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BioC 3.3: CHECK report for RNAither on oaxaca

This page was generated on 2016-10-13 12:56:46 -0700 (Thu, 13 Oct 2016).

Package 987/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAither 2.20.0
Lars Kaderali
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/RNAither
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAither
Version: 2.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.20.0.tar.gz
StartedAt: 2016-10-13 05:49:21 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 05:55:05 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 343.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAither.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RNAither.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.20.0’
* 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 ‘RNAither’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘RankProd’
  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
BScore: no visible global function definition for ‘medpolish’
BScore: no visible global function definition for ‘mad’
DRQualControl: no visible global function definition for ‘write.table’
DRQualControl: no visible global function definition for ‘axis’
DRQualControl: no visible global function definition for ‘pdf’
DRQualControl: no visible global function definition for ‘dev.off’
LiWongRank: no visible global function definition for ‘sd’
LiWongRank: no visible global function definition for ‘hist’
MannWhitney: no visible global function definition for ‘var’
MannWhitney: no visible global function definition for ‘wilcox.test’
PlotSpatialDistrib: no visible global function definition for ‘jpeg’
PlotSpatialDistrib: no visible global function definition for
  ‘brewer.pal’
PlotSpatialDistrib: no visible global function definition for ‘dev.off’
RankProduct: no visible global function definition for ‘RP’
SNRQualControl: no visible global function definition for ‘read.table’
SNRQualControl: no visible global function definition for ‘hist’
SNRQualControl: no visible global function definition for ‘x11’
SNRQualControl: no visible global function definition for ‘par’
SNRQualControl: no visible global function definition for ‘pdf’
SNRQualControl: no visible global function definition for ‘dev.off’
Ttest: no visible global function definition for ‘var’
Ttest: no visible global function definition for ‘t.test’
ZPRIMEQualControl: no visible global function definition for
  ‘write.table’
ZPRIMEQualControl: no visible global function definition for ‘axis’
ZPRIMEQualControl: no visible global function definition for ‘pdf’
ZPRIMEQualControl: no visible global function definition for ‘dev.off’
ZPRIMEQualControl: no visible global function definition for ‘png’
ZPRIMEQualControl: no visible global function definition for
  ‘read.table’
ZPrime: no visible global function definition for ‘mad’
ZPrime: no visible global function definition for ‘median’
ZScore: no visible global function definition for ‘mad’
ZScore: no visible global function definition for ‘median’
ZScorePerScreen: no visible global function definition for ‘mad’
ZScorePerScreen: no visible global function definition for ‘median’
ZScorePlot: no visible global function definition for ‘sd’
ZScorePlot: no visible global function definition for ‘axis’
ZScorePlot: no visible global function definition for ‘abline’
ZScorePlot: no visible global function definition for ‘identify’
ZScorePlot: no visible global function definition for ‘pdf’
ZScorePlot: no visible global function definition for ‘dev.off’
ZScorePlot: no visible global function definition for ‘png’
ZScorePlotTwo: no visible global function definition for ‘sd’
ZScorePlotTwo: no visible global function definition for ‘median’
ZScorePlotTwo: no visible global function definition for ‘mad’
ZScorePlotTwo: no visible global function definition for ‘abline’
ZScorePlotTwo: no visible global function definition for ‘identify’
ZScorePlotTwo: no visible global function definition for ‘pdf’
ZScorePlotTwo: no visible global function definition for ‘dev.off’
ZScorePlotTwo: no visible global function definition for ‘png’
ZScorePlotTwo: no visible global function definition for ‘plot.new’
ZScorePlotTwo: no visible global function definition for ‘text’
channelPlot: no visible global function definition for ‘x11’
channelPlot: no visible global function definition for ‘lowess’
channelPlot: no visible global function definition for ‘pdf’
channelPlot: no visible global function definition for ‘dev.off’
channelPlot: no visible global function definition for ‘png’
compareReplicaPlates: no visible global function definition for ‘x11’
compareReplicaPlates: no visible global function definition for ‘par’
compareReplicaPlates: no visible global function definition for ‘mtext’
compareReplicaPlates: no visible global function definition for ‘pdf’
