition for ‘quantile’
plotGenome: no visible global function definition for ‘pdf’
plotGenome: no visible global function definition for ‘dev.cur’
plotGenome: no visible global function definition for ‘dev.new’
plotGenome: no visible global function definition for ‘par’
plotGenome: no visible global function definition for ‘legend’
plotGenome: no visible global function definition for ‘title’
plotGenome: no visible global function definition for ‘devAskNewPage’
plotGenome: no visible global function definition for ‘graphics.off’
plotIdeogram: no visible global function definition for ‘plot’
plotIdeogram: no visible global function definition for ‘rect’
plotIdeogram: no visible global function definition for ‘mtext’
plotObs: no visible global function definition for ‘par’
plotObs: no visible global function definition for ‘plot’
plotSample: no visible global function definition for ‘pdf’
plotSample: no visible global function definition for ‘dev.cur’
plotSample: no visible global function definition for ‘dev.new’
plotSample: no visible global function definition for ‘devAskNewPage’
plotSample: no visible global function definition for ‘quantile’
plotSample: no visible global function definition for ‘par’
plotSample: no visible global function definition for ‘legend’
plotSample: no visible global function definition for ‘title’
plotSample: no visible global function definition for ‘graphics.off’
plotSegments: no visible global function definition for ‘par’
plotSegments: no visible global function definition for ‘plot’
sawMarkM: no visible global function definition for ‘quantile’
subset.abe: no visible binding for global variable ‘quantile’
subsetData: no visible global function definition for ‘read.table’
subsetSegments: no visible global function definition for ‘read.table’
winsorize: no visible global function definition for ‘read.table’
winsorize: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline axis barplot box col2rgb colorRampPalette dev.cur dev.new
  devAskNewPage graphics.off legend lines mad modifyList mtext par pdf
  plot points polygon quantile rainbow read.table rect rgb runmed
  segments text title write.table xspline
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.cur",
             "dev.new", "devAskNewPage", "graphics.off", "pdf",
             "rainbow", "rgb")
  importFrom("graphics", "abline", "axis", "barplot", "box", "legend",
             "lines", "mtext", "par", "plot", "points", "polygon",
             "rect", "segments", "text", "title", "xspline")
  importFrom("stats", "mad", "quantile", "runmed")
  importFrom("utils", "modifyList", "read.table", "write.table")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
plotCircle 9.289  0.425   9.915
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/copynumber.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL copynumber
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘copynumber’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (copynumber)

name	user	system	elapsed
SNPdata	0.019	0.005	0.024
aspcf	2.319	0.157	2.495
callAberrations	3.248	0.147	3.411
getGRangesFormat	3.378	0.140	3.525
imputeMissing	2.468	0.060	2.533
interpolate.pcf	0.568	0.019	0.587
lymphoma	0.002	0.001	0.002
micma	0.001	0.001	0.002
multipcf	0.812	0.015	0.828
pcf	0.87	0.02	0.89
pcfPlain	0.122	0.027	0.149
plotAberration	3.610	0.114	3.746
plotAllele	2.802	0.126	2.958
plotChrom	2.262	0.049	2.326
plotCircle	9.289	0.425	9.915
plotFreq	4.711	0.104	4.994
plotGamma	1.500	0.148	1.664
plotGenome	3.989	0.072	4.209
plotHeatmap	2.968	0.102	3.083
plotSample	3.280	0.092	3.438
selectSegments	0.987	0.029	1.058
subsetData	0.006	0.001	0.006
subsetSegments	3.102	0.094	3.219
winsorize	0.344	0.002	0.349