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BioC 3.5: CHECK report for copynumber on toluca2

This page was generated on 2017-04-23 14:37:16 -0400 (Sun, 23 Apr 2017).

Package 275/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
copynumber 1.15.0
Gro Nilsen
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/copynumber
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: copynumber
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings copynumber_1.15.0.tar.gz
StartedAt: 2017-04-23 02:18:38 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 02:21:11 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 153.0 seconds
RetCode: 0
Status:  OK 
CheckDir: copynumber.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings copynumber_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/copynumber.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
plotCircle 8.461   0.26   8.744
* 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-3.5-bioc/meat/copynumber.Rcheck/00check.log’
for details.


copynumber.Rcheck/00install.out:

* installing *source* package ‘copynumber’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (copynumber)

copynumber.Rcheck/copynumber-Ex.timings:

nameusersystemelapsed
SNPdata0.0180.0030.022
aspcf2.4850.1102.598
callAberrations3.4370.1043.545
getGRangesFormat3.5210.1053.632
imputeMissing2.2820.0572.344
interpolate.pcf0.5150.0170.533
lymphoma0.0010.0010.002
micma0.0020.0010.002
multipcf0.9910.0171.009
pcf0.9790.0190.999
pcfPlain0.4290.0160.445
plotAberration3.7370.1043.846
plotAllele3.3850.0933.499
plotChrom2.8150.0432.871
plotCircle8.4610.2608.744
plotFreq4.150.104.26
plotGamma1.5950.0851.708
plotGenome3.8900.0764.035
plotHeatmap3.9780.1124.150
plotSample3.4420.0653.549
selectSegments0.9420.0160.975
subsetData0.0080.0010.008
subsetSegments3.4030.1093.535
winsorize0.3720.0030.376