compareReplicaPlates: no visible global function definition for
  ‘dev.off’
compareReplicateSD: no visible global function definition for ‘sd’
compareReplicateSD: no visible global function definition for ‘x11’
compareReplicateSD: no visible global function definition for
  ‘brewer.pal’
compareReplicateSD: no visible global function definition for ‘png’
compareReplicateSD: no visible global function definition for ‘dev.off’
compareReplicateSDPerScreen: no visible global function definition for
  ‘sd’
compareReplicateSDPerScreen: no visible global function definition for
  ‘x11’
compareReplicateSDPerScreen: no visible global function definition for
  ‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
  ‘png’
compareReplicateSDPerScreen: no visible global function definition for
  ‘dev.off’
compareReplicates: no visible global function definition for ‘x11’
compareReplicates: no visible global function definition for ‘par’
compareReplicates: no visible global function definition for ‘points’
compareReplicates: no visible global function definition for ‘mtext’
compareReplicates: no visible global function definition for ‘identify’
compareReplicates: no visible global function definition for ‘pdf’
compareReplicates: no visible global function definition for ‘dev.off’
compareReplicates: no visible global function definition for ‘png’
controlDensity: no visible global function definition for ‘density’
controlDensity: no visible global function definition for ‘hist’
controlDensity: no visible global function definition for ‘par’
controlDensity: no visible global function definition for ‘axis’
controlDensity: no visible global function definition for ‘abline’
controlDensity: no visible global function definition for ‘legend’
controlDensity: no visible global function definition for ‘pdf’
controlDensity: no visible global function definition for ‘dev.off’
controlDensity: no visible global function definition for ‘png’
controlDensityPerPlate: no visible global function definition for ‘x11’
controlDensityPerPlate: no visible global function definition for ‘par’
controlDensityPerPlate: no visible global function definition for
  ‘density’
controlDensityPerPlate: no visible global function definition for
  ‘hist’
controlDensityPerPlate: no visible global function definition for
  ‘axis’
controlDensityPerPlate: no visible global function definition for
  ‘abline’
controlDensityPerPlate: no visible global function definition for
  ‘legend’
controlDensityPerPlate: no visible global function definition for ‘pdf’
controlDensityPerPlate: no visible global function definition for
  ‘plot.new’
controlDensityPerPlate: no visible global function definition for
  ‘text’
controlDensityPerPlate: no visible global function definition for
  ‘dev.off’
controlDensityPerPlate: no visible global function definition for ‘png’
controlDensityPerScreen: no visible global function definition for
  ‘par’
controlDensityPerScreen: no visible global function definition for
  ‘density’
controlDensityPerScreen: no visible global function definition for
  ‘hist’
controlDensityPerScreen: no visible global function definition for
  ‘axis’
controlDensityPerScreen: no visible global function definition for
  ‘abline’
controlDensityPerScreen: no visible global function definition for
  ‘legend’
controlDensityPerScreen: no visible global function definition for
  ‘pdf’
controlDensityPerScreen: no visible global function definition for
  ‘dev.off’
controlDensityPerScreen: no visible global function definition for
  ‘png’
controlNorm: no visible global function definition for ‘median’
doCtrlNorm: no visible global function definition for ‘median’
doCtrlNorm: no visible global function definition for ‘mad’
doPercNegNorm: no visible global function definition for ‘median’
doPocNorm: no visible global function definition for ‘median’
function1: no visible global function definition for ‘write.table’
function2: no visible global function definition for ‘write.table’
function2b: no visible global function definition for ‘write.table’
function2c: no visible global function definition for ‘write.table’
function3: no visible global function definition for ‘write.table’
function4a: no visible global function definition for ‘write.table’
function4b: no visible global function definition for ‘write.table’
function5: no visible global function definition for ‘write.table’
function6: no visible global function definition for ‘write.table’
function7: no visible global function definition for ‘write.table’
generateDatasetFile: no visible global function definition for
  ‘write.table’
gseaTableFunc: no visible global function definition for ‘write.table’
hitselectionPval: no visible global function definition for ‘median’
hitselectionPval: no visible global function definition for
  ‘write.table’
hitselectionZscore: no visible global function definition for
  ‘write.table’
hitselectionZscorePval: no visible global function definition for
  ‘write.table’
joinDatasetFiles: no visible global function definition for
  ‘read.table’
joinDatasetFiles: no visible global function definition for
  ‘write.table’
lowessNorm: no visible global function definition for ‘lowess’
mainAnalysis: no visible global function definition for ‘write.table’
mainAnalysis: no visible global function definition for ‘read.table’
mainAnalysis: no visible binding for global variable ‘median’
makeBoxplot4PlateType: no visible global function definition for ‘x11’
makeBoxplot4PlateType: no visible global function definition for
  ‘boxplot’
makeBoxplot4PlateType: no visible global function definition for
  ‘plot.new’
makeBoxplot4PlateType: no visible global function definition for ‘text’
makeBoxplot4PlateType: no visible global function definition for ‘pdf’
makeBoxplot4PlateType: no visible global function definition for
  ‘dev.off’
makeBoxplot4PlateType: no visible global function definition for ‘png’
makeBoxplotControls: no visible global function definition for
  ‘boxplot’
makeBoxplotControls: no visible global function definition for ‘pdf’
makeBoxplotControls: no visible global function definition for
  ‘dev.off’
makeBoxplotControls: no visible global function definition for ‘png’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘par’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘boxplot’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘plot.new’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘text’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘pdf’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘dev.off’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘png’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘par’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘boxplot’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘pdf’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘dev.off’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘png’
makeBoxplotOverview: no visible global function definition for ‘jpeg’
makeBoxplotOverview: no visible global function definition for
  ‘boxplot’
makeBoxplotOverview: no visible global function definition for
  ‘dev.off’
makeBoxplotPerPlate: no visible global function definition for ‘par’
makeBoxplotPerPlate: no visible global function definition for
  ‘boxplot’
makeBoxplotPerPlate: no visible global function definition for ‘pdf’
makeBoxplotPerPlate: no visible global function definition for
  ‘dev.off’
makeBoxplotPerPlate: no visible global function definition for ‘png’
makeBoxplotPerScreen: no visible global function definition for
  ‘boxplot’
makeBoxplotPerScreen: no visible global function definition for ‘pdf’
makeBoxplotPerScreen: no visible global function definition for
  ‘dev.off’
makeBoxplotPerScreen: no visible global function definition for ‘png’
makeCorrPlots: no visible global function definition for ‘jpeg’
makeCorrPlots: no visible global function definition for ‘cor’
makeCorrPlots: no visible global function definition for ‘dev.off’
makeCtrlBoxPlot: no visible global function definition for ‘jpeg’
makeCtrlBoxPlot: no visible global function definition for ‘boxplot’
makeCtrlBoxPlot: no visible global function definition for ‘dev.off’
makeCtrlDensityPlot: no visible global function definition for ‘jpeg’
makeCtrlDensityPlot: no visible global function definition for
  ‘density’
makeCtrlDensityPlot: no visible global function definition for ‘hist’
makeCtrlDensityPlot: no visible global function definition for
  ‘dev.off’
makeQCPlots: no visible global function definition for ‘jpeg’
makeQCPlots: no visible global function definition for ‘boxplot’
makeQCPlots: no visible global function definition for ‘dev.off’
makeScreenOverview: no visible global function definition for ‘jpeg’
makeScreenOverview: no visible global function definition for ‘dev.off’
makefullbarplot: no visible global function definition for ‘jpeg’
makefullbarplot: no visible global function definition for ‘abline’
makefullbarplot: no visible global function definition for ‘dev.off’
makevolcanoplot: no visible global function definition for ‘jpeg’
makevolcanoplot: no visible global function definition for ‘abline’
makevolcanoplot: no visible global function definition for ‘dev.off’
multTestAdjust: no visible global function definition for ‘p.adjust’
numCellQualControl: no visible global function definition for
  ‘read.table’
numCellQualControl: no visible global function definition for ‘sd’
numCellQualControl: no visible global function definition for ‘hist’
numCellQualControl: no visible global function definition for
  ‘write.table’
numCellQualControl: no visible global function definition for ‘pdf’
numCellQualControl: no visible global function definition for ‘dev.off’
percCellQualControl: no visible global function definition for
  ‘read.table’
percCellQualControl: no visible global function definition for ‘sd’
percCellQualControl: no visible global function definition for ‘hist’
percCellQualControl: no visible global function definition for
  ‘write.table’
percCellQualControl: no visible global function definition for ‘pdf’
percCellQualControl: no visible global function definition for
  ‘dev.off’
plotBar: no visible global function definition for ‘boxplot’
plotBar: no visible global function definition for ‘abline’
plotBar: no visible global function definition for ‘pdf’
plotBar: no visible global function definition for ‘dev.off’
plotBar: no visible global function definition for ‘png’
plotBar: no visible global function definition for ‘x11’
plotBarGeruest: no visible global function definition for ‘median’
plotBarGeruest: no visible global function definition for ‘mad’
plotControlHisto: no visible global function definition for ‘hist’
plotControlHisto: no visible global function definition for ‘par’
plotControlHisto: no visible global function definition for ‘legend’
plotControlHisto: no visible global function definition for ‘pdf’
plotControlHisto: no visible global function definition for ‘dev.off’
plotControlHisto: no visible global function definition for ‘png’
plotControlHistoPerplate: no visible global function definition for
  ‘x11’
plotControlHistoPerplate: no visible global function definition for
  ‘par’
plotControlHistoPerplate: no visible global function definition for
  ‘plot.new’
plotControlHistoPerplate: no visible global function definition for
  ‘text’
plotControlHistoPerplate: no visible global function definition for
  ‘hist’
plotControlHistoPerplate: no visible global function definition for
  ‘legend’
plotControlHistoPerplate: no visible global function definition for
  ‘mtext’
plotControlHistoPerplate: no visible global function definition for
  ‘pdf’
plotControlHistoPerplate: no visible global function definition for
  ‘dev.off’
plotControlHistoPerplate: no visible global function definition for
  ‘png’
plotControlHistoPerscreen: no visible global function definition for
  ‘par’
plotControlHistoPerscreen: no visible global function definition for
  ‘hist’
plotControlHistoPerscreen: no visible global function definition for
  ‘legend’
plotControlHistoPerscreen: no visible global function definition for
  ‘pdf’
plotControlHistoPerscreen: no visible global function definition for
  ‘dev.off’
plotControlHistoPerscreen: no visible global function definition for
  ‘png’
plotHisto: no visible global function definition for ‘hist’
plotHisto: no visible global function definition for ‘pdf’
plotHisto: no visible global function definition for ‘dev.off’
plotHisto: no visible global function definition for ‘png’
plotHistoPerplate: no visible global function definition for ‘x11’
plotHistoPerplate: no visible global function definition for ‘par’
plotHistoPerplate: no visible global function definition for ‘hist’
plotHistoPerplate: no visible global function definition for ‘mtext’
plotHistoPerplate: no visible global function definition for ‘pdf’
plotHistoPerplate: no visible global function definition for ‘dev.off’
plotHistoPerplate: no visible global function definition for ‘png’
plotHistoPerscreen: no visible global function definition for ‘par’
plotHistoPerscreen: no visible global function definition for ‘hist’
plotHistoPerscreen: no visible global function definition for ‘pdf’
plotHistoPerscreen: no visible global function definition for ‘dev.off’
plotHistoPerscreen: no visible global function definition for ‘png’
plotQQ: no visible global function definition for ‘qqnorm’
plotQQ: no visible global function definition for ‘qqline’
plotQQ: no visible global function definition for ‘pdf’
plotQQ: no visible global function definition for ‘dev.off’
plotQQ: no visible global function definition for ‘png’
plotQQperplate: no visible global function definition for ‘x11’
plotQQperplate: no visible global function definition for ‘par’
plotQQperplate: no visible global function definition for ‘qqnorm’
plotQQperplate: no visible global function definition for ‘qqline’
plotQQperplate: no visible global function definition for ‘mtext’
plotQQperplate: no visible global function definition for ‘plot.new’
plotQQperplate: no visible global function definition for ‘text’
plotQQperplate: no visible global function definition for ‘pdf’
plotQQperplate: no visible global function definition for ‘dev.off’
plotQQperplate: no visible global function definition for ‘png’
plotQQperscreen: no visible global function definition for ‘par’
plotQQperscreen: no visible global function definition for ‘qqnorm’
plotQQperscreen: no visible global function definition for ‘qqline’
plotQQperscreen: no visible global function definition for ‘pdf’
plotQQperscreen: no visible global function definition for ‘dev.off’
plotQQperscreen: no visible global function definition for ‘png’
plothist: no visible global function definition for ‘jpeg’
plothist: no visible global function definition for ‘hist’
plothist: no visible global function definition for ‘dev.off’
plotmybar: no visible global function definition for ‘median’
plotmybar: no visible global function definition for ‘mad’
plotmybar: no visible global function definition for ‘jpeg’
plotmybar: no visible global function definition for ‘boxplot’
plotmybar: no visible global function definition for ‘abline’
plotmybar: no visible global function definition for ‘dev.off’
plotqq: no visible global function definition for ‘jpeg’
plotqq: no visible global function definition for ‘dev.off’
plotscatter: no visible global function definition for ‘jpeg’
plotscatter: no visible global function definition for ‘lowess’
plotscatter: no visible global function definition for ‘dev.off’
replicatesCV: no visible global function definition for ‘par’
replicatesCV: no visible global function definition for ‘sd’
replicatesCV: no visible global function definition for ‘points’
replicatesCV: no visible global function definition for ‘identify’
replicatesCV: no visible global function definition for ‘pdf’
replicatesCV: no visible global function definition for ‘dev.off’
replicatesCV: no visible global function definition for ‘png’
replicatesSpearmancor: no visible global function definition for
  ‘write.table’
replicatesSpearmancor: no visible global function definition for ‘cor’
replicatesSpearmancor: no visible global function definition for
  ‘read.table’
rnaither: no visible global function definition for ‘quantile’
rnaither: no visible binding for global variable ‘median’
saveDataset: no visible global function definition for ‘write.table’
savepValVec: no visible global function definition for ‘write.table’
spatialDistrib: no visible global function definition for ‘x11’
spatialDistrib: no visible global function definition for ‘brewer.pal’
spatialDistrib: no visible global function definition for ‘png’
spatialDistrib: no visible global function definition for ‘dev.off’
spatialDistrib: no visible global function definition for ‘plot.new’
spatialDistrib: no visible global function definition for ‘text’
summarizeReplicates: no visible global function definition for ‘median’
summarizeReplicates: no visible global function definition for ‘mad’
summarizeReplicates: no visible global function definition for ‘sd’
summarizeReplicates: no visible global function definition for ‘t.test’
summarizeReplicates: no visible global function definition for
  ‘wilcox.test’
varAdjust: no visible global function definition for ‘mad’
vennDiag: no visible global function definition for ‘pdf’
vennDiag: no visible global function definition for ‘dev.off’
vennDiag: no visible global function definition for ‘png’
volcanoPlot: no visible global function definition for ‘abline’
volcanoPlot: no visible global function definition for ‘identify’
volcanoPlot: no visible global function definition for ‘pdf’
volcanoPlot: no visible global function definition for ‘dev.off’
volcanoPlot: no visible global function definition for ‘png’
writehitlist: no visible global function definition for ‘write.table’
writehitlist: no visible binding for global variable ‘median’
writehitlist: no visible global function definition for ‘median’
writehitlist: no visible global function definition for ‘mad’
writehitlist: no visible global function definition for ‘sd’
writehitlist: no visible global function definition for ‘t.test’
writehitlist: no visible global function definition for ‘wilcox.test’
ylabCompute: no visible global function definition for ‘sd’
ylabCompute: no visible global function definition for ‘median’
ylabCompute: no visible global function definition for ‘mad’
Undefined global functions or variables:
  RP abline axis boxplot brewer.pal cor density dev.off hist identify
  jpeg legend lowess mad median medpolish mtext p.adjust par pdf
  plot.new png points qqline qqnorm quantile read.table sd t.test text
  var wilcox.test write.table x11
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf", "png", "x11")
  importFrom("graphics", "abline", "axis", "boxplot", "hist", "identify",
             "legend", "mtext", "par", "plot.new", "points", "text")
  importFrom("stats", "cor", "density", "lowess", "mad", "median",
             "medpolish", "p.adjust", "qqline", "qqnorm", "quantile",
             "sd", "t.test", "var", "wilcox.test")
  importFrom("utils", "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 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
mainAnalysis 23.437  1.759  26.149
rnaither     14.923  1.193  17.019
gseaAnalysis  5.532  0.076  75.797
* 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-3.3-bioc/meat/RNAither.Rcheck/00check.log’
for details.


RNAither.Rcheck/00install.out:

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RNAither)

RNAither.Rcheck/RNAither-Ex.timings:

nameusersystemelapsed
BScore0.0590.0080.067
DRQualControl0.0360.0030.038
LiWongRank0.0730.0010.075
MannWhitney0.0380.0010.039
RankProduct0.2760.0070.282
SNRQualControl0.0280.0040.032
Ttest0.0270.0000.027
ZPRIMEQualControl0.0440.0060.053
ZScore0.0140.0000.015
ZScorePerScreen0.0090.0010.010
ZScorePlot0.1330.0140.168
ZScorePlotTwo0.0280.0040.049
channelPlot0.0370.0030.044
closestToZero0.0030.0000.004
compareHits0.0550.0020.057
compareReplicaPlates0.0190.0020.022
compareReplicateSD0.2140.0130.231
compareReplicateSDPerScreen0.3000.0130.318
compareReplicates0.2310.0210.283
controlDensity0.0600.0050.067
controlDensityPerPlate0.2050.0160.229
controlDensityPerScreen0.1080.0100.123
controlNorm0.0140.0010.015
createSubset0.0030.0000.004
discardLabtek0.0040.0010.005
discardWells0.0040.0000.004
divNorm0.0150.0000.016
divideChannels0.0030.0000.003
eraseDataSetColumn0.0100.0010.010
findReplicates0.0050.0000.005
furthestFromZero0.0020.0000.003
generateDatasetFile0.0180.0010.031
generateRepMatNoFilter0.0080.0010.008
generateReplicateMat0.0070.0000.007
gseaAnalysis 5.532 0.07675.797
hitselectionPval0.0190.0010.020
hitselectionZscore0.0180.0010.019
hitselectionZscorePval0.0170.0000.018
incorporatepValVec0.0110.0000.013
indexSubset0.0030.0010.004
joinDatasetFiles0.0170.0010.020
joinDatasets0.0030.0010.003
lowessNorm0.0110.0000.012
mainAnalysis23.437 1.75926.149
makeBoxplot4PlateType0.0630.0060.072
makeBoxplotControls0.0280.0030.031
makeBoxplotControlsPerPlate0.1050.0090.117
makeBoxplotControlsPerScreen0.0580.0050.064
makeBoxplotPerPlate0.0580.0050.064
makeBoxplotPerScreen0.0310.0030.034
multTestAdjust0.0030.0000.003
numCellQualControl0.0290.0020.032
orderGeneIDs0.0460.0010.047
percCellQualControl0.0260.0030.029
plotBar0.1270.0070.162
plotControlHisto0.0810.0050.086
plotControlHistoPerplate0.3280.0130.349
plotControlHistoPerscreen0.1550.0070.165
plotHisto0.0230.0030.027
plotHistoPerplate0.1190.0120.139
plotHistoPerscreen0.0530.0060.061
plotQQ0.0330.0030.038
plotQQperplate0.1110.0110.127
plotQQperscreen0.0590.0050.067
quantileNormalization0.0180.0010.019
replicatesCV0.0690.0060.079
replicatesSpearmancor0.0230.0020.025
rms0.0020.0000.002
rnaither14.923 1.19317.019
saveDataset0.0100.0000.011
saveOldIntensityColumns0.0020.0010.003
savepValVec0.0020.0000.003
spatialDistrib0.5450.0310.585
spatialDistribHits0.6010.0310.643
subtractBackground0.0070.0010.007
sumChannels0.0100.0010.011
summarizeReps0.0580.0010.059
summarizeRepsNoFiltering0.0470.0000.047
trim0.0030.0000.004
varAdjust0.0050.0010.006
vennDiag0.0680.0050.074
volcanoPlot0.0720.0050.077